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  <front>
    <journal-meta><journal-id journal-id-type="publisher">GChron</journal-id><journal-title-group>
    <journal-title>Geochronology</journal-title>
    <abbrev-journal-title abbrev-type="publisher">GChron</abbrev-journal-title><abbrev-journal-title abbrev-type="nlm-ta">Geochronology</abbrev-journal-title>
  </journal-title-group><issn pub-type="epub">2628-3719</issn><publisher>
    <publisher-name>Copernicus Publications</publisher-name>
    <publisher-loc>Göttingen, Germany</publisher-loc>
  </publisher></journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.5194/gchron-7-545-2025</article-id><title-group><article-title>StratoBayes: a Bayesian method for automated stratigraphic correlation and age modelling</article-title><alt-title>StratoBayes</alt-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Eichenseer</surname><given-names>Kilian</given-names></name>
          <email>kilian.eichenseer@gmail.com</email>
        <ext-link>https://orcid.org/0000-0002-0477-8878</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1 aff2">
          <name><surname>Sinnesael</surname><given-names>Matthias</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-0354-8250</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Smith</surname><given-names>Martin R.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-5660-1727</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Millard</surname><given-names>Andrew R.</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>Department of Earth Sciences, Durham University, South Road, DH1 3LE, Durham, United Kingdom</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Geology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Department of Archaeology, Durham University, South Road, DH1 3LE, Durham, United Kingdom</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Kilian Eichenseer (kilian.eichenseer@gmail.com)</corresp></author-notes><pub-date><day>27</day><month>October</month><year>2025</year></pub-date>
      
      <volume>7</volume>
      <issue>4</issue>
      <fpage>545</fpage><lpage>570</lpage>
      <history>
        <date date-type="received"><day>21</day><month>March</month><year>2025</year></date>
           <date date-type="accepted"><day>27</day><month>August</month><year>2025</year></date>
           <date date-type="rev-recd"><day>12</day><month>August</month><year>2025</year></date>
           <date date-type="rev-request"><day>4</day><month>April</month><year>2025</year></date>
      </history>
      <permissions>
        <copyright-statement>Copyright: © 2025 Kilian Eichenseer et al.</copyright-statement>
        <copyright-year>2025</copyright-year>
      <license license-type="open-access"><license-p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this licence, visit <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><self-uri xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025.html">This article is available from https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025.html</self-uri><self-uri xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025.pdf">The full text article is available as a PDF file from https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025.pdf</self-uri>
      <abstract><title>Abstract</title>

      <p id="d2e121">Stratigraphic correlation and age modelling are fundamental to reconstructing Earth's history, biological evolution, and palaeoclimate, and underpin the exploration for subsurface resources. Correlations are produced by integrating diverse stratigraphic data across multiple sites, typically by visual inspection. Here, we introduce “StratoBayes”, a Bayesian statistical framework that combines stratigraphic correlation and depositional age estimation of stratigraphic horizons, i.e. age modelling.  Our method aligns quantitative signals from two or more sites by shifting and scaling, allowing for sedimentation rate changes between stratigraphic partitions. The likelihood of an alignment is evaluated by how well the adjusted signals conform to a shared smooth trend, represented by a cubic spline. Tie points or independent age constraints, such as radiometric dates or biostratigraphic markers, can be integrated within this framework, providing age estimates for all sites. Our approach identifies multiple alignments where distinct alternatives exist, estimates their relative probabilities, and quantifies the uncertainty associated with correlations and age estimates. We apply StratoBayes to a lower Cambrian dataset comprising a combination of <inline-formula><mml:math id="M1" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> records, radiometric dates and astrochronology from four sites in Morocco and Siberia. The results demonstrate its capacity to quantify existing alignments, and provide the first precise age estimate for the evolutionary appearance of trilobites in Siberia, one of the hallmarks of the Cambrian Explosion. Beyond this application, StratoBayes offers a generalisable framework for probabilistic stratigraphic correlation, with potential to improve age models across a range of proxy records and time intervals.</p>
  </abstract>
    
<funding-group>
<award-group id="gs1">
<funding-source>Leverhulme Trust</funding-source>
<award-id>2019-223</award-id>
</award-group>
</funding-group>
</article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <label>1</label><title>Introduction</title>
      <p id="d2e146">Stratigraphic correlation works on the basis that rocks that were deposited under similar conditions or at the same time tend to share characteristics that allow for their attribution to a stratigraphic or temporal horizon. For example, insofar as temporal changes in the global <inline-formula><mml:math id="M2" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> composition of seawater are reflected in marine sedimentary rocks, matching trends of changing <inline-formula><mml:math id="M3" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> in rock sections from different locations can be used to place those sections on a relative time scale (Cramer and Jarvis, 2020; Saltzman et al., 2012). Quantitative signals such as isotopic compositions, elemental concentrations or geophysical well-log data present a particular challenge: in aligning those signals by eye, the stratigrapher has to make a large number of intuitive decisions about which peaks and troughs are likely to line up. Trying to integrate all the stratigraphic evidence from multiple sites often results in more than one potential alignment solution and differing interpretations between different workers (Bowyer et al., 2022, 2023; Landing and Kruse, 2017; Smith et al., 2016).</p>
      <p id="d2e175">Computer algorithms have been designed to address the problems arising from visual correlation (Agterberg, 1990; Lisiecki and Lisiecki, 2002; Rudman and Lankston, 1973). Algorithms designed for aligning quantitative signals from two or more sites typically use a point-based approach, aligning each point of site A with zero, one or multiple points from site B. This approach proposes variable sedimentation rates between points. This flexibility in principle allows the most precise alignments, though potentially at the cost of overfitting. Point-based algorithms commonly use dynamic time warping (DTW), a technique that finds the optimal match between two time-series data by adjusting their alignment (Sakoe and Chiba, 1978). For a selection of recent approaches using dynamic time warping for stratigraphic alignment, see Wheeler and Hale (2014), Hay et al. (2019), Baville et al. (2022), Sylvester (2023), and Hagen et al. (2024). The limitations of DTW-based approaches are that they commonly require known section tops and bottoms (Sylvester, 2023); and they are generally deterministic, providing only a single solution without any indication of uncertainty or alternative alignments (but see Al Ibrahim, 2022; Hay et al., 2019). The integration of additional stratigraphic information besides the quantitative signals tends to be difficult, requiring extra steps outside of the core DTW-algorithm (e.g. Hagen and Creveling, 2024).</p>
      <p id="d2e178">Probabilistic approaches overcome some of these limitations by estimating the probabilities of different outcomes, rather than producing deterministic predictions. An effective probabilistic approach is offered by the Bayesian framework, which integrates multiple sources of uncertainty by combining prior knowledge, encapsulated mathematically as a prior probability distribution, with a custom likelihood function that is used to evaluate the likelihood of observed data. Given an appropriate prior and likelihood function it is straightforward to integrate different types of stratigraphic information. Bayesian approaches are commonly employed in age-depth models that interpolate between absolute age constraints or tie points; examples include Bchron (Haslett and Parnell, 2008) and Oxcal (Ramsey, 1995). This approach can be extended by incorporating prior expectations on hiatuses, sedimentation rates, and rate variability, including external information such as astrochronological data (e.g. Blaauw and Christen, 2011; Trayler et al., 2024).</p>
      <p id="d2e181">Recent Bayesian methods have attempted to combine stratigraphic correlation and age modelling. Lee et al. (2022) have implemented a Bayesian method that uses Gaussian process regression to match Cenozoic oxygen isotope data from one site to an oxygen isotope stack, while simultaneously integrating age estimates from radiocarbon dates to produce probabilistic age-depth models (i.e. the BIGMACS model). This method improves upon earlier approaches by specifying uncertainty for tie points and integrates prior knowledge on Cenozoic sedimentation rates with absolute age information from the aligned site. However, age uncertainties from the reference site are not included, and varying sampling resolution or large sedimentation rate changes may violate model assumptions and impede the broader adoption of this method in its current form (Middleton et al., 2024). Edmonsond and Dyer (2025) have developed a different Bayesian method based on Gaussian process regression that works without prior knowledge of sedimentation rates, but requires minimum and maximum age estimates for all sections, and the absence of an explicit prior on sedimentation rates may risk overfitting. Here, we introduce a versatile Bayesian method for stratigraphic correlation and age modelling that can align quantitative signals from two or more sites without the need to specify tie points or top and bottom ages, and with no restrictions on sampling frequencies. Possible sedimentation rates can be specified by the user as priors, and the likelihood encompasses the alignment of the signals and, optionally, additional age constraints such as dated horizons. The method requires only vague prior knowledge on the ages and on the degree of overlap of the sections, along with order-of-magnitude estimates of sedimentation rates; it is not necessary to specify matching section tops or bottoms. The model is able to integrate radiometric dates from different sites, meaning that ages from well-dated sites can inform age estimates at sites with little or no age information. Age estimates with uncertainty can thus be obtained for any point within any site, and alternative alignments can be identified. Additional stratigraphic knowledge, such as hiatuses or tie points, can be readily incorporated.</p>
      <p id="d2e185">Our Bayesian model works by evaluating the fit of a single cubic spline (Heaton et al., 2020) to the combined quantitative signal of all sites. If more than one type of signal is included, e.g. <inline-formula><mml:math id="M4" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M5" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">18</mml:mn></mml:msup><mml:mi mathvariant="normal">O</mml:mi></mml:mrow></mml:math></inline-formula>, a different spline is constructed for each signal type, and their joint likelihood is used to evaluate the alignment. Different alignments are generated by shifting the sites relative to each other, and by scaling segments of the sites using different sedimentation rates. Markov chain Monte Carlo methods are used to obtain the posterior distributions of the unknown model parameters. Our method is implemented as an R package, “StratoBayes”.</p>
      <p id="d2e214">To demonstrate the potential of this method, we apply it to artificial stratigraphic data and to a real case study using lower Cambrian <inline-formula><mml:math id="M6" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> records from Morocco (Magaritz et al., 1991; Maloof et al., 2005, 2010; Tucker, 1986) and Siberia (Kouchinsky et al., 2007). Integrating radiometric dates (Landing et al., 1998, 2021; Maloof et al., 2010), we provide age estimates for the studied sections of an interval spanning several lower Cambrian carbon isotope excursions, and compare our algorithm-derived correlation with recent stratigraphic models relying on visual expert-based interpretations (Bowyer et al., 2022, 2023). Our solution also provides a fully quantitative age estimate for the appearance of the first Siberian trilobites, which are thought to be the world's oldest trilobites (Landing et al., 2021).</p>
</sec>
<sec id="Ch1.S2">
  <label>2</label><title>Bayesian stratigraphic model</title>
      <p id="d2e238">StratoBayes generates and evaluates alignments of quantitative stratigraphic signals. A signal consists of, for example, geochemical or geophysical measurements that vary across height or depth (Fig. 1a), obtained from a contiguous sedimentary sequence, which may be interrupted by hiatuses at known horizons. Alignments are generated by shifting the sites containing the signals either (a) against a fixed reference site, or (b) against each other on an absolute age scale. Additionally, the sites are scaled (“stretched” or “squeezed”) assuming different sedimentation rates. The fit of different alignments, corresponding to different shifts and sedimentation rates, is evaluated in the Bayesian framework.</p>

      <fig id="F1" specific-use="star"><label>Figure 1</label><caption><p id="d2e243">Schematic of the alignment algorithm. <bold>(a)</bold> Input data: Quantitative stratigraphic measurements (e.g. geochemical data) from two sites recorded along their section height (here given in meters). <bold>(b)</bold> Priors must be placed on the shift parameter <inline-formula><mml:math id="M7" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and on the relative sedimentation rate <inline-formula><mml:math id="M8" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>. Here, <inline-formula><mml:math id="M9" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> determines the reference height (at Site 1) corresponding to the top of the height range of Site 2, and <inline-formula><mml:math id="M10" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> corresponds to the sedimentation rate of Site 2 relative to Site 1. The vertical, dashed lines denote the <inline-formula><mml:math id="M11" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M12" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> values, 12.3 m and 3.0, respectively, that were used in the creation of the data of site 2. <bold>(c)</bold> An alignment corresponding to a single sample from the posterior. The blue dashed line indicates the position of the top of the data from Site 2 at the reference height scale (<inline-formula><mml:math id="M13" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>; median: 12.5 <inline-formula><mml:math id="M14" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi></mml:mrow></mml:math></inline-formula>). The relative sedimentation rate <inline-formula><mml:math id="M15" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> has been estimated at a median of 2.8, corresponding to a shortening of the dataset from Site 2 relative to the reference site (indicated by the dashed and solid light brown line). Note that the posterior estimates of <inline-formula><mml:math id="M16" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M17" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> are similar, although not identical to the values used in creating the data (see Sect. 3). The curved grey line shows the cubic B-spline corresponding to the alignment.</p></caption>
        <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f01.png"/>

      </fig>

      <p id="d2e341">Statistical analysis in the Bayesian framework starts by formulating a probabilistic model that includes known data <inline-formula><mml:math id="M18" display="inline"><mml:mi>y</mml:mi></mml:math></inline-formula> and unknown model parameters <inline-formula><mml:math id="M19" display="inline"><mml:mi mathvariant="italic">θ</mml:mi></mml:math></inline-formula>. Instead of trying to identify a single estimate for <inline-formula><mml:math id="M20" display="inline"><mml:mi mathvariant="italic">θ</mml:mi></mml:math></inline-formula>, Bayesian inference involves estimating probability distributions for the model parameters, termed “posterior probability distributions”. Posterior distributions are obtained by combining prior knowledge of the parameters with the data via a likelihood function. Bayes' theorem states that the probability of the parameters given the data, <inline-formula><mml:math id="M21" display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi>y</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, i.e. the posterior probability, is proportional to the probability of the data given the model parameters (i.e. the likelihood), <inline-formula><mml:math id="M22" display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mo>(</mml:mo><mml:mi>y</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, times the prior probability of the model parameters, <inline-formula><mml:math id="M23" display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>:

          <disp-formula id="Ch1.E1" content-type="numbered"><label>1</label><mml:math id="M24" display="block"><mml:mrow><mml:mi>p</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi>y</mml:mi><mml:mo>)</mml:mo><mml:mo>∝</mml:mo><mml:mi>p</mml:mi><mml:mo>(</mml:mo><mml:mi>y</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mi>p</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

        In our case, this approach requires specifying prior probability distributions for the unknown model parameters that control the shifting and scaling (Fig. 1b), and optionally for the duration of pre-determined hiatuses. Our model assumes that the measurements in each sedimentary sequence are samples (with noise) from a common underlying signal, whose value can be modelled by a smooth curve described by a cubic B-spline. Our likelihood function quantifies how well a cubic B-spline fitted to a given alignment explains the observed data (Fig. 1c). Additional likelihood components can integrate absolute age constraints such as radiometric dates or other tie points, e.g. index fossils. Using Bayes' theorem, the priors are combined with the likelihood to obtain the posterior probability for any alignment.</p>
      <p id="d2e458">We obtain probability distributions for the parameters of the model by running a Markov chain Monte Carlo (MCMC) simulation. This involves repeatedly generating parameter values over a large number of iterations. To ensure thorough exploration of the parameter space, we employ parallel tempering, i.e. we run multiple chains in parallel, flattening the likelihood of the tempered (hot) chains, which can therefore move between different posterior modes; swaps between chains are proposed at every iteration. For the posterior estimates, we retain samples only from the primary (cold) chain. An initial portion of the samples is discarded (burn-in) to remove dependency on starting values, and only every <inline-formula><mml:math id="M25" display="inline"><mml:mi>n</mml:mi></mml:math></inline-formula>th iteration is recorded to reduce autocorrelation.  Details on the MCMC implementation are provided in Appendix A.</p>
      <p id="d2e468">In the following, we will assume that measurements were taken on a height scale (increasing from the bottom to the top), but depth-scale measurements can be used interchangeably by inverting their sign.</p>
<sec id="Ch1.S2.SS1">
  <label>2.1</label><title>Evaluating alignments with a cubic B-spline</title>
      <p id="d2e478">Identifying good alignment positions requires evaluating and comparing different potential alignments. In the Bayesian framework, the measure used for this evaluation is the likelihood. We derive the likelihood of an alignment from its fit to a single cubic B-spline (Eilers and Marx, 1996), fitted to the measurements from all sites, including the reference site (see Fig. 1c).</p>
      <p id="d2e481">We model each measured value <inline-formula><mml:math id="M26" display="inline"><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> as normally distributed:

