Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes

Abstract

Modern phylogeography aims at reconstructing the geographic diffusion of organisms based on their genomic sequences and spatial information. Phylogeographic approaches usually ignore 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 characterised 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/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of diffusion that characterise the origins and evolutionary histories of different viral genes and genomic segments. phylogeography, recombination, viral evolution

Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages

“…Recombination processes decouple the evolutionary history of different viral genes/proteins, which can similarly lead to the decoupling of their inferred spatial histories. In fact, it has been shown that, in the case of recombination, the WGS does not provide a good summary of the geographic histories of each individual genomic region, whilst the FMDV genome coding for the capsid region (comprising of the structural proteins from VP1 to VP4) have highly coupled histories, both phylogenetically and geographically ( Bachanek-Bankowska et al 2018 ; Singer et al 2020 ). These factors provide confidence in the results based on the use of VP1 sequences to reconstruct spatial migration networks and estimate divergence times and evolutionary rates, although the full capsid region would be expected to provide greater resolution.…”