Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

Abstract

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation-extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.

Slow and steady: the evolution of cranial disparity in fossil and recent turtles

“…First, given that turtles originated in the Early Mesozoic, it is plausible that the initial increase of disparity is the result of random or adaptive exploration of the available morphospace. Given that turtles have extended generation times relative to most invertebrates or small amniotes [75,76], it is furthermore plausible that evolutionary rates are lower for the group [77,78] and that this diversification therefore took place over an unusually prolonged time period and was only stopped by climatic cooling. On the other hand, the early diversification of turtles also coincides with the break-up of Pangaea, as already noted for other reptile groups [79][80][81][82].…”

Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

“…Higher substitution rates and greater rate heterogeneity may be driving factors, although rate heterogeneity among nuclear and mitochondrial genes has rarely been evaluated [35]. Mitochondrial data suffer from greater NT composition bias and site saturation [27].…”

Molecular evolution and the latitudinal biodiversity gradient

“…Evidence of a link between rates of molecular evolution and netdiversification has been reported (Barraclough and Savolainen, 2001;Jobson and Albert, 2002;Eo and Dewoody, 2010;Lancaster, 2010;Lanfear et al, 2010abut see Goldie et al, 2011 where no such link was found in mammals). However, none of these studies have conclusively shown that increased rates of molecular evolution are responsible for elevated rates of speciation.…”