Evidence of Subdivisions on Evolutionary Timescales in a Large, Declining Marsupial Distributed across a Phylogeographic Barrier.

Deryn L Alpers,Faith M Walker,Birgita D Hansen,Steven Bellman,Paul Sunnucks,William B Sherwin,Andrea C Taylor

doi:10.1371/journal.pone.0162789

Abstract

Major prehistoric forces, such as the climatic shifts of the Pleistocene, can remain visible in a species’ population genetics. Inference of refuges via genetic tools is useful for conservation management as it can identify populations whose preservation may help retain a species’ adaptive potential. Such investigation is needed for Australia’s southern hairy-nosed wombat (Lasiorhinus latifrons), whose conservation status has recently deteriorated, and whose phylogeographic history during the Pleistocene may be atypical compared to other species. Its contemporary range spans approximately 2000 km of diverse habitat on either side of the Spencer Gulf, which was a land bridge during periods of Pleistocene aridity that may have allowed for migration circumventing the arid Eyrean barrier. We sampled from animals in nearly all known sites within the species’ current distribution, mainly using non-invasive methods, and employed nuclear and mitochondrial DNA analyses to assess alternative scenarios for Pleistocene impacts on population structure. We found evidence for mildly differentiated populations at the range extremes on either side of Spencer Gulf, with secondary contact between locations neighbouring each side of the barrier. These extreme western and eastern regions, and four other regions in between, were genetically distinct in genotypic clustering analyses. Estimates indicate modest, but complex gene flow patterns among some of these regions, in some cases possibly restricted for several thousand years. Prior to this study there was little information to aid risk assessment and prioritization of conservation interventions facilitating gene flow among populations of this species. The contributions of this study to that issue are outlined.

Highlights

The Pleistocene period was marked by oscillations in global climate aridity and, as a consequence, habitat fragmentation with animal species potentially surviving in refuges [1, 2]
We investigated the effects of environmental influences since the late Pleistocene on southern hairy-nosed (SHN) wombat population structure, and attempted to uncover the population genetic patterns that existed prior to land-use by European settlers and the relationships among extant populations
Our results suggest that geological events may have structured genetic variation in the SHN wombat, but in such a way that neither the Eyrean barrier nor the Spencer Gulf marks a clear genetic break in the centre of the SHN wombat distribution

Summary

Introduction

The Pleistocene period was marked by oscillations in global climate aridity and, as a consequence, habitat fragmentation with animal species potentially surviving in refuges [1, 2]. Irrespective of historical processes, conservation management policies can use information on population structure to maximize the likely retention of a species’ evolutionary history and adaptive diversity by minimizing the loss of distinct populations. These conservation management concerns are pertinent for the southern hairy-nosed (SHN) wombat (Lasiorhinus latifrons), a large, herbivorous, fossorial marsupial from semi-arid regions of southern Australia (Fig 1) [10, 11]. Identifying how the SHN wombat responded to historical habitat and climatic changes is important for both our greater understanding of its evolutionary history as well as its contemporary conservation

Methods

Results

Conclusion