Phylogeography

Phylogeography is the study of the historical processes that may be responsible for the past to present geographic distributions of genealogical lineages. This is accomplished by considering the geographic distribution of individuals in light of genetics, particularly population genetics.

This term was introduced to describe geographically structured genetic signals within and among species. An explicit focus on a species' biogeography/biogeographical past sets phylogeography apart from classical population genetics and phylogenetics.

Past events that can be inferred include population expansion, population bottlenecks, vicariance, dispersal, and migration. Recently developed approaches integrating coalescent theory or the genealogical history of alleles and distributional information can more accurately address the relative roles of these different historical forces in shaping current patterns.

The term phylogeography was first used by John Avise in his 1987 work Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics. Historical biogeography is a synthetic discipline that addresses how historical, geological, climatic and ecological conditions influenced the past and current distribution of species. As part of historical biogeography, researchers had been evaluating the geographical and evolutionary relationships of organisms years before. Two developments during the 1960s and 1970s were particularly important in laying the groundwork for modern phylogeography; the first was the spread of cladistic thought, and the second was the development of plate tectonics theory.

The resulting school of thought was vicariance biogeography, which explained the origin of new lineages through geological events like the drifting apart of continents or the formation of rivers. When a continuous population (or species) is divided by a new river or a new mountain range (i.e., a vicariance event), two populations (or species) are created. Paleogeography, geology and paleoecology are all important fields that supply information that is integrated into phylogeographic analyses.

Phylogeography takes a population genetics and phylogenetic perspective on biogeography. In the mid-1970s, population genetic analyses turned to mitochondrial markers. The advent of the polymerase chain reaction (PCR), the process where millions of copies of a DNA segment can be replicated, was crucial in the development of phylogeography.

Thanks to this breakthrough, the information contained in mitochondrial DNA sequences was much more accessible. Advances in both laboratory methods (e.g. capillary DNA sequencing technology) that allowed easier sequencing of DNA and computational methods that make better use of the data (e.g. employing coalescent theory) have helped improve phylogeographic inference. By 2000, Avise generated a seminal review of the topic in book form, in which he defined phylogeography as the study of the "principles and processes governing the geographic distributions of genealogical lineages... within and among closely related species."

Early phylogeographic work has recently been criticized for its narrative nature and lack of statistical rigor (i.e. it did not statistically test alternative hypotheses). The only real method was Alan Templeton's Nested Clade Analysis, which made use of an inference key to determine the validity of a given process in explaining the concordance between geographic distance and genetic relatedness. Recent approaches have taken a stronger statistical approach to phylogeography than was done initially.