Phylogeography

by

Bryan C. Carstens

• LAST REVIEWED: 13 January 2014
• LAST MODIFIED: 13 January 2014
• DOI: 10.1093/obo/9780199941728-0041

Introduction

The discipline of phylogeography is relatively new; it gained momentum when John Avise and colleagues coined the term phylogeography in a review of early investigations to describe investigations that characterized the geographical distribution of mitochondrial DNA lineages. Early phylogeographic studies operated under the assumption that the mitochondrial genome, due to its small effective population size and elevated mutation rate, was uniquely suited to tracking intraspecific diversification. Thus, until relatively recently, phylogeography (at least in animal systems) could be described as the investigation of the geographical distribution of mitochondrial gene lineages, and researchers hoped that these lineages would reflect organismal patterns of diversification. However, as DNA sequencing decreased in price and theoretical work suggested that any single locus was likely to be inadequate for phylogeographic investigation, the number of loci included in phylogeographic investigations increased, first by the handful and then exponentially as next-generation sequencing became widely accessible.

General Overviews

The discipline of phylogeography became popular with the advent of automated Sanger sequencing and the widening availability of primers that amplified mitochondrial genes in a variety of taxa. Avise, et al. 1987 proposes the portmanteau in a review of early studies; this provided momentum to intraspecific research aimed at taxonomic and historical questions. Phylogeography seeks to infer the intraspecific history of a species by (1) assaying genetic diversity from across its geographic range, (2) analyzing these data, by using a variety of approaches, and (3) making inferences about which models of historical demography were likely to have produced the pattern observed in the empirical data. The most-direct points of entry into the discipline are several review papers that have summarized important work in the field. Two works (Avise, et al. 1987; Knowles 2009) are particularly broad in scope and cover early and later work in the field, respectively, while Avise 1998 and Hickerson, et al. 2010 combine review with prospectives about the future of the field. Additional overviews constitute a deeper introduction to phylogeographic research. Perhaps the most widely read is Avise 2000, which introduced the field to a broad scientific audience and provided an ideal book for graduate seminars and researchers interested in conducting phylogeographic investigations in systems of interest. Other relevant books include Avise 1994 and portions of two general introductions to molecular ecology (Lowe, et al. 2004; and Beebee and Rowe 2008), which provide useful context for phylogeographic research.

• Avise, John C. 1994. Molecular markers, natural history and evolution. New York: Chapman & Hall.

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

  While not exclusively devoted to phylogeographic research, this book details the rational for conducting field-based investigations into the history of species, by using genetic markers. The review of a diverse set of genetic markers is useful to younger researchers who have come of age in the genomics era, while the applications section covers phylogeography and related disciplines.

• Avise, John C. 1998. The history and purview of phylogeography: A personal reflection. Molecular Ecology 7.4: 371–379.

  DOI: 10.1046/j.1365-294x.1998.00391.x

  Along with providing a first-hand account of the development of phylogeographic research, Avise recorded many details about how phylogeographic research fits into the broader field of evolutionary biology, and he offers opinions regarding the scope of the discipline.

• Avise, John C. 2000. Phylogeography: The history and formation of species. Cambridge, MA: Harvard Univ. Press.

  The seminal work of John Avise, this book collects and interprets hundreds of 20th-century phylogeography studies, providing a synthesis that encouraged the field to move toward multilocus data sets and increasingly sophisticated analyses.

• Avise, John C., Jonathan Arnold, R. Martin Ball, et al. 1987. Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18:489–522.

  This paper is both a review of the early work in the discipline and a description of the unique attributes of the mitochondrial genome. Avise and colleagues argue that the high mutation rate and low effective population size of animal mitochondrial DNA allow genealogies from this molecule to reflect the pattern of intraspecific divergence within species, enabling phylogeography to connect population genetics and systematics, two disciplines that were traditionally focused on different aspects of evolution and thus were conceptually isolated.

• Beebee, Trevor, and Graham Rowe. 2008. An introduction to molecular ecology. 2d ed. Oxford: Oxford Univ. Press.

  This introductory text is best suited as a general introduction to the field of molecular ecology. It contains a very accessible section devoted to phylogeography. First published in 2004.

• Hickerson, Michael J., Bryan C. Carstens, Jeanine Cavender-Bares, et al. 2010. Phylogeography’s past, present, and future: 10 years after Avise 2000. Molecular Phylogenetics and Evolution 54.1: 291–301.

  DOI: 10.1016/j.ympev.2009.09.016

  The product of a workshop organized by Jack Sites, this manuscript encourages researchers to broaden the scope of phylogeographic research. Written just as next-generation sequencing (NGS) platforms were becoming available, it represents the transition between the Sander and NGS eras of phylogeography. It argues that novel methodological advances will enable comparative studies of communities of organisms and will allow integration with other biological fields.

• Knowles, L. Lacey. 2009. Statistical phylogeography. Annual Review of Ecology, Evolution, and Systematics 40:593–612.

  DOI: 10.1146/annurev.ecolsys.38.091206.095702

  The ideal complement to Avise, et al. 1987. By the end of the first decade of the 21st century, researchers accepted that data from a single locus would provide only limited insight into the demographic history of a species, due to coalescent stochasticity. Knowles provides a compelling argument for the application of coalescent theory in phylogeographic research and argues for increased complexity of the demographic models considered by phylogeographers.

• Lowe, Andrew, Stephen Harris, and Paul Ashton. 2004. Ecological genetics: Design, analysis, and application. Malden, MA: Blackwell.

  This text is slightly more technical than other works. Important considerations regarding sampling design and data analysis are covered in the phylogeography section.