Speciation generates mosaic genomes in kangaroos

  • The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of 11 kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict. A multilocus coalescent analysis using ∼14,900 genome fragments, each 10 kb long, significantly resolved the species relationships between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) as nested inside Macropus, making this genus paraphyletic. However, the phylogenomic analyses indicate multiple conflicting phylogenetic signals in the swamp wallaby genome. This is interpreted as at least one introgression event between the ancestor of the genus Wallabia and a now extinct ghost lineage outside the genus Macropus. Additional phylogenetic signals must therefore be caused by incomplete lineage sorting and/or introgression, but available statistical methods cannot convincingly disentangle the two processes. In addition, the relationships inside the Macropus subgenus M. (Notamacropus) represent a hard polytomy. Thus, the relationships between tammar, red-necked, agile, and parma wallabies remain unresolvable even with whole-genome data. Even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting, and introgression complicate the interpretation of the phylogeny and thus taxonomy.

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Author:Maria Anna Nilsson, Yichen Zheng, Vikas Kumar, Matthew J. Phillips, Axel Janke
URN:urn:nbn:de:hebis:30:3-463749
DOI:https://doi.org/10.1093/gbe/evx245
ISSN:1759-6653
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/29182740
Parent Title (English):Genome biology and evolution
Publisher:Oxford Univ. Press
Place of publication:Oxford
Contributor(s):Ellen Pritham
Document Type:Article
Language:English
Year of Completion:2017
Date of first Publication:2017/11/22
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2018/05/03
Tag:Macropus; genomics; incomplete lineage sorting; kangaroo; polytomy
Volume:10
Issue:1
Page Number:12
First Page:33
Last Page:44
Note:
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
HeBIS-PPN:431957436
Institutes:Angeschlossene und kooperierende Institutionen / Senckenbergische Naturforschende Gesellschaft
Biowissenschaften / Institut für Ökologie, Evolution und Diversität
Fachübergreifende Einrichtungen / Biodiversität und Klima Forschungszentrum (BiK-F)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 59 Tiere (Zoologie) / 590 Tiere (Zoologie)
Sammlungen:Universitätspublikationen
Sammlung Biologie / Sondersammelgebiets-Volltexte
Open-Access-Publikationsfonds:Biowissenschaften
Licence (English):License LogoCreative Commons - Namensnennung-Nicht kommerziell 4.0