            <disp-formula id="Ch1.E2" content-type="numbered"><label>2</label><mml:math id="M27" display="block"><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>∼</mml:mo><mml:mtext>Normal</mml:mtext><mml:mo>(</mml:mo><mml:msub><mml:mi mathvariant="italic">μ</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:mi mathvariant="italic">σ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math id="M28" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">μ</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the mean, and the standard deviation <inline-formula><mml:math id="M29" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> represents the scatter around the spline. <inline-formula><mml:math id="M30" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">μ</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is given by the spline function

            <disp-formula id="Ch1.E3" content-type="numbered"><label>3</label><mml:math id="M31" display="block"><mml:mrow><mml:msub><mml:mi mathvariant="italic">μ</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:munderover><mml:mo movablelimits="false">∑</mml:mo><mml:mrow><mml:mi>j</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow><mml:mrow><mml:mi>k</mml:mi><mml:mo>+</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:munderover><mml:msub><mml:mi mathvariant="italic">β</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:msub><mml:mi>B</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

          Here, <inline-formula><mml:math id="M32" display="inline"><mml:mi mathvariant="italic">μ</mml:mi></mml:math></inline-formula> can be interpreted as an underlying common signal of which the observations from each site, including the reference site, are noisy realisations. <inline-formula><mml:math id="M33" display="inline"><mml:mi>k</mml:mi></mml:math></inline-formula> denotes the number of internal knots of the spline, with more knots implying that the spline can potentially capture higher-frequency variations. <inline-formula><mml:math id="M34" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">β</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the spline coefficient associated with the <inline-formula><mml:math id="M35" display="inline"><mml:mi>j</mml:mi></mml:math></inline-formula>th basis function, and <inline-formula><mml:math id="M36" display="inline"><mml:mrow><mml:msub><mml:mi>B</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is the <inline-formula><mml:math id="M37" display="inline"><mml:mi>j</mml:mi></mml:math></inline-formula>th B-spline basis function evaluated at a reference height <inline-formula><mml:math id="M38" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. A roughness penalty controlled by a smoothing parameter <inline-formula><mml:math id="M39" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula> is incorporated in the prior on <inline-formula><mml:math id="M40" display="inline"><mml:mi mathvariant="bold-italic">β</mml:mi></mml:math></inline-formula>, such that higher values of <inline-formula><mml:math id="M41" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula> serve to favour smoother splines (Appendix A). The number of knots and the roughness penalty each influence spline flexibility in different ways: increasing <inline-formula><mml:math id="M42" display="inline"><mml:mi>k</mml:mi></mml:math></inline-formula> provides a finer resolution for fitting local features, whereas increasing <inline-formula><mml:math id="M43" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula> penalizes abrupt changes and yields smoother fits. The knots for the spline can be distributed across the reference height range that the converted measurement heights occupy for a specific combination of shift parameters (<inline-formula><mml:math id="M44" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>) and scale parameters (<inline-formula><mml:math id="M45" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>, i.e. relative sedimentation rates). Our current model implementation uses evenly spaced knots, but knot placement could also follow, for example, the density of measurements. Alternatively, the knots can be fixed at specific heights on the reference scale, in which case combinations of <inline-formula><mml:math id="M46" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M47" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> that result in converted measurement heights falling outside the knot range cannot be evaluated.</p>
      <p id="d2e737">The likelihood of an alignment, given <inline-formula><mml:math id="M48" display="inline"><mml:mi mathvariant="bold-italic">β</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M49" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M50" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula>, is determined by the residual deviations of the <inline-formula><mml:math id="M51" display="inline"><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values from the corresponding <inline-formula><mml:math id="M52" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">μ</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values. The overall likelihood for <inline-formula><mml:math id="M53" display="inline"><mml:mi>n</mml:mi></mml:math></inline-formula> data points is obtained by taking the product over all individual likelihoods for each pair of <inline-formula><mml:math id="M54" display="inline"><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M55" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">μ</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>:

            <disp-formula id="Ch1.E4" content-type="numbered"><label>4</label><mml:math id="M56" display="block"><mml:mrow><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold">y</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="bold-italic">β</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="italic">σ</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="italic">λ</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:munderover><mml:mo movablelimits="false">∏</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:munderover><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:msqrt><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="italic">π</mml:mi><mml:msup><mml:mi mathvariant="italic">σ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:msqrt></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:msup><mml:mi mathvariant="normal">e</mml:mi><mml:mrow><mml:mfenced close=")" open="("><mml:mrow><mml:mo>-</mml:mo><mml:mstyle scriptlevel="+1"><mml:mfrac><mml:mrow><mml:mo>(</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="italic">μ</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi mathvariant="italic">σ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:math></disp-formula>

          We thus assume that the deviations of the data from the spline are independently and identically distributed according to a normal distribution with mean 0 and standard deviation <inline-formula><mml:math id="M57" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula>.</p>
      <p id="d2e916">Our model allows for using more than one type of measurement simultaneously.  In this case, a separate spline is fitted to all data, from all sites, for each type of measurement. The product of all likelihoods from all measurement types gives the overall likelihood.</p>
</sec>
<sec id="Ch1.S2.SS2">
  <label>2.2</label><title>Alignment and partitioning</title>
      <p id="d2e928">In order to generate alignments of stratigraphic signals from different sites, one site is picked as a fixed reference site. The other sites are shifted and stretched (or squeezed) relative to the fixed reference site <inline-formula><mml:math id="M58" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>. This requires specifying a shift parameter (height) <inline-formula><mml:math id="M59" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, which anchors an arbitrary, specified height of site <inline-formula><mml:math id="M60" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> to a height in the reference site <inline-formula><mml:math id="M61" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>. Here, we anchor the top of site <inline-formula><mml:math id="M62" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>, so we set <inline-formula><mml:math id="M63" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> meaning <inline-formula><mml:math id="M64" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> will be the height at site <inline-formula><mml:math id="M65" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> that aligns with the top of site <inline-formula><mml:math id="M66" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>. To stretch or squeeze site <inline-formula><mml:math id="M67" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>, a relative sedimentation rate <inline-formula><mml:math id="M68" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> can be specified, where <inline-formula><mml:math id="M69" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is defined relative to the reference site. For any height <inline-formula><mml:math id="M70" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> at site <inline-formula><mml:math id="M71" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>, the corresponding height in the reference site <inline-formula><mml:math id="M72" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> can then be calculated as

            <disp-formula id="Ch1.E5" content-type="numbered"><label>5</label><mml:math id="M73" display="block"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mi>r</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math id="M74" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the height of the top of site <inline-formula><mml:math id="M75" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>. Although we here chose the top of site <inline-formula><mml:math id="M76" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> as the reference horizon <inline-formula><mml:math id="M77" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> for simplicity, any horizon at site <inline-formula><mml:math id="M78" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> can be used as <inline-formula><mml:math id="M79" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>. A <inline-formula><mml:math id="M80" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> implies that site <inline-formula><mml:math id="M81" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> has a lower sedimentation rate than site <inline-formula><mml:math id="M82" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>, and consequently, <inline-formula><mml:math id="M83" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> has to be stretched to match <inline-formula><mml:math id="M84" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>. A <inline-formula><mml:math id="M85" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>, i.e. a higher sedimentation rate at site <inline-formula><mml:math id="M86" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> will lead to <inline-formula><mml:math id="M87" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> being squeezed to match <inline-formula><mml:math id="M88" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>.</p>
      <p id="d2e1280">The model described here is simple in that the same <inline-formula><mml:math id="M89" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> is applied to all measurements of the same site. In this scenario, any site may be used as the reference site. Below, we introduce more complex models with more than one sedimentation rate per site, and with hiatuses. With these models, it is practical to select the site with the most sedimentation rate changes and hiatuses as the reference site. This reduces the number of unknown parameters in the model, making it easier to obtain a representative sample from the posterior.</p>
<sec id="Ch1.S2.SS2.SSS1">
  <label>2.2.1</label><title>Multiple sedimentation rates per site</title>
      <p id="d2e1297">Instead of having one sedimentation rate per site, sites can be partitioned, reflecting for example lithological units, with each partition being modelled with a distinct sedimentation rate:

              <disp-formula id="Ch1.E6" content-type="numbered"><label>6</label><mml:math id="M90" display="block"><mml:mtable rowspacing="0.2ex" class="aligned" columnspacing="1em" displaystyle="true" columnalign="right left"><mml:mtr><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:msub><mml:mi>h</mml:mi><mml:mi>r</mml:mi></mml:msub><mml:mo>=</mml:mo></mml:mrow></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msubsup><mml:mo movablelimits="false">∑</mml:mo><mml:mi>l</mml:mi><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msubsup><mml:mfenced close=")" open="("><mml:mrow><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>p</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>+</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:mfenced><mml:mo>-</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mstyle displaystyle="true" class="stylechange"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mo>×</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mspace linebreak="nobreak" width="0.33em"/><mml:mo>,</mml:mo><mml:mspace linebreak="nobreak" width="1em"/><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>,</mml:mo><mml:mi mathvariant="normal">…</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:math></disp-formula>

            Here, <inline-formula><mml:math id="M91" display="inline"><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the number of partitions encountered from <inline-formula><mml:math id="M92" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mtext>top</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math id="M93" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math id="M94" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the top height of partition <inline-formula><mml:math id="M95" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> at site <inline-formula><mml:math id="M96" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>, and <inline-formula><mml:math id="M97" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>+</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the top height of the partition below partition <inline-formula><mml:math id="M98" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> at site <inline-formula><mml:math id="M99" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>. If <inline-formula><mml:math id="M100" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> falls in the first partition from the top, the calculation simplifies to the equivalent of Eq. (5), with <inline-formula><mml:math id="M101" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, the top height of the first partition being also the top height of site <inline-formula><mml:math id="M102" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>. The relative sedimentation rates of partitions, <inline-formula><mml:math id="M103" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>p</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, can differ for each partition in each site, or partitions in different positions within a site or across sites may share sedimentation rates.</p>
</sec>
<sec id="Ch1.S2.SS2.SSS2">
  <label>2.2.2</label><title>Site-specific sedimentation rate multipliers</title>
      <p id="d2e1648">The sedimentation rate model above can be further expanded by adding an overall site-specific sedimentation rate multiplier <inline-formula><mml:math id="M104" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>:

              <disp-formula id="Ch1.E7" content-type="numbered"><label>7</label><mml:math id="M105" display="block"><mml:mtable rowspacing="0.2ex" class="aligned" columnspacing="1em" displaystyle="true" columnalign="right left"><mml:mtr><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:msub><mml:mi>h</mml:mi><mml:mi>r</mml:mi></mml:msub><mml:mo>=</mml:mo></mml:mrow></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msubsup><mml:mo movablelimits="false">∑</mml:mo><mml:mi>l</mml:mi><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msubsup><mml:mfenced close=")" open="("><mml:mrow><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>p</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>+</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:mfenced></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mstyle class="stylechange" displaystyle="true"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mo>-</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mspace linebreak="nobreak" width="0.33em"/><mml:mo>,</mml:mo><mml:mspace linebreak="nobreak" width="1em"/><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>,</mml:mo><mml:mi mathvariant="normal">…</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:math></disp-formula>

            This may be useful in scenarios where sedimentation rates systematically differ between sites, perhaps due to varying distances from a sediment source, but where the sedimentation rate ratios of different partitions are assumed to be constant across sites.</p>
</sec>
<sec id="Ch1.S2.SS2.SSS3">
  <label>2.2.3</label><title>Hiatuses</title>
      <p id="d2e1863">Known hiatuses (also referred to as unconformities or stratigraphic gaps) can be included at specific pre-defined locations in a site. Expanding Eq. (5) to include gaps of height <inline-formula><mml:math id="M106" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula>, we obtain

              <disp-formula id="Ch1.E8" content-type="numbered"><label>8</label><mml:math id="M107" display="block"><mml:mtable class="split" rowspacing="0.2ex" displaystyle="true" columnalign="right left"><mml:mtr><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mi>r</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mo>-</mml:mo><mml:munderover><mml:mo movablelimits="false">∑</mml:mo><mml:mi>g</mml:mi><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:msub><mml:mi>G</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:munderover><mml:msub><mml:mi mathvariant="italic">δ</mml:mi><mml:mi>g</mml:mi></mml:msub><mml:mspace linebreak="nobreak" width="0.33em"/><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd/><mml:mtd><mml:mrow><mml:mi>g</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>,</mml:mo><mml:mi mathvariant="normal">…</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:msub><mml:mi>G</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:math></disp-formula>

            where <inline-formula><mml:math id="M108" display="inline"><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mrow><mml:msub><mml:mi>G</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the number of gaps encountered from <inline-formula><mml:math id="M109" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> until height <inline-formula><mml:math id="M110" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. In a correlation on an absolute age scale (Sect. 2.2.5), hiatuses would instead be expressed as durations, not heights.</p>
</sec>
<sec id="Ch1.S2.SS2.SSS4">
  <label>2.2.4</label><title>Tie points</title>
      <p id="d2e2046">Tie points define specific heights within an aligned site and assign a probability distribution to indicate to which horizon these heights correspond on the reference scale. For example, a tie point might be a lithological boundary, a biostratigraphic horizon, or a radiometric date. If tie points are specified, the likelihood of an alignment is expanded to include not only the fit of the signal data to the spline, but also the positions of the ties on the reference height scale relative to the specified probability distribution.</p>
      <p id="d2e2049">For example, a point in an aligned section which is tied by observation to the reference section at a position <inline-formula><mml:math id="M111" display="inline"><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> with a normally distributed uncertainty with standard deviation <inline-formula><mml:math id="M112" display="inline"><mml:mrow><mml:msub><mml:mi>s</mml:mi><mml:mi>t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> that ends up being shifted to a reference height <inline-formula><mml:math id="M113" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mi>t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (computed from the relevant <inline-formula><mml:math id="M114" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M115" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> parameters) contributes a likelihood of

              <disp-formula id="Ch1.E9" content-type="numbered"><label>9</label><mml:math id="M116" display="block"><mml:mrow><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:mi mathvariant="normal">|</mml:mi><mml:msub><mml:mi>h</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>s</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:msqrt><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="italic">π</mml:mi><mml:msubsup><mml:mi>s</mml:mi><mml:mi>t</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msubsup></mml:mrow></mml:msqrt></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:msup><mml:mi mathvariant="normal">e</mml:mi><mml:mrow><mml:mfenced close=")" open="("><mml:mrow><mml:mo>-</mml:mo><mml:mstyle scriptlevel="+1"><mml:mfrac><mml:mrow><mml:mo>(</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msubsup><mml:mi>s</mml:mi><mml:mi>t</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msubsup></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:math></disp-formula>

            to the overall likelihood of the model.</p>
</sec>
<sec id="Ch1.S2.SS2.SSS5">
  <label>2.2.5</label><title>Age-scale alignment</title>
      <p id="d2e2201">Data on an (absolute) age scale can be aligned using the methods introduced above by using ages instead of heights. However, height-scale data can be aligned on an age-scale if absolute age constraints (specified as ties) are provided from at least one site. In this case, all sites will be shifted to align on a common age scale, i.e., there is no reference site.</p>
      <p id="d2e2204">Analogous to the heights in the reference height scale in Eq. (5), ages (<inline-formula><mml:math id="M117" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>) can be calculated as:

              <disp-formula id="Ch1.E10" content-type="numbered"><label>10</label><mml:math id="M118" display="block"><mml:mrow><mml:mi>a</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>+</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

