GBE Speciation Generates Mosaic Genomes in Kangaroos Maria A. Nilsson1,*,†, Yichen Zheng1,†,VikasKumar1, Matthew J. Phillips2, and Axel Janke1,3,* 1Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft fu¨ r Naturforschung, Frankfurt am Main, Germany 2School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), Brisbane, Queensland, Australia 3Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany †These authors contributed equally to this work. *Corresponding authors: E-mails:
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[email protected]. Accepted: November 21, 2017 Data deposition: This project has been deposited at GenBank under the accession PRJEB18139 (Illumina short read data) and KY996499- KY996509 (complete mitochondrial sequences). Abstract The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary rela- tionship 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.