The effects of subsampling gene trees on coalescent methods applied to ancient divergences

Molecular Phylogenetics and Evolution
Mark P SimmonsJohn Gatesy

Abstract

Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic inference. We sampled eight empirical studies of ancient lineages with diverse numbers of taxa and genes for which the original authors applied one or more coalescent methods. We found that the average pairwise congruence among gene trees varied greatly both between studies and also often within a study. We recommend that presenting plots of pairwise congruence among gene trees in a dataset be treated as a standard practice for empirical coalescent studies so that readers can readily assess the extent and distribution of incongruence among gene trees. ASTRAL-based coalescent analyses generally outperformed MP-EST and STAR with respect to both internal consistency (congruence between analyses of subsamples of genes with the complete dataset of all genes) and congruence with the concatenation-based topology. We evaluated the approach of subsampling gene trees that are, on average, more congruent with other gene trees as a method to reduce artifacts caused by gene-tree-estimation errors on coalescent analyses. We suggest that this method is well suited to testing whether gene-tree-estimation error is a primary cause of incongruence between concate...Continue Reading

References

Feb 1, 1992·Journal of Molecular Evolution·P J LockhartA W Larkum
May 1, 1996·Molecular Biology and Evolution·J L ThorneD T Jones
Aug 30, 2001·Proceedings of the National Academy of Sciences of the United States of America·M S Rosenberg, S Kumar
Sep 14, 2002·Systematic Biology·Derrick J Zwickl, David M Hillis
Mar 20, 2003·Molecular Phylogenetics and Evolution·Mark P Simmons, John V Freudenstein
Jul 14, 2005·Systematic Biology·David M HillisKatherine St John
Oct 26, 2005·Journal of Biomedical Informatics·Paul J Planet
Mar 2, 2006·Systematic Biology·Wayne P Maddison, L Lacey Knowles
May 31, 2006·PLoS Genetics·James H Degnan, Noah A Rosenberg
Jan 30, 2008·Bioinformatics·Stephen A Smith, Casey W Dunn
Feb 22, 2008·Systematic Biology·Jessica W LeighAndrew J Roger
Oct 24, 2008·Phytopathology·A T Dyer, K J Leonard
Nov 13, 2009·Molecular Biology and Evolution·Joseph Heled, Alexei J Drummond
Apr 28, 2010·Bioinformatics·Jeet Sukumaran, Mark T Holder
Jun 9, 2010·Systematic Biology·Liang LiuScott V Edwards
Jun 9, 2010·Systematic Biology·Huateng Huang, L Lacey Knowles
Oct 13, 2010·BMC Evolutionary Biology·Liang LiuScott V Edwards
Oct 27, 2010·Journal of Molecular Evolution·Vadim V GoremykinOlaf R P Bininda-Emonds
Mar 31, 2011·Systematic Biology·Liang Liu, Lili Yu
Apr 30, 2011·Molecular Biology and Evolution·Jessica W LeighEric Bapteste
Jan 1, 2004·American Journal of Botany·John V FreudensteinMark W Chase
Jun 30, 2011·Genome Biology and Evolution·Jessica W LeighEric Bapteste
Mar 27, 2012·Molecular Phylogenetics and Evolution·Jeffrey A RosenfeldRob DeSalle
Aug 30, 2012·Proceedings of the National Academy of Sciences of the United States of America·Sen SongShaoyuan Wu
Dec 25, 2012·Molecular Phylogenetics and Evolution·R Alexander PyronRuchira Somaweera
May 10, 2013·Nature·Leonidas Salichos, Antonis Rokas
May 11, 2013·Nucleic Acids Research·Timothy I ShawLiang Liu

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Citations

Apr 23, 2016·Molecular Phylogenetics and Evolution·Mark P Simmons, John Gatesy
Oct 4, 2016·Molecular Phylogenetics and Evolution·Yuan Tian, Laura S Kubatko
Oct 28, 2017·The Journal of Heredity·Mark S Springer, John Gatesy
Oct 4, 2017·Systematic Biology·Fábio K Mendes, Matthew W Hahn
Nov 15, 2018·Evolution; International Journal of Organic Evolution·Ricardo Betancur-RGuillermo Ortí
Aug 16, 2017·Nature Ecology & Evolution·Dahiana ArcilaRicardo Betancur-R
Dec 19, 2019·Frontiers in Genetics·Mark S SpringerWilliam J Murphy
Feb 6, 2021·Molecular Phylogenetics and Evolution·Mark P Simmons, John Gatesy
Nov 6, 2018·Molecular Phylogenetics and Evolution·Mark P SimmonsJohn Gatesy
May 14, 2021·Molecular Biology and Evolution·Nicolás Mongiardino Koch
Nov 9, 2021·Molecular Phylogenetics and Evolution·Mark P SimmonsJohn Gatesy

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