Editing Phylogeography (section)

==Historical development==
The term phylogeography was first used by [[John Avise]] in his 1987 work ''Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics''.<ref>{{cite journal|last=Avise|first=J.C.|author2=J Arnold |author3=R M Ball |author4=E Bermingham |author5=T Lamb |author6=J E Neigel |author7=C A Reeb |author8=N C Saunders |journal=Annual Review of Ecology and Systematics|year=1987|volume=18 |doi=10.1146/annurev.es.18.110187.002421 |title=Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics |issue=1 |pages=489–522|bibcode=1987AnRES..18..489A |s2cid=26363881 }}</ref> 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|plate tectonics theory]].<ref>{{cite journal |author=De Queiroz, A. |year=2005 |title=The resurrection of oceanic dispersal in historical biogeography |journal=Trends in Ecology and Evolution |volume=20 |pages=68–73 |doi=10.1016/j.tree.2004.11.006 |pmid=16701345 |issue=2|url=http://doc.rero.ch/record/13905/files/PAL_E864.pdf }}</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]]s and [[phylogenetic]] perspective on [[biogeography]]. In the mid-1970s, population genetic analyses turned to mitochondrial markers.<ref name="Avise98">{{cite journal |author=Avise, J. C. |year=1998 |title=The history and purview of phylogeography: a personal reflection |journal=Molecular Ecology |volume=7 |pages=371–379 | doi=10.1046/j.1365-294x.1998.00391.x |issue=4|bibcode=1998MolEc...7..371A |s2cid=16711956 |url=https://escholarship.org/uc/item/1hv4f8vk }}</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 (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.<ref name="Avise98" /> 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."<ref name="Avise00" />

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.<ref name="K&M02" /><ref>{{cite journal |author1=Templeton, A. R. |author2=E. Routman |author3=C. A. Phillips |year=1995 |title=Separating Population Structure from Population History: A Cladistic Analysis of the Geographical Distribution of Mitochondrial DNA Haplotypes in the Tiger Salamander, Ambystoma Tigrinum |journal=[[Genetics (journal)|Genetics]] |volume=140 |pages=767–782 |pmid=7498753 |issue=2 |doi=10.1093/genetics/140.2.767 |pmc=1206651}}</ref><ref>{{cite journal |author=Templeton, A. R. |year=1998 |title=Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history |journal=Molecular Ecology |volume=7 |pages=381–397 | doi=10.1046/j.1365-294x.1998.00308.x |pmid=9627999 |issue=4|bibcode=1998MolEc...7..381T |s2cid=19496196 }}</ref>

'''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 (where the main effect of glaciation is increasing [[arid]]ity, i.e. the expansion of savanna and retraction of [[tropical rainforest]])<ref name="Schneider">{{cite journal |author1=Schneider, C. J. |author2=M. Cunningham |author3=C. Moritz |year=1998 |title=Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia |journal=Molecular Ecology |volume=7 |pages=487–498 | doi=10.1046/j.1365-294x.1998.00334.x |issue=4|s2cid=84601584 |doi-access=free |bibcode=1998MolEc...7..487S }}</ref><ref>{{cite journal |author=Da Silva, M. N. F. and J. L. Patton |year=1998 |title=Molecular phylogeography and the evolution and conservation of Amazonian mammals |journal=Molecular Ecology |volume=7 |pages=475–486 |doi=10.1046/j.1365-294x.1998.00276.x |pmid=9628001 |issue=4|bibcode=1998MolEc...7..475D |s2cid=28482137 }}</ref> as well as temperate regions that were directly influenced by glaciers.<ref>{{cite journal |author1=Taberlet, P. |author2=L. Fumagalli |author3=A.G. Wust-Saucy |author4=J.F. Cossons |year=1998 |title=Comparative phylogeography and postglacial colonization routes in Europe |journal=Molecular Ecology |volume=7 |pages=453–464 | doi=10.1046/j.1365-294x.1998.00289.x |pmid=9628000 |issue=4|bibcode=1998MolEc...7..453T |s2cid=6365966 }}</ref>