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Howell LG, Mawson PR, Comizzoli P, Witt RR, Frankham R, Clulow S, O'Brien JK, Clulow J, Marinari P, Rodger JC. Modeling genetic benefits and financial costs of integrating biobanking into the conservation breeding of managed marsupials. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14010. [PMID: 36178038 DOI: 10.1111/cobi.14010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/10/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Managed breeding programs are an important tool in marsupial conservation efforts but may be costly and have adverse genetic effects in unavoidably small captive colonies. Biobanking and assisted reproductive technologies (ARTs) could help overcome these challenges, but further demonstration of their potential is required to improve uptake. We used genetic and economic models to examine whether supplementing hypothetical captive populations of dibblers (Parantechinus apicalis) and numbats (Myrmecobius fasciatus) with biobanked founder sperm through ARTs could reduce inbreeding, lower required colony sizes, and reduce program costs. We also asked practitioners of the black-footed ferret (Mustela nigripes) captive recovery program to complete a questionnaire to examine the resources and model species research pathways required to develop an optimized biobanking protocol in the black-footed ferret. We used data from this questionnaire to devise similar costed research pathways for Australian marsupials. With biobanking and assisted reproduction, inbreeding was reduced on average by between 80% and 98%, colony sizes were on average 99% smaller, and program costs were 69- to 83-fold lower. Integrating biobanking made long-standing captive genetic retention targets possible in marsupials (90% source population heterozygosity for a minimum of 100 years) within realistic cost frameworks. Lessons from the use of biobanking technology that contributed to the recovery of the black-footed ferret include the importance of adequate research funding (US$4.2 million), extensive partnerships that provide access to facilities and equipment, colony animals, appropriate research model species, and professional and technical staff required to address knowledge gaps to deliver an optimized biobanking protocol. Applied research investment of A$133 million across marsupial research pathways could deliver biobanking protocols for 15 of Australia's most at-risk marsupial species and 7 model species. The technical expertise and ex situ facilities exist to emulate the success of the black-footed ferret recovery program in threatened marsupials using these research pathways. All that is needed now for significant and cost-effective conservation gains is greater investment by policy makers in marsupial ARTs.
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Affiliation(s)
- Lachlan G Howell
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria, Australia
- FAUNA Research Alliance, Kahibah, New South Wales, Australia
| | - Peter R Mawson
- Perth Zoo, Department of Biodiversity, Conservation and Attractions, South Perth, Western Australia, Australia
| | - Pierre Comizzoli
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, D.C., USA
| | - Ryan R Witt
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
- FAUNA Research Alliance, Kahibah, New South Wales, Australia
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
- Australian Museum, Sydney, New South Wales, Australia
| | - Simon Clulow
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Justine K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society, Mosman, New South Wales, Australia
| | - John Clulow
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
- FAUNA Research Alliance, Kahibah, New South Wales, Australia
| | - Paul Marinari
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, Virginia, USA
| | - John C Rodger
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
- FAUNA Research Alliance, Kahibah, New South Wales, Australia
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2
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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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Blanchard AM, Emes RD, Greenwood AD, Holmes N, Loose MW, McEwen GK, Meers J, Speight N, Tarlinton RE. Genome Reference Assembly for Bottlenecked Southern Australian Koalas. Genome Biol Evol 2022; 15:6948355. [PMID: 36542479 PMCID: PMC9887267 DOI: 10.1093/gbe/evac176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Koala populations show marked differences in inbreeding levels and in the presence or absence of the endogenous Koala retrovirus (KoRV). These genetic differences among populations may lead to severe disease impacts threatening koala population viability. In addition, the recent colonization of the koala genome by KoRV provides a unique opportunity to study the process of retroviral adaptation to vertebrate genomes and the impact this has on speciation, genome structure, and function. The genome build described here is from an animal from the bottlenecked Southern population free of endogenous and exogenous KoRV. It provides a more contiguous genome build than the previous koala reference derived from an animal from a more outbred Northern population and is the first koala genome from a KoRV polymerase-free animal.
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Affiliation(s)
| | - Richard David Emes
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | | | - Nadine Holmes
- School of Life Sciences, University of Nottingham, United Kingdom
| | | | | | - Joanne Meers
- School of Veterinary Science, University of Queensland, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, University of Adelaide, Australia
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4
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Cristescu RH, Strickland K, Schultz AJ, Kruuk LEB, de Villiers D, Frère CH. Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression. Mol Ecol 2022; 31:5455-5467. [PMID: 36043238 PMCID: PMC9826501 DOI: 10.1111/mec.16676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/11/2023]
Abstract
The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and, to date, we know little about the determinants of individual susceptibility to disease. Here, we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95% CI: 0.06-0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population.
