New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

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When studying infectious diseases it is often important to understand how germs spread from location-to-location, person-to-person, or even one part of the body to another. Using phylogeographic methods, it is possible to recover the history of spread of pathogens (or other organisms) by studying their genetic material. Here we reveal that some popular, fast phylogeographic methods are inaccurate, and we introduce a new more reliable method to address the problem. By comparing different phylogeographic methods based on principled population models and fast alternatives, we found that different approaches can give diametrically opposed results, and we offer concrete examples in the context of the ongoing Ebola outbreak in West Africa and the world-wide outbreaks of Avian Influenza Virus and Tomato Yellow Leaf Curl Virus. We found that the most popular phylogeographic method often produces completely inaccurate conclusions. One of the reasons for its popularity has been its computational speed, which has allowed users to analyse large genetic datasets with complex models. More accurate approaches have until now been considerably slower, and therefore we propose a new method called BASTA that achieves good accuracy in a reasonable time. We are relying more and more on genetic sequencing to learn about the origin and spread of infections, and as this role continues to grow, it will be essential to use accurate phylogeographic methods when designing policies to prevent or curb the spread of disease.

Vyšlo v časopise: New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation. PLoS Genet 11(8): e32767. doi:10.1371/journal.pgen.1005421
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005421

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