Estimation of Primate Speciation Dates Using Local Molecular Clocks

Department of Cell and Molecular Biology, Northwestern University Medical School, Chicago, Illinois, USA.
Molecular Biology and Evolution (Impact Factor: 9.11). 08/2000; 17(7):1081-90. DOI: 10.1093/oxfordjournals.molbev.a026389
Source: PubMed


Protein-coding genes of the mitochondrial genomes from 31 mammalian species were analyzed to estimate the speciation dates within primates and also between rats and mice. Three calibration points were used based on paleontological data: one at 20-25 MYA for the hominoid/cercopithecoid divergence, one at 53-57 MYA for the cetacean/artiodactyl divergence, and the third at 110-130 MYA for the metatherian/eutherian divergence. Both the nucleotide and the amino acid sequences were analyzed, producing conflicting results. The global molecular clock was clearly violated for both the nucleotide and the amino acid data. Models of local clocks were implemented using maximum likelihood, allowing different evolutionary rates for some lineages while assuming rate constancy in others. Surprisingly, the highly divergent third codon positions appeared to contain phylogenetic information and produced more sensible estimates of primate divergence dates than did the amino acid sequences. Estimated dates varied considerably depending on the data type, the calibration point, and the substitution model but differed little among the four tree topologies used. We conclude that the calibration derived from the primate fossil record is too recent to be reliable; we also point out a number of problems in date estimation when the molecular clock does not hold. Despite these obstacles, we derived estimates of primate divergence dates that were well supported by the data and were generally consistent with the paleontological record. Estimation of the mouse-rat divergence date, however, was problematic.

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Available from: Anne D Yoder
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    • "Early studies achieved this by considering the evolutionary rate to be constant over time, that is, assuming a global molecular clock (also called a strict clock; Zuckerkandl and Pauling 1965). More recent methods allow the rate to vary over time under constraints specified by a relaxed-clock model, typically using a Bayesian inference framework (Hasegawa et al. 1989; Kishino et al. 1990; Thorne et al. 1998; Huelsenbeck et al. 2000; Yoder and Yang 2000; Kishino et al. 2001; Thorne and Kishino 2002; Aris-Brosou and Yang 2002; Yang and Yoder 2003; Drummond et al. 2006; Lepage et al. 2006; 2007; Rannala and Yang 2007; Drummond and Suchard 2010; Heath et al. 2012; Heath and Moore 2014). "
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    ABSTRACT: Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of datasets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants and bees). Previous total-evidence dating analyses of this dataset were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push towards more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.
    Full-text · Article · Oct 2015 · Systematic Biology
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    • "Improvements made in recent years to molecular dating approaches for timing divergence events 1 Advancement of molecular phylogeny: In the past decade, advances in sequencing technologies have resulted in the rapid accumulation of molecular data and increased access to genomic-scale data. Various tree-building methods have been developed to process large datasets; these have led to more accurate resolution of phylogenetic relationships and genetic distances between living taxa (Yang & Rannala, 2012). 2 Increasing variety of molecular clock models: Various molecular clock models, such as local molecular clocks (Li & Tanimura, 1987; Yoder & Yang, 2000 "

    Full-text · Article · Sep 2015 · New Phytologist
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    • "Over the past couple of years this has been the method of choice among investigators interested in divergence time estimation. Additional models have also been proposed, like the local-clocks model of Yoder and Yang (2000) and others (Yang and Yoder 2003; Drummond and Suchard 2010), a compound Poisson process of punctuated change (Huelsenbeck et al. 2000), as well as mixture models of evolutionary rates (Heath et al. 2012). "
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    ABSTRACT: Abstract— Divergence time analyses have become increasingly popular over the past several decades, partly due to the proliferation of molecular data, but also because of the development of methods that do not assume a strict molecular clock. In this review, I provide a brief background to the topic, then highlight several methods for “relaxing” the assumptions of a strict molecular clock. I discuss the pros and cons of many of these methods. Finally, I discuss the various techniques for incorporating fossils in molecular studies to estimate absolute ages of clades.
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