Data from: Comparing phylogeographies to reveal incompatible geographical histories within genomes

Modern phylogeography aims at reconstructing the geographic movement of
organisms based on their genomic sequences and spatial information.
Phylogeographic approaches are often applied to pathogen sequences and
therefore tend to neglect the possibility of recombination, which
decouples the evolutionary and geographic histories of different parts of
the genome. Genomic regions of recombining or reassorting pathogens often
originate and evolve at different times and locations, which characterise
their unique spatial histories. Measuring the extent of these differences
requires new methods to compare geographic information on phylogenetic
trees reconstructed from different parts of the genome. Here we develop
for the first time a set of measures of phylogeographic incompatibility,
aimed at detecting differences between geographical histories in terms of
distances between phylogeographies. We study the effect of varying
demography and recombination on phylogeographic incompatibilities using
coalescent simulations. We further apply these measures to the
evolutionary history of human and livestock pathogens, either reassorting
or recombining, such as the Victoria and Yamagata lineages of influenza B
and the O/ME-SA/Ind-2001 foot-and-mouth disease virus strain. Our results
reveal diverse geographical paths of migration that characterise the
origins and evolutionary histories of different viral genes and genomic
segments. These incompatibility measures can be applied to any
phylogeography, and more generally to any phylogeny where each tip has
been assigned either a continuous or discrete “trait” independent of the
sequence. We illustrate this flexibility with an analysis of the interplay
between the phylogeography and phylolinguistics of Uralic-speaking human
populations, hinting at patrilinear language transmission.