Tighter estimation of hominoid divergence times by hierarchical Bayesian analysis of dated fossil morphology and incompletely so

This poster was presented at SMBE 2013, Chicago, IL.

Citation: Matzke, Nicholas J.; Schraiber, Joshua G.; Collard, Mark; Dembo, Mana; Yang, Melinda A. (2013). "Tighter estimation of hominoid divergence times by hierarchical Bayesian analysis of dated fossil morphology and incompletely sorted genes." Society For Molecular Biology and Evolution 2013 Annual Meeting, Poster Session B, Poster B205, slot 865. SMBE 2013 Scientific Program, p. 100.

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Abstract

Tighter estimation of hominoid divergence times by hierarchical Bayesian analysis of dated fossil morphology and incompletely sorted genes

Authors: Nicholas J. Matzke1*†, Joshua G. Schraiber1†, Mark Collard2, Mana Dembo2,
Melinda A. Yang1†

Affiliations:

1 Center for Theoretical and Evolutionary Genomics, Department of Integrative Biology,
University of California, Berkeley.

2 Human Evolutionary Studies Program and Department of Archaeology, Simon Fraser
University, Burnaby, British Columbia, Canada

  • Correspondence to: ude.yelekreb|ekztam#ude.yelekreb|ekztam

† Current address: 1005 Valley Life Sciences Building #3140, Berkeley, CA 94720-3140

The date of the human-chimp divergence remains frustratingly uncertain, with estimates collated in TimeTree ranging from 4-10 million years ago (Mya), with little evidence of convergence (Figure 2, middle). All hominoid divergence times show similar uncertainty, despite their fundamental importance for human genetics and evolution, due to difficulties in extrapolating the long-term substitution rate from modern measurements of the mutation rate, and uncertainty in the phylogenetic placement of fossil taxa. Here we use a hierarchical Bayesian model, implemented in BEAST, to simultaneously estimate (1) a dated tree based on discrete morphological characters from 39 fossil and living terminal taxa, and (2) a dated species tree of living taxa based on 100 noncoding genomic loci evolving under the multispecies coalescent. Only the dates (sometimes uncertain) of fossil tips are used to inform the dating of the tree; the problem of the subjectivity of prior distributions on node dates is avoided completely. The fossil data overwhelm even a strong prior favoring a high substitution rate, despite inclusion of all uncertainty in the dating and phylogenetic placement of fossils. The advantage of combined analysis is striking: a dated morphology-only analysis yields a 95% highest posterior density (HPD) on the human-chimp divergence time of 4.5-8.95 Mya, but in the combined analysis the 95% HPD is 4.38-5.54 Mya, despite the uncertain phylogenetic position of some fossils. In fossil-rich situations, the precision of estimates of node dates may soon approach the timescale of speciation events themselves (less than 1 My).

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