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Journal article
Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
Nature ecology & evolution, v 1(2), pp 20-20
01 Feb 2017
PMID: 28812610
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species. Initial results using a suite of standard methodologies revealed conflicting phylogenetic signal, which supports ten alternative evolutionary histories among early otophysan lineages. By contrast, GGI revealed that the vast majority of gene genealogies supports a single tree topology grounded on morphology that was not obtained by previous molecular studies. We also reanalysed published data sets for exemplary groups with recalcitrant resolution to assess the power of this approach. GGI supports the notion that ctenophores are the earliest-branching animal lineage, and adds insight into relationships within clades of yeasts, birds and mammals. GGI opens up a promising avenue to account for incompatible signals in large data sets and to discern between estimation error and actual biological conflict explaining gene tree discordance.
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Details
- Title
- Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
- Creators
- Dahiana Arcila - National Museum of Natural HistoryGuillermo Orti - George Washington UniversityRichard Vari - National Museum of Natural HistoryJonathan W. Armbruster - Auburn UniversityMelanie L. J. Stiassny - American Museum of Natural HistoryKyung D. Ko - George Washington UniversityMark H. Sabaj - Drexel UniversityJohn Lundberg - Academy of Natural Sciences of Drexel UniversityLiam J. Revell - University of Massachusetts BostonRicardo Betancur-R - Massachusetts Rehabilitation Commission
- Publication Details
- Nature ecology & evolution, v 1(2), pp 20-20
- Publisher
- Springer Nature
- Number of pages
- 10
- Grant note
- George Washington University Natural History Museum (Smithsonian) 1541554 / Division Of Environmental Biology; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) Smithsonian Peter Buck fellowship DEB-147184; DEB-1541491; DEB-1457426; DEB-1541554; DEB-0315963; DEB-1023403; DEB-1350474 / National Science Foundation (NSF)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Academy of Natural Sciences of Drexel University
- Web of Science ID
- WOS:000417169600005
- Scopus ID
- 2-s2.0-85021988665
- Other Identifier
- 991019330622504721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Ecology
- Evolutionary Biology