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Hogg CJ, Silver L, McLennan EA, Belov K. Koala Genome Survey: An Open Data Resource to Improve Conservation Planning. Genes (Basel) 2023; 14:genes14030546. [PMID: 36980819 PMCID: PMC10048327 DOI: 10.3390/genes14030546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.
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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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3
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Kjeldsen SR, Raadsma HW, Leigh KA, Tobey JR, Phalen D, Krockenberger A, Ellis WA, Hynes E, Higgins DP, Zenger KR. Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments. Heredity (Edinb) 2019; 122:525-544. [PMID: 30209291 PMCID: PMC6461856 DOI: 10.1038/s41437-018-0144-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/07/2018] [Accepted: 08/01/2018] [Indexed: 02/05/2023] Open
Abstract
The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHecorr=0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene flow and adapt across divergent environments as long as the required food source is available.
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Affiliation(s)
- Shannon R Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia.
| | - Herman W Raadsma
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia
| | - Kellie A Leigh
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia
- Science for Wildlife, PO Box 286, Cammeray, NSW, 2062, Australia
| | - Jennifer R Tobey
- San Diego Zoo Institute for Conservation Research, Escondido, CA, 92027, USA
| | - David Phalen
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia
| | - Andrew Krockenberger
- Centre for Tropical Biodiversity and Climate Change, Division of Research and Innovation, James Cook University, Cairns, QLD, 4878, Australia
| | - William A Ellis
- School of Agriculture and Food Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Emily Hynes
- Ecoplan Australia, PO Box 968, Torquay, VIC, 3228, Australia
| | - Damien P Higgins
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
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4
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Schultz AJ, Cristescu RH, Littleford-Colquhoun BL, Jaccoud D, Frère CH. Fresh is best: Accurate SNP genotyping from koala scats. Ecol Evol 2018; 8:3139-3151. [PMID: 29607013 PMCID: PMC5869377 DOI: 10.1002/ece3.3765] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/29/2017] [Accepted: 12/07/2017] [Indexed: 12/25/2022] Open
Abstract
Maintaining genetic diversity is a crucial component in conserving threatened species. For the iconic Australian koala, there is little genetic information on wild populations that is not either skewed by biased sampling methods (e.g., sampling effort skewed toward urban areas) or of limited usefulness due to low numbers of microsatellites used. The ability to genotype DNA extracted from koala scats using next‐generation sequencing technology will not only help resolve location sample bias but also improve the accuracy and scope of genetic analyses (e.g., neutral vs. adaptive genetic diversity, inbreeding, and effective population size). Here, we present the successful SNP genotyping (1272 SNP loci) of koala DNA extracted from scat, using a proprietary DArTseq™ protocol. We compare genotype results from two‐day‐old scat DNA and 14‐day‐old scat DNA to a blood DNA template, to test accuracy of scat genotyping. We find that DNA from fresher scat results in fewer loci with missing information than DNA from older scat; however, 14‐day‐old scat can still provide useful genetic information, depending on the research question. We also find that a subset of 209 conserved loci can accurately identify individual koalas, even from older scat samples. In addition, we find that DNA sequences identified from scat samples through the DArTseq™ process can provide genetic identification of koala diet species, bacterial and viral pathogens, and parasitic organisms.
