Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity |
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Authors: | Katherine A Harrisson Stephen J Amish Alexandra Pavlova Shawn R Narum Marina Telonis‐Scott Meaghan L Rourke Jarod Lyon Zeb Tonkin Dean M Gilligan Brett A Ingram Mark Lintermans Han Ming Gan Christopher M Austin Gordon Luikart Paul Sunnucks |
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Institution: | 1. School of Biological Sciences, Monash University, Clayton, Vic., Australia;2. Department of Ecology Environment and Evolution, School of Life Sciences, La Trobe University, Bundoora, Vic., Australia;3. Arthur Rylah Institute for Environmental Research, Heidelberg, Vic., Australia;4. Conservation Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, USA;5. Flathead Lake Biological Station, University of Montana, Polson, MT, USA;6. Columbia River Inter‐Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, ID, USA;7. Department of Primary Industries, DPI Fisheries, Narrandera, NSW, Australia;8. Department of Primary Industries, DPI Fisheries, Batemans Bay Fisheries Office, Batemans Bay, NSW, Australia;9. Victorian Fisheries Authority, Alexandra, Vic., Australia;10. Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia;11. Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic., Australia;12. School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia;13. Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia |
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Abstract: | Adaptive differences across species’ ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene–environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired‐end restriction site‐associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene–association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature‐ and precipitation‐related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies. |
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Keywords: | candidate genes landscape genomics local adaptation natural populations spatial genetics wildlife management |
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