Family level phylogenies reveal modes of macroevolution in RNA viruses

Andrew Kitchen; Laura A Shackelton; Edward C Holmes

doi:10.1073/pnas.1011090108

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Family level phylogenies reveal modes of macroevolution in RNA viruses

Journal article

Open access

Peer reviewed

Family level phylogenies reveal modes of macroevolution in RNA viruses

Andrew Kitchen, Laura A Shackelton and Edward C Holmes

Proceedings of the National Academy of Sciences - PNAS, Vol.108(1), pp.238-243

01/04/2011

DOI: 10.1073/pnas.1011090108

PMCID: PMC3017157

PMID: 21173251

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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.

Amino Acid Sequence

Likelihood Functions

Sequence Alignment

Host Specificity - genetics

Genetic Speciation

Bayes Theorem

Computational Biology

RNA Viruses - classification

RNA Viruses - genetics

Models, Genetic

Phylogeny

Evolution, Molecular

Details

Title: Subtitle: Family level phylogenies reveal modes of macroevolution in RNA viruses
Creators: Andrew Kitchen - Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
Laura A Shackelton
Edward C Holmes
Resource Type: Journal article
Publication Details: Proceedings of the National Academy of Sciences - PNAS, Vol.108(1), pp.238-243
DOI: 10.1073/pnas.1011090108
PMID: 21173251
PMCID: PMC3017157
NLM abbreviation: Proc Natl Acad Sci U S A
ISSN: 0027-8424
eISSN: 1091-6490
Publisher: United States
Grant note: R01 GM080533 / NIGMS NIH HHS
Language: English
Date published: 01/04/2011
Academic Unit: Anthropology; International Programs
Record Identifier: 9983984517502771

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