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Affiliation(s)
- Anthony J Schultz
- GeneCology Research Centre University of the Sunshine Coast Maroochydore DC Qld Australia.,Global Change Ecology Research Centre University of the Sunshine Coast Maroochydore DC Qld Australia
| | - Romane H Cristescu
- Global Change Ecology Research Centre University of the Sunshine Coast Maroochydore DC Qld Australia
| | - Bethan L Littleford-Colquhoun
- GeneCology Research Centre University of the Sunshine Coast Maroochydore DC Qld Australia.,Global Change Ecology Research Centre University of the Sunshine Coast Maroochydore DC Qld Australia
| | - Damian Jaccoud
- Diversity Arrays Technology University of Canberra Bruce ACT Australia
| | - Céline H Frère
- Global Change Ecology Research Centre University of the Sunshine Coast Maroochydore DC Qld Australia
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5
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Wedrowicz F, Mosse J, Wright W, Hogan FE. Genetic structure and diversity of the koala population in South Gippsland, Victoria: a remnant population of high conservation significance. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1049-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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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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7
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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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8
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Dennison S, Frankham GJ, Neaves LE, Flanagan C, FitzGibbon S, Eldridge MDB, Johnson RN. Population genetics of the koala (Phascolarctos cinereus) in north-eastern New South Wales and south-eastern Queensland. AUST J ZOOL 2016. [DOI: 10.1071/zo16081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Habitat loss and fragmentation are key threats to local koala (Phascolarctos cinereus) populations. Broad-scale management is suboptimal for koalas because distribution models are not easily generalised across regions. Therefore, it is imperative that data relevant to local management bodies are available. Genetic data provides important information on gene flow and potential habitat barriers, including anthropogenic disturbances. Little genetic data are available for nationally significant koala populations in north-eastern New South Wales, despite reported declines due to urbanisation and habitat loss. In this study, we develop 14 novel microsatellite loci to investigate koala populations in north-eastern New South Wales (Port Macquarie, Coffs Harbour, Tyagarah, Ballina) and south-eastern Queensland (Coomera). All locations were significantly differentiated (FST = 0.096–0.213; FʹST = 0.282–0.582), and this pattern was not consistent with isolation by distance (R2 = 0.228, P = 0.058). Population assignment clustered the more northern populations (Ballina, Tyagarah and Coomera), suggesting contemporary gene flow among these sites. For all locations, low molecular variation among (16%) rather than within (84%) sites suggests historical connectivity. These results suggest that koala populations in north-eastern New South Wales and south-eastern Queensland are experiencing contemporary impediments to gene flow, and highlight the importance of maintaining habitat connectivity across this region.
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9
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Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0784-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Abstract
Toll-like receptors (TLRs) play a crucial role in the early defence against invading pathogens, yet our understanding of TLRs in marsupial immunity is limited. Here, we describe the characterisation of nine TLRs from a koala immune tissue transcriptome and one TLR from a draft sequence of the koala genome and the subsequent development of an assay to study genetic diversity in these genes. We surveyed genetic diversity in 20 koalas from New South Wales, Australia and showed that one gene, TLR10 is monomorphic, while the other nine TLR genes have between two and 12 alleles. 40 SNPs (16 non-synonymous) were identified across the ten TLR genes. These markers provide a springboard to future studies on innate immunity in the koala, a species under threat from two major infectious diseases.
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11
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Seddon JM, Lee KE, Johnston SD, Nicolson VN, Pyne M, Carrick FN, Ellis WAH. Testing the regional genetic representativeness of captive koala populations in South-East Queensland. WILDLIFE RESEARCH 2014. [DOI: 10.1071/wr13103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Context Captive breeding for release back to the wild is an important component of ex situ conservation but requires genetic diversity that is representative of the wild population and has the ultimate goal of producing ecologically sustainable and resilient populations. However, defining and testing for representativeness of captive populations is difficult. Koalas (Phascolarctos cinereus) are bred for educational and tourism purposes in zoos and wildlife parks in South-East Queensland, but there are drastic declines evident in some wild koala populations in this region. Aim We compared genetic diversity at microsatellite loci and mitochondrial DNA in two captive koala populations with that of the local, wild koalas of South-East Queensland, determining the degree to which genetic diversity of neutral loci had been preserved and was represented in the captive populations. Key results The expected heterozygosity and the allelic richness was significantly greater in one captive colony than one wild South-East Queensland population. There was low but significant differentiation of the captive from wild populations using FST, with greater differentiation described by Jost’s Dest. In contrast, a newly introduced Kullback–Leibler divergence measure, which assesses similarity of allele frequencies, showed no significant divergence of colony and wild populations. The captive koalas lacked many of the mitochondrial haplotypes identified from South-East Queensland koalas and possessed seven other haplotypes. Conclusions Captive colonies of koalas have maintained levels of overall neutral genetic diversity similar to wild populations at microsatellite loci and low but significant differentiation likely resulted from drift and founder effects in small captive colonies or declining wild populations. Mitochondrial DNA suggests that captive founders were from a wider geographic source or that haplotypes have been lost locally. Implications Overall, tested captive koalas maintain sufficient microsatellite diversity to act as an in situ reservoir for neutral genetic diversity of regional populations.
