TY - JOUR
T1 - Empirical landscape genetic comparison of single nucleotide polymorphisms and microsatellites in three arid-zone mammals with high dispersal capacity
AU - Skey, Ebony D
AU - Ottewell, Kym M
AU - Spencer, Peter B
AU - Shaw, Robyn E
N1 - Funding Information:
This study was part of an Australian Research Council Linkage Project (LP170100061), with the Australian National University, Biologic, CSIRO, Department of Biodiversity, Conservation and Attractions (DBCA), Murdoch University, Roy Hill Iron Ore Pty Ltd, the Western Australian Biodiversity Science Institute, and the Western Australian Museum. The work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. We gratefully acknowledge the many Traditional Owners of the Pilbara region; on whose country these data were collected. We are also grateful for data and support provided by Murdoch University and DBCA. In particular, we acknowledge the personnel involved with the Pilbara biological survey and Janine Kinloch for providing spatial data. Open access publishing facilitated by Australian National University, as part of the Wiley ‐ Australian National University agreement via the Council of Australian University Librarians.
Funding Information:
This study was part of an Australian Research Council Linkage Project (LP170100061), with the Australian National University, Biologic, CSIRO, Department of Biodiversity, Conservation and Attractions (DBCA), Murdoch University, Roy Hill Iron Ore Pty Ltd, the Western Australian Biodiversity Science Institute, and the Western Australian Museum. The work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. We gratefully acknowledge the many Traditional Owners of the Pilbara region; on whose country these data were collected. We are also grateful for data and support provided by Murdoch University and DBCA. In particular, we acknowledge the personnel involved with the Pilbara biological survey and Janine Kinloch for providing spatial data. Open access publishing facilitated by Australian National University, as part of the Wiley - Australian National University agreement via the Council of Australian University Librarians.
Publisher Copyright:
© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
PY - 2023/5
Y1 - 2023/5
N2 - 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.
AB - 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.
KW - arid zone
KW - isolation-by-resistance
KW - landscape genetics
KW - microsatellites
KW - single nucleotide polymorphisms
KW - small mammals
UR - http://www.scopus.com/inward/record.url?scp=85160915643&partnerID=8YFLogxK
U2 - 10.1002/ece3.10037
DO - 10.1002/ece3.10037
M3 - Article
C2 - 37153020
SN - 2045-7758
VL - 13
SP - 1
EP - 17
JO - Ecology and Evolution
JF - Ecology and Evolution
IS - 5
M1 - e10037
ER -