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Affiliation(s)
- Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Kasha Strickland
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Anthony J. Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia,Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Loeske E. B. Kruuk
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK,Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | | | - Céline H. Frère
- School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
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Cooley M, Whiteley P, Thornton G, Stevenson M. Health surveillance representative of koala (Phascolarctos cinereus) distribution in Victoria, Australia. Aust Vet J 2022; 100:605-612. [PMID: 36261878 PMCID: PMC10092863 DOI: 10.1111/avj.13208] [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: 05/11/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/28/2022]
Abstract
Health surveillance of wildlife populations is essential for conservation and reduction of the impacts of disease. Population declines and areas of overabundance of koalas (Phascolarctos cinereus) can disrupt the overall survival of the species as well as its habitat. This retrospective study was conducted to describe population distributions, identify areas which need increased surveillance and improve koala health surveillance methodology by Wildlife Health Victoria: Surveillance (WHV:S) at the Veterinary School of The University of Melbourne. Twelve years of Victorian koala observation data from the Atlas of Living Australia combined with surveillance data from WHV:S were used to create choropleth maps, using Quantum Geographic Information Systems of populations and surveillance events, visually representing hot spots. This data was further used to calculate health surveillance efforts between 2008 to the beginning of 2020. Analysis ranked postcodes throughout Victoria from low surveillance efforts to high, using standardised surveillance ratio's 95% confidence interval upper limits which were mapped using a colour gradient. This identified postcodes which need increased surveillance effort, corresponding to areas with high koala observations and low surveillance submissions. This analysis can guide surveillance for postcodes with koalas that were under-represented and inform improved methodology of future surveillance by WHV:S. The specific advice for improvements to WHV:S includes utilisation of citizen science and syndromic surveillance, website improvement, increasing community awareness and more. The limitations of this study were discussed.
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Affiliation(s)
- M Cooley
- School of Veterinary Medicine, Royal Veterinary College, Hatfield, Hertfordshire, AL9 7TA, UK
| | - P Whiteley
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - G Thornton
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - M Stevenson
- Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, 3010, Australia
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Howell LG, Johnston SD, O’Brien JK, Frankham R, Rodger JC, Ryan SA, Beranek CT, Clulow J, Hudson DS, Witt RR. Modelling Genetic Benefits and Financial Costs of Integrating Biobanking into the Captive Management of Koalas. Animals (Basel) 2022; 12:ani12080990. [PMID: 35454237 PMCID: PMC9028793 DOI: 10.3390/ani12080990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Managed wildlife breeding faces high costs and genetic diversity challenges associated with caring for small populations. Biobanking (freezing of sex cells and tissues for use in assisted breeding) and associated reproductive technologies could help alleviate these issues in koala captive management by enhancing retention of genetic diversity in captive-bred animals and lowering program costs through reductions in the size of the required live captive colonies. Australia’s zoos and wildlife hospitals provide rare opportunities to refine and cost-effectively integrate these tools into conservation outcomes for koalas due to extensive already-existing infrastructure, technical expertise, and captive animals. Abstract Zoo and wildlife hospital networks are set to become a vital component of Australia’s contemporary efforts to conserve the iconic and imperiled koala (Phascolarctos cinereus). Managed breeding programs held across zoo-based networks typically face high economic costs and can be at risk of adverse genetic effects typical of unavoidably small captive colonies. Emerging evidence suggests that biobanking and associated assisted reproductive technologies could address these economic and genetic challenges. We present a modelled scenario, supported by detailed costings, where these technologies are optimized and could be integrated into conservation breeding programs of koalas across the established zoo and wildlife hospital network. Genetic and economic modelling comparing closed captive koala populations suggest that supplementing them with cryopreserved founder sperm using artificial insemination or intracytoplasmic sperm injection could substantially reduce inbreeding, lower the required colony sizes of conservation breeding programs, and greatly reduce program costs. Ambitious genetic retention targets (maintaining 90%, 95% and 99% of source population heterozygosity for 100 years) could be possible within realistic cost frameworks, with output koalas suited for wild release. Integrating biobanking into the zoo and wildlife hospital network presents a cost-effective and financially feasible model for the uptake of these tools due to the technical and research expertise, captive koala colonies, and ex situ facilities that already exist across these networks.
