On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity

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dc.contributor.authorRenzette, Nicholas
dc.contributor.authorKowalik, Timothy F.
dc.contributor.authorJensen, Jeffrey D.
dc.contributor.departmentDepartment of Microbiology and Physiological Systems
dc.date2022-08-11T08:11:03.000
dc.date.accessioned2022-08-23T17:30:12Z
dc.date.available2022-08-23T17:30:12Z
dc.date.issued2015-09-03
dc.date.submitted2015-09-25
dc.description.abstractA central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, though these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analyzing the relationship among intraspecies diversity, interspecies divergence, and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centered on long non-coding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.
dc.identifier.citation<p>Mol Ecol. 2015 Jul 24. doi: 10.1111/mec.13331. [Epub ahead of print]. <a href="http://dx.doi.org/10.1111/mec.13331">Link to article on publisher's site</a></p>
dc.identifier.contextkey7641689
dc.identifier.doi10.1111/mec.13331
dc.identifier.issn0962-1083 (Linking)
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/umccts_pubs/41
dc.identifier.pmid26211679
dc.identifier.submissionpathumccts_pubs/41
dc.identifier.urihttps://hdl.handle.net/20.500.14038/50469
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=26211679&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706826/
dc.source.journaltitleMolecular ecology
dc.subjectUMCCTS funding
dc.subjectEcology and Evolutionary Biology
dc.subjectGenetics and Genomics
dc.subjectPopulation Biology
dc.subjectTranslational Medical Research
dc.titleOn the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity
dc.typeJournal Article
dspace.entity.typePublication
html.description.abstract<p>A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, though these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analyzing the relationship among intraspecies diversity, interspecies divergence, and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centered on long non-coding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.</p>
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