            Here, <inline-formula><mml:math id="M119" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">α</mml:mi><mml:mrow><mml:mtext>top</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the top age (minimum age), rather than top height (maximum height), of site <inline-formula><mml:math id="M120" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>. Sedimentation rates <inline-formula><mml:math id="M121" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ν</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> need to be expressed on the common age scale, rather than relative to a reference site. Equations (6)–(8) can be modified accordingly for an analysis on the age scale.</p>
      <p id="d2e2308">It should be noted that due to sedimentation rates being fixed for an entire site or within partitions, our current model implementation does not necessarily result in increasing age uncertainty away from absolute age constraints. Potential sedimentation rate changes within sites or partitions could lead to our model underestimating age uncertainty with growing stratigraphic distance from absolute age constraints (see De Vleeschouwer and Parnell, 2014).</p>
</sec>
</sec>
<sec id="Ch1.S2.SS3">
  <label>2.3</label><title>Priors</title>
      <p id="d2e2320">The Bayesian framework requires priors to be placed on all unknown model parameters. In our model, these include the alignment parameters (e.g. <inline-formula><mml:math id="M122" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M123" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>), the smoothing parameter <inline-formula><mml:math id="M124" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula>, the residual standard deviation <inline-formula><mml:math id="M125" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> (if it is not fixed), and the spline coefficients <inline-formula><mml:math id="M126" display="inline"><mml:mi mathvariant="bold-italic">β</mml:mi></mml:math></inline-formula>. The priors on the alignment parameters determine the range of possible alignments and need to be chosen with care. For the other parameters, weakly informative priors with minimal influence on the analysis are preferred (Appendix A). In addition to those priors, we penalise a lack of overlap by specifying a prior probability of data points from different sites overlapping each other.</p>
<sec id="Ch1.S2.SS3.SSS1">
  <label>2.3.1</label><title>Alignment parameters</title>
      <p id="d2e2365">The priors on the alignment parameters should reflect the stratigraphic knowledge on the input data. The user may specify different types of prior distributions (e.g., normal, uniform, exponential) for the alignment parameters during model setup. <list list-type="bullet"><list-item>
      <p id="d2e2370"><inline-formula><mml:math id="M127" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> determines the reference site (site <inline-formula><mml:math id="M128" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>) height or age that a specific position within the aligned site (site <inline-formula><mml:math id="M129" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>) corresponds to. In the absence of prior knowledge on how the sites are likely to align, a uniform prior can be placed on <inline-formula><mml:math id="M130" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>. For example, if <inline-formula><mml:math id="M131" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> refers to the top of site <inline-formula><mml:math id="M132" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>, a uniform prior on <inline-formula><mml:math id="M133" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> with <inline-formula><mml:math id="M134" display="inline"><mml:mo>min⁡</mml:mo></mml:math></inline-formula> and <inline-formula><mml:math id="M135" display="inline"><mml:mo>max⁡</mml:mo></mml:math></inline-formula> equal to the height or age range of site <inline-formula><mml:math id="M136" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula> implies that the top of site <inline-formula><mml:math id="M137" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> will be placed within the height range of site <inline-formula><mml:math id="M138" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>.</p></list-item><list-item>
      <p id="d2e2458"><inline-formula><mml:math id="M139" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> is either a relative (<italic>height scale alignment</italic>) or an absolute (<italic>age scale alignment</italic>) sedimentation rate. In our model implementation, priors are placed on the natural logarithm of <inline-formula><mml:math id="M140" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M141" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, rather than on <inline-formula><mml:math id="M142" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> directly. Specifying rate parameters on the logarithmic scale ensures that their priors are symmetric: a doubling or halving of a rate has equivalent distances on the logarithmic scale. If the sedimentation rate is relative, <inline-formula><mml:math id="M143" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:math></inline-formula> (i.e. <inline-formula><mml:math id="M144" display="inline"><mml:mrow><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>) results in “stretching”, and <inline-formula><mml:math id="M145" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:math></inline-formula> (i.e. <inline-formula><mml:math id="M146" display="inline"><mml:mrow><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>) results in “squeezing” of site <inline-formula><mml:math id="M147" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> relative to site <inline-formula><mml:math id="M148" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>. In the absence of strong prior knowledge about the relative sedimentation rate, a normal prior on <inline-formula><mml:math id="M149" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> with a mean of 0 places equal prior probability on “stretching” or “squeezing” of site <inline-formula><mml:math id="M150" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> relative to site <inline-formula><mml:math id="M151" display="inline"><mml:mi>r</mml:mi></mml:math></inline-formula>. The standard deviation requires at least a broad guess of the potential magnitude of sedimentation rate differences. For example, a standard deviation of <inline-formula><mml:math id="M152" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mn mathvariant="normal">4</mml:mn><mml:mo>)</mml:mo><mml:mo>/</mml:mo><mml:mn mathvariant="normal">1.96</mml:mn></mml:mrow></mml:math></inline-formula> places 95 % of prior probability on <inline-formula><mml:math id="M153" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:mn mathvariant="normal">4</mml:mn><mml:mo>&lt;</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:math></inline-formula> for <inline-formula><mml:math id="M154" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo><mml:mo>∼</mml:mo><mml:mtext>Normal</mml:mtext><mml:mo>(</mml:mo><mml:mn mathvariant="normal">0</mml:mn><mml:mo>,</mml:mo><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mn mathvariant="normal">4</mml:mn><mml:mo>)</mml:mo><mml:mo>/</mml:mo><mml:mn mathvariant="normal">1.96</mml:mn><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. If <inline-formula><mml:math id="M155" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> is an absolute sedimentation rate, the range of plausible prior sedimentation rates may be estimated from the absolute age constraints.</p></list-item><list-item>
      <p id="d2e2691"><inline-formula><mml:math id="M156" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is a multiplier applied to all relative or absolute sedimentation rates <inline-formula><mml:math id="M157" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> corresponding to a single site <inline-formula><mml:math id="M158" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>. As with <inline-formula><mml:math id="M159" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M160" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:math></inline-formula> (i.e. <inline-formula><mml:math id="M161" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>) causes additional “stretching”, and <inline-formula><mml:math id="M162" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> (i.e. <inline-formula><mml:math id="M163" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:math></inline-formula>) causes additional “squeezing” of site <inline-formula><mml:math id="M164" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>.</p></list-item><list-item>
      <p id="d2e2806"><inline-formula><mml:math id="M165" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula> is the reference height range or duration of a hiatus. An exponential prior may be useful when little is known about the extent of the hiatus, placing higher probabilities on short extents. The rate needs to be chosen to make sense in the context of the height of the sections, or of the anticipated age range of the sites.</p></list-item></list></p>
</sec>
<sec id="Ch1.S2.SS3.SSS2">
  <label>2.3.2</label><title>Penalising a lack of overlap</title>
      <p id="d2e2823">Individual splines fitted to data from each site separately can almost always follow the data more closely than a single spline fitted to aligned data from all sites. Given enough knots, alignments in which the data do not overlap, or only overlap little, will thus generally result in a higher likelihood than alignments with a partial or full overlap. This means that if the priors allow non-overlapping alignments, those will generally be preferred in the model inference. To counteract this tendency, we impose a prior on the overlap of each individual data point from all sites that penalises non-overlap with data from other sites.</p>
      <p id="d2e2826">The prior on overlap for data point <inline-formula><mml:math id="M166" display="inline"><mml:mi>i</mml:mi></mml:math></inline-formula> from site <inline-formula><mml:math id="M167" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula> is

              <disp-formula id="Ch1.E11" content-type="numbered"><label>11</label><mml:math id="M168" display="block"><mml:mrow><mml:mi>P</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi>i</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:msup><mml:mi mathvariant="normal">e</mml:mi><mml:mrow><mml:mfenced open="(" close=")"><mml:mrow><mml:mo>-</mml:mo><mml:msqrt><mml:mrow><mml:mi>S</mml:mi><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msqrt><mml:mo>+</mml:mo><mml:msqrt><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mrow><mml:mtext>overlap</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msqrt></mml:mrow></mml:mfenced><mml:mo>×</mml:mo><mml:msub><mml:mi>c</mml:mi><mml:mtext>overlap</mml:mtext></mml:msub></mml:mrow></mml:msup></mml:mrow></mml:math></disp-formula>

            where <inline-formula><mml:math id="M169" display="inline"><mml:mi>S</mml:mi></mml:math></inline-formula> is the number of sites in the analysis, <inline-formula><mml:math id="M170" display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mrow><mml:mtext>overlap</mml:mtext><mml:mo>,</mml:mo><mml:mi>s</mml:mi><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the number of other sites overlapping the reference height <inline-formula><mml:math id="M171" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mi>r</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> or age <inline-formula><mml:math id="M172" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> of point <inline-formula><mml:math id="M173" display="inline"><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math id="M174" display="inline"><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mtext>overlap</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> is a constant. This formulation implies that the penalty for a point <inline-formula><mml:math id="M175" display="inline"><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> that overlaps all other sites is 0, and the penalty is strongest (most negative) if <inline-formula><mml:math id="M176" display="inline"><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> overlaps no other sites. To work effectively, the penalty needs to be stronger for data sets with little noise (low residual <inline-formula><mml:math id="M177" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula>), to offset the larger likelihood differences resulting from fitting a spline with low <inline-formula><mml:math id="M178" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula>. A range of <inline-formula><mml:math id="M179" display="inline"><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mtext>overlap</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> values may work in practice. A formulation that we have found works well in many scenarios sets

              <disp-formula id="Ch1.E12" content-type="numbered"><label>12</label><mml:math id="M180" display="block"><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mtext>overlap</mml:mtext></mml:msub><mml:mo>=</mml:mo><mml:mi>c</mml:mi><mml:mo>×</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mi>S</mml:mi></mml:mfrac></mml:mstyle><mml:munderover><mml:mo movablelimits="false">∑</mml:mo><mml:mrow><mml:mi>s</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow><mml:mi>S</mml:mi></mml:munderover><mml:msup><mml:mfenced close=")" open="("><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mrow><mml:mi>y</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:mi>q</mml:mi></mml:msup></mml:mrow></mml:math></disp-formula>

            where <inline-formula><mml:math id="M181" display="inline"><mml:mi>c</mml:mi></mml:math></inline-formula> is a constant determining the strength of the overlap penalty (set to a default of <inline-formula><mml:math id="M182" display="inline"><mml:mrow><mml:mi>c</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:math></inline-formula>), <inline-formula><mml:math id="M183" display="inline"><mml:mrow><mml:mi>q</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> if <inline-formula><mml:math id="M184" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> is fixed, and <inline-formula><mml:math id="M185" display="inline"><mml:mrow><mml:mi>q</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula> if <inline-formula><mml:math id="M186" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> is variable (i.e. estimated in the model inference). Here, <inline-formula><mml:math id="M187" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mrow><mml:mi>y</mml:mi><mml:mo>,</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the standard deviation of all data <inline-formula><mml:math id="M188" display="inline"><mml:mi>y</mml:mi></mml:math></inline-formula> from site <inline-formula><mml:math id="M189" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>, and <inline-formula><mml:math id="M190" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the residual standard deviation of a Bayesian spline fitted to the data <inline-formula><mml:math id="M191" display="inline"><mml:mi>y</mml:mi></mml:math></inline-formula> from site <inline-formula><mml:math id="M192" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>, using the same priors as for the overall model inference.</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S3">
  <label>3</label><title>Model illustration</title>
      <p id="d2e3209">We illustrate the performance of our stratigraphic alignment method with a simple, artificial dataset (Fig. 2a). We generated measurements from a reference site (<inline-formula><mml:math id="M193" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>ref</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>) using a sine wave covering 3.5 periods, where each period corresponds to <inline-formula><mml:math id="M194" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula> radians. To generate the signal data, we intercepted this sine wave at heights <inline-formula><mml:math id="M195" display="inline"><mml:mi>h</mml:mi></mml:math></inline-formula> with 250 evenly spaced points per period, i.e. the number of data points (<inline-formula><mml:math id="M196" display="inline"><mml:mi>n</mml:mi></mml:math></inline-formula>) is <inline-formula><mml:math id="M197" display="inline"><mml:mrow><mml:mn mathvariant="normal">3.5</mml:mn><mml:mo>×</mml:mo><mml:mn mathvariant="normal">250</mml:mn><mml:mo>=</mml:mo><mml:mn mathvariant="normal">875</mml:mn></mml:mrow></mml:math></inline-formula>. Each signal value <inline-formula><mml:math id="M198" display="inline"><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> was generated with random white noise <inline-formula><mml:math id="M199" display="inline"><mml:mrow><mml:mi mathvariant="italic">σ</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mn mathvariant="normal">1</mml:mn><mml:mn mathvariant="normal">5</mml:mn></mml:mfrac></mml:mstyle></mml:mrow></mml:math></inline-formula> added, such that

          <disp-formula id="Ch1.E13" content-type="numbered"><label>13</label><mml:math id="M200" display="block"><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>∼</mml:mo><mml:mtext>Normal</mml:mtext><mml:mfenced open="(" close=")"><mml:mrow><mml:msub><mml:mi mathvariant="italic">η</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mi>sin⁡</mml:mi><mml:mfenced close=")" open="("><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mn mathvariant="normal">2</mml:mn></mml:mfrac></mml:mstyle><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:mfenced><mml:mo>,</mml:mo><mml:mi mathvariant="italic">σ</mml:mi></mml:mrow></mml:mfenced><mml:mspace linebreak="nobreak" width="0.33em"/><mml:mo>,</mml:mo><mml:mspace width="1em" linebreak="nobreak"/><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>,</mml:mo><mml:mi mathvariant="normal">…</mml:mi><mml:mo>,</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:math></disp-formula>

        The factor <inline-formula><mml:math id="M201" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">η</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> modulates the amplitude of the sine wave at each height <inline-formula><mml:math id="M202" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. It was set to <inline-formula><mml:math id="M203" display="inline"><mml:mrow><mml:mi mathvariant="italic">η</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> for the heights ranging from <inline-formula><mml:math id="M204" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">0.5</mml:mn><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math id="M205" display="inline"><mml:mrow><mml:mn mathvariant="normal">5</mml:mn><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula>, and to <inline-formula><mml:math id="M206" display="inline"><mml:mrow><mml:mi mathvariant="italic">η</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.75</mml:mn></mml:mrow></mml:math></inline-formula> from heights <inline-formula><mml:math id="M207" display="inline"><mml:mrow><mml:mn mathvariant="normal">5</mml:mn><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math id="M208" display="inline"><mml:mrow><mml:mn mathvariant="normal">6.5</mml:mn><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula>, which reduces the amplitude beginning in the middle of the third period of the sine wave. The aligned signal was simulated as above, but from a sine wave covering one period, sampling 250 data points, again with random noise using <inline-formula><mml:math id="M209" display="inline"><mml:mrow><mml:mi mathvariant="italic">σ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M210" display="inline"><mml:mrow><mml:mi mathvariant="italic">η</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>. To simulate a sedimentation rate twice as high as at the reference site, we multiplied the heights of <inline-formula><mml:math id="M211" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> by 2. The heights of <inline-formula><mml:math id="M212" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> were then shifted to start at 0.</p>

      <fig id="F2" specific-use="star"><label>Figure 2</label><caption><p id="d2e3497">Model illustration using artificial data. <bold>(a)</bold> Input data: Quantitative stratigraphic data from two sites. The blue line indicates the range in which <inline-formula><mml:math id="M213" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>ref</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> was created with <inline-formula><mml:math id="M214" display="inline"><mml:mrow><mml:mi mathvariant="italic">η</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>, and the purple line above indicates the range for which <inline-formula><mml:math id="M215" display="inline"><mml:mi mathvariant="italic">η</mml:mi></mml:math></inline-formula> was set to 0.75 to lower the amplitude. <bold>(b)</bold> Two alignments identified by the inference, with (<inline-formula><mml:math id="M216" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; blue squares) matching the first or second period of (<inline-formula><mml:math id="M217" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>ref</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; red points). The alignments shown here correspond to two distinct samples from the posterior; other samples will result in slightly different positions of (<inline-formula><mml:math id="M218" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>). The curved dark lines show the cubic spline corresponding to each alignment. <bold>(c)</bold> Posterior densities of <inline-formula><mml:math id="M219" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M220" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. The two modes of <inline-formula><mml:math id="M221" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> correspond to the two distinct alignments in <bold>(b)</bold>. The dotted lines indicate the <inline-formula><mml:math id="M222" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> values with which (<inline-formula><mml:math id="M223" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>) was simulated, and the two plausible <inline-formula><mml:math id="M224" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> values. <bold>(d)</bold> Trace plots of <inline-formula><mml:math id="M225" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M226" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. The three distinct colours correspond to the three independent model runs. For visual clarity, only 75 selected samples are shown from each run.</p></caption>
        <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f02.png"/>

      </fig>

      <p id="d2e3661">The aligned signal should thus match either the first or the second, but not the third period of the reference signal. To align the two sites, we used a simple model with a site-specific shift <inline-formula><mml:math id="M227" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, referring to the top of <inline-formula><mml:math id="M228" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and relative sedimentation rate <inline-formula><mml:math id="M229" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> as in Eq. (5). From the data generation, we know that the posterior of <inline-formula><mml:math id="M230" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> should be <inline-formula><mml:math id="M231" display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula>, with <inline-formula><mml:math id="M232" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">0.69</mml:mn></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math id="M233" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> (defined as the reference height corresponding to the top height of <inline-formula><mml:math id="M234" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>) should be <inline-formula><mml:math id="M235" display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula> (top of first period) or <inline-formula><mml:math id="M236" display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">4</mml:mn><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula> (top of second period).</p>
      <p id="d2e3768">To minimise the influence of the priors, we used a uniform prior on <inline-formula><mml:math id="M237" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> that extends well beyond the alignment positions known from generating the data, and a broad normal prior on <inline-formula><mml:math id="M238" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> that encompasses the known sedimentation rate <inline-formula><mml:math id="M239" display="inline"><mml:mrow><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula> (Fig. 2b):

