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Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes

View ORCID ProfileBenjamin Singer, View ORCID ProfileAntonello Di Nardo, Jotun Hein, View ORCID ProfileLuca Ferretti
doi: https://doi.org/10.1101/2020.01.10.902460
Benjamin Singer
1Department of Zoology, University of Oxford, UK
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Antonello Di Nardo
2The Pirbright Institute, Pirbright, Woking, Surrey, UK
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Jotun Hein
3Department of Statistics, University of Oxford, UK
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Luca Ferretti
2The Pirbright Institute, Pirbright, Woking, Surrey, UK
4Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, UK
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  • For correspondence: luca.ferretti@gmail.com
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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

Footnotes

  • ↵† e-mail: luca.ferretti{at}bdi.ox.ac.uk

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted January 11, 2020.
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Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes
Benjamin Singer, Antonello Di Nardo, Jotun Hein, Luca Ferretti
bioRxiv 2020.01.10.902460; doi: https://doi.org/10.1101/2020.01.10.902460
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Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes
Benjamin Singer, Antonello Di Nardo, Jotun Hein, Luca Ferretti
bioRxiv 2020.01.10.902460; doi: https://doi.org/10.1101/2020.01.10.902460

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