Phylogeography
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.
[6] 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.
[6] 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.
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.
[12] A recent study on imperiled cave crayfish in the Appalachian Mountains of eastern North America[13] demonstrates how phylogenetic analyses along with geographic distribution can aid in recognizing conservation priorities.
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.
[9] 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.
An example study of poison frogs living in the South American neotropics (illustrated to the left) is used to demonstrate how phylogeographers combine genetics and paleogeography to piece together the ecological history of organisms in their environments.
Several major geoclimatic events have greatly influenced the biogeographic distribution of organisms in this area, including the isolation and reconnection of South America, the uplift of the Andes, an extensive Amazonian floodbasin system during the Miocene, the formation of Orinoco and Amazon drainages, and dry−wet climate cycles throughout the Pliocene to Pleistocene epochs.
The same phylogenetic tree is duplicated four more times to show where each lineage is distributed and is found (illustrated in the inset maps below, including Amazon basin, Andes, Guiana-Venezuela, Central America-Chocó).
This study rejected the null model and found that the origin for all extant Amazonian poison frog species primarily stem from fourteen lineages that dispersed into their respective areas after the Miocene floodbasin receded.
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.
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.
In light of these recent data from the 1000 genomes project, genomic-scale SNP databases sampling thousands of individuals globally and samples taken from two non-Homo sapiens hominins (Neanderthals and Denisovans), the picture of human evolutionary has become more resolved and complex involving possible Neanderthal and Denisovan admixture, admixture with archaic African hominins, and Eurasian expansion into the Australasian region that predates the standard out of African expansion.
[20] 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.
