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Biodiversity and Conservation

, Volume 25, Issue 14, pp 2907–2927 | Cite as

Ancient DNA reveals complexity in the evolutionary history and taxonomy of the endangered Australian brush-tailed bettongs (Bettongia: Marsupialia: Macropodidae: Potoroinae)

  • Dalal Haouchar
  • Carlo Pacioni
  • James Haile
  • Matthew C. McDowell
  • Alexander Baynes
  • Matthew J. Phillips
  • Jeremy J. Austin
  • Lisa C. Pope
  • Michael Bunce
Original Paper

Abstract

The three surviving ‘brush-tailed’ bettong species—Bettongia gaimardi (Tasmania), B. tropica (Queensland) and B. penicillata (Western Australia), are all classified as threatened or endangered. These macropodids are prolific diggers and are recognised as important ‘ecosystem engineers’ that improve soil quality and increase seed germination success. However, a combination of introduced predators, habitat loss and disease has seen populations become increasingly fragmented and census numbers decline. Robust phylogenies are vital to conservation management, but the extent of extirpation and fragmentation in brush-tailed bettongs is such that a phylogeny based upon modern samples alone may provide a misleading picture of former connectivity, genetic diversity and species boundaries. Using ancient DNA isolated from fossil bones and museum skins, we genotyped two mitochondrial DNA (mtDNA) genes: cytochrome b (266 bp) and control region (356 bp). These ancient DNA data were combined with a pre-existing modern DNA data set on the historically broadly distributed brush-tailed bettongs (~300 samples total), to investigate their phylogenetic relationships. Molecular dating estimates the most recent common ancestor of these bettongs occurred c. 2.5 Ma (million years ago), which suggests that increasing aridity likely shaped their modern-day distribution. Analyses of the concatenated mtDNA sequences of all brush-tailed bettongs generated five distinct and well-supported clades including: a highly divergent Nullarbor form (Clade I), B. tropica (Clade II), B. penicillata (Clades III and V), and B. gaimardi (Clade IV). The generated phylogeny does not reflect current taxonomy and the question remains outstanding of whether the brush-tailed bettongs consisted of several species, or a single widespread species. The use of nuclear DNA markers (single nucleotide polymorphisms and/or short tandem repeats) will be needed to better inform decisions about historical connectivity and the appropriateness of ongoing conservation measures such as translocations and captive breeding.

Keywords

Ancient DNA Bettongia Conservation Past biodiversity Phylogenetics Phylogeography 

Notes

Acknowledgments

Thanks to the WA Museum, Museum of Victoria and the Australian National Wildlife Collection (CSIRO) for access to historical samples and assistance. Work was funded by Australian Research Council grants: FT0991741 (MB) DP120104435 (Gavin Prideaux and MB). We thank Gavin Prideaux (Flinders University) for helpful discussions and the Pawsey Supercomputer Centre, Western Australia, and CIPRES (http://www.phylo.org/sub_sections/portal/cite.php) for providing computational support.

Supplementary material

10531_2016_1210_MOESM1_ESM.pdf (578 kb)
Supplementary material 1 (PDF 577 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Dalal Haouchar
    • 1
    • 2
  • Carlo Pacioni
    • 1
    • 2
  • James Haile
    • 2
    • 3
  • Matthew C. McDowell
    • 4
  • Alexander Baynes
    • 5
  • Matthew J. Phillips
    • 6
  • Jeremy J. Austin
    • 7
  • Lisa C. Pope
    • 8
  • Michael Bunce
    • 2
  1. 1.Ancient DNA Laboratory, School of Veterinary and Life SciencesMurdoch UniversityMurdochAustralia
  2. 2.Trace and Environmental DNA Laboratory, Department of Environment and AgricultureCurtin UniversityBentleyAustralia
  3. 3.PalaeoBARN, Research Laboratory for Archaeology and History of ArtUniversity of OxfordOxfordUK
  4. 4.School of Biological SciencesFlinders University of South AustraliaBedford ParkAustralia
  5. 5.Western Australian MuseumWelshpool DCAustralia
  6. 6.School of Earth, Environmental and Biological SciencesQueensland University of TechnologyBrisbaneAustralia
  7. 7.School of Biological Sciences, Australian Centre for Ancient DNAUniversity of AdelaideAdelaideAustralia
  8. 8.School of Biological SciencesThe University of QueenslandSt LuciaAustralia

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