Evolution and Development: Genes and Mutations Underlying Phenotypic Variation

by

Virginie Courtier-Orgogozo, Arnaud Martin

• LAST REVIEWED: 13 January 2014
• LAST MODIFIED: 13 January 2014
• DOI: 10.1093/obo/9780199941728-0003

Introduction

While the study of evolution has long been equated with theoretical computations of changes in allele frequencies in populations, the elucidation of the actual genes and mutations responsible for measurable differences (i.e., phenotypic variation) between individuals and species, which started in the 1980s, has revolutionized the field. From “Mendelian” traits underlined by single genes to polygenic traits such as human height that are influenced by many determinants across the genome (called quantitative trait loci, or QTL), a wide array of powerful methods are now accessible to biologists to tackle the molecular basis of variation. The accumulating empirical data on the “loci of evolution” provides unprecedented insights into multiple aspects of evolution. The molecular nature of the causative mutations illuminates certain observations (e.g., unstable phenotypes due to epigenetic mutations) and clarifies how genotypes connect to phenotypes and fitness. Analysis of the number, effect size, and distribution of loci reveals that the genetic basis of certain phenotypic changes is limited and thus at least partly predictable. Elucidation of the causative mutations also makes it possible to investigate the historical origin of phenotypic traits. This bibliography represents an overview of this ongoing transdisciplinary research program and mainly includes representative studies that have connected genetic modifications to morphological, physiological, or behavioral traits in eukaryotes, be it in the wild or in features selected for breeding. Also included here are a few articles with no direct link to organism-level phenotypes (e.g., theoretical papers and papers focusing on gene expression levels or enzymatic activities) when the reported results led to significant progress in our general understanding of the genetic basis of evolution. Experimental evolution studies as well as genetic studies of bacteria have not been included here, but should be remembered as an essential and complementary part of our body of empirical knowledge.

General Overviews

This section provides recent general overviews that are important for understanding evolutionary genetics as a field. Stern 2010 stresses that the study of evolution of development must integrate a variety of disciplines, and that the field is now tending to reunify population genetics (the study of allele frequencies across space and time) with developmental biology (the study of processes that integrate genotypic and environmental factors into phenotypes). Orr 2005 summarizes the discordance between theoretical predictions and emerging empirical data on the genes and mutations responsible for phenotypic evolution. Carroll, et al. 2004 and Nei 2007 represent one of the first syntheses of such empirical data, while Stern and Orgogozo 2008; Alonso-Blanco, et al. 2009; and O’Bleness, et al. 2012 convey more recent overviews of the field. Rockman 2011 is a necessary paper that condemns rapid generalizations from empirical data due to inescapable experimental biases.

• Alonso-Blanco, Carlos, Mark G. M. Aarts, Leonie Bentsink, et al. 2009. What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell 21.7: 1877–1996.

  DOI: 10.1105/tpc.109.068114

  A comprehensive review of the loci of natural and agricultural variation that have been identified in plants.

• Carroll, Sean B., Jennifer K. Grenier, and Scott D. Weatherbee. 2004. From DNA to diversity: Molecular genetics and the evolution of animal design. 2d ed. Malden, MA: Blackwell Science.

  This edition, along with its first edition (2001), represents a very accessible and beautifully illustrated synthesis of the field of evolutionary developmental biology. Of particular interest is the testable hypothesis that morphological evolution occurs primarily via the regulation of expression of a restricted set of architect genes, the so-called developmental toolkit.

• Nei, Masatoshi. 2007. The new mutation theory of phenotypic evolution. Proceedings of the National Academy of Sciences 104.30: 12235–12242.

  DOI: 10.1073/pnas.0703349104

  Against the view held by most evolutionary biologists, Masatoshi Nei argues that the primary driving force of phenotypic evolution is mutation, rather than natural selection.

• O’Bleness, M., V. B. Searles, A. Varki, P. Gagneux, and J. M. Sikela. 2012. Evolution of genetic and genomic features unique to the human lineage. Nature Reviews Genetics 13.12: 853–866.

  DOI: 10.1038/nrg3336

  An overview of the emerging genetic data on the changes that have shaped some of the peculiarities of our own species.

• Orr, H. Allen. 2005. The genetic theory of adaptation: A brief history. Nature Review Genetics 6.2: 119–127.

  DOI: 10.1038/nrg1523

  An informal description of the literature on theories of adaptation, recommended to understand what past and modern models predict about the number and the effect size of evolutionarily relevant mutations.

• Rockman, Matthew V. 2011. The QTN program and the alleles that matter for evolution: All that’s gold does not glitter. Evolution 66.1: 1–17.

  DOI: 10.1111/j.1558-5646.2011.01486.x

  Matthew Rockman reminds us with eloquence that only mutations of large-phenotypic effect are accessible to geneticists, and that the lack of information on mutations with infinitesimal effects prevents us from using empirical data to derive quantitative statements about the genetic basis of evolution in general.

• Stern, David L. 2010. Evolution, development, and the predictable genome. Greenwood Village, CO: Roberts.

  A concise and thoughtful introduction to the genetics of phenotypic evolution and its main concepts, explaining how fields such as evolutionary developmental biology and population genomics illuminate each other.

• Stern, David L., and Virginie Orgogozo. 2008. The loci of evolution: How predictable is genetic evolution? Evolution 62.9: 2155–2177.

  DOI: 10.1111/j.1558-5646.2008.00450.x

  A meta-analysis of the mutations responsible for phenotypic evolution, which uses the literature for testing various predictions about the relative importance of coding and regulatory changes. Of particular interest is the intriguing possibility that intraspecific and interspecific evolution might involve different kinds of causing mutations.