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Neaves LE, Frankham GJ, Dennison S, FitzGibbon S, Flannagan C, Gillett A, Hynes E, Handasyde K, Helgen KM, Tsangaras K, Greenwood AD, Eldridge MDB, Johnson RN. Phylogeography of the Koala, (Phascolarctos cinereus), and Harmonising Data to Inform Conservation. PLoS One 2016; 11:e0162207. [PMID: 27588685 PMCID: PMC5010259 DOI: 10.1371/journal.pone.0162207] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/18/2016] [Indexed: 11/18/2022] Open
Abstract
The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus), one of Australia’s most iconic species, was historically widely distributed throughout much of eastern Australia but currently represents a complex conservation challenge. To better understand the challenges to koala genetic health, we assessed the phylogeographic history of the koala. Variation in the maternally inherited mitochondrial DNA (mtDNA) Control Region (CR) was examined in 662 koalas sampled throughout their distribution. In addition, koala CR haplotypes accessioned to Genbank were evaluated and consolidated. A total of 53 unique CR haplotypes have been isolated from koalas to date (including 15 haplotypes novel to this study). The relationships among koala CR haplotypes were indicative of a single Evolutionary Significant Unit and do not support the recognition of subspecies, but were separated into four weakly differentiated lineages which correspond to three geographic clusters: a central lineage, a southern lineage and two northern lineages co-occurring north of Brisbane. The three geographic clusters were separated by known Pleistocene biogeographic barriers: the Brisbane River Valley and Clarence River Valley, although there was evidence of mixing amongst clusters. While there is evidence for historical connectivity, current koala populations exhibit greater structure, suggesting habitat fragmentation may have restricted female-mediated gene flow. Since mtDNA data informs conservation planning, we provide a summary of existing CR haplotypes, standardise nomenclature and make recommendations for future studies to harmonise existing datasets. This holistic approach is critical to ensuring management is effective and small scale local population studies can be integrated into a wider species context.
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Affiliation(s)
- Linda E. Neaves
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, United Kingdom
- * E-mail:
| | - Greta J. Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
| | - Siobhan Dennison
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
| | - Sean FitzGibbon
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Cheyne Flannagan
- Koala Hospital Port Macquarie, PO Box 236, Port Macquarie, NSW, 2444, Australia
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, Queensland, 4519, Australia
| | - Emily Hynes
- Ecoplan Australia Pty Ltd, PO Box 968 Torquay, Victoria, 3228, Australia
| | - Kathrine Handasyde
- School of BioSciences, The University of Melbourne, Victoria, 3010, Australia
| | - Kristofer M. Helgen
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Kyriakos Tsangaras
- Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, 6 International Airport Ave., 2370 Nicosia, Cyprus
| | - Alex D. Greenwood
- Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Mark D. B. Eldridge
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
| | - Rebecca N. Johnson
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
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Ruiz-Rodriguez CT, Ishida Y, Murray ND, O'Brien SJ, Graves JAM, Greenwood AD, Roca AL. Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria. J Hered 2016; 107:573-580. [PMID: 27515769 PMCID: PMC5063317 DOI: 10.1093/jhered/esw049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/04/2016] [Indexed: 11/12/2022] Open
Abstract
The koala (Phascolarctos cinereus) suffered population declines and local extirpation due to hunting in the early 20th century, especially in southern Australia. Koalas were subsequently reintroduced to the Brisbane Ranges (BR) and Stony Rises (SR) by translocating individuals from a population on French Island descended from a small number of founders. To examine genetic diversity and north-south differentiation, we genotyped 13 microsatellite markers in 46 wild koalas from the BR and SR, and 27 Queensland koalas kept at the US zoos. The Queensland koalas displayed much higher heterozygosity (H O = 0.73) than the 2 southern Australian koala populations examined: H O = 0.49 in the BR, whereas H O = 0.41 in the SR. This is consistent with the historical accounts of bottlenecks and founder events affecting the southern populations and contrasts with reports of high genetic diversity in some southern populations. The 2 southern Australian koala populations were genetically similar (F ST = 0.018, P = 0.052). By contrast, northern and southern Australian koalas were highly differentiated (F ST = 0.27, P < 0.001), thereby suggesting that geographic structuring should be considered in the conservation management of koalas. Sequencing of 648bp of the mtDNA control region in Queensland koalas found 8 distinct haplotypes, one of which had not been previously detected among koalas. Queensland koalas displayed high mitochondrial haplotype diversity (H = 0.753) and nucleotide diversity (π = 0.0072), indicating along with the microsatellite data that North American zoos have maintained high levels of genetic diversity among their Queensland koalas.
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Affiliation(s)
- Christina T Ruiz-Rodriguez
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Yasuko Ishida
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Neil D Murray
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Stephen J O'Brien
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Jennifer A M Graves
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Alex D Greenwood
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Alfred L Roca
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca).
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