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Affiliation(s)
- Lachlan G. Howell
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University Geelong, Melbourne Burwood Campus, 221 Burwood Highway, Burwood, VIC 3125, Australia
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
- Correspondence: (L.G.H.); (R.R.W.)
| | - Stephen D. Johnston
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia;
| | - Justine K. O’Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society, Bradleys Head Rd., Mosman, NSW 2088, Australia;
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia;
| | - John C. Rodger
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
| | - Shelby A. Ryan
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
| | - Chad T. Beranek
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
| | - John Clulow
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
| | - Donald S. Hudson
- Port Stephens Koala & Wildlife Preservation Society LTD., t/a Port Stephens Koala Hospital, One Mile, NSW 2316, Australia;
| | - Ryan R. Witt
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
- Correspondence: (L.G.H.); (R.R.W.)
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7
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Schultz AJ, Strickland K, Cristescu RH, Hanger J, de Villiers D, Frère CH. Testing the effectiveness of genetic monitoring using genetic non-invasive sampling. Ecol Evol 2022; 12:e8459. [PMID: 35127011 PMCID: PMC8794716 DOI: 10.1002/ece3.8459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/26/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023] Open
Abstract
Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.
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Affiliation(s)
- Anthony James Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Kasha Strickland
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Department of Aquaculture and Fish BiologyHólar UniversityHólarIceland
| | - Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
| | | | | | - Céline H. Frère
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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TESTIS ABNORMALITIES IN A POPULATION OF SOUTH AUSTRALIAN KOALAS (PHASCOLARCTOS CINEREUS). J Wildl Dis 2021; 58:158-167. [PMID: 34797903 DOI: 10.7589/jwd-d-21-00055] [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: 04/09/2021] [Accepted: 08/20/2021] [Indexed: 11/20/2022]
Abstract
Testis asymmetry, in which the testes in an individual differ in size, has recently been reported in koalas (Phascolarctos cinereus) in the Mount Lofty Ranges population of South Australia. We describe the morphology and histology of both testes from affected individuals in this population (n=56) and the parameters of koalas with normal-sized testes based on age and breeding season (n=56). Morphologic measurements included testis weight, length, width, and volume; histologic parameters included seminiferous tubule diameter, seminiferous epithelial height, and seminiferous tubule (interstitial tissue ratio and presence or absence of spermatozoa). Of the 56 koalas with intraindividual variation in testes size, 47 were classified as asymmetric and nine as microtestes. For koalas with asymmetric testes, all morphologic parameters were significantly decreased in the smaller testes compared with normal-sized testes, but for the histologic parameters, only seminiferous tubule diameter was significantly less. Histopathologic examination of the asymmetric testes showed 38 with normal parenchyma histologically indistinguishable between intraindividual testes, four with degeneration and atrophy, and three with hypoplasia, whereas examination of microtestes showed degeneration and atrophy in seven, hypoplasia in one, and aplasia in one. No association of testis size difference with Chlamydia pecorum infection was found in a subset of animals. For the 56 koalas with normal-sized testes, morphologic parameters were found to increase with age, and juvenile and young adults were found to have smaller seminiferous tubule diameters than adults. No differences were found between testes of koalas in the breeding and nonbreeding season. Overall, these findings indicate that testis asymmetry in koalas from the Mount Lofty Ranges population is common but not associated with decreased function, except where testis malformations such as hypoplasia or aplasia occur or when parenchyma has been disrupted by acquired disease.
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Tarlinton RE, Fabijan J, Hemmatzadeh F, Meers J, Owen H, Sarker N, Seddon JM, Simmons G, Speight N, Trott DJ, Woolford L, Emes RD. Transcriptomic and genomic variants between koala populations reveals underlying genetic components to disorders in a bottlenecked population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01340-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractHistorical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.
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10
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Schultz AJ, Cristescu RH, Hanger J, Loader J, de Villiers D, Frère CH. Inbreeding and disease avoidance in a free-ranging koala population. Mol Ecol 2020; 29:2416-2430. [PMID: 32470998 DOI: 10.1111/mec.15488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 05/11/2020] [Indexed: 11/30/2022]
Abstract
Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex-biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free-ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether free-ranging female koalas avoid mating with (a) more closely related males; and (b) males infected with sexually transmitted Chlamydia pecorum. We found no evidence that female koalas avoid mating with relatively more related available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas can avoid mating with males infected with C. pecorum. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.
