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Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol

Department of Cell and Molecular Biology, Northwestern University Medical School, Chicago, Illinois, USA.
Molecular Biology and Evolution (Impact Factor: 14.31). 08/2000; 17(7):1081-90. DOI: 10.1093/oxfordjournals.molbev.a026389
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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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Available from: Anne D Yoder, Aug 19, 2015
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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.
    Systematic Botany 02/2015; 40(1):6-13. DOI:10.1600/036364415X686297 · 1.11 Impact Factor
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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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    ABSTRACT: Absolute times from calibrated DNA phylogenies can be used to infer lineage diversification, the origin of new ecological niches, or the role of long distance dispersal in shaping current distribution patterns. Molecular-clock dating of non-vascular plants, however, has lagged behind flowering plant and animal dating. Here, we review dating studies that have focused on bryophytes with several goals in mind, (i) To facilitate cross-validation by comparing rates and times obtained so far; (ii) to summarize rates that have yielded plausible results and that could be used in future studies; and (iii) to calibrate a species-level phylogeny for Nothoceros, a model for plastid genome evolution in hornworts. Including the present work, there have been 18 molecular clock studies of liverworts, mosses, or hornworts, the majority with fossil calibrations, a few with geological calibrations or dated with previously published plastid substitution rate. Over half the studies cross-validated inferred divergence times by using alternative calibration approaches. Plastid substitution rates inferred for "bryophytes" are in line with those found in angiosperm studies, implying that bryophyte clock models can be calibrated either with published substitution rates or with fossils, with the two approaches testing and cross-validating each other. Our phylogeny of Nothoceros is based on 44 accessions representing all suspected species and a matrix of six markers of nuclear, plastid, and mitochondrial DNA. The results show that Nothoceros comprises 10 species, nine in the Americas and one in New Zealand (N. giganteus), with the divergence between the New Zealand species and its Chilean sister species dated to the Miocene and therefore due to long-distance dispersal. Based on the new tree, we formally transfer two species of Megaceros into Nothoceros, resulting in the new combinations N. minarum (Nees) J.C.Villarreal and N. schizophyllus (Gottsche ex Steph.) J.C.Villarreal, and we also newly synonymize eight names described in Megaceros.
    Molecular Phylogenetics and Evolution 09/2014; 78(1):25–35. DOI:10.1016/j.ympev.2014.04.014 · 4.02 Impact Factor
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    • "Under a 'relaxed-clock' model, substitution rates change over the tree in a constrained manner, thus separating the rate and time parameters associated with each branch and allowing inference of lineage divergence times. A considerable amount of effort has been directed at modeling lineage-specific substitution rate variation, with many different relaxed-clock models described in the literature [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]. When such models are coupled with a model on the distribution of speciation events over time (e.g., the Yule model [20] or birth-death process [21]), molecularsequence data can then inform the relative rates and node ages in a phylogenetic analysis. "
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    ABSTRACT: Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data-most commonly, fossil age estimates-are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the "fossilized birth-death" (FBD) process-a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene.
    Proceedings of the National Academy of Sciences 07/2014; 111(29). DOI:10.1073/pnas.1319091111 · 9.81 Impact Factor
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