RRphylogeography code and data

1.     One of the main goals of
historical biogeography is understanding where species originated, and how
climate change and ecological interactions shaped their distribution. The
task is complicated by both active and passive mechanisms, including
habitat tracking, the separation of species into metapopulations of
variably interconnected demes, and long-distance dispersal which may all
obscure the geographic signature of species origin.
2.     Current historical biogeography
tools use phylogenies to infer the area of origin. They work by
discretizing the geographic range occupied by the species into distinct
areas and then applying ancestral character estimation to identify the
area occupied at speciation. These methods are powerful and can account
for different modes of speciation. Yet, they are bound to assume that the
discrete areas currently occupied by the species are faithful
representation of their climatic and historic affiliation and ignore
metapopulation structures. Still, most methods cannot take advantage from
the fossil information or work with phylogenies including extinct species.
Although explicit bioclimatic modeling is now possible under some
implementations, these limitations are partly unresolved, which burdens
the accuracy of the area of origin estimation process.
3.     We present a new tool written
in R, named RRphylogeography, meant to find the area of origin of species,
and to locate feasible zones of contact between species throughout their
history. RRphylogeography starts from the bioclimatic modelling of the
species, identifies potential habitat patches occupied during speciation,
and finds the habitat patches most likely to represent the area of origin
or contact.