Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons

Molecular Biology and Evolution
Cheng-Min Shi, Ziheng Yang

Abstract

The phylogenetic relationships among extant gibbon species remain unresolved despite numerous efforts using morphological, behavorial, and genetic data and the sequencing of whole genomes. A major challenge in reconstructing the gibbon phylogeny is the radiative speciation process, which resulted in extremely short internal branches in the species phylogeny and extensive incomplete lineage sorting with extensive gene-tree heterogeneity across the genome. Here, we analyze two genomic-scale data sets, with ∼10,000 putative noncoding and exonic loci, respectively, to estimate the species tree for the major groups of gibbons. We used the Bayesian full-likelihood method bpp under the multispecies coalescent model, which naturally accommodates incomplete lineage sorting and uncertainties in the gene trees. For comparison, we included three heuristic coalescent-based methods (mp-est, SVDQuartets, and astral) as well as concatenation. From both data sets, we infer the phylogeny for the four extant gibbon genera to be (Hylobates, (Nomascus, (Hoolock, Symphalangus))). We used simulation guided by the real data to evaluate the accuracy of the methods used. Astral, while not as efficient as bpp, performed well in estimation of the species ...Continue Reading

References

Sep 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·C W Birky, J B Walsh
Jul 1, 1994·Journal of Molecular Evolution·Z Yang
Apr 1, 1996·Genetical Research·M NordborgD Charlesworth
Aug 5, 1998·Proceedings of the National Academy of Sciences of the United States of America·B G Baldwin, M J Sanderson
Mar 26, 2002·Biological Reviews of the Cambridge Philosophical Society·Thomas Geissmann
Oct 22, 2003·Human Genetics·Stefan MüllerJohannes Wienberg
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Aug 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·Dick G Hwang, Phil Green
Mar 29, 2005·Evolution; International Journal of Organic Evolution·James H Degnan, Laura A Salter
Jun 14, 2005·Molecular Phylogenetics and Evolution·Zoltan TakacsDon J Melnick
Mar 9, 2006·Systematic Biology·Nicolas Lartillot, Hervé Philippe
May 31, 2006·PLoS Genetics·James H Degnan, Noah A Rosenberg
Dec 22, 2006·PloS One·Esther ClarkeKlaus Zuberbühler
Dec 23, 2006·Genome Research·Roberta RobertoEvan E Eichler
Mar 17, 2007·Systematic Biology·Laura Salter Kubatko, James H Degnan
Mar 30, 2007·Proceedings of the National Academy of Sciences of the United States of America·Scott V EdwardsDennis K Pearl
Jul 31, 2007·Molecular Biology and Evolution·Ingo EbersbergerArndt von Haeseler
Jul 16, 1976·Science·J T Marshall, E R Marshall
May 9, 2009·PLoS Genetics·Graham McVickerPhil Green
Oct 29, 2009·BMC Evolutionary Biology·Helen J ChatterjeeColin Groves
Nov 13, 2009·Molecular Biology and Evolution·Joseph Heled, Alexei J Drummond
Dec 4, 2009·Molecular Biology and Evolution·Jody Hey
Feb 9, 2010·Molecular Phylogenetics and Evolution·Kazunari Matsudaira, Takafumi Ishida
Mar 17, 2010·BMC Evolutionary Biology·Van Ngoc ThinhChristian Roos
Jun 9, 2010·Systematic Biology·Huateng Huang, L Lacey Knowles
Jul 24, 2010·Journal of Mathematical Biology·Elizabeth S AllmanJohn A Rhodes
Oct 13, 2010·BMC Evolutionary Biology·Liang LiuScott V Edwards
Feb 18, 2011·Molecular Biology and Evolution·Eric Y DurandMontgomery Slatkin
Oct 25, 2011·Current Biology : CB·Heather R L LernerRobert C Fleischer
Jan 5, 2012·Systematic Biology·Hayley C Lanier, L Lacey Knowles
Feb 24, 2012·Systematic Biology·Fredrik RonquistJohn P Huelsenbeck
Jun 12, 2012·Molecular Biology and Evolution·Thomas J MeyerMark A Batzer
Aug 23, 2012·BMC Evolutionary Biology·Yi-Chiao ChanLinda Vigilant
Jan 24, 2013·PloS One·Jeffrey D WallAnna Di Rienzo
May 10, 2013·Nature·Leonidas Salichos, Antonis Rokas
Aug 16, 2013·Systematic Biology·Adam D LeachéZiheng Yang
Nov 22, 2013·Statistical Applications in Genetics and Molecular Biology·Nengjun YiHimel Mallick
Aug 12, 2014·Bioinformatics·Julia Chifman, Laura Kubatko

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Citations

Mar 3, 2018·Genes·Mark S Springer, John Gatesy
Jul 10, 2018·Systematic Biology·Adam D LeachéZiheng Yang
Aug 23, 2018·Evolutionary Anthropology·Julia M Zichello
Jul 28, 2018·Molecular Biology and Evolution·Tomáš FlouriZiheng Yang
Dec 12, 2019·Molecular Biology and Evolution·Tomáš FlouriZiheng Yang
May 18, 2020·Systematic Biology·Matthew Wascher, Laura Kubatko
Jul 4, 2020·Systematic Biology·Xiyun Jiao, Ziheng Yang
Jul 2, 2020·Bioinformatics·Anastasiia Kim, James H Degnan
May 20, 2020·Nature Reviews. Genetics·Paschalia KapliMaximilian J Telford
Jul 22, 2020·Proceedings of the National Academy of Sciences of the United States of America·Mariam OkhovatLucia Carbone
Dec 21, 2019·Molecular Biology and Evolution·Anastasiia KimJames H Degnan
Apr 9, 2021·Molecular Phylogenetics and Evolution·Anastasiia Kim, James H Degnan
May 14, 2021·Molecular Biology and Evolution·Gabrielle A HartleyLucia Carbone
Jan 26, 2021·Molecular Biology and Evolution·Tianqi Zhu, Ziheng Yang
Jul 6, 2021·Molecular Phylogenetics and Evolution·Hernán Vázquez-Miranda, F Keith Barker
May 15, 2021·Genome Biology and Evolution·Sree Rohit Raj KoloraKatja Nowick
Oct 27, 2021·Cladistics : the International Journal of the Willi Hennig Society·David OrtizMalahat Dianat

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