Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii)

Andrew M Ritchie,Lindell Bromham,Xia Hua

doi:10.1007/s00239-022-10052-6

Abstract

Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.

Highlights

IntroductionVariation in the tempo and mode of evolution is an important feature of the tree of life, which can potentially reveal evolutionary patterns and processes
Empirical patterns of molecular rate variation may be significantly correlated to variation in life history characters such as body size (Barrera-Redondo et al 2018; Berv and Field 2018), lifespan (Galtier et al 2009) or the rate of reproduction (Welch et al 2008)
We performed additional tests and data transformations to check whether the size of contrasts was affected by the depth of the pair, as represented by the inferred age of the most recent common ancestor (MRCA) of each sister pair, or by the ancestral value of the diversification or substitution rates, but these analyses did not materially alter the results, so the analysis presented here uses comparisons without any adjustment for age or ancestral values

Summary

Introduction

Variation in the tempo and mode of evolution is an important feature of the tree of life, which can potentially reveal evolutionary patterns and processes. Empirical patterns of molecular rate variation may be significantly correlated to variation in life history characters such as body size (Barrera-Redondo et al 2018; Berv and Field 2018), lifespan (Galtier et al 2009) or the rate of reproduction (Welch et al 2008). These findings of consistent patterns of rate variation between lineages open the door to viewing the Journal of Molecular Evolution (2022) 90:200–214 rate of molecular evolution as a trait that can itself evolve and diversify (Bromham 2009, 2011), subject both to selective pressures and random variation (Dobzhansky 1970; Lynch et al 2016)

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