Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins

Molecular Ecology
Elizabeth J BeckmanChristopher C Witt

Abstract

Genetic introgression among closely related species is a widespread phenomenon across the Tree of Life and could be an important source of adaptive variation during early stages of diversification. In particular, genomic studies have revealed that many rapidly radiating clades tend to have complex, reticulate evolutionary histories. Although rapid radiations appear to be susceptible to introgression, they present special challenges for its detection because formal tests require accurate phylogenies, and paradoxically, introgression itself may obscure evolutionary relationships. To address this methodological challenge, we assessed introgression in a recent, rapid avian radiation in the Andes, the South American siskins (Spinus). Using ~45,000 SNPs, we estimated the Spinus phylogeny using multiple analytical approaches and recovered four strongly conflicting topologies. We performed a series of complimentary introgression tests that included valid tests for each of the likely species trees. From the consilience of test results, we inferred multiple introgression events among Andean Spinus in a way that was robust to phylogenetic uncertainty in the species tree. Positive tests for introgression were corroborated by independent po...Continue Reading

References

Jan 2, 2003·Proceedings of the National Academy of Sciences of the United States of America·Dan MishmarDouglas C Wallace
Mar 12, 2004·Molecular Ecology·J William O Ballard, Michael C Whitlock
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jun 7, 2005·The American Naturalist·Peter R GrantK Petren
Jan 13, 2006·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Pierre U BlierHélène Lemieux
May 17, 2006·Trends in Ecology & Evolution·Ole Seehausen
May 17, 2006·Trends in Ecology & Evolution·James Mallet
Sep 12, 2006·The Plant Journal : for Cell and Molecular Biology·Radhika DesikanSteven J Neill
Mar 17, 2007·Systematic Biology·Laura Salter Kubatko, James H Degnan
Apr 22, 2008·Nature Genetics·John Novembre, Matthew Stephens
Jan 17, 2009·Evolution; International Journal of Organic Evolution·Scott V Edwards
Aug 4, 2009·Genome Research·David H AlexanderKenneth Lange
Sep 26, 2009·Nature·David ReichLalji Singh
May 8, 2010·Science·Richard E GreenSvante Pääbo
Aug 6, 2010·Molecular Biology and Evolution·Graham R ScottWilliam K Milsom
Feb 18, 2011·Molecular Biology and Evolution·Eric Y DurandMontgomery Slatkin
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
Sep 20, 2011·Bioinformatics·Thibaut Jombart, Ismaïl Ahmed
Nov 25, 2011·Molecular Biology and Evolution·Martin J Genner, George F Turner
Dec 14, 2011·BMC Evolutionary Biology·Zbyszek BoratyńskiJosé Melo-Ferreira
Feb 10, 2012·Molecular Biology and Evolution·Robert LanfearStephane Guindon
Mar 3, 2012·G3 : Genes - Genomes - Genetics·Julian M CatchenJohn H Postlethwait
Mar 13, 2012·Molecular Ecology·Thomas L ParchmanC Alex Buerkle
Mar 17, 2012·Molecular Biology and Evolution·David BryantArindam RoyChoudhury
Jun 23, 2012·Nature·UNKNOWN Heliconius Genome Consortium
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Nov 21, 2012·PLoS Genetics·Joseph K Pickrell, Jonathan K Pritchard
May 25, 2013·Molecular Ecology·Julian CatchenWilliam A Cresko
Jul 31, 2013·Evolution; International Journal of Organic Evolution·Rongfeng CuiGil G Rosenthal
Mar 8, 2014·Bioinformatics·Deren A R Eaton
Apr 12, 2014·PLoS Computational Biology·Remco BouckaertAlexei J Drummond
Jun 13, 2014·PLoS Computational Biology·Kevin J LiuLuay Nakhleh
Aug 12, 2014·Bioinformatics·Julia Chifman, Laura Kubatko
Sep 24, 2014·Molecular Biology and Evolution·Simon H MartinChris D Jiggins

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