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12
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Wedrowicz F, Karsa M, Mosse J, Hogan FE. Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet. Mol Ecol Resour 2013; 13:634-41. [PMID: 23582171 DOI: 10.1111/1755-0998.12101] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 02/24/2013] [Accepted: 02/28/2013] [Indexed: 11/30/2022]
Abstract
The koala, an Australian icon, has been added to the threatened species list. Rationale for the listing includes proposed declines in population size, threats to populations (e.g. disease) and loss and fragmentation of habitat. There is now an urgent need to obtain accurate data to assess the status of koala populations in Australia, to ensure the long-term viability of this species. Advances in genetic techniques have enabled DNA analysis to study and inform the management of wild populations; however, sampling of individual koalas is difficult in tall, often remote, eucalypt forest. The collection of faecal pellets (scats) from the forest floor presents an opportunistic sampling strategy, where DNA can be collected without capturing or even sighting an individual. Obtaining DNA via noninvasive sampling can be used to rapidly sample a large proportion of a population; however, DNA from noninvasively collected samples is often degraded. Factors influencing DNA quality and quantity include environmental exposure, diet and methods of sample collection, storage and DNA isolation. Reduced DNA quality and quantity can introduce genotyping errors and provide inaccurate DNA profiles, reducing confidence in the ability of such data to inform management/conservation strategies. Here, we present a protocol that produces a reliable individual koala genotype from a single faecal pellet and highlight the importance of optimizing DNA isolation and analysis for the species of interest. This method could readily be adapted for genetic studies of mammals other than koalas, particularly those whose diet contains high proportions of volatile materials that are likely to induce DNA damage.
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Affiliation(s)
- Faye Wedrowicz
- School of Applied Sciences and Engineering, Monash University Gippsland Campus, Northways Road, Churchill, Victoria, Australia
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Tsangaras K, Ávila-Arcos MC, Ishida Y, Helgen KM, Roca AL, Greenwood AD. Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus). BMC Genet 2012; 13:92. [PMID: 23095716 PMCID: PMC3518249 DOI: 10.1186/1471-2156-13-92] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 09/27/2012] [Indexed: 02/04/2023] Open
Abstract
Background The koala (Phascolarctos cinereus) is an arboreal marsupial that was historically widespread across eastern Australia until the end of the 19th century when it suffered a steep population decline. Hunting for the fur trade, habitat conversion, and disease contributed to a precipitous reduction in koala population size during the late 1800s and early 1900s. To examine the effects of these reductions in population size on koala genetic diversity, we sequenced part of the hypervariable region of mitochondrial DNA (mtDNA) in koala museum specimens collected in the 19th and 20th centuries, hypothesizing that the historical samples would exhibit greater genetic diversity. Results The mtDNA haplotypes present in historical museum samples were identical to haplotypes found in modern koala populations, and no novel haplotypes were detected. Rarefaction analyses suggested that the mtDNA genetic diversity present in the museum samples was similar to that of modern koalas. Conclusions Low mtDNA diversity may have been present in koala populations prior to recent population declines. When considering management strategies, low genetic diversity of the mtDNA hypervariable region may not indicate recent inbreeding or founder events but may reflect an older historical pattern for koalas.
