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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Rivera-Arroyo RC, Escalante-Pliego P, Aguilar-Torres D, Úbeda-Olivas MF. Phylogeography of the white-crowned parrot (Pionus senilis). Biota Neotrop 2022. [DOI: 10.1590/1676-0611-bn-2022-1382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Abstract The white-crowned parrot Pionus senilis (von Spix, 1824) is distributed throughout Middle America, inhabiting the Gulf of Mexico coastal area from Tamaulipas (Mexico) to northern Panama. We used mitochondrial data (COI, ND2 and ND4) from 55 specimens to infer phylogenetic relationships, and analyzed the phylogeographic structure, genetic diversity, divergence periods, and historical demography to explore phylogeographic patterns. We found three divergent lineages: two geographically separated by the Isthmus of Tehuantepec, and the third, in Costa Rica by the Nicaragua Depression. The analysis of molecular variance and statistical analyses were consistent with genetically distinct populations. The Central American lineage diverged 1.33 million years ago, whereas the other two lines branched off 1.19 million years ago. This phylogenetic pattern has been reported in other species of Middle American birds.
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