SRA

The iconic Australasian kangaroos and wallabies (genera Macropus and Wallabia) represent a successful marsupial radiation. However, the evolutionary relationship and timing of the kangaroo evolution is controversial. We sequenced the genomes of nine of the 13 species in the Macropus and Wallabia taxon complex to investigate the evolutionary cause of the conflicting trees. A multi-locus coalescent analysis using ~14,900 genome fragments could significantly resolve the species relationship between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) nested inside Macropus, making the genus paraphyletic. However, the genomic analyses show that the swamp wallaby genome is a mix of phylogenetic signals. One introgression event must have taken place between the ancestor of the genus Wallabia and a now extinct ghost lineage. The relationships inside one of the Macropus subgenera (M. (Notamacropus)) are hard polytomy. Thus, evolution of species can be complex, even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting and gene flow making it necessary to rethink speciation and evolutionary models.