THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION

By H. Hoekstra, J. Coyne. Evolution; international journal of organic evolution, 2007

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Abstract An important tenet of evolutionary developmental biology (“evo devo”) is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis-regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis-regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis-regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis-regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/7e4325660b960a398e6408e83add5e244272a1bd

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Citations in the corpus

Mechanistic approaches to the study of evolution: the functional synthesis (2007, background): “How important are changes in cis -regulatory regions versus those in protein-coding sequences for the evolution of adaptive phenotype”
Bridging the gap between the genotype and the phenotype: linking genetic variation, selection and adaptation in fishes (2008, background): “In fact, there is some debate about the relative importance of regulatory and protein categories in phenotypic evolution (Hoekstra and Coyne 2007; Wray 2007).”
The genetics of quantitative traits: challenges and prospects (2009, background): “Determining the functional consequences of QTNs addresses the long-standing debate about the relative contribution of protein-coding changes versus regulatory changes in phenotypic evolutio”
The Molecular Basis of Phenotypic Convergence (2014, background): “There is a long-standing debate over whether structural or regulatory changes fuel adaptive evolutionary change (e.g., King & Wilson 1975, Hoekstra & Coyne 2007, Carroll 2008, Wittkopp & Kalay 2012).”
Whole-genome duplication in teleost fishes and its evolutionary consequences (2014, background): “This may often be the appropriate conclusion; however, the methods used might not always detect alternatively spliced variants of a paralogue which might be prevalent in a certain tissue, and mRNA abundances can also be altered through changes in mRNA stability (Hoekstra and Coyne 2007).”