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Bayesian phylogenetic estimation of fossil ages.

Drummond AJ, Stadler T - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2016)

Bottom Line: In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated.The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa.We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, University of Auckland, Auckland 1010, New Zealand Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4058 Basel, Switzerland alexei@cs.auckland.ac.nz.

No MeSH data available.


Related in: MedlinePlus

The Bayesian phylogenetic estimate of fossil age (median of marginal posterior) for each of the 36 penguin fossils plotted against their palaeontological age estimates, under two alternative site and molecular clock models. The palaeontological age estimates are represented by the mid-point of the range and the upper and lower limits. The Bayesian estimates are represented by the median of the marginal posterior distribution and the upper and lower limits of the 95% HPD interval. The diagonal line shows the x = y. If the vertical line does not cross x = y, then the mid-point of the geological range is not in the phylogenetic 95% HPD. If the horizontal line does not cross x = y, then the median phylogenetic estimate is not contained in the palaeontological age range. The labelled fossils have posterior probability of less than 0.05 for their age being within the palaeontological age interval. (Online version in colour.)
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RSTB20150129F2: The Bayesian phylogenetic estimate of fossil age (median of marginal posterior) for each of the 36 penguin fossils plotted against their palaeontological age estimates, under two alternative site and molecular clock models. The palaeontological age estimates are represented by the mid-point of the range and the upper and lower limits. The Bayesian estimates are represented by the median of the marginal posterior distribution and the upper and lower limits of the 95% HPD interval. The diagonal line shows the x = y. If the vertical line does not cross x = y, then the mid-point of the geological range is not in the phylogenetic 95% HPD. If the horizontal line does not cross x = y, then the median phylogenetic estimate is not contained in the palaeontological age range. The labelled fossils have posterior probability of less than 0.05 for their age being within the palaeontological age interval. (Online version in colour.)

Mentions: Although Mk-1 is a very simple model, the phylogenetic estimates of the ages of the penguin fossils were remarkably consistent with their palaeontological age ranges. Figure 2a plots the geological age and range against the phylogenetic estimates of fossil age. The points in this plot have R2 = 0.903. The median error (where the error is the difference between the phylogenetic median and the geological median) is 1.96 Myr. The median relative error (where the relative error is the error divided by the geological median) was 5.7% and the median relative standard deviation (RSD; defined as the standard deviation of the marginal posterior divided by the posterior median estimate) was 9.2%. A summary of the individual estimates are tabulated in table 1.Figure 2.


Bayesian phylogenetic estimation of fossil ages.

Drummond AJ, Stadler T - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2016)

The Bayesian phylogenetic estimate of fossil age (median of marginal posterior) for each of the 36 penguin fossils plotted against their palaeontological age estimates, under two alternative site and molecular clock models. The palaeontological age estimates are represented by the mid-point of the range and the upper and lower limits. The Bayesian estimates are represented by the median of the marginal posterior distribution and the upper and lower limits of the 95% HPD interval. The diagonal line shows the x = y. If the vertical line does not cross x = y, then the mid-point of the geological range is not in the phylogenetic 95% HPD. If the horizontal line does not cross x = y, then the median phylogenetic estimate is not contained in the palaeontological age range. The labelled fossils have posterior probability of less than 0.05 for their age being within the palaeontological age interval. (Online version in colour.)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920331&req=5

RSTB20150129F2: The Bayesian phylogenetic estimate of fossil age (median of marginal posterior) for each of the 36 penguin fossils plotted against their palaeontological age estimates, under two alternative site and molecular clock models. The palaeontological age estimates are represented by the mid-point of the range and the upper and lower limits. The Bayesian estimates are represented by the median of the marginal posterior distribution and the upper and lower limits of the 95% HPD interval. The diagonal line shows the x = y. If the vertical line does not cross x = y, then the mid-point of the geological range is not in the phylogenetic 95% HPD. If the horizontal line does not cross x = y, then the median phylogenetic estimate is not contained in the palaeontological age range. The labelled fossils have posterior probability of less than 0.05 for their age being within the palaeontological age interval. (Online version in colour.)
Mentions: Although Mk-1 is a very simple model, the phylogenetic estimates of the ages of the penguin fossils were remarkably consistent with their palaeontological age ranges. Figure 2a plots the geological age and range against the phylogenetic estimates of fossil age. The points in this plot have R2 = 0.903. The median error (where the error is the difference between the phylogenetic median and the geological median) is 1.96 Myr. The median relative error (where the relative error is the error divided by the geological median) was 5.7% and the median relative standard deviation (RSD; defined as the standard deviation of the marginal posterior divided by the posterior median estimate) was 9.2%. A summary of the individual estimates are tabulated in table 1.Figure 2.

Bottom Line: In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated.The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa.We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, University of Auckland, Auckland 1010, New Zealand Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4058 Basel, Switzerland alexei@cs.auckland.ac.nz.

No MeSH data available.


Related in: MedlinePlus