Rates of Genome Evolution and Branching Order from Whole Genome Analysis

Abstract

Accurate estimation of any phylogeny is important as a framework for evolutionary analysis of form and function at all levels of organization from sequence to whole organism. Using alignments of nonrepetitive components of opossum, human, mouse, rat, and dog genomes we evaluated two alternative tree topologies for eutherian evolution. We show with very high confidence that there is a basal split between rodents (as represented by the mouse and rat) and a branch joining primates (as represented by humans) and carnivores (as represented by dogs), consistent with some but not the most widely accepted mammalian phylogenies. The result was robust to substitution model choice with equivalent inference returned from a spectrum of models ranging from a general time reversible model, a model that treated nucleotides as either purines and pyrimidines, and variants of these that incorporated rate heterogeneity among sites. By determining this particular branching order we are able to show that the rate of molecular evolution is almost identical in rodent and carnivore lineages and that sequences evolve approximately 11%-14% faster in these lineages than in the primate lineage. In addition by applying the chicken as outgroup the analyses suggested that the rate of evolution in all eutherian lineages is approximately 30% slower than in the opossum lineage. This pattern of relative rates is inconsistent with the hypothesis that generation time is an important determinant of substitution rates and, by implication, mutation rates. Possible factors causing rate differences between the lineages include differences in DNA repair and replication enzymology, and shifts in nucleotide pools. Our analysis demonstrates the importance of using multiple sequences from across the genome to estimate phylogeny and relative evolutionary rate in order to reduce the influence of distorting local effects evident even in relatively long sequences.

Genome analysis of the platypus reveals unique signatures of evolution

“…Genome landscape. To establish phylogeny we extended the basic data sampling approach described previously 73 to protein-coding genes, and used established techniques to analyse protein-coding indels 74 and retrotransposon insertions 75 ( Supplementary Notes 19).…”

Genomics, biogeography, and the diversification of placental mammals

“…Among the placental mammals, phylogenetic branching events have been inferred by using either nucleotide sequence data (4)(5)(6)(7)(8)(9)(10)(11) or rare insertion/deletion patterns (12)(13)(14)(15). Many of the results recognize four primary eutherian groups: Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires.…”

“…The Euarchontoglires includes the species from five living mammalian orders (e.g., primates, treeshrews, flying lemurs, rabbits, and rodents). This last group remains the most controversial, and a number of recent studies have suggested it is not valid (4,6,7). The studies that have identified and supported these primary groupings have been able to resolve the branching pattern within some of the clades, but a statistically robust determination of the branching order at the base of the placental clade continues to be elusive.…”

“…Based on a parsimony analysis of nuclear-encoded genes, it was reported (8) that murid rodents as represented by mouse and rat were the sister group to all other placental mammals, and that rabbits were the next branching clade. More recently, a number of large-scale genomic studies (4,6) have reported that primates grouped more closely to laurasiatherians than to Glires.…”

Breakpoint graphs and ancestral genome reconstructions

“…9). While the morphology studies support the primate-rodent clade (Shoshani and McKenna 1998), the early molecular studies supported the primate-carnivore clade (Graur 1993;Janke et al 1994;Kumar and Hedges 1998; Murphy et al (2001), the phylogeny based on the primate-rodent clade (Madsen et al 2001;Poux et al 2002;Amrine-Madsen et al 2003;Thomas et al 2003;Reyes et al 2004) has become widely accepted, the question is far from being settled: recent studies provided arguments against the primate-rodent clade (Arnason et al 2002;Misawa and Janke 2003;Jorgensen et al 2005;Cannarozzi et al 2007;Huerta-Cepas et al 2007;Huttley et al 2007;Niimura and Nei 2007). Below we analyze some rearrangement-based characters supporting both the primate-carnivore and (to a smaller extent) the primaterodent clade.…”