Bringing next generation approaches to conservation genomics using museum collections – Rock wallaby museum skinomics

Ignition Grant Round 3 (June 2014)

  • Sally Potter, ANU
  • Maxine Piggott, ANU
  • Jason Bragg, ANU
  • Matthew Morgan, CSIRO
  • Leo Joseph, CSIRO

Traditional genetic approaches have been valuable in identifing patterns of diversity where sampling is good, however for many Australian taxa sampling is poor. Existing frozen tissue collections often provide limited sampling but vouchered musuem collections can offer much better sampling.

It is more only recently, using new genomic methods (next generation sequencing; NGS; e.g. Bi et al. 2013), that we can make use of existing  museum collections and provide us the necessary sampling to evaluate evolutionary history and taxonomy within many elusive or rare species. 

Since these methods are yet to be tested with Australian collections, we propose to develop methods for applying NGS to museum skins, testing the largest collection of rock-wallaby skins in Australia at the Australian National Wildlife Collection (CSIRO). There is limited information about errors associated with damaged DNA (tanned skins) in NGS approaches and we aim to assess how reliable and consistent NGS appraoches are in use of museum collections.

More specifically, our objectives are to:

  1. Optimise genomic techniques, including extraction methods & library preparation in use of museum specimens in exon capture hybridisation experiments.
  2. Use the experiment to generate data to evaluate the genetic diversity within the three currently recognised species of northern Australian rock-wallabies.
  3. Use the genetic outcomes to assist in conservation management planning for northern Australian rock-wallabies and in providing a suitable protocol for non-invasive conservation genomics.
  4. Incorporate the phylogenetic data in spatial modelling predictions to assist in identifying areas of refugia across northern Australia.

Once the technique is developed and tested in our lab, we hope it will provide a valubale resource for other conservation genomic studies within Australia. Museum collections in Australia provide a wealth of resources for evolutionary studies and using these specimens in conservation management, we hope to further highlight the importance of collections in Australia. Once the methods are optimised, we aim to further the focus to other Australian taxa.

The main outcome of this project will be to demonstrate application of NGS methods to museum collections and applicability of such techniques for other research. There will be a lot of troubleshooting required in the bioinformatics of this project and our experimental design will help to establish what we can gain from museum samples.

Despite this, focusing on rock-wallabies where we will have species specific outcomes and gain better insight into northern Australia biodiversity, the application of such methods has potential for climate change and adapatation research, conservation planning and threatened species policies.

We aim to provide useful protocols for non-invasive monitoring for conservation surveys, assisting in future efforts to understand and protect endangered or cryptic species within Australia.