              <disp-formula specific-use="align" content-type="numbered"><mml:math id="M240" display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E14"><mml:mtd><mml:mtext>14</mml:mtext></mml:mtd><mml:mtd><mml:mstyle class="stylechange" displaystyle="true"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mi>P</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">α</mml:mi><mml:mo>)</mml:mo><mml:mo>∼</mml:mo><mml:mtext>Uniform</mml:mtext><mml:mo>(</mml:mo><mml:mo>-</mml:mo><mml:mi mathvariant="italic">π</mml:mi><mml:mo>,</mml:mo><mml:mn mathvariant="normal">8</mml:mn><mml:mi mathvariant="italic">π</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E15"><mml:mtd><mml:mtext>15</mml:mtext></mml:mtd><mml:mtd><mml:mstyle displaystyle="true" class="stylechange"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mi>P</mml:mi><mml:mo>(</mml:mo><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo><mml:mo>)</mml:mo><mml:mo>∼</mml:mo><mml:mtext>Normal</mml:mtext><mml:mo>(</mml:mo><mml:mn mathvariant="normal">0</mml:mn><mml:mo>,</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>)</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

        These priors place 95 % of prior probability for the relative sedimentation rate of <inline-formula><mml:math id="M241" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> between 0.14 and 7.1, and place the top of <inline-formula><mml:math id="M242" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> anywhere from half a period below the start of the first period (<inline-formula><mml:math id="M243" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula>) up to one period above the third period (<inline-formula><mml:math id="M244" display="inline"><mml:mrow><mml:mn mathvariant="normal">8</mml:mn><mml:mi mathvariant="italic">π</mml:mi></mml:mrow></mml:math></inline-formula>). For the cubic spline, we specify 20 evenly spaced knots, which is more than enough to approximate the three periods of the sine wave.</p>
      <p id="d2e3927">We estimated the posterior of the model with three independent runs, each with 16 chains and 60 000 iterations. The first 10 000 samples were discarded as burn-in, and every 25th iteration was recorded, resulting a total of 6000 samples after burn-in across all three independent model runs.</p>
      <p id="d2e3930">The results show that the analysis identified both matching alignments, corresponding to the first and second period of the reference site (Fig. 2b). The posterior probability for (<inline-formula><mml:math id="M245" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>) matching period 1 is 50.1 %, and 49.9 % for matching period 2. A density plot of the posterior of <inline-formula><mml:math id="M246" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M247" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> shows that <inline-formula><mml:math id="M248" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> has a bimodal posterior, corresponding to the two alignments (Fig. 2c). The trace plots indicate good mixing of the chains (Fig. 2d), suggesting that the posterior estimates are robust.</p>
      <p id="d2e3972">It is notable that the model estimate for the relative sedimentation rate <inline-formula><mml:math id="M249" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> is lower at 1.90 (95 % credible interval: 1.82–1.99) than the value used for the data generation (2.00). Reported values, here and throughout, represent the posterior median, with 95 <inline-formula><mml:math id="M250" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:math></inline-formula> credible intervals – given in brackets – referring to the interval between the 2.5 <inline-formula><mml:math id="M251" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:math></inline-formula> and 97.5 <inline-formula><mml:math id="M252" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:math></inline-formula> points of the posterior distribution. This deviation of the posterior from the known sedimentation rate estimate arises because the priors favour greater overlap (see Sect. 2.3.2). The posterior alignment tends to “compress” the data from <inline-formula><mml:math id="M253" display="inline"><mml:mrow><mml:msub><mml:mtext>Site</mml:mtext><mml:mtext>align</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> slightly less than expected, leading to an increased overlap of points (see also Fig. 5b).</p>
</sec>
<sec id="Ch1.S4">
  <label>4</label><title>Case study: Lower Cambrian <inline-formula><mml:math id="M254" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> records</title>
      <p id="d2e4039">To demonstrate the utility of this method, we use it to align stable carbon isotope records (<inline-formula><mml:math id="M255" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula>) from lower Cambrian marine shelf carbonates (Fig. 3). We integrate a combination of radiometric dates, <inline-formula><mml:math id="M256" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> and astrochronological information from four sites to obtain age estimates for the sampled intervals from all sites, and use this age model for dating the first documented occurrence of Siberian trilobites.</p>
<sec id="Ch1.S4.SS1">
  <label>4.1</label><title>Data</title>
      <p id="d2e4075">We selected three records from the Anti-Atlas mountains in Southern Morocco, corresponding to the Oued Sdas, the Tiout and the Talat n' Yissi sections, which were part of West-Gondwana during the early Cambrian (Magaritz et al., 1991; Maloof et al., 2005, 2010; Tucker, 1986). Oued Sdas and Tiout harbour multiple precise U–Pb radiometric ages (Landing et al., 2021; Maloof et al., 2010). Talat n' Yissi has no radiometric dates, but a radiometric date exists from the stratigraphically equivalent Lemdad syncline (Landing et al., 1998) that has been correlated biostratigraphically to Talat n'Yissi with the <italic>Antatlasia gutta-pluviae</italic> zone (Maloof et al., 2005); we include this date in the analysis.  We will align these sites with each other, and with a <inline-formula><mml:math id="M257" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> record from the Sukharikha section from the northwestern Siberian platform (Kouchinsky et al., 2007), corresponding to the palaeocontinent Siberia.  There are no radiometric dates available for the Siberian section for this stratigraphic interval. Data that was inferred to be below the lower leg of the prominent “5p” excursion (lowest peak in Fig. 3a and d) was excluded to simplify the correlation, reducing the number of modelled sedimentation rates unconstrained by radiometric dates. This cropping of data affects the Oued Sdas and Sukharikha sections; Fig. 3 shows all data that was included in the analysis. <inline-formula><mml:math id="M258" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> values were used as reported by the authors of the respective publications without any scaling or other adjustments.</p>

      <fig id="F3" specific-use="star"><label>Figure 3</label><caption><p id="d2e4109">Cambrian <inline-formula><mml:math id="M259" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> data and radiometric dates from Morocco <bold>(a–c)</bold> and Siberia <bold>(d)</bold>. Different colours, in conjunction with different symbols, delineate different lithological units or formations. Circles indicate the position of radiometric dates, with mean age and 2 standard deviations denoting the uncertainty. Stars denote the positions where the oldest trilobite remains are found in Morocco <bold>(a)</bold> and Siberia <bold>(d)</bold>. The dashed line in <bold>(d)</bold> indicates a hiatus. <inline-formula><mml:math id="M260" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> indicates the reference horizon chosen for specifying the prior on the shift parameter <inline-formula><mml:math id="M261" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> for each site.</p></caption>
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f03.png"/>

        </fig>

</sec>
<sec id="Ch1.S4.SS2">
  <label>4.2</label><title>Model specification</title>
      <p id="d2e4169">To align the four sites on the age scale, we specify an <inline-formula><mml:math id="M262" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> parameter on the absolute age scale (<inline-formula><mml:math id="M263" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>) for each site, and use absolute, rather than relative sedimentation rates (expressed in <inline-formula><mml:math id="M264" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>). We encapsulate variation in sedimentation rates (<inline-formula><mml:math id="M265" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>) by partitioning sites into members, formations or lithological units, leading to multiple sedimentation rates per site. As there are few radiometric dates to constrain sedimentation rates, partitions shared between the Moroccan sites are set to have the same relative sedimentation rate across sites. To account for potentially faster or slower sedimentation rates at different sites, a site-specific sedimentation rate multiplier <inline-formula><mml:math id="M266" display="inline"><mml:mi mathvariant="italic">ζ</mml:mi></mml:math></inline-formula> is added for Oued Sdas and Talat n'Yissi that is multiplied with the <inline-formula><mml:math id="M267" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> from those sites. The <inline-formula><mml:math id="M268" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> for a partition applies to all sites at which this partition occurs; for Tiout, they are used unaltered, and no <inline-formula><mml:math id="M269" display="inline"><mml:mi mathvariant="italic">ζ</mml:mi></mml:math></inline-formula> is needed for Sukharikha as there are no shared partitions with other sites. We partition the Moroccan data based on the lithostratigraphy from Maloof et al. (2005). We divide the Adoudounian Tifnout Member into a lower part (Tifnout l.), and an upper stromatolitic part (Tifnout stromatolite), as preliminary results suggested pronounced sedimentation variability between those parts. We subdivide the Lie de Vin Formation into three members; the Igoudine Formation is subdivided into two members. The Amouslek and Isaafen formations are not subdivided. The Sukharikha section is divided into two formations, which we assign separate sedimentation rates. At the boundary, a substantial hiatus is evinced by the truncation of the “7p” <inline-formula><mml:math id="M270" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> peak (Kouchinsky et al., 2007).  We include the duration of this hiatus (<inline-formula><mml:math id="M271" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula>) as an additional unknown parameter in the model.</p>
      <p id="d2e4260">The model requires priors to be specified for each of its 18 alignment parameters: Four <inline-formula><mml:math id="M272" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, eleven <inline-formula><mml:math id="M273" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>, two <inline-formula><mml:math id="M274" display="inline"><mml:mi mathvariant="italic">ζ</mml:mi></mml:math></inline-formula> and one <inline-formula><mml:math id="M275" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula> (Fig. 4). These priors are broadly guided by the radiometric dates and by previous work (Bowyer et al., 2023; Landing et al., 2021; Sinnesael et al., 2024). The <inline-formula><mml:math id="M276" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> for the Tiout and Sukharikha sites are placed at the height positions of the first trilobite fossil remains found at Tiout (Sinnesael et al., 2024), and the first appearance of Siberian trilobites correlated to Sukharikha (Landing et al., 2021; Varlamov et al., 2008).  Here, we place normal distributed priors with mean age 520 <inline-formula><mml:math id="M277" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> and a wide standard deviation of 2 Myr on the <inline-formula><mml:math id="M278" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> parameters at Tiout and Sukharikha. This prior reflects the notion that first appearance dates of trilobites may be broadly similar at <inline-formula><mml:math id="M279" display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">520</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula>, but not necessarily identical, and the data is allowed to determine the exact age of each <inline-formula><mml:math id="M280" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>. The <inline-formula><mml:math id="M281" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> priors for Oued Sdas and Talat n'Yissi are placed at the position of the lowest or the only available radiometric date, respectively, consisting of normal distributions with mean age equal to the mean age estimate of the radiometric data and a wide standard deviation of 2 <inline-formula><mml:math id="M282" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula>.</p><fig id="F4" specific-use="star"><label>Figure 4</label><caption><p id="d2e4352">Priors on the 18 alignment parameters for the Cambrian model. Prior probability density is shown <bold>(a)</bold> for four <inline-formula><mml:math id="M283" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> parameters corresponding to one site each (priors for Tiout and Sukharikha in grey are identical), <bold>(b)</bold> for six <inline-formula><mml:math id="M284" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> (sedimentation rate) parameters with little prior knowledge, <bold>(c)</bold> for five <inline-formula><mml:math id="M285" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> parameters from Morocco with tight priors based on astrochronology, <bold>(d)</bold> for <inline-formula><mml:math id="M286" display="inline"><mml:mi mathvariant="italic">ζ</mml:mi></mml:math></inline-formula> parameters (site-specific sedimentation rate multipliers) for Oued Sdas and Talat n'Yissi (identical), and <bold>(e)</bold> for the duration of the hiatus between the Sukharikha and the Krasnoporog formations. The width of the red bar in <bold>(b)</bold> visualises the range of sedimentation rates spanned by <bold>(c)</bold>. Panel <bold>(f)</bold> visualises two alignments generated by randomly drawing parameter values from their respective priors, to give an indication of the broad range of alignments that the priors on the alignment parameters allow; colours correspond to the four sites (see Fig. 6). Panels <bold>(b–d)</bold> are depicted with a logarithmic <inline-formula><mml:math id="M287" display="inline"><mml:mi>x</mml:mi></mml:math></inline-formula> axis as the priors were specified on <inline-formula><mml:math id="M288" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M289" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ζ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>.</p></caption>
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f04.png"/>

        </fig>

      <p id="d2e4454">For the sedimentation rates, priors informed by an astrochronology of the Tiout section (Sinnesael et al., 2024) are used for the following five stratigraphic partitions: The lower, middle and upper members of the Lie de Vin Formation, and for the lower and upper (Tiout Member) members of the Igoudine Formation. Those priors are chosen such that the 95 percentile interval of <inline-formula><mml:math id="M290" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> spans the minimum and maximum of the astrochronological sedimentation rate estimates when using an uncertainty of <inline-formula><mml:math id="M291" display="inline"><mml:mrow><mml:mo>±</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> short eccentricity cycle for each partition, with an estimated duration of short (<inline-formula><mml:math id="M292" display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">100</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mrow class="unit"><mml:mi mathvariant="normal">kyr</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula>) eccentricity cycles ranging from 92.5–100.5 <inline-formula><mml:math id="M293" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">kyr</mml:mi></mml:mrow></mml:math></inline-formula> (two standard deviations, following Lantink et al., 2022).</p>
      <p id="d2e4496">To specify priors for the remaining Moroccan partitions (lower part of Tifnout Fm., Tifnout stromatolite, Amouslek Fm., and Isaafen Fm.), sedimentation rates between the radiometric dates from Oued Sdas and Tiout are calculated using the mean ages of the dates. The prior on <inline-formula><mml:math id="M294" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is defined as a normal distribution with a mean of 5.39, corresponding to the mean of the empirical sedimentation rates from Oued Sdas and Tiout, calculated on the logarithmic scale. A wide standard deviation of 0.75 is set, resulting in the 95 percentile interval of <inline-formula><mml:math id="M295" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> spanning 50.3–951 <inline-formula><mml:math id="M296" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>.  This interval significantly exceeds the range of sedimentation rates inferred from the radiometric dates at Oued Sdas and Tiout, 147 to 314 <inline-formula><mml:math id="M297" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, allowing for the possibility of lower or higher sedimentation rates in some partitions.</p>
      <p id="d2e4554">Prior sedimentation rate estimates for the Siberian formations are estimated in the absence of radiometric dates, very broadly based on global correlations by Bowyer et al. (2023). These correlations suggest average sedimentation rates on the order of 20–30 <inline-formula><mml:math id="M298" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>; we place a normal prior on <inline-formula><mml:math id="M299" display="inline"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> with a mean of 3.30 and a standard deviation of 0.75, resulting in a 95 percentile interval of <inline-formula><mml:math id="M300" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula> spanning 6.23–117.9 <inline-formula><mml:math id="M301" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, which allows for the possibility of significantly different sedimentation rates from those inferred by Bowyer et al. (2023).</p>
      <p id="d2e4612">Finally, a prior needs to be placed on the duration of the hiatus <inline-formula><mml:math id="M302" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula> between the Sukharikha and the Krasnoporog formations. Kouchinsky et al.  (2007) do not give an indication of the potential duration of this hiatus, but if the under- and overlying <inline-formula><mml:math id="M303" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> peaks are correlated as indicated by previous work (Bowyer et al., 2022; Landing et al., 2021), a relatively short hiatus of <inline-formula><mml:math id="M304" display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula> is likely. To express considerable uncertainty about the duration of the hiatus, we place an exponential prior on <inline-formula><mml:math id="M305" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula> with a rate of 1, which places <inline-formula><mml:math id="M306" display="inline"><mml:mrow><mml:mn mathvariant="normal">95</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula> of prior probability on the duration being <inline-formula><mml:math id="M307" display="inline"><mml:mrow><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">3</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula>, with 5 <inline-formula><mml:math id="M308" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:math></inline-formula> probability accounting for the possibility of a longer gap.</p>
      <p id="d2e4691">The cubic spline comprises 40 evenly spaced knots, allowing it to closely follow trends in the <inline-formula><mml:math id="M309" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> records while keeping the MCMC runtime manageable, as a higher knot count increases computational cost. For the smoothing parameter <inline-formula><mml:math id="M310" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula>, we applied a gamma prior with StratoBayes' default values of <inline-formula><mml:math id="M311" display="inline"><mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mi mathvariant="italic">λ</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M312" display="inline"><mml:mrow><mml:msub><mml:mi>b</mml:mi><mml:mi mathvariant="italic">λ</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1000</mml:mn></mml:mrow></mml:math></inline-formula>. We fixed <inline-formula><mml:math id="M313" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula>, which is the residual standard deviation of the overall spline, at 0.66, which is the average residual standard deviation of individual cubic splines fitted to each <inline-formula><mml:math id="M314" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> record from the four respective sites. These individual splines were constructed with 40 knots evenly spaced across the height range of each respective site and fitted with Gibbs sampling using 2000 iterations, discarding 25 <inline-formula><mml:math id="M315" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:math></inline-formula> of samples as burn-in. The same default <inline-formula><mml:math id="M316" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula> priors as described above were applied, while the prior for these splines' standard deviations was specified as a gamma prior on the precision <inline-formula><mml:math id="M317" display="inline"><mml:mi mathvariant="italic">τ</mml:mi></mml:math></inline-formula>, with <inline-formula><mml:math id="M318" display="inline"><mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mi mathvariant="italic">τ</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>b</mml:mi><mml:mi mathvariant="italic">τ</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.01</mml:mn></mml:mrow></mml:math></inline-formula> (see Appendix A for details).</p>
</sec>
<sec id="Ch1.S4.SS3">
  <label>4.3</label><title>Parameter estimation</title>
      <p id="d2e4818">This model is more complex than our earlier examples, and hence requires longer runs with more chains. We conducted four independent model runs, each with 750 000 iterations and 24 chains. The runs were executed in parallel using four workers on a desktop computer (Intel i7-10700 CPU, 8 cores/16 threads, 40 GB RAM) and completed within 5 days. The first 150 000 iterations were discarded as burn-in. From the remaining 600 000, every 50th iteration was retained, resulting in 12 000 samples per run and 48 000 samples in total.</p>
      <p id="d2e4821">Inspection of trace plots of the model runs indicates stationarity and good mixing of the chains with the exception of infrequent visits of secondary posterior modes (Appendix B, Fig. B1). The potential scale reduction factor (using Eq. 4 in Vats and Knudson, 2021) is between 1.00 and 1.05 for all alignment parameters, suggesting approximate convergence of the MCMC. The multivariate effective sample size (Vats et al., 2019) of the 48 000 samples is 4161.</p>
</sec>
<sec id="Ch1.S4.SS4">
  <label>4.4</label><title>Results</title>
      <p id="d2e4833">To identify distinctly different alignments in the posterior, a hierarchical density-based cluster analysis (Campello et al., 2015) was conducted using the inferred ages of all partition boundaries of the four sites (Fig. 4a and b).  We specified 1 % of samples (480) as the minimum number of points per cluster, resulting in three distinct clusters with 93 %, 2.8 % and 2.6 % of posterior samples, respectively, and 1.5 % of samples not being assigned to any cluster. These alignment clusters also differ in the prior probabilities and likelihoods associated with individual posterior samples.  On average, samples from alignment 1 tend to exhibit a lower degree of overlap, but a higher likelihood (Fig. 4c), indicating a better fit to the data.</p>

