Editing Phylogeography (section)

==Comparing phylogenetic relationships==
[[File:Phylogeography poisonfrogs.jpg|thumb|450px|These figures map out the phylogeographic history of [[Poison dart frog|poison frogs]] in South America.]]

The field of comparative phylogeography seeks to explain the mechanisms responsible for the phylogenetic relationships and distribution of ''different'' species. For example, comparisons across multiple taxa can clarify the histories of biogeographical regions.<ref name="Riginos">{{cite journal |author1=Riginos, C. |year=2005 |title=Cryptic vicariance in Gulf of California fishes parallels vicariant patterns found in Baja California mammals and reptiles |journal=[[Evolution (journal)|Evolution]] |volume=59 |issue=12 | pages=2678–2690 |doi=10.1554/05-257.1|pmid=16526514 |s2cid=9500433 }}</ref> For example, phylogeographic analyses of terrestrial vertebrates on the [[Baja California]] peninsula<ref>{{cite journal |author1=Riddle, B. R. |author2=D. J. Hafner |author3=L. F. Alexander |author4=J. R. Jaeger |year=2000 |title=Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota |journal=[[Proceedings of the National Academy of Sciences]] |volume=97 |pages=14438–14443 |doi=10.1073/pnas.250413397 |pmid=11095731 |issue=26 |pmc=18937|bibcode=2000PNAS...9714438R |doi-access=free }}</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 affected 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.

Phylogeography integrates biogeography and genetics to study in greater detail the lineal history of a species in context of the geoclimatic history of the planet. 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 [[Great American Interchange|the isolation and reconnection of South America]], the uplift of the Andes, an extensive [[Amazon Rainforest|Amazonian]] floodbasin system during the Miocene, the formation of [[Orinoco]] and [[Amazon River#Drainage area|Amazon drainages]], and dry−wet climate cycles throughout the [[Pliocene]] to [[Pleistocene]] epochs.<ref name="Santos09"/>

Using this contextual paleogeographic information (paleogeographic time series is shown in panels A-D) the authors of this study<ref name="Santos09">{{Cite journal  | last1 = Santos  | first1 = J. C.  | last2 = Coloma  | first2 = L. A.  | last3 = Summers | first3 = K.  | last4 = Caldwell  | first4 = J. P.  | last5 = Ree  | first5 = R.  | title = Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages  | journal = PLOS Biol  | volume = 7  | issue = 3 | pages = e1000056  | year = 2009  | doi = 10.1371/journal.pbio.1000056  | pmid = 19278298  | pmc = 2653552  | last6 = Moritz  | first6 = Craig  | editor1-last = Moritz  | editor1-first = Craig|display-authors=etal | doi-access = free }}</ref> proposed a null-hypothesis that assumes no spatial structure and two alternative hypothesis involving dispersal and other biogeographic constraints (hypothesis are shown in panels E-G, listed as SMO, SM1, and SM2). The phylogeographers visited the ranges of each frog species to obtain tissue samples for genetic analysis; researchers can also obtain tissue samples from museum collections.

The evolutionary history and relations among different poison frog species is reconstructed using [[phylogenetic tree]]s derived from molecular data. The molecular trees are mapped in relation to paleogeographic history of the region for a complete phylogeographic study. The tree shown in the center of the figure has its branch lengths calibrated to a [[molecular clock]], with the geological time bar shown at the bottom. 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).<ref name="Santos09"/>

The combination of techniques used in this study exemplifies more generally how phylogeographic studies proceed and test for patterns of common influence. Paleogeographic data establishes geological time records for historical events that explain the branching patterns in the molecular trees. 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.<ref name="Santos09" /> Regionally based phylogeographic studies of this type are repeated for different species as a means of independent testing. Phylogeographers find broadly concordant and repeated patterns among species in most regions of the planet that is due to a common influence of [[paleoclimatic]] history.<ref name="Avise00"/>