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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

Comparison of Mk-1 against Mk-8 analyses for the penguin dataset. (a) Phylogenetic estimate of fossil age of Mk-1 against Mk-8 with x = y line, (b) regression of error in phylogenetic estimate of fossil age of Mk-1 against Mk-8, (c) regression of posterior probability of palaeontological range of Mk-1 against Mk-8, (d) regression of BF for palaeontological range of Mk-1 against Mk-8. (Online version in colour.)
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RSTB20150129F5: Comparison of Mk-1 against Mk-8 analyses for the penguin dataset. (a) Phylogenetic estimate of fossil age of Mk-1 against Mk-8 with x = y line, (b) regression of error in phylogenetic estimate of fossil age of Mk-1 against Mk-8, (c) regression of posterior probability of palaeontological range of Mk-1 against Mk-8, (d) regression of BF for palaeontological range of Mk-1 against Mk-8. (Online version in colour.)

Mentions: Overall the results of analysing the penguin dataset with the Mk-1 and Mk-8 models were strikingly concordant. Figure 5 shows four regressions between the two models: (i) regression of estimated phylogenetic estimates of fossil ages of Mk-1 against Mk-8, (ii) regression of the error in the phylogenetic estimates of fossil ages of Mk-1 against Mk-8, (iii) regression of posterior probability of palaeontological range of Mk-1 against Mk-8 and (iv) regression of BF for palaeontological range of Mk-1 against Mk-8. Under Mk-8, all fossils have positive evidence for their geological age range, whereas under Mk-1 there are a handful of fossils with negative evidence for the corresponding geological age range. Furthermore, assuming the median geological age is the truth, the variance in the phylogenetic estimation error of the fossil ages is larger under Mk-1 than under Mk-8. This evidence, along with the previous result that Mk-8 has a higher marginal likelihood than Mk-1 [23], suggests that the relaxed model is overall a better fit to the data. Under both models, there is a positive correlation between the precision of the age estimate and the number of non-ambiguous characters coded for the fossil taxon (figure 6).Figure 5.


Bayesian phylogenetic estimation of fossil ages.

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

Comparison of Mk-1 against Mk-8 analyses for the penguin dataset. (a) Phylogenetic estimate of fossil age of Mk-1 against Mk-8 with x = y line, (b) regression of error in phylogenetic estimate of fossil age of Mk-1 against Mk-8, (c) regression of posterior probability of palaeontological range of Mk-1 against Mk-8, (d) regression of BF for palaeontological range of Mk-1 against Mk-8. (Online version in colour.)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSTB20150129F5: Comparison of Mk-1 against Mk-8 analyses for the penguin dataset. (a) Phylogenetic estimate of fossil age of Mk-1 against Mk-8 with x = y line, (b) regression of error in phylogenetic estimate of fossil age of Mk-1 against Mk-8, (c) regression of posterior probability of palaeontological range of Mk-1 against Mk-8, (d) regression of BF for palaeontological range of Mk-1 against Mk-8. (Online version in colour.)
Mentions: Overall the results of analysing the penguin dataset with the Mk-1 and Mk-8 models were strikingly concordant. Figure 5 shows four regressions between the two models: (i) regression of estimated phylogenetic estimates of fossil ages of Mk-1 against Mk-8, (ii) regression of the error in the phylogenetic estimates of fossil ages of Mk-1 against Mk-8, (iii) regression of posterior probability of palaeontological range of Mk-1 against Mk-8 and (iv) regression of BF for palaeontological range of Mk-1 against Mk-8. Under Mk-8, all fossils have positive evidence for their geological age range, whereas under Mk-1 there are a handful of fossils with negative evidence for the corresponding geological age range. Furthermore, assuming the median geological age is the truth, the variance in the phylogenetic estimation error of the fossil ages is larger under Mk-1 than under Mk-8. This evidence, along with the previous result that Mk-8 has a higher marginal likelihood than Mk-1 [23], suggests that the relaxed model is overall a better fit to the data. Under both models, there is a positive correlation between the precision of the age estimate and the number of non-ambiguous characters coded for the fossil taxon (figure 6).Figure 5.

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