      <fig id="F5" specific-use="star"><label>Figure 5</label><caption><p id="d2e4838"><bold>(a, b)</bold> 2D density plots of the inferred top ages of the four sites, representing some of the ages used for obtaining alignment clusters from posterior samples. <bold>(c)</bold> 2D density plot of the ln prior probability of overlap against the overall ln likelihood. Areas with more opaque shadings correspond to a higher density of individual posterior samples. Colours correspond to alignment clusters: alignment 1 – violet; alignment 2 – blue; alignment 3 – green; outlier samples not assigned to any cluster – yellow.</p></caption>
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f05.png"/>

        </fig>

      <p id="d2e4852">Using samples from the posterior of the model parameters, alignments can be generated. Figure 6 visualises three alignments drawn from the three alignment clusters identified in the posterior. For each alignment cluster, the iteration with partition boundary ages that are, on average, closest to the median ages of the partition boundaries within that cluster is selected for displaying. All three alignments exhibit a good match between the long-term trends of the <inline-formula><mml:math id="M319" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> curves from the four sites and the common spline curve, although many shorter-term deviations are visible (Fig. 6a–c).  The spline curve notably follows the more densely sampled sites (Oued Sdas, Talat n'Yissi) more so than the thinly sampled sites (Tiout, Sukharikha), resulting in greater deviations of the latter two sites.</p>

      <fig id="F6" specific-use="star"><label>Figure 6</label><caption><p id="d2e4871">Three possible alignments identified by the inference with Cambrian data. <bold>(a)</bold> Exemplary sample from the cluster of the most likely alignment (93 % of posterior samples). <bold>(b, c)</bold> Exemplary samples from a second and third identified alignment cluster (2.8 % and 2.6 % of posterior samples, respectively). Each shown alignment corresponds to a single sample from the posterior; other samples will result in slightly different alignments. 1.5 % of samples were not assigned to any cluster (see Fig. 5). The curved dark lines show the cubic B-splines corresponding to each visualised sample. The coloured bars to the right of each alignment show the median duration of the stratigraphic partitions under each respective alignment cluster, based on the median ages of partition boundaries, with colours repeating the colour scheme of Fig. 2. <bold>(d)</bold> Posterior density of the inferred ages corresponding to the radiometric dates to the left (3 from Tiout, 4 from Oued Sdas, and 1 from Talat n'Yissi) and the first occurrences of trilobites at Tiout (Ti tril.) and Sukharikha (Sh tril.) to the right, in colours. All samples from all alignment clusters were included. Greater width corresponds to higher posterior density; all densities are scaled to have the same maximum for better visibility. Densities representing the uncertainties of radiometric dates based on their mean and standard deviation are shown in grey (left). The faint yellow shading to the right shows the prior density on <inline-formula><mml:math id="M320" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, i.e. the first appearance of trilobites at Tiout and Siberia based on a mean age of (520 <inline-formula><mml:math id="M321" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>) and a standard deviation of <inline-formula><mml:math id="M322" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula> (identical for Tiout and Siberia). Colours and shapes of the points correspond to the four sites: Tiout – brown circles; Oued Sdas – pink squares; Talat n'Yissi – green diamonds; Sukharikha – blue triangles.</p></caption>
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f06.png"/>

        </fig>

      <p id="d2e4917">The posterior age estimates for the stratigraphic positions of the radiometric dates broadly match the age estimates that were used as inputs in the analysis (Fig. 6d). The deviations are greatest for the Talat n'Yissi date (<inline-formula><mml:math id="M323" display="inline"><mml:mrow><mml:msub><mml:mtext>Ta</mml:mtext><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>), which has large uncertainty and therefore less influence on the analysis, and the second date from Oued Sdas (<inline-formula><mml:math id="M324" display="inline"><mml:mrow><mml:msub><mml:mtext>Ou</mml:mtext><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>). The first appearances of trilobites are visualised alongside the dates in Fig. 6d, and are dated to 519.46 <inline-formula><mml:math id="M325" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (519.25–519.68 <inline-formula><mml:math id="M326" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>) at Tiout. The age estimate for the first Siberian trilobites differs considerably between the different alignment solutions: For the most likely alignment 1, the age estimate is 520.79 <inline-formula><mml:math id="M327" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (520.98–520.61 <inline-formula><mml:math id="M328" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>), and for alignment 2 the estimate is somewhat higher at 521.05 <inline-formula><mml:math id="M329" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (521.19–520.91 <inline-formula><mml:math id="M330" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>). Alignment 3 suggests a significantly later appearance of Siberian trilobites at 519.98 <inline-formula><mml:math id="M331" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (520.15–519.84 <inline-formula><mml:math id="M332" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>). All three alignments place the appearance of the first Siberian trilobites before their appearance at Tiout, with the temporal gap (computed directly from the posterior distribution) being estimated at 1.33 <inline-formula><mml:math id="M333" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula> (1.09–1.54 <inline-formula><mml:math id="M334" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula>) for alignment 1, 1.71 <inline-formula><mml:math id="M335" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula> (1.54–1.87 <inline-formula><mml:math id="M336" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula>) for alignment 2, and 0.63 <inline-formula><mml:math id="M337" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula> (0.53–0.74 <inline-formula><mml:math id="M338" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula>) for alignment 3.</p>
      <p id="d2e5056">The posterior of the model runs allows the construction of age models that span the entire height of each site (Fig. 7). As sedimentation rates are constrained to be constant within the pre-defined partitions, sedimentation rate changes are visible as inflections at the boundaries of these partitions. Age uncertainties are relatively low at Tiout and most of Oued Sdas, which are relatively well constrained by radiometric dates in the top (Tiout) and middle (Oued Sdas) parts of the sections, as well as by astronomical priors on sedimentation rates. Uncertainty noticably increases towards the top and bottom of Oued Sdas. The lowest partition of Oued Sdas is constrained only by its match to the lower part of the Sukharikha Fm., their age estimates are thus varying considerably between different alignments (Fig. 6). Differences in the positioning of the <inline-formula><mml:math id="M339" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> curves between alignments are greatest at Talat n'Yissi and the Siberian Krasnoporog Fm. (Fig. 6), which results in large uncertainties in the age models (Fig. 7c and d).</p>

      <fig id="F7" specific-use="star"><label>Figure 7</label><caption><p id="d2e5074">Age-depth model for each of the four sites. The solid lines indicate the median posterior ages corresponding to the respective heights; the shaded interval denotes the 95 % credible interval of posterior ages. Colours correspond to the colours of partitions introduced in Fig. 3. Circles indicate the mean age estimates of radiometric dates, with vertical lines spanning two standard deviations around the mean of these age estimates. Stars denote the first appearances of trilobites in Morocco and Siberia. See Fig. B2 for separate visualisations of age-depth models for different alignment solutions.</p></caption>
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f07.png"/>

