DOI: 10.5061/dryad.15dv41p4s
title: Data from: Comparing phylogeographies to reveal incompatible geographical histories within genomes

description: 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.
description: ## 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
 Yamagata lineages (Bedford et al. 2015; Langat et al. 2017),
 characterising five out of the eight gene segments and encoding: the
 polymerase basic subunits 1 and 2 (PB1 and PB2), the hemagglutinin (HA)
 and neuraminidase (NA) glycoproteins, and the non-structural protein 1
 (NS1), along with the the joint sequences of all these genes (~8.6 kb).
 MCC trees resulting from the analyses are included. ### 3\_FMDV folder XML
 files generated in BEAST 1.10.4 and used to run discrete phylogeographic
 reconstructions for Foot-and-Mouth Disease Vius (FMDV) O/ME-SA/Ind-2001
 lineage. For FMD we selected 74 whole-genome sequences (Bachanek-Bankowska
 et al. 2018), extracting separate alignments for each of the four
 structural (VP1 to VP4) and six non-structural (2A to 2C, and 3A to 3D)
 proteins, along with the leader polypeptide (Lpro) and both the 3'
 and 5' UTR alignments. MCC trees resulting from the analyses are
 included. ### 4\_Phyloling folder We retrieved previously published
 genotype data of autosomal chromosomes (1_auto folder), mtDNAs (3_mt
 folder) and chrY (4_y folder) of Uralic-speaking individuals (Tambets et
 al. 2018). Conventional FST distance matrices derived for each genotype
 data along with linguistic (lexical) data were used to infer distinct
 phylogenies in FastME 2.1.6.1 (.nex files), which were subsequently
 re-projected in time using the chronos function implemented in the R
 package ape (_CH.tree files). The linguistic data we used is composed of a
 set of 226 words translated into each language. The linguistic space was
 build using the default MDS projection routines in R based on lexical
 distances. XML files generated in BEAST 1.10.4 for each genotype data and
 used to run continuous phylogeographies using the 2-dimensional lexical or
 geographic spaces as continuous traits. MCC trees resulting from the
 analyses are included. ## Reference * Bachanek-Bankowska K, Di Nardo A,
 Wadsworth J, Mioulet V, Pezzoni G, Grazioli S, Brocchi E, Kafle SC,
 Hettiarachchi R, Kumarawadu PL, et al. 2018. Reconstructing the
 evolutionary history of pandemic foot-and-mouth disease viruses: the
 impact of recombination within the emerging O/ME-SA/Ind-2001 lineage. Sci
 Rep, 8(1): 14693. * Bedford T, Riley S, Barr IG, Broor S, Chadha M, Cox
 NJ, Daniels RS, Gunasekaran CP, Hurt AC, Kelso A, et al. 2015. Global
 circulation patterns of seasonal influenza viruses vary with antigenic
 drift. Nature, 523(7559): 217–220. * Langat P, Raghwani J, Dudas G, Bowden
 620 TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA,
 et al. 2017. Genome-wide evolutionary dynamics of influenza B viruses on a
 global scale. PLOS Pathog, 13(12): 1–26. * Tambets K, Yunusbayev B,
 Hudjashov G, Iluma¨e AM, Rootsi S, Honkola T, Vesakoski O, Atkinson Q,
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 recent demographic history for most of the uralic-speaking populations.
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