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Affiliation(s)
- Anthony J Schultz
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Romane H Cristescu
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Jon Hanger
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, QLD, Australia
| | - Jo Loader
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, QLD, Australia
| | | | - Celine H Frère
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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11
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Major RE, Ewart KM, Portelli DJ, King A, Tsang LR, O’Dwyer T, Carlile N, Haselden C, Bower H, Alquezar‐Planas DE, Johnson RN, Eldridge MDB. Islands within islands: genetic structuring at small spatial scales has implications for long‐term persistence of a threatened species. Anim Conserv 2020. [DOI: 10.1111/acv.12603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. E. Major
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
| | - K. M. Ewart
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
| | - D. J. Portelli
- Department of Environment and Natural Resources Alice Springs NT Australia
| | - A. King
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
| | - L. R. Tsang
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
| | - T. O’Dwyer
- NSW Department of Planning, Industry and Environment Hurstville NSW Australia
| | - N. Carlile
- NSW Department of Planning, Industry and Environment Hurstville NSW Australia
| | - C. Haselden
- Lord Howe Island Board Lord Howe Island NSW Australia
| | - H. Bower
- Lord Howe Island Board Lord Howe Island NSW Australia
| | | | - R. N. Johnson
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
| | - M. D. B. Eldridge
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
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12
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Whisson DA, Ashman KR. When an iconic native animal is overabundant: The koala in southern Australia. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Desley A. Whisson
- Deakin University, Geelong, AustraliaSchool of Life and Environmental Sciences, 221 Burwood Highway Burwood Victoria Australia
| | - Kita R. Ashman
- Deakin University, Geelong, AustraliaSchool of Life and Environmental Sciences, 221 Burwood Highway Burwood Victoria Australia
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13
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Integrating measures of long-distance dispersal into vertebrate conservation planning: scaling relationships and parentage-based dispersal analysis in the koala. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01203-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Brandies PA, Grueber CE, Ivy JA, Hogg CJ, Belov K. Disentangling the mechanisms of mate choice in a captive koala population. PeerJ 2018; 6:e5438. [PMID: 30155356 PMCID: PMC6108315 DOI: 10.7717/peerj.5438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/23/2018] [Indexed: 11/29/2022] Open
Abstract
Successful captive breeding programs are crucial to the long-term survival of many threatened species. However, pair incompatibility (breeding failure) limits sustainability of many captive populations. Understanding whether the drivers of this incompatibility are behavioral, genetic, or a combination of both, is crucial to improving breeding programs. We used 28 years of pairing data from the San Diego Zoo koala colony, plus genetic analyses using both major histocompatibility complex (MHC)-linked and non-MHC-linked microsatellite markers, to show that both genetic and non-genetic factors can influence mating success. Male age was reconfirmed to be a contributing factor to the likelihood of a koala pair copulating. This trend could also be related to a pair's age difference, which was highly correlated with male age in our dataset. Familiarity was reconfirmed to increase the probability of a successful copulation. Our data provided evidence that females select mates based on MHC and genome-wide similarity. Male heterozygosity at MHC class II loci was associated with both pre- and post-copulatory female choice. Genome-wide similarity, and similarity at the MHC class II DAB locus, were also associated with female choice at the post-copulatory level. Finally, certain MHC-linked alleles were associated with either increased or decreased mating success. We predict that utilizing a variety of behavioral and MHC-dependent mate choice mechanisms improves female fitness through increased reproductive success. This study highlights the complexity of mate choice mechanisms in a species, and the importance of ascertaining mate choice mechanisms to improve the success of captive breeding programs.
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Affiliation(s)
- Parice A. Brandies
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- San Diego Zoo Global, San Diego, CA, USA
| | | | - Carolyn J. Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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15
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Johnson RN, O'Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O'Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AYY, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Graves JAM, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K. Adaptation and conservation insights from the koala genome. Nat Genet 2018; 50:1102-1111. [PMID: 29967444 PMCID: PMC6197426 DOI: 10.1038/s41588-018-0153-5] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/30/2018] [Indexed: 11/16/2022]
Abstract
The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.
