Multi-Species Phylogeography of Arid-Zone Sminthopsinae (Marsupialia: Dasyuridae) Reveals Evidence of Refugia and Population Expansion in Response to Quaternary Change.

Linette S Umbrello,Joel A Huey,Raphael K Didham,Ric A How

doi:10.3390/genes11090963

Linette S Umbrello, Joel A Huey + Show 2 more

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https://doi.org/10.3390/genes11090963

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Abstract

Historical population contraction and expansion events associated with Pleistocene climate change are important drivers of intraspecific population structure in Australian arid-zone species. We compared phylogeographic patterns among arid-adapted Dasyuridae (Sminthopsis and Planigale) with close phylogenetic relationships and similar ecological roles to investigate the drivers of phylogeographic structuring and the importance of historical refugia. We generated haplotype networks for two mitochondrial (control region and cytochrome b) and one nuclear (omega-globin) gene from samples distributed across each species range. We used ΦST to test for a genetic population structure associated with the four Pilbara subregions, and we used expansion statistics and Bayesian coalescent skyline analysis to test for signals of historical population expansion and the timing of such events. Significant population structure associated with the Pilbara and subregions was detected in the mitochondrial data for most species, but not with the nuclear data. Evidence of population expansion was detected for all species, and it likely began during the mid-late Pleistocene. The timing of population expansion suggests that these species responded favorably to the increased availability of arid habitats during the mid-late Pleistocene, which is when previously patchy habitats became more widespread. We interpret our results to indicate that the Pilbara region could have acted as a refugium for small dasyurids.

Highlights

In the northern hemisphere, environmental change during the Pleistocene elicited range contraction into southern refugia during repeated glacial maxima (GM) [1], or, expansion in the case of cold-tolerant species [2]
The study species each have different habitat preferences and exhibit a range of potential dispersal abilities (Table 1). Both Planigale species are endemic to the greater Pilbara region [40], while the four Sminthopsis occur in the Pilbara and in the adjacent arid regions (Figure 1b)
The strongest evidence we found was for the Pilbara as an evolutionary refugium for widely distributed dasyurid species within the Western Australia (WA) lineage of S. macroura

Summary

Introduction

Environmental change during the Pleistocene elicited range contraction into southern refugia during repeated glacial maxima (GM) [1], or, expansion in the case of cold-tolerant species [2]. In non-glaciated regions, the absence of widespread ice-sheets has led to idiosyncratic rather than leading-edge phylogeographic patterns, resulting in multiple, species-specific refugia distributed in climatically altered landscapes [3]. Habitat shifts were associated with the activation of mobile dune systems as vegetation patterns accommodated climate change and resulted in a complex array of species responses to change during the Quaternary [4], including in Australian deserts [5,6]. Over 75% of the Australian continent falls within arid climate zones [7]. Global Pleistocene glacial cycles resulted in extremely low levels of precipitation and sea levels during GM, most recently the last

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