About: Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence

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About: Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence
Creator	Bloom, Jesse Hilton, Sarah
Source	Medline; PMC
abstract	Molecular phylogenetics is often used to estimate the time since the divergence of modern gene sequences. For highly diverged sequences, such phylogenetic techniques sometimes estimate surprisingly recent divergence times. In the case of viruses, independent evidence indicates that the estimates of deep divergence times from molecular phylogenetics are sometimes too recent. This discrepancy is caused in part by inadequate models of purifying selection leading to branch-length underestimation. Here we examine the effect on branch-length estimation of using models that incorporate experimental measurements of purifying selection. We find that models informed by experimentally measured site-specific amino-acid preferences estimate longer deep branches on phylogenies of influenza virus hemagglutinin. This lengthening of branches is due to more realistic stationary states of the models, and is mostly independent of the branch-length extension from modeling site-to-site variation in amino-acid substitution rate. The branch-length extension from experimentally informed site-specific models is similar to that achieved by other approaches that allow the stationary state to vary across sites. However, the improvements from all of these site-specific but time homogeneous and site independent models are limited by the fact that a protein’s amino-acid preferences gradually shift as it evolves. Overall, our work underscores the importance of modeling site-specific amino-acid preferences when estimating deep divergence times—but also shows the inherent limitations of approaches that fail to account for how these preferences shift over time.
has issue date	2018-11-06(xsd:dateTime)
bibo:doi	10.1093/ve/vey033
bibo:pmid	30425841
has license	cc-by
sha1sum (hex)	d9622ec04bc88f584cd280c9dccd177066960cf0
schema:url	https://doi.org/10.1093/ve/vey033
resource representing a document's title	Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence
has PubMed Central identifier	PMC6220371
has PubMed identifier	30425841
schema:publication	Virus Evol
resource representing a document's body	covid:d9622ec04bc88f584cd280c9dccd177066960cf0#body_text
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