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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    • "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 "

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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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    • ") so that no substitutions rates could be calculated. Obviously, rate heterogeneity among lineages is real (Lewis et al., 1997; Yoder and Yang, 2000; Smith and Donoghue, 2008; Rothfels and Schuettpelz, 2014), and where such heterogeneity is punctuated, it can sometimes be accommodated by local clocks, i.e., separate strict clocks in different parts of the tree (Yoder and Yang, 2000; Rothfels and Schuettpelz, 2014; Bellot and Renner, in preparation). Rate heterogeneity is expected to increase with the size of datasets, and the desire to include nodes suitable for fossil calibration often requires the inclusion of distant outgroups, potentially introducing further rate variation. "
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