Biological species in the viral world
- 21 May 2018
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 115 (23), 6040-6045
- https://doi.org/10.1073/pnas.1717593115
Abstract
Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.Funding Information
- HHS | National Institutes of Health (R35GM118038)
This publication has 73 references indexed in Scilit:
- Why do RNA viruses recombine?Nature Reviews Microbiology, 2011
- Family level phylogenies reveal modes of macroevolution in RNA virusesProceedings of the National Academy of Sciences of the United States of America, 2010
- Search and clustering orders of magnitude faster than BLASTBioinformatics, 2010
- Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene SizeJournal of Molecular Biology, 2010
- Shifting the genomic gold standard for the prokaryotic species definitionProceedings of the National Academy of Sciences of the United States of America, 2009
- Diversity among the tailed-bacteriophages that infect the EnterobacteriaceaeResearch in Microbiology, 2008
- Pattern pluralism and the Tree of Life hypothesisProceedings of the National Academy of Sciences of the United States of America, 2007
- Identifying bacterial genes and endosymbiont DNA with GlimmerBioinformatics, 2007
- RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsBioinformatics, 2006
- Application of Phylogenetic Networks in Evolutionary StudiesMolecular Biology and Evolution, 2005