Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution.

Abstract

Controversies over the molecular clock hypothesis were reviewed. Since it is evident that the molecular clock does not hold in an exact sense, accounting for evolution of the rate of molecular evolution is a prerequisite when estimating divergence times with molecular sequences. Recently proposed statistical methods that account for this rate variation are overviewed and one of these procedures is applied to the mitochondrial protein sequences and to the nuclear gene sequences from many mammalian species in order to estimate the time scale of eutherian evolution. This Bayesian method not only takes account of the variation of molecular evolutionary rate among lineages and among genes, but it also incorporates fossil evidence via constraints on node times. With denser taxonomic sampling and a more realistic model of molecular evolution, this Bayesian approach is expected to increase the accuracy of divergence time estimates.Key words: Bayesian method, divergence times, variation of evolutionary MOLECULAR CLOCKSince Pauling (1962, 1965) first recognized the possibility that proteins evolve at steady rates, the notion has aroused many controversies (Wilson et al., 1977;Kimura, 1983;Britten, 1986;Gillespie, 1991;Graur and Li, 2000). This hypothetical constancy of molecular evolution is called the molecular clock.The neutral theory provides a simple and successful explanation for a large number of observations of molecular evolution (Kimura, 1968(Kimura, , 1983). Yet the theory does not necessarily predict the molecular clock, since it simply predicts that the rate of molecular evolution is equal to the rate of neutral mutation, and the mutation rate may possibly be related to generation time rather than absolute time as suggested by many authors (e.g., Laird et al., 1969;Kohne, 1970). The generation time in rodents is much shorter than that in humans, and therefore the number of germline replications per year might be much higher in rodents than in humans.Britten (1986) showed that the rate of DNA evolution has been retarded in anthropoids compared with the rates in prosimians and in rodents. Wu and Li (1985) suggested that the rate of nucleotide substitution in rodents such as mice and rats is higher than that in humans, and that the ratio of the number of nucleotide substitutions in the rodent line to that in the human line since their divergence is 1.3 for nonsynonymous (amino acid replacing) substitutions and 2.0 for synonymous substitutions. It seems plausible that mice and rats evolve more rapidly than higher primates in the nuclear genes (Waterston et al., 2002), but the difference of the rate between rodents and humans seems smaller than the difference of the generation time between the two lineages. Genetic changes in evolution are the results of fixation of mutations that occurred in the germ cells, that is, eggs and sperms, and mutation rate may differ between female and male gametogenesis. Since the number of germ cell divisions is expected to be larger in males than in females, males are expected to ...

Highly conserved linkage homology between birds and turtles: Bird and turtle chromosomes are precise counterparts of each other

“…The present study reveals extensive chromosomal homologies between chicken and the Chinese soft-shelled turtle, although the two lineages diverged from the common ancestor more than 210 MYA. By 16 contrast, chromosomal rearrangements have occurred more frequently between mouse and human than between chicken and the turtle (Carver & Stubbs 1997, Burt 2002, although the lineage of human and mouse diverged more recently (80-90 MYA) (Hasegawa et al 2003). Our data suggest that the karyotypes of birds and turtles, consisting of few macrochromosomes and a large number of microchromosomes, have remained relatively stable and conserved, and thus inter-and intrachromosomal rearrangements have hardly occurred in the two lineages after divergence from the common ancestor.…”

Placing confidence limits on the molecular age of the human–chimpanzee divergence

“…The first chimpanzee fossil, for example, was only just reported in 2005 (1). As recently as the mid-1960s (2), the African apes were considered to be distant relatives of the human lineage, but subsequent molecular phylogenetic analyses have shown that the chimpanzee and human are sister species and have led to a revision of the age of their divergence (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). Currently, the earliest unequivocal upright hominids at 4.2 millions of years ago (Ma) provide the minimum age for human-chimpanzee divergence (14), and some recently proposed early hominids dated between 5 and slightly more than 6 Ma are thought to provide an estimate close to the actual species divergence (15)(16)(17)(18)(19).…”

“…However, studies using molecular data have yielded disparate values as well (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13), because of differences in the number of genes used, types of substitutions (synonymous, noncoding, and nonsynonymous) analyzed, calibration points used, and statistical methods used (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). Furthermore, current estimates of C.I.s of molecular divergence times fail to consider a comprehensive set of factors contributing to variance, such as a limited number of genes (gene sampling error), a limited number of sites for each gene (variance contributed by sequence divergence-estimation procedures), rate differences among lineages, and inherent uncertainty in the time used for calibrating lineage-specific and relaxed molecular clocks (21,22).…”

Paleontology: Outrunning Time

“…The fossil record provides hard minimum and soft maximum ages to help calibrate molecular phylogenies (Benton et al 2009). In turn, relaxed clock methods, which do not assume constancy of the molecular clock, instead allow multiple models with freely "evolving" substitution rates to compete, with the nodes of the branching tree constrained by dates from the fossil record (Hasegawa et al 2003). Since it is automatically the case that allowing substitution rates to vary will improve goodness of fit to the data, model selection criteria, such as the Akaike Information Criterion (Forster and Sober 1994), must be used to find those models that will achieve the best fit with the fewest independently estimated substitution rates (Hasegawa et al 2003).…”