Ecological Genomics

by

Patrick Abbot

• LAST REVIEWED: 31 August 2021
• LAST MODIFIED: 15 January 2015
• DOI: 10.1093/obo/9780199830060-0129

Introduction

Ecological genomics seeks to understand genomic responses to environmental variation and in turn how genomic variation shapes the responses of organisms to their environment. Often associated with evolutionary, population, or functional genomics, with which it shares many of the same analytical tools and technologies, ecological genomics addresses interactions between environments and genomes, with the goal of gaining a better understanding of the roles organisms play in their ecosystems. Technological and analytical advances in 21st century underpin the emergence of ecological genomics as a coherent field of study. Not unlike ecology itself, ecological genomics is interdisciplinary and draws on concepts and techniques spanning environmental sciences, evolutionary biology, population genetics, molecular biology, toxicology, environmental microbiology, physiology, and even chemistry. Typical questions include: What are the genome-wide patterns of gene expression in organisms under physiological or metabolic stress? How are microbial communities structured, and how do they vary over ecological gradients? How are life history patterns and mating systems influenced by genomic variation? What is the genomic basis of phenotypic plasticity? What genes or genetic markers underlie adaptive traits? How do epigenetic modifications of genomes affect ecologically important traits? Such questions are broad, and answers can touch on a dizzying expanse of biological terrain. The references listed here are weighted toward those that emphasize ecological applications of genomics, such as those in conservation biology or microbial ecology. However, many overviews are included that aggregate ecological, evolutionary, and functional genomics under a single banner. Of the many emerging themes in ecological genomics, a major one is the need and now opportunity to account for diversity in the patterns and mechanisms that affect natural phenotypic variation both within and between species, particularly in non-model organisms. There is much hope that ecological genomics will reveal new insights across the spectrum of biology, and even upend perceived wisdoms.

General Overviews

As a relatively new area of specialization within genomics, there are few book-length overviews. The first book devoted solely to ecological genomics was published in 2006 by Nico van Straalen and Dick Roelofs (Oxford University Press). A second edition was published in 2012 and is the starting point for entry into the concepts and literature in ecological genomics. Landry and Aubin-Horth 2013 is a multiauthor volume. There are also number of books devoted to the application of ecological genomics to specific taxa or that address subjects related to theory and computation used in ecological genomics (cited under van Straalen and Roelofs 2012). Prior to these, many researchers would point to Avise 1994 (Molecular Markers, Natural History and Evolution) as an important landmark. Published only two years before the first full bacterial genome was sequenced, Avise 1994 provided a synopsis of the growing integration of molecular biology with ecology, evolution, and conservation. It helped to establish the nascent field of molecular ecology, and it laid the foundation for ecological genomics. Ecological genomics or “ecogenomics” began to appear in the literature in the late 1990s, mostly devoted to microbial research. However, things moved quickly, and by the time the first draft of the human genome was published in 2000, Streelman and Kocher 2000 was able to summarize a number of genomic and transcriptomic studies of heritable factors potentially of evolutionary or ecological importance. Since then, new technologies have emerged, commonly known as next generation sequencing technologies (NGS), that have spurred the development of the field, and a number of reviews have appeared in journals devoted to various aspects of ecological genomics. Notable are those that integrate ecological genomics with more evolutionary and functional perspectives, such as Feder and Mitchell-Olds 2003, and Rokas and Abbot 2009. There are also those that describe the interface between ecological genomics and quantitative genetics, such as Stinchcombe and Hoekstra 2007 and that focus on applications of genomics to ecology, such as Ungerer, et al. 2007. A number of reviews focus more on the technology or analytical tools themselves and explain new technologies in terms of their ecological and evolutionary applications. See, for example, Hudson 2008, Ekblom and Galindo 2011, and Pavey, et al. 2012. As described in the introduction, most reviews are rooted in functional and evolutionary genomics or recent advances in biotechnology and computational biology. It is less common to find reviews that integrate modern ecological concepts and genomics (but see van Straalen and Roelofs 2012). Since 2003 an annual symposium devoted to ecological genomics has been hosted by Kansas State University.

• Avise, J. C. 1994. Molecular Markers, Natural History, and Evolution. 1st ed. New York: Chapman and Hall.

  DOI: 10.1007/978-1-4615-2381-9

  NNNThis book, as well as the second edition published in 2004, provides historical and conceptual perspectives on several issues in ecological genomics. Its emphasis is on the integration of molecular techniques and organismal biology.

• Feder, M. E., and T. Mitchell-Olds. 2003. Evolutionary and ecological functional genomics. Nature Reviews Genetics 4:649–655.

  DOI: 10.1038/nrg1128

  NNNComing soon after the completion of the human genome but prior to the emergence of NGS technologies, this paper helped to define ecological genomics and related fields. It outlined several ideal features that define organisms serving as models for the study of ecological genomics.

• Hudson, M. E. 2008. Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources 8:3–17.

  DOI: 10.1111/j.1471-8286.2007.02019.x

  NNNThis paper was one of the first to review NGS technologies aimed at ecologists and evolutionary biologists. It provided an important introduction to the principles behind NGS at the time it was published.

• Landry, C. R., and N. Aubin-Horth. 2013. Ecological genomics: Ecology and the evolution of genes and genomes. New York: Springer.

  NNNThis is a multiauthor volume that focuses on the contributions of genomics to life- history evolution, phenotypic plasticity, adaptation, and speciation.

• Rokas, A., and Abbot P. 2009. Harnessing genomics for evolutionary insights. Trends in Ecology and Evolution 24:192–200.

  DOI: 10.1016/j.tree.2008.11.004

  NNNProvides an overview of some NGS technologies as of 2009, and includes several examples of how NGS technologies can produce novel advances in evolution and ecology.

• Streelman, J. T., and T. D. Kocher. 2000. From phenotype to genotype. Evolution and Development 2:166–173.

  DOI: 10.1046/j.1525-142x.2000.00056.x

  NNNThis paper was prescient when it was published, outlining general features of a research program that integrates genomics, evolution, and ecology in order to discover the genomic architecture of adaptive phenotypes. Its treatment of the utility of whole genomic approaches versus reductive methods may be even more relevant in the early 21st century than when it was published.

• Ungerer, M. C., L. C. Johnson, and M. A. Herman. 2007. Ecological genomics: Understanding gene and genome function in the natural environment. Heredity 100:178–183.

  DOI: 10.1038/sj.hdy.6800992

  NNNOne of the articles inaugurating ecological genomics as a field, and published by researchers who also initiated an annual symposium at Kansas State University, this paper defines the scope, goals, and general research methodologies of ecological genomics.

• van Straalen, N., and D. Roelofs. 2012. Introduction to ecological genomics. New York: Oxford Univ. Press.

  NNNAs the title implies, this is the most thorough introduction to ecological genomics. A must-read for those just entering the field or for those wanting an introduction to the integrative nature of ecological genomics.