First comparative study of primate morphological and molecular evolutionary rates including muscle data: implications for the tempo and mode of primate and human evolution

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 CO 3. 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.

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Wing shape and environmental energy are associated with molecular evolutionary rates in a large avian radiation

10.1101/2020.01.16.908368 ◽

2020 ◽

Author(s):

David Alejandro Duchêne ◽

Paola Montoya ◽

Carlos Daniel Cadena

Keyword(s):

Uv Radiation ◽

Positive Association ◽

Evolutionary Rates ◽

Wing Morphology ◽

Geographic Ranges ◽

Molecular Evolutionary Rates ◽

Strong Positive Association ◽

Genomic Regions ◽

Avian Family

AbstractAmong the macroevolutionary drivers of molecular evolutionary rates, metabolic demands and environmental energy have been a central topic of discussion. The large number of studies examining these associations have found mixed results, and have rarely explored the interactions among various factors impacting molecular evolutionary rates. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with a proxy of metabolic demands imposed by flight (wing morphology) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found a strong positive association between molecular rates in genomic regions that can change the coded amino-acid with wing morphology, environmental temperature, and UV radiation. Strikingly, however, we did not find evidence of such associations with molecular rates at sites not impacting amino-acids. Our results suggest that the demands of flight and environmental energy primarily impact genome evolution by placing selective constraints, instead of being associated with basal mutation rates.

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Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

Biology Letters ◽

10.1098/rsbl.2009.0419 ◽

2009 ◽

Vol 5 (6) ◽

pp. 812-816 ◽

Cited By ~ 74

Author(s):

Davin H. E. Setiamarga ◽

Masaki Miya ◽

Yusuke Yamanoue ◽

Yoichiro Azuma ◽

Jun G. Inoue ◽

...

Keyword(s):

Comparative Genomics ◽

Molecular Clock ◽

Divergence Time ◽

Evolutionary Rates ◽

Implicit Assumption ◽

Molecular Evolutionary Rates ◽

Clock Analysis ◽

The Japanese Archipelago ◽

Two Populations ◽

Rates Of Molecular Evolution

The southern and northern Japanese populations of the medaka fish provide useful tools to gain insights into the comparative genomics and speciation of vertebrates, because they can breed to produce healthy and fertile offspring despite their highly divergent genetic backgrounds compared with those of human–chimpanzee. Comparative genomics analysis has suggested that such large genetic differences between the two populations are caused by higher molecular evolutionary rates among the medakas than those of the hominids. The argument, however, was based on the assumption that the two Japanese populations diverged approximately at the same time (4.0–4.7 Myr ago) as the human–chimpanzee lineage (5.0–6.0 Myr ago). This can be misleading, because the divergence time of the two populations was calculated based on estimated, extremely higher molecular evolutionary rates of other fishes with an implicit assumption of a global molecular clock. Here we show that our estimate, based on a Bayesian relaxed molecular-clock analysis of whole mitogenome sequences from 72 ray-finned fishes (including 14 medakas), is about four times older than that of the previous study (18 Myr). This remarkably older estimate can be reconciled with the vicariant events of the Japanese archipelago, and the resulting rates of molecular evolution are almost identical between the medaka and hominid lineages. Our results further highlight the fact that reproductive isolation may not evolve despite a long period of geographical isolation.

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