The identity of the Depuch Island rock-wallaby revealed through ancient DNA

Abstract

Abstract. Ancient DNA is becoming increasingly recognised as a tool in conservation biology to audit past biodiversity. The widespread loss of Australian biodiversity, especially endemic mammal populations, is of critical concern. An extreme example occurred on Depuch Island, situated off the north-west coast of Western Australia, where an unidentified species of rock-wallaby (Petrogale sp.) became extinct as a result of predation by red foxes. Two potential candidate species, Petrogale lateralis and P. rothschildi, both have ranges adjacent to Depuch Island, making identification based on geography difficult. A museum bone (one of the only surviving Depuch Island specimens) was subjected to standard ancient DNA analyses and procedures. Mitochondrial DNA cytochrome b and hypervariable control region were targeted for species identification. Ancient DNA was successfully recovered from the bone: 200 base pairs (bp) of control region and 975 bp of the cytochrome b gene. Bayesian phylogenetic analyses were employed to model the Depuch Island rock-wallaby DNA sequences together with sequences of other rock-wallaby taxa from GenBank. Evidence suggests that of the two Petrogale lateralis subspecies proposed to have inhabited Depuch Island, Petrogale lateralis lateralis was identified as the most likely. The identification of the Depuch Island rock-wallaby population may assist in the reintroduction of an insurance population of Petrogale lateralis lateralis, which is becoming increasingly threatened on mainland Australia.

Late-Holocene mammal fauna from southern Australia reveals rapid species declines post-European settlement: Implications for conservation biology

“…Genetic analysis using methods optimised for ancient DNA (e.g. Haouchar et al, 2013; Willerslev and Cooper, 2005) could potentially establish fossil relationships to extant populations.…”

Holocene vertebrate fossils aid the management and restoration of Australian ecosystems

“…Recent advances in ancient DNA analyses have made it possible to audit the genetic composition of past biodiversity by directly sampling DNA from Holocene fossils (Haouchar et al . ). This allows characterisation of pre‐European parameters such as population sizes, levels of gene flow and population relatedness, providing critical information for wildlife management and conservation goal setting (Ramakrishnan et al .…”

“…However, European landscape modifications have caused severe range and population size reductions in most native mammals, resulting in accelerated random genetic drift, rapid decline of genetic diversity and increased population differentiation, complicating the estima-tion of past population conditions (Leonard 2008;Pacioni et al 2011). Recent advances in ancient DNA analyses have made it possible to audit the genetic composition of past biodiversity by directly sampling DNA from Holocene fossils (Haouchar et al 2013). This allows characterisation of pre-European parameters such as population sizes, levels of gene flow and population relatedness, providing critical information for wildlife management and conservation goal setting (Ramakrishnan et al 2005;Leonard 2008;de Bruyn et al 2011).…”

“…Molecular techniques may also be applied to differentiate species that are morphologically indistinct. This technique was recently applied to identify the Depuch Island rock-wallaby (Haouchar et al 2013) and could easily be applied to differentiate other morphologically indistinct species pairs (e.g. Pseudocheirus occidentalis and P. peregrinus) and species complexes (e.g.…”

Novel mitochondrial haplotype of spotted-tailed quoll (Dasyurus maculatus) present on Kangaroo Island (South Australia) prior to extirpation

“…In this endeavour, ancient DNA (aDNA) information retrieved from fossils is necessary, particularly when taxa are morphologically cryptic. For example, aDNA has been used to identify the subspecies of rock wallaby ( Petrogale lateralis ) that inhabited Depuch Island (Western Australia) prior to extirpation by foxes (Haouchar et al, 2013). Because aDNA is degraded, the authors targeted mitochondrial loci as there are many more copies of the mitogenome than the nuclear genome.…”