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Affiliation(s)
- Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
| | - Denis O'Meally
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Zhiliang Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | | | - Simon Y W Ho
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Will J Nash
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- San Diego Zoo Global, San Diego, CA, USA
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- UQ Genomics Initiative, University of Queensland, St Lucia, Queensland, Australia
| | - Camilla M Whittington
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Siobhan Dennison
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | | | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Don Colgan
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Tonia L Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Kensington, New South Wales, Australia
| | | | - Val Attenbrow
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Sydney, New South Wales, Australia
| | - Parice A Brandies
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Amanda Yoon-Yee Chong
- Earlham Institute, Norwich Research Park, Norwich, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Norwich, UK
- Department of Biological Sciences, University of East Anglia, Norwich, UK
| | - Zachary Duda
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Greta J Frankham
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Amber K Gillett
- Australia Zoo Wildlife Hospital, Beerwah, Queensland, Australia
| | - Merran Govendir
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Japan
- Japan Monkey Centre, Inuyama, Japan
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- School of Biological Sciences, Environment Institute, Centre for Applied Conservation Science, and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew Hobbs
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Clare E Holleley
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Thomas N Heider
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Elizabeth A Jones
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew King
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Danielle Madden
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Jennifer A Marshall Graves
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
- School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Katrina M Morris
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia
| | - Adam Polkinghorne
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Marilyn B Renfree
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Charles Robin
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Ryan Salinas
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Kyriakos Tsangaras
- Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Shafagh A Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Belinda Wright
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Ramaciotti Centre for Genomics, University of New South Wales, Kensington, New South Wales, Australia
| | - Peter Timms
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
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16
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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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17
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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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18
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Isolating DNA sourced non-invasively from koala scats: a comparison of four commercial DNA stool kits. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-0994-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Phillips S. Differing mortality rates in two concurrently radio-tracked populations of koala (Phascolarctos cinereus). AUSTRALIAN MAMMALOGY 2018. [DOI: 10.1071/am16047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Radio-tracking studies enable insights into factors that contribute to koala mortality. Two radio-tracking studies investigating the impacts of disturbance events on koalas were undertaken in different areas over the same period. Both studies employed similar techniques for koala capture, processing and monitoring. In one study, none of nine koalas died during a 5-month monitoring program following their translocation into a new habitat area, while in the second study 6 of 11 koalas died over the same period during an in situ impact-monitoring study. The two populations differed morphologically and genetically: that with the higher mortality rate notable for a smaller head and neck circumference and lower genetic diversity. Differing outcomes from the two studies lend support to a hypothesis that inbreeding and the loss of genetic information may predispose some individuals and/or populations of koalas to an elevated stress response and/or increased susceptibility to disease, the expression of which may become exacerbated in the presence of ongoing disturbance or novel stressors that can include research activities. If this is the case, the endocrinology and genetic structure of free-ranging koala populations needs to be afforded greater consideration in terms of predicting a given population’s immunological response to potential isolation and/or disturbance events.
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20
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van der Geer AAE, Galis F. High incidence of cervical ribs indicates vulnerable condition in Late Pleistocene woolly rhinoceroses. PeerJ 2017; 5:e3684. [PMID: 28875067 PMCID: PMC5580387 DOI: 10.7717/peerj.3684] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 07/22/2017] [Indexed: 11/20/2022] Open
Abstract
Mammals as a rule have seven cervical vertebrae, a number that remains remarkably constant. Changes of this number are associated with major congenital abnormalities (pleiotropic effects) that are, at least in humans, strongly selected against. Recently, it was found that Late Pleistocene mammoths (Mammuthus primigenius) from the North Sea have an unusually high incidence of abnormal cervical vertebral numbers, approximately ten times higher than that of extant elephants. Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, indicating a homeotic change from a cervical rib-less vertebra into a thoracic rib-bearing vertebra. The high incidence of cervical ribs indicates a vulnerable condition and is thought to be due to inbreeding and adverse conditions that may have impacted early pregnancies in declining populations. In this study we investigated the incidence of cervical ribs in another extinct Late Pleistocene megaherbivore from the North Sea and the Netherlands, the woolly rhinoceros (Coelodonta antiquitatis). We show that the incidence of abnormal cervical vertebral numbers in the woolly rhinoceros is unusually high for mammals (15,6%, n = 32) and much higher than in extant Rhinoceratidae (0%, n = 56). This indicates that woolly rhinoceros lived under vulnerable conditions, just like woolly mammoths. The vulnerable condition may well have contributed to their eventual extinction.