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LEE KRISTENE, ELLIS WILLIAMAH, CARRICK FRANKN, CORLEY SEANW, JOHNSTON STEPHEND, BAVERSTOCK PETERR, NOCK CATHERINEJ, ROWE KEVINC, SEDDON JENNIFERM. Anthropogenic changes to the landscape resulted in colonization of koalas in north-east New South Wales, Australia. AUSTRAL ECOL 2012. [DOI: 10.1111/j.1442-9993.2012.02414.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lee KE, Seddon JM, Johnston S, FitzGibbon SI, Carrick F, Melzer A, Bercovitch F, Ellis W. Genetic diversity in natural and introduced island populations of koalas in Queensland. AUST J ZOOL 2012. [DOI: 10.1071/zo12075] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Island populations of animals are expected to show reduced genetic variation and increased incidence of inbreeding because of founder effects and the susceptibility of small populations to the effects of genetic drift. Koalas (Phascolarctos cinereus) occur naturally in a patchy distribution across much of the eastern Australian mainland and on a small number of islands near the Australian coast. We compared the genetic diversity of the naturally occurring population of koalas on North Stradbroke Island in south-east Queensland with other island populations including the introduced group on St Bees Island in central Queensland. The population on St Bees Island shows higher diversity (allelic richness 4.1, He = 0.67) than the North Stradbroke Island population (allelic richness 3.2, He = 0.55). Koalas on Brampton, Newry and Rabbit Islands possessed microsatellite alleles that were not identified from St Bees Island koalas, indicating that it is most unlikely that these populations were established by a sole secondary introduction from St Bees Island. Mitochondrial haplotypes on the central Queensland islands were more similar to a haplotype found at Springsure in central Queensland and the inland clades in south-east Queensland, rather than the coastal clade in south-east Queensland.
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Lee T, Zenger KR, Close RL, Jones M, Phalen DN. Defining spatial genetic structure and management units for vulnerable koala (Phascolarctos cinereus) populations in the Sydney region, Australia. WILDLIFE RESEARCH 2010. [DOI: 10.1071/wr09134] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context. Mammal populations around the world are increasingly threatened with population fragmentation because of loss of habitat or barriers to gene flow. The investigation of koala populations in the Sydney region not only provides valuable information about this vulnerable species, but also serves as a model for other species that have suffered major rapid declines in population size, and are now recovering in fragmented habitat. The peri-urban study region allows investigation of the impact of landscape features such as major roads and housing developments on koala gene flow. Aims. Animals originating from four geographic sampling areas around Sydney, New South Wales, Australia, were examined to determine population structure and gene flow and to identify barriers to gene flow and management units. Methods. The present study examined 12 microsatellite loci and used Bayesian assignment methods and genic frequency analysis methods to identify demographically separate populations and barriers to gene flow between those populations. Key results. Three discrete populations were resolved, with all displaying moderate to high levels of genetic differentiation among them (θ = 0.141–0.224). The allelic richness and heterozygosity of the Blue Mountains population (A = 6.46, HO = 0.66) is comparable to the highest diversity found in any koala population previously investigated. However, considerably lower genetic diversity was found in the Campbelltown population (A = 3.17, HO = 0.49), which also displayed evidence of a recent population bottleneck (effective population size estimated at 16–21). Conclusions. Animals separated by a military reserve were identified as one population, suggesting that the reserve maintains gene flow within this population. By contrast, strong differentiation of two geographically close populations separated by several potential barriers to gene flow suggested these land-use features pose barriers to gene flow. Implications. Implications of these findings for management of koala populations in the Greater Sydney region are discussed. In particular, the need to carefully consider the future of a military reserve is highlighted, along with possible solutions to allow gene flow across the proposed barrier regions. Because these are demographically separate populations, specific management plans tailored to the needs of each population will need to be formulated.
