Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies

Bastien Llamas, Paul Brotherton, Kieren Mitchell, Jennifer Templeton, Vicki Thomson, Jessica Metcalf, Kyle Armstrong, Marta Kasper, Stephen Richards, Aaron Camens, Mike Lee, Alan Cooper

    Research output: Contribution to journalArticle

    11 Citations (Scopus)

    Abstract

    Understanding the evolution of Australia's extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39-52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46-50 and 40-45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA.We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.

    Original languageEnglish
    Pages (from-to)574-584
    Number of pages11
    JournalMOLECULAR BIOLOGY AND EVOLUTION
    Volume32
    Issue number3
    DOIs
    Publication statusPublished - 2015

    Fingerprint Dive into the research topics of 'Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies'. Together they form a unique fingerprint.

  • Cite this

    Llamas, B., Brotherton, P., Mitchell, K., Templeton, J., Thomson, V., Metcalf, J., Armstrong, K., Kasper, M., Richards, S., Camens, A., Lee, M., & Cooper, A. (2015). Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies. MOLECULAR BIOLOGY AND EVOLUTION, 32(3), 574-584. https://doi.org/10.1093/molbev/msu338