Article

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

ABSTRACT

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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    • "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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    • "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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