So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

PloS One
Stephen A SmithJoseph F Walker

Abstract

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. "Gene shopping", wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-s...Continue Reading

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Citations

Apr 25, 2019·Proceedings. Biological Sciences·Joanna M WolfeHeather D Bracken-Grissom
Dec 7, 2019·Systematic Biology·Tom CarruthersRobert W Scotland
Oct 22, 2019·Systematic Biology·Michael R McGowenStephen J Rossiter
Jan 9, 2020·Proceedings of the National Academy of Sciences of the United States of America·Andrea Del CortonaFrederik Leliaert
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Nov 21, 2019·Systematic Biology·Stephen A SmithJoseph W Brown
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Oct 4, 2019·PeerJ·Joseph F WalkerGregory W Stull
Sep 26, 2020·Proceedings of the National Academy of Sciences of the United States of America·Katja T C A PeijnenburgFerdinand Marlétaz
Oct 14, 2020·Evolution; International Journal of Organic Evolution·Oscar M VargasKathleen M Kay
Dec 6, 2020·Proceedings of the National Academy of Sciences of the United States of America·Andrew J HelmstetterThomas L P Couvreur
Jan 29, 2021·Systematic Biology·Catherine S McFaddenEstefanía Rodríguez
Dec 29, 2020·Systematic Biology·Silas BossertBryan N Danforth
Sep 4, 2020·Systematic Biology·Nicolás Mongiardino Koch, Jeffrey R Thompson
May 25, 2021·Ecology and Evolution·Friðgeir GrímssonReinhard Zetter
May 14, 2021·Molecular Biology and Evolution·Nicolás Mongiardino Koch
May 15, 2021·Genome Biology and Evolution·Emmanuel F A ToussaintNadir Alvarez
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Nov 1, 2021·Molecular Biology and Evolution·Xiao-Mei XiaXiao-Quan Wang
Dec 7, 2021·G3 : Genes - Genomes - Genetics·Shane D WidanagamaAaron B A Shafer

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Software Mentioned

pxlstr
SortaDate
pxlog
r8s
RAxML
PhyloBayes
Phyx package
MrBayes
pxbp
NELSI

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