Consistent variation in amino-acid substitution rate, despite uniformity of mutation rate: protein evolution in mammals is not neutral

Examining the role of effective population size on mitochondrial and multilocus divergence time discordance in a songbird

Estimates of speciation times are subject to a number of potential errors. One source of bias is that effective population size (Ne) has been shown to influence substitution rates. This issue is of particular interest for phylogeographic studies because population sizes can vary dramatically among genetically structured populations across species' ranges. In this study, we used multilocus data to examine temporal phylogeographic patterns in a widespread North American songbird, the Northern Cardinal (Cardinalis cardinalis). Species tree estimation indicated that the phylogeographic structure of C. cardinalis was comprised of four well-supported mainland lineages with large population sizes (large Ne) and two island lineages comprised of much smaller populations (small Ne). We inferred speciation times from mtDNA and multilocus data and found there was discordance between events that represented island-mainland divergences, whereas both estimates were similar for divergences among mainland lineages. We performed coalescent simulations and found that the difference in speciation times could be attributed to stochasticity for a recently diverged island lineage. However, the magnitude of the change between speciation times estimated from mtDNA and multilocus data of an older island lineage was substantially greater than predicted by coalescent simulations. For this divergence, we found the discordance in time estimates was due to a substantial increase in the mtDNA substitution rate in the small island population. These findings indicate that in phylogeographic studies the relative tempo of evolution between mtDNA and nuclear DNA can become highly discordant in small populations.

Heterogeneous genomic molecular clocks in primates

Using data from primates, we show that molecular clocks in sites that have been part of a CpG dinucleotide in recent past (CpG sites) and non-CpG sites are of markedly different nature, reflecting differences in their molecular origins. Notably, single nucleotide substitutions at non-CpG sites show clear generation-time dependency, indicating that most of these substitutions occur by errors during DNA replication. On the other hand, substitutions at CpG sites occur relatively constantly over time, as expected from their primary origin due to methylation. Therefore, molecular clocks are heterogeneous even within a genome. Furthermore, we propose that varying frequencies of CpG dinucleotides in different genomic regions may have contributed significantly to conflicting earlier results on rate constancy of mammalian molecular clock. Our conclusion that different regions of genomes follow different molecular clocks should be considered when inferring divergence times using molecular data and in phylogenetic analysis.

Size of the protein-coding genome and rate of molecular evolution

In diploid populations of size N, there will be 2 Nmu mutations per nucleotide (nt) site (or per locus) per generation (mu stands for mutation rate). If either the population or the coding genome double in size, one expects 4 Nmu mutations. What is important is not the population size per se but the number of genes (coding sites), the two being often interconverted. Here we compared the total physical length of protein-coding genomes (n) with the corresponding absolute rates of synonymous substitution (K(S)), an empirical neutral reference. In the classical occupancy problem and in the coupons collector (CC) problem, n was expressed as the mean rate of change (K(CC)). Despite inherently very low power of the approaches involving averaging of rates, the mode of molecular evolution of the total size phenotype of the coding genome could be evidenced through differences between the genomic estimates of K(CC) [K(CC)=1/(ln n + 0.57721) n] and rate of molecular evolution, K(S). We found that (1) the estimates of n and K(S) are reciprocally correlated across taxa (r=0.812; p<< 0.001); (2) the gamete-cell division hypothesis (Chang et al. Proc Natl Acad Sci USA 91:827-831, 1994) can be confirmed independently in terms of K(CC)/K(S) ratios; (3) the time scale of molecular evolution changes with change in mutation rate, as previously shown by Takahata (Proc Natl Acad Sci USA 87:2419-2423, 1990), Takahata et al. (Genetics 130:925-938, 1992), and Vekemans and Slatkin (Genetics 137:1157-1165, 1994); (4) the generation time and population size (Lynch and Conery, Science 302:1401-1404, 2003) effects left their "signatures" at the level of the size phenotype of the protein-coding genome.

Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence

Several lines of indirect evidence suggest that hominoids (apes and humans) and cercopithecoids (Old World monkeys) diverged around 23-25 Mya. Importantly, although this range of dates has been used as both an initial assumption and as a confirmation of results in many molecular-clock analyses, it has not been critically assessed on its own merits. In this article we test the robusticity of the 23- to 25-Mya estimate with approximately 150,000 base pairs of orthologous DNA sequence data from two cercopithecoids and two hominoids by using quartet analysis. This method is an improvement over other estimates of the hominoid-cercopithecoid divergence because it incorporates two calibration points, one each within cercopithecoids and hominoids, and tests for a statistically appropriate model of molecular evolution. Most comparisons reject rate constancy in favor of a model incorporating two rates of evolution, supporting the "hominoid slowdown" hypothesis. By using this model of molecular evolution, the hominoid-cercopithecoid divergence is estimated to range from 29.2 to 34.5 Mya, significantly older than most previous analyses. Hominoid-cercopithecoid divergence dates of 23-25 Mya fall outside of the confidence intervals estimated, suggesting that as much as one-third of ape evolution has not been paleontologically sampled. Identifying stem cercopithecoids or hominoids from this period will be difficult because derived features that define crown catarrhines need not be present in early members of these lineages. More sites that sample primate habitats from the Oligocene of Africa are needed to better understand early ape and Old World monkey evolution.

Molecular clocks and explosive radiations

Molecular data are ideal for exploring evolutionary history because of its universality, stochasticity, and abundance. These features provide a means of exploring the evolutionary history of all organisms (including those that do not tend to leave fossils), potentially within a statistical framework that allows testing of evolutionary hypotheses. However, the discrepancy between molecular and paleontological dates for three key "explosive" radiations inferred from the fossil record--the Cambrian explosion of animal phyla and the post-KT radiations of modern orders of mammals and birds--have led to a reexamination of the assumptions on which molecular dates are based. Could variation in the rate of molecular evolution, perhaps associated with "explosive" radiations, cause overestimation of diversification dates? Here I examine four hypothetical causes of fast molecular rates in explosive radiations--body size, morphological rate, speciation rate, and ecological diversification--using available empirical evidence on patterns of variation in rate of molecular evolution.

Mutation rates in mammalian genomes

Knowledge of the rate of point mutation is of fundamental importance, because mutations are a vital source of genetic novelty and a significant cause of human diseases. Currently, mutation rate is thought to vary many fold among genes within a genome and among lineages in mammals. We have conducted a computational analysis of 5,669 genes (17,208 sequences) from species representing major groups of placental mammals to characterize the extent of mutation rate differences among genes in a genome and among diverse mammalian lineages. We find that mutation rate is approximately constant per year and largely similar among genes. Similarity of mutation rates among lineages with vastly different generation lengths and physiological attributes points to a much greater contribution of replication-independent mutational processes to the overall mutation rate. Our results suggest that the average mammalian genome mutation rate is 2.2 x 10(-9) per base pair per year, which provides further opportunities for estimating species and population divergence times by using molecular clocks.

Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate

The neutralist perspective on molecular evolution maintains that the vast majority of mutations affecting gene function are neutral or deleterious. After a gene duplication where both genes are retained, it predicts that original and duplicate genes diverge at clock-like rates. This prediction is usually tested for coding sequences, but can also be applied to another important aspect of gene function, the genes' expression pattern. Moreover, if both sequence and expression pattern diverge at clock-like rates, a correlation between divergence in sequence and divergence in expression patterns is expected. Duplicate gene pairs with more highly diverged sequences should also show more highly diverged expression patterns. This prediction is tested for a large sample of duplicated genes in the yeast Saccharomyces cerevisiae, using both genome sequence and microarray expression data. Only a weak correlation is observed, suggesting that coding sequence and mRNA expression patterns of duplicate gene pairs evolve independently and at vastly different rates. Implications of this finding for the neutralist-selectionist debate are discussed.

Molecular evidence from the nuclear genome for the time frame of human evolution

Evolutionary divergence times can be inferred from molecular distances if a molecular clock can be assumed and if the substitution rate can be estimated. We present new evidence from relative rate tests that the rate of substitution at fourfold degenerate sites of nuclear genome-coding DNA is uniform in primate and rodent lineages. We also review recent relative rate test results showing substitution rate uniformity in the nuclear genome of simian primates. DNA distances between a range of mammalian taxa shows that a molecular clock is inconsistent with many assumed divergence times irrespective of the assumed substitution rate. We find that the substitution rate that implies the best compromise fit with divergence times across the range of taxa is 2.0-2.25 x 10(-9). This range of substitution rates implies a divergence time of humans and chimpanzees of 4.0-3.6 million years ago. This postdates the occurrence of Ardipithecus ramidus and the earliest occurrence of Australopithecus afarensis, suggesting that the common ancestor of humans and chimpanzees was bipedal and that the trait has been lost in chimpanzees rather than gained in humans.