Genome Evolution

by

Xiao Chen, Kelsi Lindblad, Laura F. Landweber

• LAST REVIEWED: 29 September 2015
• LAST MODIFIED: 29 September 2015
• DOI: 10.1093/obo/9780199941728-0068

Introduction

While modern evolutionary biologists achieved a deep theoretical understanding of how genetic material changes in response to diverse evolutionary forces well before the genomics era, evolutionary studies used to be restricted to small numbers of genetic sequences, due to limited availability of molecular biological data. Since the 1990s, however, rapid advances in sequencing technology have led to the availability of genomes for both model and non-model organisms. This has allowed us to perform comparative genomics on a much broader scale, shedding light on evolutionary questions that were previously out of reach. One can now study the molecular and evolutionary forces underlying genome evolution through whole-genome comparisons across multiple taxa, detect genomic regions under either purifying evolution—suggesting conserved biological functions, or adaptive evolution—suggesting potential evolutionary innovations, and the field can also resolve many long-standing phylogenetic controversies across the tree of life. The emerging field of evolutionary genomics lies at the interface between molecular and evolutionary biology, revolutionizing the way scientists infer patterns and mechanisms of genome evolution.

General Overviews

General overviews on genome evolution include Lynch 2007, which offers a population genetics perspective, and Gregory 2011, which is a comprehensive compendium with a historical approach, as well as Anisimova 2012, which emphasizes methodologies implemented in genome evolution studies. Jobling, et al. 2013 provides an overview of human genome evolution. Graur and Li 2000 is a good textbook reference for theories and applications of molecular evolution.

• Anisimova, M., ed. 2012. Evolutionary genomics: Statistical and computational methods. New York: Humana.

  This book is a collection of articles that review recent developments in statistical and computational methodologies in genomic data analyses, driven by rapid growth in sequencing technologies. In addition, this book also discusses important biological insights into genome evolution that improved methodologies can provide.

• Graur, D., and W.-H. Li. 2000. Fundamentals of molecular evolution. Sunderland, MA: Sinauer.

  This book provides an excellent summary of the fundamental principles of molecular evolution, covering both the evolutionary forces acting on molecular processes, such as natural selection and random genetic drift, as well as the methodologies for analyzing molecular data in an evolutionary framework. New evolutionary insights from classic genomics studies are also discussed.

• Gregory, T. R. 2011. The evolution of the genome. New York: Academic Press.

  This book provides a comprehensive overview of genome evolution. It discusses a wide range of topics, including genome size evolution, genomic parasites, gene and genome duplications, and genome evolution theories. This book also reviews the history of each respective field, highlighting the critical questions and how they are studied.

• Jobling, M., E. Hollox, M. Hurles, T. Kivisild, and C. Tyler-Smith. 2013. Human evolutionary genetics. New York: Garland Science.

  This book synthesizes current knowledge of human genetics and evolution. It also incorporates insights drawn from genomic technologies and resources—including ancient human genomes and other primate genomes that have recently become available, and sheds light on how genomics have shaped our understanding of human genome and evolution.

• Lynch, M. 2007. The origins of genome architecture. Sunderland, MA: Sinauer.

  One of the first books to discuss evolutionary genomics thoroughly as a combination of molecular biology and molecular evolution, covering major topics such as the origin of eukaryotes, mobile genetic elements, origin of introns, and evolution of organelle genomes. Population genetics is reviewed in the context of genome evolution. Lynch also provides an insightful discussion on the contribution of non-adaptive forces in shaping genome evolution.