Empirical landscape genetic comparison of single nucleotide polymorphisms and microsatellites in three arid-zone mammals with high dispersal capacity

Ebony D Skey; Kym M Ottewell; Peter B Spencer; Robyn E Shaw

doi:10.1002/ece3.10037

Empirical landscape genetic comparison of single nucleotide polymorphisms and microsatellites in three arid-zone mammals with high dispersal capacity

Ecol Evol. 2023 May 2;13(5):e10037. doi: 10.1002/ece3.10037. eCollection 2023 May.

Authors

Ebony D Skey^{1

2}, Kym M Ottewell², Peter B Spencer¹, Robyn E Shaw^{1

2

3}

Affiliations

¹ Environmental & Conservation Sciences Murdoch University Perth Western Australia Australia.
² Biodiversity and Conservation Science Department of Biodiversity, Conservation and Attractions Perth Western Australia Australia.
³ Present address: Division of Ecology and Evolution, Research School of Biology The Australian National University Canberra Australian Capital Territory Australia.

Abstract

Landscape genetics is increasingly transitioning away from microsatellites, with single nucleotide polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial-genetic structure. This is particularly pertinent for research in arid-zone mammals due to challenges associated with unique life history traits, such as boom-bust population dynamics and long-distance dispersal capacities. Here, we provide a case study comparing SNPs versus microsatellites for testing three explicit landscape genetic hypotheses (isolation-by-distance, isolation-by-barrier, and isolation-by-resistance) in a suite of small, arid-zone mammals in the Pilbara region of Western Australia. Using clustering algorithms, Mantel tests, and linear mixed effects models, we compare functional connectivity between genetic marker types and across species, including one marsupial, Ningaui timealeyi, and two native rodents, Pseudomys chapmani and P. hermannsburgensis. SNPs resolved subtle genetic structuring not detected by microsatellites, particularly for N. timealeyi where two genetic clusters were identified. Furthermore, stronger signatures of isolation-by-distance and isolation-by-resistance were detected when using SNPs, and model selection based on SNPs tended to identify more complex resistance surfaces (i.e., composite surfaces of multiple environmental layers) in the best-performing models. While we found limited evidence for physical barriers to dispersal across the Pilbara for all species, we found that topography, substrate, and soil moisture were the main environmental drivers shaping functional connectivity. Our study demonstrates that new analytical and genetic tools can provide novel ecological insights into arid landscapes, with potential application to conservation management through identifying dispersal corridors to mediate the impacts of ongoing habitat fragmentation in the region.

Keywords: arid zone; isolation‐by‐resistance; landscape genetics; microsatellites; single nucleotide polymorphisms; small mammals.