The Loci of Evolution: How Predictable is Genetic Evolution?

By D. Stern, Virginie Orgogozo. Evolution; international journal of organic evolution, 2008

755 citations recorded by the source corpus.

Abstract Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This “cis-regulatory hypothesis” has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question “Do coding or cis-regulatory mutations cause more phenotypic evolution?” hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/0e922beaeb72dd1921d7e0abd233fed92f45640e

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Citations in the corpus

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation (2009, background): “In addition, recent literature suggests that much of morphological evolution is tied to mutation in cis-regulatory regions (for reviews, see [57,58]).”
The Molecular Basis of Phenotypic Convergence (2014, background): “…candidate gene studies, quantitative trait locus analysis, population genomic scans for selection, whole genome sequencing, gene expression analysis, functional assays) have been reviewed elsewhere (e.g., Nielsen 2005, Arendt & Reznick 2008, Stinchcombe & Hoekstra 2008, Springer et al. 2011).”
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence (2011, background): “This evidence includes expression divergence that correlates with phenotypic divergence, manipulations of gene expression that are sufficient for recreating phenotypic differences and genetic mapping identifying regulatory loci as being responsible for divergent phenotype”
The QTN Program and the Alleles That Matter for Evolution: All That’s Gold Does Not Glitter (2011, positive): “Recently, Stern and Orgogozo (2008) compiled a valuable catalog of the evolutionarily relevant mutations characterized to date.”
Chapter 1: Subspecies Represent Geographically Partitioned Variation, A Gold Mine of Evolutionary Biology, and a Challenge for Conservation (2010, background): “…2008). further, interspecific morphological differences appear to involve cisregulatory element changes more than intraspecific ones do, which led Stern and Orgogozo (2008) to conclude that speciation causes fixation of a certain subset of the genetic variation that causes phenotypic variation…”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “These data have sparked a vigorous scientific dialogue regarding the nature of genetic mutations that contribute to evolutionary change (Stern, 2000; Hoekstra and Coyne, 2007; Wray, 2007; Carroll, 2008; Stern and Orgogozo, 2008; Wagner and Lynch, 2008; Streisfeld and Rausher, 2010).”
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (2016, positive): “…regulatory and coding regions, these meth-ods may fail to capture variation involved in gene regulation — such as enhancers and copy number variation — that may underlie the majority of adaptive phenotypic variation (Wray et al. 2003; Perry et al. 2007; Rockman 2012; Stern and Orgogozo 2008).”
Fitness and its role in evolutionary genetics (2009, background): “Are these mutations, for example, often in cis -regulatory sequences — as several researchers in evolutionary developmental biology (evo–devo) have suggeste”