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Genetic variation and structuring in the threatened koala populations of Southeast Queensland. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9987-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wang XM, Cao LR, Liu ZS, Fang SG. Mitochondrial DNA variation and matrilineal structure in blue sheep populations of Helan Mountain, China. CAN J ZOOL 2006. [DOI: 10.1139/z06-137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondrial DNA (mtDNA) control region (5′ hypervariable region, 554 bp) sequences from 71 samples of blue sheep ( Pseudois nayaur Hodgson, 1833) collected from six study localities throughout Helan Mountain Nature Reserve in Ningxia province of China were investigated to analyse distribution patterns of genetic variability, elucidate matrilineal structure, and investigate population history. Haplotype diversity (h) among the 71 samples was estimated to be 0.792 ± 0.037, and nucleotide diversity (Π) was relatively low (0.00392 ± 0.00046). A χ2contingency analysis of all mtDNA haplotype frequencies revealed that these haplotypes were distributed in a nonrandom fashion among study localities (χ2= 86.205, P = 0.092). Additional evidence of matrilineal structure was provided by the finding that a significant amount (9.02%; P < 0.01) of mtDNA variation was partitioned among different localities in the study area. We conclude that blue sheep of Helan Mountain Nature Reserve are structured spatially along matrilines. Pairwise computations of Φstand an AMOVA indicated that some sampling localities are differentiated relative to a random collection of genotypes and reflected differences in the spatial distribution of genetic variation. Isolation-by-distance (IBD) models (Mantel tests) revealed no obvious association between genetic differentiation and geographical distance. These results could be a basis for the development of suitable management strategies for conservation purposes. This work represents the first analysis of blue sheep mitochondrial control region DNA to be performed from a population genetics perspective.
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Affiliation(s)
- Xiao-Ming Wang
- School of Life Science, East China Normal University, 3663 Zhongshan Road N, Shanghai 200062, China
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wildlife of Ministry of Education, Zhejiang University, Hangzhou 310029, China
- The State Conservation Center for Gene Resources of Endangered Wildlife, Hangzhou 310029, China
| | - Li-Rong Cao
- School of Life Science, East China Normal University, 3663 Zhongshan Road N, Shanghai 200062, China
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wildlife of Ministry of Education, Zhejiang University, Hangzhou 310029, China
- The State Conservation Center for Gene Resources of Endangered Wildlife, Hangzhou 310029, China
| | - Zhen-Sheng Liu
- School of Life Science, East China Normal University, 3663 Zhongshan Road N, Shanghai 200062, China
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wildlife of Ministry of Education, Zhejiang University, Hangzhou 310029, China
- The State Conservation Center for Gene Resources of Endangered Wildlife, Hangzhou 310029, China
| | - Sheng-Guo Fang
- School of Life Science, East China Normal University, 3663 Zhongshan Road N, Shanghai 200062, China
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wildlife of Ministry of Education, Zhejiang University, Hangzhou 310029, China
- The State Conservation Center for Gene Resources of Endangered Wildlife, Hangzhou 310029, China
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de Moraes-Barros N, Silva JAB, Miyaki CY, Morgante JS. Comparative Phylogeography of the Atlantic Forest Endemic Sloth (Bradypus torquatus) and the Widespread Three-toed Sloth (Bradypus variegatus) (Bradypodidae, Xenarthra). Genetica 2006; 126:189-98. [PMID: 16502095 DOI: 10.1007/s10709-005-1448-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The comparative phylogeographic study of the maned sloth (Bradypus torquatus) and the three-toed sloth (Bradypus variegatus) was performed using a segment of mitochondrial DNA (mtDNA) control region. We examined 19 B. torquatus from two regions and 47 B. variegatus from three distant regions of Atlantic forest. This first characterization of molecular diversity indicates a great diversity (B. torquatus: h = 0.901 +/- 0.039 and pi = 0.012 +/- 0.007; B. variegatus: h = 0.699 +/- 0.039 and pi = 0.010 +/- 0.006) and very divergent mitochondrial lineages within each sloth species. The different sampled regions carry distinct and non-overlapping sets of mtDNA haplotypes and are genetically divergent. This phylogeographic pattern may be characteristic of sloth species. In addition, we infer that two main phylogeographic groups exist in the Atlantic forest representing a north and south distinct divergence.
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Affiliation(s)
- Nadia de Moraes-Barros
- Departamento de Genética e Biologia Evolutiva Laboratório de Biologia Evolutiva e Conservação de Vertebrados, Universidade de São Paulo, C.P. 11.461, 05422-970, São Paulo, SP, Brazil.
