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Incomplete lineage sorting and phenotypic evolution in marsupials

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  • Shaohong Feng, BGI-Shenzhen, CAS - Kunming Institute of Zoology
  • ,
  • Ming Bai, CAS - Institute of Zoology, Ningxia University, Hebei Agricultural University
  • ,
  • Iker Rivas-González
  • Cai Li, Sun Yat-Sen University
  • ,
  • Shiping Liu, BGI-Shenzhen
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  • Yijie Tong, CAS - Institute of Zoology, Hebei Agricultural University, Hainan Yazhou Bay Seed Lab
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  • Haidong Yang, CAS - Institute of Zoology, Guangdong Academy of Sciences
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  • Guangji Chen, BGI-Shenzhen, University of Chinese Academy of Sciences
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  • Duo Xie, Chinese Academy of Sciences
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  • Karen E. Sears, University of California at Los Angeles
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  • Lida M. Franco, Universidad de Ibague
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  • Juan Diego Gaitan-Espitia, University of Hong Kong
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  • Roberto F. Nespolo, Universidad Austral de Chile, Pontificia Universidad Catolica de Chile, Millenium Institute for Integrative Biology (iBio), Millennium Nucleus of Patagonian Limit of Life (LiLi)
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  • Warren E. Johnson, Smithsonian Institution, Walter Reed Army Institute of Research
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  • Huanming Yang, BGI-Shenzhen, James D. Watson Institute of Genome Sciences
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  • Parice A. Brandies, University of Sydney
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  • Carolyn J. Hogg, University of Sydney
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  • Katherine Belov, University of Sydney
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  • Marilyn B. Renfree, School of Biosciences
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  • Kristofer M. Helgen, Australian Museum, University of New South Wales
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  • Jacobus J. Boomsma, University of Copenhagen
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  • Mikkel Heide Schierup
  • Guojie Zhang, BGI-Shenzhen, CAS - Kunming Institute of Zoology, University of Copenhagen, Chinese Academy of Sciences

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.

Original languageEnglish
JournalCell
Volume185
Issue10
Pages (from-to)1646-1660.e18
Number of pages15
ISSN0092-8674
DOIs
Publication statusPublished - May 2022

    Research areas

  • biogeography, CoalHMM, gene-phenotype incongruence, hemiplasy, incomplete lineage sorting, marsupial, monito del monte, phylogenetic inference, rapid speciation, trait evolution

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