Family level phylogenies reveal modes of macroevolution in RNA viruses
Andrew Kitchen a,1, Laura A. Shackelton a,b,1, and Edward C. Holmes a,c,2
- Author Affiliations
aCenter for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, Pennsylvania State University, University Park, PA 16802;
bGlobal Health Discovery, Bill and Melinda Gates Foundation, Seattle, WA 98105; and
cFogarty International Center, National Institutes of Health, Bethesda, MD 20892
Edited by Peter Palese, Mount Sinai School of Medicine, New York, NY, and approved November 22, 2010 (received for review July 27, 2010)
↵1A.K. and L.A.S. contributed equally to this work.
Abstract
Despite advances in understanding the patterns and processes of microevolution in RNA viruses, little is known about the determinants of viral diversification at the macroevolutionary scale. In particular, the processes by which viral lineages assigned as different “species” are generated remain largely uncharacterized. To address this issue, we use a robust phylogenetic approach to analyze patterns of lineage diversification in five representative families of RNA viruses. We ask whether the process of lineage diversification primarily occurs when viruses infect new host species, either through cross-species transmission or codivergence, and which are defined here as analogous to allopatric speciation in animals, or by acquiring new niches within the same host species, analogous to sympatric speciation. By mapping probable primary host species onto family level viral phylogenies, we reveal a strong clustering among viral lineages that infect groups of closely related host species. Although this is consistent with lineage diversification within individual hosts, we argue that this pattern more likely represents strong biases in our knowledge of viral biodiversity, because we also find that better-sampled human viruses rarely cluster together. Hence, although closely related viruses tend to infect related host species, it is unlikely that they often infect the same host species, such that evolutionary constraints hinder lineage diversification within individual host species. We conclude that the colonization of new but related host species may represent the principle mode of macroevolution in RNA viruses.
emergence, molecular evolution, host jumping
Footnotes
2To whom correspondence should be addressed. E-mail: ech15@psu.edu.
Author contributions: A.K., L.A.S., and E.C.H. designed research; A.K. and L.A.S. performed research; A.K. and L.A.S. analyzed data; and A.K., L.A.S., and E.C.H. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
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