        </fig>

</sec>
</sec>
<sec id="Ch1.S5">
  <label>5</label><title>Discussion</title>
<sec id="Ch1.S5.SS1">
  <label>5.1</label><title>Lower Cambrian stratigraphy</title>
      <p id="d2e5100">We used StratoBayes to correlate and date four lower Cambrian carbonate sections using <inline-formula><mml:math id="M340" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> records, radiometric dates and astrochronological sedimentation rate estimates. From a large space of possible alignment configurations (Fig. 4), the software identified alignment solutions that visibly match the large-scale features in the <inline-formula><mml:math id="M341" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> records from multiple sites, while simultaneously achieving an approximate fit to the radiometric dates (Fig. 6).</p>
      <p id="d2e5129">The most likely alignment solution from the posterior, alignment 1 (<inline-formula><mml:math id="M342" display="inline"><mml:mrow><mml:mtext>probability</mml:mtext><mml:mo>=</mml:mo><mml:mn mathvariant="normal">93</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula>), results in a correlation of the three Moroccan sites that has much in common with that proposed by Maloof et al. (2005). In our model, we used common sedimentation rates for the stratigraphic partitions (members, formations) shared between the sites, whilst allowing sedimentation rates to systematically differ from the reference sedimentation rates at Tiout by adding a site-specific multiplier.  This multiplier, <inline-formula><mml:math id="M343" display="inline"><mml:mi mathvariant="italic">ζ</mml:mi></mml:math></inline-formula>, is 1.02 (95 <inline-formula><mml:math id="M344" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:math></inline-formula> credible interval: 0.97–1.08) for Oued Sdas, meaning the model estimates very similar sedimentation rates for Tiout and Oued Sdas (Fig. 6a), consistent with their close geographical proximity. Sedimentation rates for the shared partitions at Talat n'Yissi are lower by a factor of 0.86 (0.76–0.96), which would be consistent with a moderately lower accommodation space at Talat n'Yissi relative to Tiout and Oued Sdas (as suggested by Fig. 3b in Maloof et al., 2005). We deliberately chose broad priors that did not explicitly enforce a relationship between sedimentation rates and palaeogeography; nonetheless, the model identified a geologically plausible solution. In contrast, the higher <inline-formula><mml:math id="M345" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mtext>Talat n'Yssi</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> of alignment 2 (<inline-formula><mml:math id="M346" display="inline"><mml:mrow><mml:mtext>probability</mml:mtext><mml:mo>=</mml:mo><mml:mn mathvariant="normal">2.8</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula>, 1.07–1.37) and alignment 3 (<inline-formula><mml:math id="M347" display="inline"><mml:mrow><mml:mtext>probability</mml:mtext><mml:mo>=</mml:mo><mml:mn mathvariant="normal">2.6</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula>, 2.07–2.45) are harder to reconcile with the palaeogeographic context.</p>
      <p id="d2e5207">Alignments 2 and 3 also suggest different sedimentation rates between Tiout and Oued Sdas, with a higher value of <inline-formula><mml:math id="M348" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mtext>Oued Sdas</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (1.13–1.26) being estimated by alignment 2, and a lower value of <inline-formula><mml:math id="M349" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ζ</mml:mi><mml:mtext>Oued Sdas</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (0.83–0.88) by alignment 3. The most consistent lithostratigraphic alignment between Tiout and Oued Sdas is achieved by alignment 1, meaning that the age estimates for partition boundaries (based on members or formations) are most similar (Fig. 6). For the more distant Talat n'Yissi, age estimates of partition boundaries differ to varying degrees across all three alignments.</p>
      <p id="d2e5232">Breaking down the posterior probability into individual components – likelihood (fit of <inline-formula><mml:math id="M350" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> measurements to the spline, fit of age estimates to the radiometric dates) and prior probability from the overlap penalty – reveals that samples from alignment 1 have a higher likelihood, on average (Fig. 5c). In contrast, alignments 2 and 3 have a greater number of overlapping <inline-formula><mml:math id="M351" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> points, which results in higher overlap prior probabilities (Fig. 5c). The overlap prior reflects the prior belief that substantial parts of the sections involved in the correlation should be overlapping. However, the weight of that prior is somewhat arbitrary and reflects the technical requirement to facilitate overlap despite non-overlap allowing for closer fit to the spline, similar to the role of the “edge value” in some DTW implementations (Hay et al., 2019). A lower prior weight on overlap would thus have caused alignments 2 and 3 to receive lower posterior probabilities relative to alignment 1. Taken together, the evidence from above leads us to strongly favour alignment 1, and we will focus further discussion on that most likely alignment solution.</p>
      <p id="d2e5262">A radiometric date of 517.0 <inline-formula><mml:math id="M352" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math id="M353" display="inline"><mml:mrow><mml:mo>±</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula> SD: 515.5–518.5 <inline-formula><mml:math id="M354" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>) has been recovered from the Lemdad Syncline in the Atlas mountains (Landing et al., 1998), and has been correlated biostratigraphically to a horizon in the lower Isaafen Fm. at Talat n'Yissi (Maloof et al., 2005). In our alignment 1, this horizon has a posterior age estimate of 519 <inline-formula><mml:math id="M355" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (519.2–518.8 <inline-formula><mml:math id="M356" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>) – <inline-formula><mml:math id="M357" display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula> older than the mean of the radiometric date. This date has informed the age estimates for Talat n'Yssi in Maloof et al. (2005) and Maloof et al. (2010), whereas alignment 1 produces age estimates close to those of Bowyer et al. (2022) and Bowyer et al. (2023).  Age estimates deviating from radiometric dates are not necessarily incorrect: Although radiometric dates are sometimes treated as “absolute truth” within the stratigraphic community, they are the result of various sources of technical uncertainties (Condon et al., 2024) and geological interpretations like the actual zircon crystallisation versus eruption age (Keller et al., 2018). This is illustrated by the recalculation of the radiometric date from Landing et al. (1998) to 515.56 <inline-formula><mml:math id="M358" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math id="M359" display="inline"><mml:mrow><mml:mo>±</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula> SD: 514.40–516.72 <inline-formula><mml:math id="M360" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>) in the Geological Time Scale 2012 (Schmitz et al., 2012).</p>
      <p id="d2e5348">The two radiometric dates measured at Tiout at the bottom of and within the Amouslek Formation suggest a sedimentation rate of 146 <inline-formula><mml:math id="M361" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math id="M362" display="inline"><mml:mrow><mml:mo>±</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula> SD: 78.7–613 <inline-formula><mml:math id="M363" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>) for the Amouslek formation.  However, the posterior estimates for the sedimentation rate in the Amouslek formation are poorly constrained and high compared to the sedimentation rates of all other partitions, at 3030 <inline-formula><mml:math id="M364" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (800–17 300 <inline-formula><mml:math id="M365" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">m</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">Myr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>). It appears that the model has overestimated the Amouslek sedimentation rate in aligning the <inline-formula><mml:math id="M366" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> record of the overlying Isaafen formation with a part of the Siberian Krasnoporog formation which has similar <inline-formula><mml:math id="M367" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> values (Fig. 6a). The alignments of Bowyer et al. (2022) imply significant sedimentation rate changes within the Krasnoporog formation, allowing the <inline-formula><mml:math id="M368" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> records to be better reconciled with the radiometric dates. We didn't allow for sedimentation rate changes within the Krasnoporog formation because the stratigraphic log of Kouchinsky et al. (2007) indicates a uniform facies.  Additional sedimentation rate changes might lead to a closer alignment with the radiometric dates, at the cost of greater model complexity.</p>
      <p id="d2e5469">The alignment of the Siberian Sukharikha section with the Moroccan sites is relatively precise in the lower half of the records: The prominent positive <inline-formula><mml:math id="M369" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> excursions interpreted as the “5p” and “6p” excursions have a similar magnitude both at Oued Sdas and Sukharikha, and are readily aligned visually (Bowyer et al., 2022) and by our model (Fig. 6). Our model aligns the main 6p peak of Sukharikha with the first subpeak of the second large excursion at Oued Sdas, as in model C in Bowyer et al. (2022). The lesser, positive excursion below the hiatus at the top of the Sukharikha formation lines up with the positive excursion in the lower Lie-de-Vin formation, representing the “II” peak as in model C in Bowyer et al.  (2022). The upper parts of the Moroccan records and the Siberian Krasnoporog formation appear to be aligned primarily by matching the prominent positive excursion interpreted as excursion “IV” (Bowyer et al., 2022; Kouchinsky et al., 2007). The “III” peak below is only weakly expressed at Oued Sdas, leading to uncertainty in the alignment with the corresponding part of the Krasnoporog formation, and in the inferred duration of the hiatus even within alignment solution 1 (Fig. B3a–c). Similarly, considerable uncertainty exists in how the top of Talat n'Yissi corresponds to the Krasnoporog formation. This is evident from variations between samples in alignment solution 1 (Fig. B3a–c) and in the wide credible intervals of those parts of the age models (Fig. 7). The relatively small magnitude of <inline-formula><mml:math id="M370" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> changes limits the model's ability to identify a definitive alignment solution for that part of the record.</p>
      <p id="d2e5498">Our estimate for the Moroccan first appearance of trilobites at Tiout from alignment 1, 519.47 <inline-formula><mml:math id="M371" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (519.68–519.26 <inline-formula><mml:math id="M372" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>), is slightly younger and somewhat less precise than the recent, astrochronological estimate of 519.62 <inline-formula><mml:math id="M373" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (95 <inline-formula><mml:math id="M374" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">%</mml:mi></mml:mrow></mml:math></inline-formula> highest posterior distribution: 519.70–519.54 <inline-formula><mml:math id="M375" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>) by Sinnesael et al. (2024). We attribute this difference to our model simultaneously combining different data types from multiple sites.  Additionally, Sinnesael et al. (2024) allowed sedimentation rates to vary between cycles, whereas our model assumed a single sedimentation rate per member. In our alignment 1 solution, the highest <inline-formula><mml:math id="M376" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> values of Tiout correlate to shortly after the peak of the IV <inline-formula><mml:math id="M377" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> excursion. This correlation suggests that the actual peak of the excursion at Tiout has not been sampled by Magaritz et al. (1991) and Tucker (1986), which may result in misalignments when correlating the record to other sections. Further <inline-formula><mml:math id="M378" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> samples from the lower Igoudine and upper Lie-de-Vin formation at Tiout are required to improve correlation with other sections, including the correlation presented herein.</p>
      <p id="d2e5581">Our model successfully reconstructs the first appearance of trilobites at Tiout, within error, despite using a simpler astrochronology and enforcing a less variable sedimentation rate history than Sinnesael et al. (2024). It also provides the first fully quantitative estimate for the first appearance of trilobites in Siberia based on chemostratigraphic correlation and the Moroccan radiometric dates and astrochronology, at 520.79 <inline-formula><mml:math id="M379" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula> (520.98–520.61 <inline-formula><mml:math id="M380" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:math></inline-formula>). This refines earlier estimates of <inline-formula><mml:math id="M381" display="inline"><mml:mrow><mml:mo>≈</mml:mo><mml:mn mathvariant="normal">521</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mrow class="unit"><mml:mi mathvariant="normal">Ma</mml:mi></mml:mrow></mml:mrow></mml:math></inline-formula> (Landing et al., 2021), and quantifies the temporal gap between the appearance of trilobites in Siberia and Morocco as 1.33 <inline-formula><mml:math id="M382" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula> (1.09–1.54 <inline-formula><mml:math id="M383" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Myr</mml:mi></mml:mrow></mml:math></inline-formula>). We do not suggest that these estimates are definitive; indeed, we anticipate that the incorporation of additional <inline-formula><mml:math id="M384" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> data from Tiout, the inclusion of astrochronological estimates of individual short eccentricity cycles, and the relaxation of the assumption of constant sedimentation rates within partitions may update the estimate. A high-resolution temporal sequence of trilobite first occurrence dates could be used to delineate trilobite evolutionary rates and dispersal; to evaluate evolutionary hypotheses on the origins and biomineralisation of trilobites (Holmes and Budd, 2022; Paterson et al., 2019); and to inform the definition of the base of the Cambrian Series 2 (Zhang et al., 2017).</p>
</sec>
<sec id="Ch1.S5.SS2">
  <label>5.2</label><title>Statistical alignment and age modelling</title>
<sec id="Ch1.S5.SS2.SSS1">
  <label>5.2.1</label><title>Advantages of Bayesian stratigraphic alignment</title>
      <p id="d2e5659">As shown above, our algorithm can identify the correct alignment positions in scenarios with one (Fig. 1) or more than one (Fig. 2) known solution. In scenarios where more than one distinctly different alignment is identified, the probability of each solution, given the specified data and model, is identified. This can be used to evaluate the likelihood of competing models for the alignment of stratigraphic records found by visual (e.g. Bowyer et al., 2023; Landing and Kruse, 2017) or algorithmic (e.g. Hay et al., 2019) correlation. The requirement to specify priors for the alignment parameters can be leveraged to provide information beyond that which is contained in the signals: for example, information on sedimentation rates may be expressed in the prior.</p>
      <p id="d2e5662">Because our model can integrate absolute age constraints such as radiometric dates, a user is able to correlate stratigraphic records and construct probabilistic age models in a single step. In our Cambrian example, the posterior alignment and the posterior age model are thus influenced by the priors, the quantitative signals and the radiometric dates. In contrast, age models constructed in a separate step after identifying alignments do not reflect uncertainty arising during the alignment stage (Hagen and Creveling, 2024).</p>
      <p id="d2e5665">In our integrated approach, discrepancies between radiometric dates and signal alignment are resolved probabilistically, with the model weighting the available evidence based on its likelihood and prior information. This means that posterior age estimates may diverge from the age information provided by radiometric dates, as seen with the <inline-formula><mml:math id="M385" display="inline"><mml:mrow><mml:msub><mml:mtext>Ou</mml:mtext><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> date in Fig. 6d. This is not necessarily a deficiency of the model; rather, it indicates that the priors and non-radiometric data provide sufficiently strong evidence to suggest that the actual age of the horizon associated with the radiometric date falls toward the tails of its confidence interval, or that the radiometric uncertainty may be underestimated. Some degree of discrepancy is expected when integrating multiple data types rather than relying on a single proxy (see also Lee et al., 2022).</p>
      <p id="d2e5679">If, on the other hand, the user wishes to increase the influence of radiometric dates on the posterior age estimates, this can potentially be achieved by introducing additional sedimentation rate changes to allow more flexible alignment of the proxy signals, reducing the weight of the proxy signal records – such as by imposing a larger <inline-formula><mml:math id="M386" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> for the cubic spline – or by weakening priors.</p>
</sec>
<sec id="Ch1.S5.SS2.SSS2">
  <label>5.2.2</label><title>Model choice and priors</title>
      <p id="d2e5697">Stratigraphic alignment using algorithms has the advantage of removing some of the inherent subjectivity of visual alignment (Sylvester, 2023). Yet, somewhat subjective decisions are still explicitly or implicitly made with every alignment algorithm. In the case of DTW, subjectivity is introduced e.g. with restrictions on the warping path (i.e. relative sedimentation rates, Sakoe and Chiba, 1978), with the amount of overlap required between sections (Hay et al., 2019), or with the choice of an exponent controlling the weight of outlier values (Wheeler and Hale, 2014). All of those settings can alter the outcome of DTW-based alignments. Likewise, our Bayesian approach comes with a number of subjective choices. The appropriate model structure can be readily determined when the data-generating process is known (Sect. 3), but has to be carefully considered and potentially revised when dealing with complex real-world data (Sect. 4). Lithological data may guide the partitioning of data and can inform somewhat objective choices of horizons with likely sedimentation rate changes (Sect. 4.2), but such information may not be readily available with some datasets, such as with well logs.</p>
      <p id="d2e5700">Besides the model structure, StratoBayes requires the user to specify priors for several model parameters: relative or absolute sedimentation rates (<inline-formula><mml:math id="M387" display="inline"><mml:mrow><mml:mi mathvariant="italic">ν</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="italic">ζ</mml:mi></mml:mrow></mml:math></inline-formula>), the shifts of sections relative to one another (<inline-formula><mml:math id="M388" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>), the duration of hiatuses (<inline-formula><mml:math id="M389" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula>), the degree of smoothing of the spline (<inline-formula><mml:math id="M390" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula>), the extent to which overlap of signal points should be favoured (<inline-formula><mml:math id="M391" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mtext>overlap</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>), and optionally the residual standard deviation of the spline (<inline-formula><mml:math id="M392" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula>). Although the choice of any of those parameters has the potential to affect posterior alignments and age models, they also offer a chance to explicitly include geological information that could otherwise only be incorporated by discarding or modifying alignment solutions after the algorithmic alignment.</p>
      <p id="d2e5755">While it is relatively straightforward to express prior beliefs on the alignment parameters <inline-formula><mml:math id="M393" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M394" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M395" display="inline"><mml:mi mathvariant="italic">ζ</mml:mi></mml:math></inline-formula>, and <inline-formula><mml:math id="M396" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula>, it is hard to specify suitable priors for <inline-formula><mml:math id="M397" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M398" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M399" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mtext>overlap</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, as they do not correspond to measures used by geologists. The default priors on <inline-formula><mml:math id="M400" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M401" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M402" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mtext>overlap</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> in the StratoBayes software were chosen iteratively by working with various test data sets. Users should avoid fine-tuning these priors directly on the data sets to which they intend to apply StratoBayes, as this could introduce unintended circularity.  Instead, analogous independent data sets could be used to identify suitable priors for <inline-formula><mml:math id="M403" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M404" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M405" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mtext>overlap</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>. For example, priors on <inline-formula><mml:math id="M406" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M407" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> for correlating <inline-formula><mml:math id="M408" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> curves could be meaningfully specified from pre-existing reconstructed <inline-formula><mml:math id="M409" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> composite curves.</p>
</sec>
<sec id="Ch1.S5.SS2.SSS3">
  <label>5.2.3</label><title>Challenges with the proxy and sedimentary record</title>
      <p id="d2e5912">Chemostratigraphy, and, more broadly, correlating geological sections based on proxy data relies on the proxies accurately reflecting a common, underlying signal. Several processes may disrupt this assumption. For example, <inline-formula><mml:math id="M410" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> recorded in carbonates differs between different depositional environments, water depths, and grain types (Geyman and Maloof, 2021), while the <inline-formula><mml:math id="M411" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> recorded in restricted basins may be offset significantly relative to contemporary carbonates elsewhere (Uhlein et al., 2019). Where known, such offsets could be accounted for by subtracting or adding the estimated offset relative to global values.  Alternatively, anticipated offsets could be modelled as additional unknown variables, as in Edmonsond and Dyer (2025). This approach will likely require substantial prior knowledge on the potential magnitude and direction of offsets; otherwise, the combination of variation along the height or time axis and along the proxy value axis may result in a large range of mathematically feasible alignments.</p>
      <p id="d2e5941">A more fundamental problem is posed when similar patterns in a proxy curve are asynchronous in different sections: Shifting and stretching proxy data from multiple sites may result in a strongly correlated composite curve, but this correlation does not prove that the patterns or excursions observed at different sites were in fact synchronous (Blaauw, 2012). Unless supported by independent evidence such as precise radiometric dates, relative age estimates derived from proxy correlations (e.g. <inline-formula><mml:math id="M412" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula>) are conditional on the assumption of synchronicity.</p>
      <p id="d2e5957">Several challenges arise from the variability of sedimentation and the incompleteness of the sedimentary record. Sediment accumulation rates vary with measurement scale (Sadler, 1981): closer spacing between measurements allows more variability to be identified, with actual sedimentation rate histories displaying fractal properties (Miall, 2015). This implies that depositional ages tend to vary non-linearly along a vertically sampled sedimentary section, with substantial incompleteness in shallow-water records (Curtis et al., 2025). These discontinuities can lead to drastically altered shapes of proxy curves from different depositional settings, and cycles from periodic proxy fluctuations may be missed due to insufficient preservation or sampling (Curtis et al., 2025). This issue is evident in the Sukharikha section, where it is somewhat ambiguous whether the hiatus represents a fraction of a <inline-formula><mml:math id="M413" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> excursion (alignment 1 and 2) or extends over more than one full cycle (alignment 3, Fig. 6). For correlations within sedimentary basins, the method of Bloem and Curtis (2024) could help resolve ambiguous alignments by reconstructing depositional histories through geological process modelling, but this method requires exceptionally high-resolution sampling and its utility has yet to be demonstrated with real-world data sets.</p>
      <p id="d2e5973">Besides the completeness, the sampling density of proxy records may influence correlations. In StratoBayes, densely sampled sections or parts of sections exert more influence on the shape of the spline than those that are thinly sampled, which can be seen in the spline curve primarily following the densely sampled Oued Sdas and Talat n'Yissi records in Fig. 6. Despite this, our Cambrian case study demonstrates that sections with differing sampling densities – both between and within sites – can still be effectively aligned. Varying sampling density would, however, pose a challenge for reconstructing a global average proxy curve from local records, as the global curve would primarily reflect the more densely sampled sites.</p>
      <p id="d2e5977">StratoBayes introduces a simplification in modelling sedimentary histories by forcing uniform sedimentation rates within pre-defined segments of a stratigraphic section. An effect of this simplification can be seen in the age-depth plots in Fig. 7: Due to sedimentation rates being modelled as uniform within stratigraphic partitions, the uncertainty of age estimates does not necessarily increase away from the radiometric dates. We acknowledge that this may underestimate the uncertainty associated with potential sedimentation rate variability (De Vleeschouwer and Parnell, 2014), especially when allowing for few sedimentation rate changes.  Similarly, our method currently only allows for specifying potential hiatuses with an unknown duration at fixed, predetermined heights.</p>
      <p id="d2e5980">In principle, our method could be used to divide stratigraphic sections into an arbitrary number of segments with differing sedimentation rates, and with an arbitrary number of potential hiatuses. In practice, estimating the parameters of a model with more than a low double-digit number of alignment parameters (shift parameters, sedimentation rates, hiatuses) represents a challenge for the current implementation of the MCMC algorithm within StratoBayes, as finding and exploring the posterior becomes increasingly difficult as more parameters are added. This limitation could be alleviated by incorporating MCMC methods suited for higher dimensional problems and difficult posterior geometries. Alternatively, a continuous process model such as the compound Poisson-gamma process of BChron (Haslett and Parnell, 2008) might be integrated with our model for the proxy signal, but again the complexity of the MCMC would increase. Another approach would be to divide the alignment problem into sub-problems, e.g. by multiple pairwise correlation of sites (e.g. Hagen et al., 2024; Sylvester, 2023), or by correlating shorter sections.</p>
</sec>
</sec>
<sec id="Ch1.S5.SS3">
  <label>5.3</label><title>Towards quantitative stratigraphy</title>
      <p id="d2e5992">Quantitative stratigraphic correlation and age modelling of diverse geological data represent a long-standing challenge in stratigraphic research. Although many algorithms exist for correlating geochemical and geophysical stratigraphic data (e.g. Baville et al., 2022; Bloem and Curtis, 2024; Hay et al., 2019; Sylvester, 2023); few can readily provide uncertainty estimates or incorporate different types of data simultaneously (e.g. Al Ibrahim, 2022; Edmonsond and Dyer, 2025; Lee et al., 2022).  Consequently, integrated statistical approaches have only rarely been applied to complex real-world stratigraphic problems (Hagen et al., 2024; Lee et al., 2022).</p>
      <p id="d2e5995">Our new method has the potential to be applied to diverse datasets; examples range from shallow borehole data from the Holocene (Finlay et al., 2022) to Proterozoic carbonates (Halverson et al., 2010). The ability of our model to incorporate multiple proxy records simultaneously opens new possibilities for refining stratigraphic correlations. For instance, correlations involving both <inline-formula><mml:math id="M414" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M415" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">87</mml:mn></mml:msup><mml:mi mathvariant="normal">Sr</mml:mi></mml:mrow></mml:math></inline-formula> records could benefit from a probabilistic framework that accounts for their respective uncertainties (Bowyer et al., 2022). The integration of multiple proxies, e.g. multiple element ratios, in the StratoBayes framework could allow correlations based on the entire record of all proxies, rather than a few visually distinct transitions (Craigie, 2015).</p>
      <p id="d2e6024">Beyond geochemical records, our approach could also be applied e.g. to geophysical well-logs such as gamma ray or density logs, and magnetostratigraphic records could be correlated directly rather than relying on visually interpreted polarity reversals (Langereis et al., 2010).  While index fossils can currently be integrated as tie points, the modelling framework could be expanded to explicitly model first and last occurrences to better incorporate biostratigraphic uncertainty. Similarly, astrochronological constraints can be expressed as priors on sedimentation rates, but an additional model component would be needed to incorporate all astrochronological information from a given site (Sinnesael et al., 2024).</p>
</sec>
</sec>
<sec id="Ch1.S6" sec-type="conclusions">
  <label>6</label><title>Conclusions</title>
      <p id="d2e6036">StratoBayes is a Bayesian modelling framework for the probabilistic alignment of stratigraphic proxy records and age modelling. It correlates quantitative proxy signals such as isotope ratios, and integrates additional stratigraphic information such radiometric dates, to construct probabilistic age models. Applying our model to both simulated data and real-world stratigraphic records from the lower Cambrian of Morocco and Siberia, we have demonstrated its ability to account for uncertainty from all model components and to identify multiple plausible alignment solutions. Our lower Cambrian case study provides a fully probabilistic estimate for the first appearance of trilobites in Siberia, and quantifies the temporal gap between their first occurrence and the oldest Moroccan trilobites. While our results remain dependent on model assumptions, they represent a step towards a more objective and reproducible approach to early Palaeozoic stratigraphy; they also highlight sources of uncertainty and identify targets for future research. Beyond this case study, StratoBayes has broad applicability to stratigraphic problems across all time intervals that involve the correlation of quantitative proxy records.</p>
</sec>