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Affiliation(s)
- Alexandra A E van der Geer
- Naturalis Biodiversity Center, Leiden, the Netherlands.,Department of Geology and Geoenvironment, National and Kapodistrian University of Athens, Zografou, Greece
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21
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Reckless HJ, Murray M, Crowther MS. A review of climatic change as a determinant of the viability of koala populations. WILDLIFE RESEARCH 2017. [DOI: 10.1071/wr16163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The koala (Phascolarctos cinereus) occupies a broad range of eastern and southern Australia, extending over tropical coastal, semiarid inland and temperate regions. In many areas koala populations are under threat, in particular from the direct and indirect effects of ongoing habitat destruction due to increased urbanisation and other anthropogenic processes. Climate change presents additional threats to the integrity of koala habitats because many species of food and non-food trees have narrow climate envelopes and are unable to adapt to altered temperatures and rainfall. Climate extremes also produce physiological stresses in koalas that may increase the likelihood of outbreaks of chlamydiosis and other diseases. Climate change–related increases in the relative content of toxic chemicals in leaves are further stresses to the koala after ingestion. In addition, populations that originated from a small number of founder individuals are at potential risk due to their relatively low genetic diversity. Strategies that maintain residual habitat fragments and promote the construction of new refugia are now being formulated. Modelling of the impact of habitat metrics on koala distribution is providing important information that can be used in the rehabilitation of koala refugia. In future these models could be augmented with metrics that describe koala homeostasis to inform local conservation strategies. These considerations are also relevant for the maintenance of other taxa in the wider ecosystem that are also at risk from habitat destruction and climate change.
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22
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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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23
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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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24
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Trask AE, Bignal EM, McCracken DI, Monaghan P, Piertney SB, Reid JM. Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern. J Anim Ecol 2016; 85:879-91. [PMID: 26996516 DOI: 10.1111/1365-2656.12503] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/15/2016] [Indexed: 11/27/2022]
Abstract
Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However, affected families had larger initial brood sizes than unaffected families. Such high fecundity of carriers of a lethal recessive allele might reflect overdominance, potentially reducing purging and increasing allele persistence probability. We thereby demonstrate the phenotypic expression of a lethal recessive allele in a wild population of conservation concern, and provide a general framework for inferring allele distribution and persistence and informing management responses.
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Affiliation(s)
- Amanda E Trask
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Eric M Bignal
- Scottish Chough Study Group, Kindrochaid, Bridgend, Isle of Islay, Argyll, PA44 7PT, UK
| | - Davy I McCracken
- Future Farming Systems, Scotland's Rural College, Auchincruive, Ayr, KA6 5HW, UK
| | - Pat Monaghan
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Stuart B Piertney
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Jane M Reid
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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25
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Adams-Hosking C, McBride MF, Baxter G, Burgman M, de Villiers D, Kavanagh R, Lawler I, Lunney D, Melzer A, Menkhorst P, Molsher R, Moore BD, Phalen D, Rhodes JR, Todd C, Whisson D, McAlpine CA. Use of expert knowledge to elicit population trends for the koala (Phascolarctos cinereus). DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12400] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Christine Adams-Hosking
- School of Geography, Planning and Environmental Management; Global Change Institute, The University of Queensland; Brisbane Qld 4072 Australia
| | - Marissa F. McBride
- School of Botany; The University of Melbourne; Melbourne Vic. 3010 Australia
- Department of Biosciences; University of Helsinki; Helsinki 00014 Finland
| | - Greg Baxter
- School of Geography Planning and Environmental Management; The University of Queensland, Landscape Ecology and Conservation Group; Brisbane Qld 4072 Australia
| | - Mark Burgman
- School of Botany, Environmental Science; The University of Melbourne; Melbourne Vic. 3010 Australia
| | - Deidre de Villiers
- Endeavour Veterinary Ecology; 1695 Pumicestone Rd Toorbul Qld 4510 Australia
| | - Rodney Kavanagh
- The Australian National University; Research School of Biology; Canberra 0200 Australia; Niche Environment and Heritage; PO Box 2443 North Parramatta NSW 2150 Australia
| | - Ivan Lawler
- Wildlife Heritage and Marine Division; Department of the Environment; Marine and Freshwater Species Conservation Section; Canberra ACT 2700 Australia
| | - Daniel Lunney