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Higgins DP, Hemsley S, Canfield PJ. Association of uterine and salpingeal fibrosis with chlamydial hsp60 and hsp10 antigen-specific antibodies in Chlamydia-infected koalas. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2005; 12:632-9. [PMID: 15879024 PMCID: PMC1112079 DOI: 10.1128/cdli.12.5.632-639.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Infection by Chlamydia pneumoniae or Chlamydia pecorum commonly causes chronic, fibrotic disease of the urogenital tracts of female koalas. Studies of humans have associated titers of serum immunoglobulin G (IgG) against chlamydial hsp60 and hsp10 antigens with chronic infection, salpingeal fibrosis, and tubal infertility. To determine whether a similar relationship exists in Chlamydia-infected koalas, samples were collected opportunistically from 34 wild female koalas and examined by gross pathology and histopathology, PCR, and immunohistochemistry for Chlamydia spp. and enzyme-linked immunosorbent assay for serological responses to chlamydial hsp10 and hsp60 antigens. Greater anti-hsp titers occurred in Chlamydia-infected koalas with fibrous occlusion of the uterus or uterine tube than in other Chlamydia-infected koalas (for hsp10 IgG, P = 0.005; for hsp60 IgG, P = 0.001; for hsp10 IgA, P = 0.04; for hsp60 IgA, P = 0.09). However, as in humans, some koalas with tubal occlusion had low titers. Among Chlamydia-infected koalas with tubal occlusion, those with low titers were more likely to have an active component to their ongoing uterine or salpingeal inflammation (P = 0.007), such that the assay predicted, with 79% sensitivity and 92% specificity, tubal occlusion where an active component of inflammation was absent. Findings of this study permit advancement of clinical and epidemiological studies of host-pathogen-environment interactions and pose intriguing questions regarding the significance of the Th1/Th2 paradigm and antigen-presenting and inflammation-regulating capabilities of uterine epithelial cells and the roles of latency and reactivation of chlamydial infections in pathogenesis of upper reproductive tract disease of koalas.
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Affiliation(s)
- Damien P Higgins
- Faculty of Veterinary Science, B01, University of Sydney, Sydney, NSW 2006, Australia.
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Glenn TC, Staton JL, Vu AT, Davis LM, Bremer JRA, Rhodes WE, Brisbin IL, Sawyer RH. Low mitochondrial DNA variation among American alligators and a novel non-coding region in crocodilians. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 2002; 294:312-24. [PMID: 12461811 DOI: 10.1002/jez.10206] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We analyzed 1317-1823 base pairs (bp) of mitochondrial DNA sequence beginning in the 5' end of cytochrome b (cyt b) and ending in the central domain of the control region for 25 American alligators (Alligator mississippiensis) and compared these to a homologous sequence from a Chinese alligator (A. sinensis). Both species share a non-coding spacer between cyt b and tRNA(Thr). Chinese alligator cyt b differs from that of the American alligator by 17.5% at the nucleotide level and 13.8% for inferred amino acids, which is consistent with their presumed ancient divergence. Only two cyt b haplotypes were detected among the 25 American alligators (693-1199 bp surveyed), with one haplotype shared among 24 individuals. One alligator from Mississippi differed from all other alligators by a single silent substitution. The control region contained only slightly more variation among the 25 American alligators, with two variable positions (624 bp surveyed), yielding three haplotypes with 22, two, and one individuals in each of these groups. Previous genetic studies examining allozymes and the proportion of variable microsatellite DNA loci also found low levels of genetic diversity in American alligators. However, in contrast with allozymes, microsatellites, and morphology, the mtDNA data shows no evidence of differentiation among populations from the extremes of the species range. These results suggest that American alligators underwent a severe population bottleneck in the late Pleistocene, resulting in nearly homogenous mtDNA among all American alligators today.
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Affiliation(s)
- Travis C Glenn
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA.
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