      
      </body>
    <back><app-group>

<app id="App1.Ch1.S1">
  <label>Appendix A</label><title>Markov chain Monte Carlo sampling scheme</title>
      <p id="d2e6051">Appendix A details the Metropolis-within-Gibbs sampling scheme and the parallel tempering framework that are used within the StratoBayes software to sample from the posterior of the unknown model parameters.</p>
<sec id="App1.Ch1.S1.SS1">
  <label>A1</label><title>Sampling strategy</title>
      <p id="d2e6061">The MCMC sampling scheme used in this study includes an adaptive phase.  During this phase, proposal distributions and the probabilities with which different proposal types are selected for the Metropolis–Hastings updates are adjusted based on the history of the MCMC chains to improve acceptance rates and mixing. Additionally, the temperature ladder of the parallel tempering framework is updated to improve the swap rates of chains. After the adaptive phase, the proposal distributions and probabilities, as well as chain temperatures, remain fixed for the remainder of the run to ensure proper sampling from the posterior.</p>
      <p id="d2e6064">In the current implementation, the length of the adaptive phase is pre-determined by the user, specified as a fixed number of iterations.  However, the user has the option to extend the adaptation period by continuing the run if needed. More generally, adaptation could also be stopped automatically based on criteria such as mixing within chains (Yang and Rosenthal, 2017) or convergence criteria.</p>
      <p id="d2e6067">Adaptive MCMC algorithms do not always preserve the stationarity of the target distribution during the adaptive phase (Roberts and Rosenthal, 2009).  Therefore, all samples from the adaptive phase are discarded as burn-in.  Additionally, if diagnostic checks suggest that the MCMC has not converged by the end of the adaptive phase, further samples may need to be discarded.</p>
</sec>
<sec id="App1.Ch1.S1.SS2">
  <label>A2</label><title>Gibbs sampling scheme for the cubic B-splines</title>
      <p id="d2e6078">The following sampling scheme was adapted from Heaton et al. (2020). The spline coefficients are sampled from a multivariate normal distribution of the form:

            <disp-formula id="App1.Ch1.S1.E16" content-type="numbered"><label>A1</label><mml:math id="M416" display="block"><mml:mrow><mml:mi mathvariant="bold-italic">β</mml:mi><mml:mo>∼</mml:mo><mml:mtext>MVN</mml:mtext><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">b</mml:mi><mml:mi mathvariant="bold">Q</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="bold">Q</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math id="M417" display="inline"><mml:mi mathvariant="bold-italic">b</mml:mi></mml:math></inline-formula> is given by

            <disp-formula id="App1.Ch1.S1.E17" content-type="numbered"><label>A2</label><mml:math id="M418" display="block"><mml:mrow><mml:mi mathvariant="bold-italic">b</mml:mi><mml:mo>=</mml:mo><mml:mo>(</mml:mo><mml:mi mathvariant="bold">B</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">h</mml:mi><mml:mo>)</mml:mo><mml:msup><mml:mo>)</mml:mo><mml:mtext>T</mml:mtext></mml:msup><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mi mathvariant="bold-italic">y</mml:mi><mml:mrow><mml:msup><mml:mi mathvariant="italic">σ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:math></disp-formula>

          <inline-formula><mml:math id="M419" display="inline"><mml:mrow><mml:mi mathvariant="bold">B</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">h</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> are cubic B-splines (Eilers and Marx, 1996) at a set of <inline-formula><mml:math id="M420" display="inline"><mml:mi>k</mml:mi></mml:math></inline-formula> knots evaluated at heights <inline-formula><mml:math id="M421" display="inline"><mml:mi mathvariant="bold-italic">h</mml:mi></mml:math></inline-formula> at which <inline-formula><mml:math id="M422" display="inline"><mml:mi mathvariant="bold-italic">y</mml:mi></mml:math></inline-formula>, the composite stratigraphic signal of all sites, was observed. Here, <inline-formula><mml:math id="M423" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> is the residual standard deviation.</p>
      <p id="d2e6190">The other element needed for sampling from the posterior of <inline-formula><mml:math id="M424" display="inline"><mml:mi mathvariant="bold-italic">b</mml:mi></mml:math></inline-formula> is <inline-formula><mml:math id="M425" display="inline"><mml:mi>Q</mml:mi></mml:math></inline-formula>, given by

            <disp-formula id="App1.Ch1.S1.E18" content-type="numbered"><label>A3</label><mml:math id="M426" display="block"><mml:mrow><mml:mi mathvariant="bold">Q</mml:mi><mml:mo>=</mml:mo><mml:mo>(</mml:mo><mml:mi mathvariant="bold">H</mml:mi><mml:mo>+</mml:mo><mml:mi mathvariant="italic">λ</mml:mi><mml:mi mathvariant="bold">D</mml:mi><mml:msup><mml:mo>)</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math id="M427" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula> is a smoothing parameter, <inline-formula><mml:math id="M428" display="inline"><mml:mi mathvariant="bold">D</mml:mi></mml:math></inline-formula> is a penalty matrix to prevent the spline from overfitting the data, and

            <disp-formula id="App1.Ch1.S1.E19" content-type="numbered"><label>A4</label><mml:math id="M429" display="block"><mml:mrow><mml:mi mathvariant="bold">H</mml:mi><mml:mo>=</mml:mo><mml:msup><mml:mfenced close=")" open="("><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="bold">B</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">h</mml:mi><mml:mo>)</mml:mo></mml:mrow><mml:mi mathvariant="italic">σ</mml:mi></mml:mfrac></mml:mstyle></mml:mfenced><mml:mtext>T</mml:mtext></mml:msup><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="bold">B</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">h</mml:mi><mml:mo>)</mml:mo></mml:mrow><mml:mi mathvariant="italic">σ</mml:mi></mml:mfrac></mml:mstyle></mml:mrow></mml:math></disp-formula>

          The standard deviation <inline-formula><mml:math id="M430" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> can be fixed as

            <disp-formula id="App1.Ch1.S1.E20" content-type="numbered"><label>A5</label><mml:math id="M431" display="block"><mml:mrow><mml:mi mathvariant="italic">σ</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mi>S</mml:mi></mml:mfrac></mml:mstyle><mml:munderover><mml:mo movablelimits="false">∑</mml:mo><mml:mrow><mml:mi>s</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow><mml:mi>S</mml:mi></mml:munderover><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math id="M432" display="inline"><mml:mi>S</mml:mi></mml:math></inline-formula> is the number of sites, and <inline-formula><mml:math id="M433" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the standard deviation of individual splines fitted to the data of site <inline-formula><mml:math id="M434" display="inline"><mml:mi>s</mml:mi></mml:math></inline-formula>. This often provides a good approximation of <inline-formula><mml:math id="M435" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula>, while removing an unknown model parameter, potentially facilitating quicker convergence of the model run.</p>
      <p id="d2e6363">Alternatively, <inline-formula><mml:math id="M436" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> can be estimated within the Gibbs sampling scheme from the data, by placing a conjugate gamma prior on the inverse of the variance (precision, <inline-formula><mml:math id="M437" display="inline"><mml:mrow><mml:mi mathvariant="italic">τ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mi mathvariant="italic">σ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula>):

            <disp-formula id="App1.Ch1.S1.E21" content-type="numbered"><label>A6</label><mml:math id="M438" display="block"><mml:mrow><mml:msup><mml:mi mathvariant="italic">σ</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup><mml:mo>∼</mml:mo><mml:mtext>Gamma</mml:mtext><mml:mfenced close=")" open="("><mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mi mathvariant="italic">σ</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mi>y</mml:mi></mml:msub></mml:mrow><mml:mn mathvariant="normal">2</mml:mn></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo><mml:mspace width="0.33em" linebreak="nobreak"/><mml:mspace width="0.33em" linebreak="nobreak"/><mml:msub><mml:mi>b</mml:mi><mml:mi mathvariant="italic">σ</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mn mathvariant="normal">2</mml:mn></mml:mfrac></mml:mstyle><mml:mover><mml:mo movablelimits="false">∑</mml:mo><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mi>y</mml:mi></mml:msub></mml:mrow></mml:mover><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">y</mml:mi><mml:mo>-</mml:mo><mml:mi mathvariant="bold-italic">β</mml:mi><mml:mi mathvariant="bold">B</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">h</mml:mi><mml:mo>)</mml:mo><mml:msup><mml:mo>)</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:mfenced></mml:mrow></mml:math></disp-formula>

          The smoothing parameter <inline-formula><mml:math id="M439" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula> is estimated by placing a gamma prior on <inline-formula><mml:math id="M440" display="inline"><mml:mi mathvariant="italic">λ</mml:mi></mml:math></inline-formula>:

            <disp-formula id="App1.Ch1.S1.E22" content-type="numbered"><label>A7</label><mml:math id="M441" display="block"><mml:mrow><mml:mi mathvariant="italic">λ</mml:mi><mml:mo>∼</mml:mo><mml:mtext>Gamma</mml:mtext><mml:mfenced close=")" open="("><mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mi mathvariant="italic">λ</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mi>k</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo><mml:mspace width="1em" linebreak="nobreak"/><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:msub><mml:mi>b</mml:mi><mml:mi mathvariant="italic">λ</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>+</mml:mo><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mn mathvariant="normal">1</mml:mn><mml:mn mathvariant="normal">2</mml:mn></mml:mfrac></mml:mstyle><mml:msup><mml:mo>∑</mml:mo><mml:mi>k</mml:mi></mml:msup><mml:mi mathvariant="bold-italic">β</mml:mi><mml:mi mathvariant="bold">D</mml:mi><mml:mo>×</mml:mo><mml:mi mathvariant="bold-italic">β</mml:mi></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mfenced></mml:mrow></mml:math></disp-formula></p>
</sec>
<sec id="App1.Ch1.S1.SS3">
  <label>A3</label><title>Metropolis–Hastings step</title>
      <p id="d2e6567">The starting heights or ages <inline-formula><mml:math id="M442" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, sedimentation rates <inline-formula><mml:math id="M443" display="inline"><mml:mi mathvariant="italic">ν</mml:mi></mml:math></inline-formula>, site multipliers <inline-formula><mml:math id="M444" display="inline"><mml:mi mathvariant="italic">ζ</mml:mi></mml:math></inline-formula> and gaps <inline-formula><mml:math id="M445" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula> are updated in a Metropolis–Hastings step. For each unknown parameter, a new value is randomly sampled from a proposal distribution. Initially, proposals are sampled independently for each parameter from its respective prior, or alternatively from a custom proposal distribution.</p>
      <p id="d2e6598">In the following, the current set of parameter values is labelled <inline-formula><mml:math id="M446" display="inline"><mml:mi mathvariant="italic">θ</mml:mi></mml:math></inline-formula>, and the proposed set is labelled <inline-formula><mml:math id="M447" display="inline"><mml:mrow><mml:msup><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>. To decide whether to accept or reject the new set of parameters, an acceptance probability <inline-formula><mml:math id="M448" display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> is calculated, and the proposal is randomly accepted or rejected with a probability of <inline-formula><mml:math id="M449" display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula>. This probability is calculated as

            <disp-formula id="App1.Ch1.S1.E23" content-type="numbered"><label>A8</label><mml:math id="M450" display="block"><mml:mrow><mml:mi>A</mml:mi><mml:mo>=</mml:mo><mml:mtext>min</mml:mtext><mml:mfenced open="(" close=")"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>,</mml:mo><mml:mspace width="1em" linebreak="nobreak"/><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="italic">π</mml:mi><mml:mo>(</mml:mo><mml:msup><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mo>)</mml:mo></mml:mrow><mml:mrow><mml:mi mathvariant="italic">π</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mfenced></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math id="M451" display="inline"><mml:mrow><mml:mi mathvariant="italic">π</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is the unnormalised posterior probability of the current values, and <inline-formula><mml:math id="M452" display="inline"><mml:mrow><mml:mi mathvariant="italic">π</mml:mi><mml:mo>(</mml:mo><mml:msup><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is the unnormalised posterior probability of the proposed values. These can be calculated as

            <disp-formula id="App1.Ch1.S1.E24" content-type="numbered"><label>A9</label><mml:math id="M453" display="block"><mml:mrow><mml:mi mathvariant="italic">π</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mi>p</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mo>×</mml:mo><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:mtext>data</mml:mtext><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math id="M454" display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is the prior probability of <inline-formula><mml:math id="M455" display="inline"><mml:mi mathvariant="italic">θ</mml:mi></mml:math></inline-formula>, and <inline-formula><mml:math id="M456" display="inline"><mml:mrow><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:mtext>data</mml:mtext><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> the likelihood of the data given <inline-formula><mml:math id="M457" display="inline"><mml:mi mathvariant="italic">θ</mml:mi></mml:math></inline-formula>.</p>
      <p id="d2e6793">We calculate the likelihood of the data given <inline-formula><mml:math id="M458" display="inline"><mml:mi mathvariant="italic">θ</mml:mi></mml:math></inline-formula> as a product of the probability densities of each data point of the signal <inline-formula><mml:math id="M459" display="inline"><mml:mi mathvariant="bold-italic">y</mml:mi></mml:math></inline-formula> (recorded at two or more sites) and of all absolute age information. For the signal, we assume that the observed values <inline-formula><mml:math id="M460" display="inline"><mml:mi mathvariant="bold-italic">y</mml:mi></mml:math></inline-formula> are normally distributed and centred around the values predicted by the splines, <inline-formula><mml:math id="M461" display="inline"><mml:mi mathvariant="bold-italic">μ</mml:mi></mml:math></inline-formula>, at height <inline-formula><mml:math id="M462" display="inline"><mml:mi mathvariant="bold-italic">h</mml:mi></mml:math></inline-formula>, with a standard deviation <inline-formula><mml:math id="M463" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> which has been introduced earlier. The likelihood of a data point <inline-formula><mml:math id="M464" display="inline"><mml:mi>i</mml:mi></mml:math></inline-formula> from the signal <inline-formula><mml:math id="M465" display="inline"><mml:mi>y</mml:mi></mml:math></inline-formula> is thus

            <disp-formula id="App1.Ch1.S1.E25" content-type="numbered"><label>A10</label><mml:math id="M466" display="block"><mml:mrow><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:msqrt><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="italic">π</mml:mi><mml:msup><mml:mi mathvariant="italic">σ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:msqrt></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:msup><mml:mi mathvariant="normal">e</mml:mi><mml:mrow><mml:mfenced close=")" open="("><mml:mrow><mml:mo>-</mml:mo><mml:mstyle scriptlevel="+1"><mml:mfrac><mml:mrow><mml:mo>(</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="italic">μ</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi mathvariant="italic">σ</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:math></disp-formula>

          and the log-likelihood for all data points of the signal is calculated as

            <disp-formula id="App1.Ch1.S1.E26" content-type="numbered"><label>A11</label><mml:math id="M467" display="block"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">y</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:munder><mml:mo movablelimits="false">∑</mml:mo><mml:mi>i</mml:mi></mml:munder><mml:mi>ln⁡</mml:mi><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

