Phylogeography
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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 <ref>Template:Cite book</ref>. 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 <ref name="K&M02">Template:Cite journal2</ref>. Phylogeographical inferences are usually made by studying the reconstructed genealogical histories of individual genes (gene trees) sampled from different populations <ref name="K&M02" />. 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 <ref name="C&T00">Template:Cite journal2 </ref>.
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Development
While the term phylogeography was first coined in 1987 <ref>Template:Cite journal2</ref>, it has existed as a field of study for much longer. Historical biogeography addresses how historical geological, climatic and ecological conditions influenced the 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 <ref>Template:Cite journal2</ref>. 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 genetic and phylogenetic perspective on biogeography. In the mid-1970s, population genetic analyses turned to mitochondrial markers <ref name="Avise98">Template:Cite journal2</ref>. 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 <ref name="Avise98" />.
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. <ref>Template:Cite journal2</ref> <ref>Template:Cite journal2</ref> <ref name="K&M02" />).
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 <ref name="C&T00" />. This has occurred both in the tropics <ref name="Schneider">Template:Cite journal2</ref><ref>Template:Cite journal2</ref> as well as temperate regions that were influenced by glaciers <ref>Template:Cite journal2</ref>.
Phylogeography and Conservation
Phylogeography can help in the prioritization of areas of high value for conservation. Phylogeographic analyses have also played an important role in defining evolutionary significant units (ESU), a unit of conservation below the species level that is often defined on unique geographic distribution and mitochondrial genetic patterns <ref>Template:Cite journal2</ref>.
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)<ref>Template:Cite journal2</ref>. Another recent study on imperiled cave crayfish in the Appalachian Mountains of eastern North America <ref>Template:Cite journal2</ref> 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 <ref>Template:Cite journal2</ref>. 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
The field of comparative phylogeography seeks to accomplish a variety of objectives. For example, comparisons across multiple taxa can clarify the histories of biogeographical regions <ref name="Riginos">Template:Cite journal2</ref>. For example, phylogeographic analyses of terrestrial vertebrates on the Baja California peninsula <ref>Template:Cite journal2</ref> and marine fish on both the Pacific and gulf sides of the peninsula <ref name="Riginos" /> display genetic signatures that suggest a vicariance event effected multiple taxa during the Pleistocene or Pliocene.
Phylogeography also gives an important historical perspective on community composition. History is relevant to regional and local diversity in two ways <ref name="Schneider" />. One, the size and makeup of the regional species pool results from the balance of speciation and extinction. Two, at a local level community composition is influenced by the interaction between local extinction of species’ populations and recolonization <ref name="Schneider" />. A comparative phylogenetic approach in the Australian Wet Tropics indicates that regional patterns of species distribution and diversity are largely determined by local extinctions and subsequent recolonizations corresponding to climatic cycles.
Human phylogeography
Phylogeography has also proven to be useful in understanding the origin and dispersal patterns of our own species, Homo sapiens. Based primarily on observations of skeletal remains of ancient human remains and estimations of their age, anthropologists proposed two competing hypotheses about human origins. The first hypothesis is referred to as the Out-of-Africa with replacement model, which contends that the last expansion out of Africa around 100,000 years ago resulted in the modern humans displacing all previous Homo spp. populations in Eurasia that were the result of an earlier wave of emigration out of Africa. The multiregional scenario claims that individuals from the recent expansion out of Africa intermingled genetically with those human populations of more ancient African emigrations. A phylogeographic study that uncovered a Mitochondrial Eve that lived in Africa 150,000 years ago provided early support for the Out-of-Africa model <ref>Template:Cite journal2</ref>. While this study had its shortcomings, it received significant attention both within scientific circles and a wider audience. A more thorough phylogeographic analysis that used ten different genes instead of a single mitochondrial marker indicates that at least two major expansions out of Africa after the initial range extension of Homo erectus played an important role shaping the modern human gene pool and that recurrent genetic exchange is pervasive <ref>Template:Cite journal2</ref>. These findings strongly demonstrated Africa’s central role in the evolution of modern humans, but also indicated that the multiregional model had some validity.
Phylogeography of viruses
Viruses are informative in understanding the dynamics of evolutionary change due to their rapid mutation rate and fast generation time <ref name="Holmes">Template:Cite journal2</ref>. Phylogeography is a useful tool in understanding the origins and distributions of different viral strains. A phylogeographic approach has been taken for many diseases that threaten human health, including dengue, rabies, influenza and HIV <ref name="Holmes" />. Similarly, a phylogeographic approach will likely play a key role in understanding the vectors and spread of avian influenza (HPAI H5N1), demonstrating the relevance of phylogeography to the general public.
References
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