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Lott MJ, Wright BR, Neaves LE, Frankham GJ, Dennison S, Eldridge MDB, Potter S, Alquezar-Planas DE, Hogg CJ, Belov K, Johnson RN. Future-proofing the koala: synergising genomic and environmental data for effective species management. Mol Ecol 2022; 31:3035-3055. [PMID: 35344635 DOI: 10.1111/mec.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/19/2022] [Accepted: 03/04/2022] [Indexed: 11/30/2022]
Abstract
Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250 specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial divergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (∼ 430-300 kya), a major climatic reorganization that increased the amplitude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of threatened populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g. guiding translocations), as existing management divisions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.
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Affiliation(s)
- Matthew J Lott
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Belinda R Wright
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia.,Sydney School of Veterinary Sciences, Faculty of Science, the University of Sydney, 2006, New South Wales, Australia
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,Fenner School of Environment and Society, the Australian National University, Canberra, Australian Capital Territory, 2600, Australia
| | - Greta J Frankham
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Siobhan Dennison
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Sally Potter
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,Division of Ecology & Evolution, Research School of Biology, the Australian National University, Australian Capital Territory, Canberra, 2600, Australia
| | - David E Alquezar-Planas
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,National Museum of Natural History, District of Columbia, Washington, 20560, United States
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Ofori BY, Stow AJ, Baumgartner JB, Beaumont LJ. Influence of adaptive capacity on the outcome of climate change vulnerability assessment. Sci Rep 2017; 7:12979. [PMID: 29021590 PMCID: PMC5636830 DOI: 10.1038/s41598-017-13245-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 09/22/2017] [Indexed: 11/09/2022] Open
Abstract
Climate change vulnerability assessment (CCVA) has become a mainstay conservation decision support tool. CCVAs are recommended to incorporate three elements of vulnerability – exposure, sensitivity and adaptive capacity – yet, lack of data frequently leads to the latter being excluded. Further, weighted or unweighted scoring schemes, based on expert opinion, may be applied. Comparisons of these approaches are rare. In a CCVA for 17 Australian lizard species, we show that membership within three vulnerability categories (low, medium and high) generally remained similar regardless of the framework or scoring scheme. There was one exception however, where, under the warm/dry scenario for 2070, including adaptive capacity lead to five fewer species being classified as highly vulnerable. Two species, Eulamprus leuraensis and E. kosciuskoi, were consistently ranked the most vulnerable, primarily due to projected losses in climatically suitable habitat, narrow thermal tolerance and specialist habitat requirements. Our findings provide relevant information for prioritizing target species for conservation and choosing appropriate conservation actions. We conclude that for the species included in this study, the framework and scoring scheme used had little impact on the identification of the most vulnerable species. We caution, however, that this outcome may not apply to other taxa or regions.
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Affiliation(s)
- Benjamin Y Ofori
- Department of Biological Sciences, Macquarie University, North Ryde, Macquarie Park, NSW 2019, Australia. .,Department Animal Biology and Conservation Science, University of Ghana, Legon-Accra, Ghana.
| | - Adam J Stow
- Department of Biological Sciences, Macquarie University, North Ryde, Macquarie Park, NSW 2019, Australia
| | - John B Baumgartner
- Department of Biological Sciences, Macquarie University, North Ryde, Macquarie Park, NSW 2019, Australia
| | - Linda J Beaumont
- Department of Biological Sciences, Macquarie University, North Ryde, Macquarie Park, NSW 2019, Australia
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Pepper M, Hamilton DG, Merkling T, Svedin N, Cser B, Catullo RA, Pryke SR, Keogh JS. Phylogeographic structure across one of the largest intact tropical savannahs: Molecular and morphological analysis of Australia’s iconic frilled lizard Chlamydosaurus kingii. Mol Phylogenet Evol 2017; 106:217-227. [DOI: 10.1016/j.ympev.2016.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 11/24/2022]
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Ofori BY, Beaumont LJ, Stow AJ. Cunningham's skinks show low genetic connectivity and signatures of divergent selection across its distribution. Ecol Evol 2016; 7:48-57. [PMID: 28070274 PMCID: PMC5214970 DOI: 10.1002/ece3.2627] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/25/2016] [Accepted: 10/25/2016] [Indexed: 11/24/2022] Open
Abstract
Establishing corridors of connecting habitat has become a mainstay conservation strategy to maintain gene flow and facilitate climate‐driven range shifts. Yet, little attention has been given to ascertaining the extent to which corridors will benefit philopatric species, which might exhibit localized adaptation. Measures of genetic connectivity and adaptive genetic variation across species’ ranges can help fill this knowledge gap. Here, we characterized the spatial genetic structure of Cunningham's skink (Egernia cunninghami), a philopatric species distributed along Australia's Great Dividing Range, and assessed evidence of localized adaptation. Analysis of 4,274 SNPs from 94 individuals sampled at four localities spanning 500 km and 4° of latitude revealed strong genetic structuring at neutral loci (mean FST ± SD = 0.603 ± 0.237) among the localities. Putatively neutral SNPs and those under divergent selection yielded contrasting spatial patterns, with the latter identifying two genetically distinct clusters. Given low genetic connectivity of the four localities, we suggest that the natural movement rate of this species is insufficient to keep pace with spatial shifts to its climate envelope, irrespective of habitat availability. In addition, our finding of localized adaptation highlights the risk of outbreeding depression should the translocation of individuals be adopted as a conservation management strategy.
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Affiliation(s)
- Benjamin Y Ofori
- Department of Biological Sciences Macquarie University North Ryde Macquarie Park NSW Australia; Department Animal Biology and Conservation Science University of Ghana Legon-Accra Ghana
| | - Linda J Beaumont
- Department of Biological Sciences Macquarie University North Ryde Macquarie Park NSW Australia
| | - Adam J Stow
- Department of Biological Sciences Macquarie University North Ryde Macquarie Park NSW Australia
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Welton LJ, Siler CD, Grismer LL, Diesmos AC, Sites JW, Brown RM. Archipelago-wide survey of Philippine forest dragons (Agamidae:Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Luke J. Welton
- Department of Biology; 4102 LSB, Brigham Young University; Provo UT 84602 USA
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; 1345 Jayhawk Blvd., University of Kansas; Lawrence KS 66045-7561 USA
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology; 2401 Chautauqua Ave., University of Oklahoma; Norman OK 73072-7029 USA
| | - L. L. Grismer
- Department of Biology; 4500 Riverwalk Parkway, La Sierra University; Riverside CA 92515-8247 USA
| | - Arvin C. Diesmos
- Herpetology Section; Zoology Division; National Museum of the Philippines; Rizal Park Padre Burgos Avenue Manila Philippines
| | - Jack W. Sites
- Department of Biology; 4102 LSB, Brigham Young University; Provo UT 84602 USA
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; 1345 Jayhawk Blvd., University of Kansas; Lawrence KS 66045-7561 USA
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