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Phylogeography is the study of the processes controlling the geographic distributions of lineages by constructing the genealogies of populations and genes . This term was introduced to describe geographically structured genetic signal within a single species. An explicit focus on a species' biogeographical past sets phylogeography apart from classical population genetics . Phylogeographical inferences are usually made by studying the reconstructed genealogical histories of individual genes (gene trees) sampled from different populations . Past events that can be inferred include population expansion, population bottlenecks, vicariance and migration. One of the goals of phylogeographic analyses is to evaluate the relative role of history in shaping the genetic structure of populations relative to important ongoing processes. Approaches integrating genealogical and distributional information can address the relative roles of different historical forces in shaping current patterns  .

Development

Phylogeography takes a population genetic 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 that allowed easier sequencing DNA and computational methods that make better use of the data have helped improve phylogeographic inference. The development of coalescent theory has also played an important role .

Early phylogeographic work was sometimes criticized for its narrative nature and lack of statistical rigor. Hypothesis testing was rarely done, and the explanation of genealogical patterns was essentially story telling. Recent approaches have taken a stronger statistical approach to phylogeography that was done initially. Statistical phylogeography has received an increasing amount of attention (e.g. ).

Example

Climate change, such as the glaciation cycles of the past 2.4 million years, has periodically restricted some species into disjunct refugia. These restricted ranges may result in population bottlenecks that reduce genetic variation. Once a reversal in climate change allows for rapid migration out of refugial areas, these species spread rapidly into newly available habitat. A number of empirical studies find genetic signatures of both animal and plant species that support this scenario of refugia and postglacial expansion . This has occurred both in the tropics  as well as temperate regions that were influenced by glaciers .

Phylogeography and conservation

A somewhat surprising result of a phylogenetic analysis with high conservation value was the finding that the African elephant was in fact two divergent species, the forest elephant (Loxodonta cyclotis) and the savannah elephant (Loxodonta africana). Another recent study on imperiled cave crayfish in the Appalachian Mountains of eastern North America  demonstrates how phylogenetic analyses can aid in recognizing conservation priorities. Using phylogeographical approaches, the authors found that hidden within what was thought to be a single, widely distributed species an ancient and previously undetected species was also present. Conservation decisions can now be made to ensure that both lineages received protection. Results like this are not an uncommon outcome from phylogeographic studies.

An analysis of salamanders of the genus Eurycea, also in the Appalachians, found that the current taxonomy of the group greatly underestimated species level diversity . The authors of this study also found that patterns of phylogeographic diversity were more associated with historical (rather than modern) drainage connections, indicating that major shifts in the drainage patterns of the region played an important role in the generation of diversity of these salamanders. A thorough understanding of phylogeographic structure will thus allow informed choices in prioritizing areas for conservation.

Comparative phylogeography