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..., , , ## Description

### 1\_MASTER\_sim folder

XML files generated in MASTER 6.1.1 (via BEAST 2.6.1) and used to run structured coalescent simulations and generate ancestral recombination graphs. The simulation uses an island model of population structure with three populations of 20 individuals each and different patterns of migration between all populations. The structured coalescent model is implemented backward in time as a combination of coalescence events (two lineages within the same island that coalesce into one) with rate 1, migration events with rate \mu for each arrow, and recombination events (a lineage that splits into two lineages within the same island) with rate \rho.

### 2\_InfB folder

XML files generated in BEAST 1.10.4 and used to run discrete phylogeographic reconstructions for both Influenza B Victoria (1_Victoria folder) and Yamagata (2_Yamagata folder) lineages. For influenza B virus we selected 122 and 120 unique genome sequences of, respectively, the Victoria and ...