          If more than one type of signal is used, the log-likelihood of additional signals can be calculated analogously and added in Eq. (A14).</p>
      <p id="d2e6977">Age constraints are incorporated by using an age estimate from radiometric dates <inline-formula><mml:math id="M468" display="inline"><mml:mi mathvariant="bold-italic">d</mml:mi></mml:math></inline-formula> with, for example, mean ages <inline-formula><mml:math id="M469" display="inline"><mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mtext>mean</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and uncertainties given by standard deviations <inline-formula><mml:math id="M470" display="inline"><mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mtext>sd</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>. The probability density of a date <inline-formula><mml:math id="M471" display="inline"><mml:mrow><mml:msub><mml:mi>d</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is then calculated as

            <disp-formula id="App1.Ch1.S1.E27" content-type="numbered"><label>A12</label><mml:math id="M472" display="block"><mml:mrow><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi>d</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn mathvariant="normal">1</mml:mn><mml:msqrt><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="italic">π</mml:mi><mml:msubsup><mml:mi>a</mml:mi><mml:mrow><mml:mtext>sd</mml:mtext><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow><mml:mn mathvariant="normal">2</mml:mn></mml:msubsup></mml:mrow></mml:msqrt></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:msup><mml:mi mathvariant="normal">e</mml:mi><mml:mrow><mml:mfenced open="(" close=")"><mml:mrow><mml:mo>-</mml:mo><mml:mstyle scriptlevel="+1"><mml:mfrac><mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mrow><mml:mtext>mean</mml:mtext><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>a</mml:mi><mml:mrow><mml:mtext>predicted</mml:mtext><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msubsup><mml:mi>a</mml:mi><mml:mrow><mml:mtext>sd</mml:mtext><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow><mml:mn mathvariant="normal">2</mml:mn></mml:msubsup></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math id="M473" display="inline"><mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mrow><mml:mtext>predicted</mml:mtext><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the age predicted by the age-height transform at the height <inline-formula><mml:math id="M474" display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mrow><mml:mi>s</mml:mi><mml:mo>,</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, the height at the site at which date <inline-formula><mml:math id="M475" display="inline"><mml:mrow><mml:msub><mml:mi>d</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> was obtained.</p>
      <p id="d2e7160">The log-likelihood for all age constraints is calculated as

            <disp-formula id="App1.Ch1.S1.E28" content-type="numbered"><label>A13</label><mml:math id="M476" display="block"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">d</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:munder><mml:mo movablelimits="false">∑</mml:mo><mml:mi>i</mml:mi></mml:munder><mml:mi>ln⁡</mml:mi><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi>d</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>

          and the overall likelihood, if absolute age constraints are included, is

            <disp-formula id="App1.Ch1.S1.E29" content-type="numbered"><label>A14</label><mml:math id="M477" display="block"><mml:mrow><mml:mi>ln⁡</mml:mi><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">y</mml:mi><mml:mo mathvariant="bold">,</mml:mo><mml:mi mathvariant="bold-italic">d</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mi>ln⁡</mml:mi><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">y</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo><mml:mo>+</mml:mo><mml:mi>ln⁡</mml:mi><mml:mi>L</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="bold-italic">d</mml:mi><mml:mi mathvariant="normal">|</mml:mi><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula></p>
</sec>
<sec id="App1.Ch1.S1.SS4">
  <label>A4</label><title>Proposal types</title>
      <p id="d2e7274">In order to allow for a broad search of the parameter space, proposals are initially selected independently for each parameter, and are selected independently of the current parameter values. These proposals lead to a decreasing acceptance rate over time, and the chain tends to arrive at a single set of values with high posterior probability, <inline-formula><mml:math id="M478" display="inline"><mml:mrow><mml:mi mathvariant="italic">π</mml:mi><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, remaining there for many iterations due to frequent rejections.  Therefore, different types of proposals are used after an initial period: <list list-type="order"><list-item>
      <p id="d2e7293">Proposing from the prior or a custom distribution: This proposal is used exclusively for a small number of initial iterations and is alternated with other proposals later on.</p></list-item><list-item>
      <p id="d2e7297">Adaptive independent (univariate) proposals: Proposals for each parameter are selected independently from other parameter values. Proposals are dependent on the current state of the parameter <inline-formula><mml:math id="M479" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">θ</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, and sampled from a normal distribution <inline-formula><mml:math id="M480" display="inline"><mml:mrow><mml:mi>N</mml:mi><mml:mo>(</mml:mo><mml:msub><mml:mi mathvariant="italic">θ</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, where <inline-formula><mml:math id="M481" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">σ</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is a standard deviation that is estimated based on the history of the MCMC chain, i.e. based on the sampled <inline-formula><mml:math id="M482" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">θ</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> from previous iterations.</p></list-item><list-item>
      <p id="d2e7358">Adaptive dependent (multivariate) proposals (Roberts and Rosenthal, 2009): Proposals for the parameters are selected jointly and are dependent on the current state of the parameters <inline-formula><mml:math id="M483" display="inline"><mml:mi mathvariant="italic">θ</mml:mi></mml:math></inline-formula>. Proposals are sampled from a multivariate normal distribution <inline-formula><mml:math id="M484" display="inline"><mml:mrow><mml:mtext>MVN</mml:mtext><mml:mo>(</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">Σ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, where <inline-formula><mml:math id="M485" display="inline"><mml:mi mathvariant="normal">Σ</mml:mi></mml:math></inline-formula> is a covariance matrix that is estimated based on the history of the MCMC chain, i.e. based on the sampled <inline-formula><mml:math id="M486" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">θ</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> from previous iterations.</p></list-item><list-item>
      <p id="d2e7405">Shifting some or all <inline-formula><mml:math id="M487" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> and or <inline-formula><mml:math id="M488" display="inline"><mml:mi mathvariant="italic">δ</mml:mi></mml:math></inline-formula> parameters while keeping the other parameters constant. This can accelerate the convergence of the MCMC in cases where some sites are aligned with each other, but offset relative to other sites.</p></list-item></list> Proposal types are chosen with a probability that broadly corresponds to the relative acceptance probability of the respective proposal type, i.e. proposal types that are rejected often are chosen less frequently.  Adaptation for types (2) and (3), and the adjustment of proposal type probabilities ends after the adaptive phase. Posterior samples from the adaptive phase have to be discarded as burn-in, to ensure the correct convergence of the chain.</p>
</sec>
<sec id="App1.Ch1.S1.SS5">
  <label>A5</label><title>Parallel tempering</title>
      <p id="d2e7431">To avoid the MCMC chain becoming trapped at isolated peaks of the posterior probability distribution, we implement a parallel tempering framework, following Sambridge (2014). This involves running multiple chains in parallel. The target chain, the chain from which the posterior samples will be taken, is left unaltered (“cold chain”). The other chains are tempered, i.e. their unnormalised log posterior probabilities are raised to the power of <inline-formula><mml:math id="M489" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:mi>T</mml:mi></mml:mrow></mml:math></inline-formula>, with <inline-formula><mml:math id="M490" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> being the temperature. The higher <inline-formula><mml:math id="M491" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula>, the more “flattened” the posterior probability landscape becomes, and the easier it is for the chain to explore the landscape. Frequently, chain swaps are proposed, during which the model parameter values of different chains are exchanged with a Metropolis–Hastings acceptance probability based on the ratios of posterior probabilities of the states of the two chains, evaluated at both temperatures as in Appendix A2 of Sambridge (2014).</p>
      <p id="d2e7460">The initial temperatures for a number of chains <inline-formula><mml:math id="M492" display="inline"><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are selected using a geometric spacing, with <inline-formula><mml:math id="M493" display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> (cold chain) and <inline-formula><mml:math id="M494" display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant="normal">∞</mml:mi></mml:mrow></mml:math></inline-formula> (hottest chain). The infinite temperature of the hottest chain implies that all proposals during the MCMC will be accepted, and we let that chain sample from the prior probability distributions of the parameters. If <inline-formula><mml:math id="M495" display="inline"><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula>, intermediate chain temperatures are selected as

            <disp-formula id="App1.Ch1.S1.E30" content-type="numbered"><label>A15</label><mml:math id="M496" display="block"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:msubsup><mml:mo movablelimits="false">∑</mml:mo><mml:mrow><mml:mi>j</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow><mml:mi>c</mml:mi></mml:msubsup><mml:msub><mml:mi>d</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:msup></mml:mrow></mml:math></disp-formula>

          where

            <disp-formula id="App1.Ch1.S1.E31" content-type="numbered"><label>A16</label><mml:math id="M497" display="block"><mml:mtable class="aligned" columnspacing="1em" rowspacing="0.2ex" displaystyle="true" columnalign="right left"><mml:mtr><mml:mtd><mml:mstyle displaystyle="true" class="stylechange"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:msub><mml:mi>d</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mo>(</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:msup><mml:mo>)</mml:mo><mml:mrow><mml:mo>(</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:mo>/</mml:mo><mml:mn mathvariant="normal">3</mml:mn><mml:mo>)</mml:mo></mml:mrow></mml:msup></mml:mrow><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>+</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi>c</mml:mi><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>)</mml:mo><mml:mo>/</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow><mml:mrow><mml:mn mathvariant="normal">1.5</mml:mn><mml:mo>×</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mstyle displaystyle="true" class="stylechange"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mspace linebreak="nobreak" width="1em"/><mml:mi>c</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:mo>,</mml:mo><mml:mi mathvariant="normal">…</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:math></disp-formula>

          This leads to the spacing of temperatures decreasing with increasing number of chains, and temperature spacing is narrower for lower temperatures on the log scale. A small amount of white noise from a normal distribution with zero mean and a standard deviation of <inline-formula><mml:math id="M498" display="inline"><mml:mrow><mml:mo>(</mml:mo><mml:mn mathvariant="normal">5</mml:mn><mml:mo>×</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> is added to each <inline-formula><mml:math id="M499" display="inline"><mml:mrow><mml:msub><mml:mi>d</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> to vary the initial temperature ladders between independent model runs. Temperatures are updated in the adaptive phase of the MCMC to increase the swap rates of chains (Vousden et al., 2016).</p>
</sec>
</app>

<app id="App1.Ch1.S2">
  <label>Appendix B</label><title>Inspecting the posterior of the lower Cambrian case study</title>
      <p id="d2e7728">Appendix B provides additional details on the posterior of the inference with lower Cambrian <inline-formula><mml:math id="M500" display="inline"><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="italic">δ</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msup><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> data and radiometric dates.</p>
<sec id="App1.Ch1.S2.SS1">
  <label>B1</label><title>Trace plots</title>
      <p id="d2e7751">Trace plots visualise the evolution of chains from an MCMC and, together with tools such as the potential scale reduction factor (Gelman and Rubin, 1992; Vats and Knudson, 2021), allow for assessing convergence of model runs. The trace plot indicative of a well-behaved model run should be stationary after the burn-in phase, with different chains mixing well (Gelman et al., 1995). An example of a well-behaved trace plot is the first panel of Fig. B1. Inspecting the trace plots of the 18 model parameters of the lower Cambrian case study reveals that all parameters seem to have reached stationarity, this said; some chains occasionally visit distinctly different values (e.g. Fig. B1, column 1, row 2). The chains are not mixing well in those regions of the parameter space. Running the model for considerably more iterations is likely to overcome this problem. However, this affects only the less likely alignments; the most likely alignment (alignment cluster 1) is well explored across all parameters.</p>

      <fig id="FB1" specific-use="star"><label>Figure B1</label><caption><p id="d2e7756">Trace plots of the 18 alignment parameters. Each colour corresponds to a distinct run. For visual clarity, only 250 samples are displayed per run. The burn-in phase (the first 150 iterations) is omitted.</p></caption>
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f08.png"/>

        </fig>


</sec>
<sec id="App1.Ch1.S2.SS2">
  <label>B2</label><title>Age-depth models for different alignments</title>
      <p id="d2e7775">The age-depth models for each of the four sites are shown for each alignment cluster separately in Fig. B2 (instead of for all samples combined as in Fig. 7).</p>

      <fig id="FB2"><label>Figure B2</label><caption><p id="d2e7780">Age-depth model for each of the four sites. The solid lines indicate the median posterior ages corresponding to the respective heights; the shaded interval denotes the 95 % credible interval of posterior ages. Colours correspond to the three different alignment clusters and outlier samples. Circles indicate the mean age estimates of radiometric dates, with vertical lines spanning two standard deviations around the mean of these age estimates. Crosses denote the first appearances of trilobites in Morocco and Siberia.</p></caption>
          
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f09.png"/>

        </fig>


</sec>
<sec id="App1.Ch1.S2.SS3">
  <label>B3</label><title>Variation within alignment clusters</title>
      <p id="d2e7801">Summarising the posterior by grouping samples into clusters of similar alignments facilitates discussion of the results but risks oversimplifying the variation within each cluster. Each cluster represents a set of posterior samples that share similar inferred ages for the partition boundaries, but differences still exist between individual samples within the same cluster. As an example, three distinct alignments from cluster 1 are visualised in Fig. B3. An alignment from a sample not assigned to any cluster is shown in Fig. B3d.</p>

      <fig id="FB3"><label>Figure B3</label><caption><p id="d2e7806">Alternative alignments, each corresponding to a single sample from the posterior. <bold>(a)</bold> A sample from the most likely cluster 1, corresponding to that shown in Fig. 6a. <bold>(b, c)</bold> Alignments corresponding to other samples from cluster 1. <bold>(d)</bold> Alignment corresponding to an outlier sample that was not assigned to any cluster. The curved dark lines show the cubic B-splines corresponding to each alignment.</p></caption>
          
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f10.png"/>

        </fig>


</sec>
<sec id="App1.Ch1.S2.SS4">
  <label>B4</label><title>Posterior of alignment parameters</title>
      <p id="d2e7837">The posterior distributions of the alignment parameters are summarised in histograms in Fig. B4.</p>

      <fig id="FB4"><label>Figure B4</label><caption><p id="d2e7842">Comparison of prior and posterior probability densities. Histograms in colour denote the posterior probability densities of the 18 alignment parameters; the grey, smooth shadings represent prior probability densities. The four colours correspond to the four independent model runs.</p></caption>
          
          <graphic xlink:href="https://gchron.copernicus.org/articles/7/545/2025/gchron-7-545-2025-f11.png"/>

        </fig>


</sec>
</app>
  </app-group><notes notes-type="codedataavailability"><title>Code and data availability</title>

      <p id="d2e7860">The StratoBayes R package is available for download as a binary at <uri>https://stratobayes.github.io</uri> (last access:  22 October 2025). The data and R scripts used to generate the results are available at <ext-link xlink:href="https://doi.org/10.5281/zenodo.15065336" ext-link-type="DOI">10.5281/zenodo.15065336</ext-link> (Eichenseer, 2025).</p>
  </notes><notes notes-type="authorcontribution"><title>Author contributions</title>

      <p id="d2e7872">MRS and ARM conceived the idea. MRS, ARM and MS designed the initial model version, and all authors contributed to the design of the final model. MS, ARM and MRS coded the software prototype. KE, MRS and ARM modified and expanded the software. MS curated the lower Cambrian data. KE conducted the analyses and visualised the results. KE wrote the initial manuscript draft, and all authors contributed to the final version. MRS coordinated the project. MRS and ARM acquired the funding.</p>
  </notes><notes notes-type="competinginterests"><title>Competing interests</title>

      <p id="d2e7878">The contact author has declared that none of the authors has any competing interests.</p>
  </notes><notes notes-type="disclaimer"><title>Disclaimer</title>

      <p id="d2e7884">Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this paper. While Copernicus Publications makes every effort to include appropriate place names, the final responsibility lies with the authors. Views expressed in the text are those of the authors and do not necessarily reflect the views of the publisher.</p>
  </notes><ack><title>Acknowledgements</title><p id="d2e7890">We thank the participants of the StratoBayes workshop (Durham, 2024) for feedback on an early version of the StratoBayes software. We thank Tim Heaton for sharing his code for spline fitting. We thank Andrew Valentine for discussions on the model. We thank Nasrrddine Youbi and Kamal Mghazli for hosting an exploratory field visit to the lower Cambrian sections in Morocco. We thank Maarten Blaauw, Andrew Curtis and Norman MacLeod for their helpful feedback on an earlier version of this manuscript.</p></ack><notes notes-type="financialsupport"><title>Financial support</title>

      <p id="d2e7895">This research has been supported by the Leverhulme Trust (grant-no. 2019-223).</p>
  </notes><notes notes-type="reviewstatement"><title>Review statement</title>

      <p id="d2e7902">This paper was edited by Stewart Fallon and reviewed by Maarten Blaauw and Andrew Curtis.</p>
  </notes><ref-list>
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