- Office of Environment and Heritage NSW; Hurstville NSW 2220 Australia
- School of Biological Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Alistair Melzer
- Koala Research Centre of Central Queensland; School of Medical and Applied Sciences; CQ University; Rockhampton Qld 4702 Australia
| | - Peter Menkhorst
- Department of Environment, Land, Water & Planning; Arthur Rylah Institute for Environmental Research; Heidelberg Vic. 3084 Australia
| | - Robyn Molsher
- Department of Environment, Water and Natural Resources; PO Box 39 Kingscote SA 5223 Australia
| | - Ben D. Moore
- Hawkesbury Institute for the Environment; Western Sydney University; Locked Bag 1797 Penrith 2751 NSW Australia
| | - David Phalen
- Faculty of Veterinary Science; University of Sydney; Sydney NSW 2006 Australia
| | - Jonathan R. Rhodes
- ARC Centre of Excellence for Environmental Decisions; The University of Queensland; Brisbane Qld 4072 Australia
| | - Charles Todd
- Department of Environment, Land, Water & Planning; Arthur Rylah Institute for Environmental Research; Heidelberg Vic. 3084 Australia
| | - Desley Whisson
- School of Life and Environmental Sciences; Faculty of Science Engineering & Built Environment; Deakin University; Burwood Vic. 3125 Australia
| | - Clive A. McAlpine
- Landscape Ecology and Conservation Group; School of Geography, Planning, and Environmental Management; The University of Queensland; Brisbane Qld 4072 Australia
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26
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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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27
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Ishida Y, McCallister C, Nikolaidis N, Tsangaras K, Helgen KM, Greenwood AD, Roca AL. Sequence variation of koala retrovirus transmembrane protein p15E among koalas from different geographic regions. Virology 2014; 475:28-36. [PMID: 25462343 DOI: 10.1016/j.virol.2014.10.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 09/04/2014] [Accepted: 10/28/2014] [Indexed: 11/30/2022]
Abstract
The koala retrovirus (KoRV), which is transitioning from an exogenous to an endogenous form, has been associated with high mortality in koalas. For other retroviruses, the envelope protein p15E has been considered a candidate for vaccine development. We therefore examined proviral sequence variation of KoRV p15E in a captive Queensland and three wild southern Australian koalas. We generated 163 sequences with intact open reading frames, which grouped into 39 distinct haplotypes. Sixteen distinct haplotypes comprising 139 of the sequences (85%) coded for the same polypeptide. Among the remaining 23 haplotypes, 22 were detected only once among the sequences, and each had 1 or 2 non-synonymous differences from the majority sequence. Several analyses suggested that p15E was under purifying selection. Important epitopes and domains were highly conserved across the p15E sequences and in previously reported exogenous KoRVs. Overall, these results support the potential use of p15E for KoRV vaccine development.
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Affiliation(s)
- Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801, USA.
| | - Chelsea McCallister
- Department of Biological Science and Center for Applied Biotechnology Studies, California State University, Fullerton, 800 North State College Blvd, Fullerton, CA 92834, USA.
| | - Nikolas Nikolaidis
- Department of Biological Science and Center for Applied Biotechnology Studies, California State University, Fullerton, 800 North State College Blvd, Fullerton, CA 92834, USA.
| | - Kyriakos Tsangaras
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany.
| | - Kristofer M Helgen
- National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 108, Washington, DC 20013, USA.
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany.
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801, USA; The Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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28
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Lau Q, Jaratlerdsiri W, Griffith JE, Gongora J, Higgins DP. MHC class II diversity of koala (Phascolarctos cinereus) populations across their range. Heredity (Edinb) 2014; 113:287-96. [PMID: 24690756 PMCID: PMC4181066 DOI: 10.1038/hdy.2014.30] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 11/04/2013] [Accepted: 02/10/2014] [Indexed: 11/08/2022] Open
Abstract
Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in the north (Queensland and New South Wales) relative to the south (Victoria), confirmed by STRUCTURE analyses and genetic differentiation using analysis of molecular variance. The higher MHCII diversity in the north relative to south could potentially be attributed to (i) significant founder effect in Victorian populations linked to historical translocation of bottlenecked koala populations and (ii) increased pathogen-driven balancing selection and/or local genetic drift in the north. Low MHCII genetic diversity in koalas from the south could reduce their potential response to disease, although the three DAB variants found in the south had substantial sequence divergence between variants. This study assessing MHCII diversity in the koala with historical translocations in some populations contributes to understanding the effects of population translocations on functional genetic diversity.
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Affiliation(s)
- Q Lau
- Faculty of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - W Jaratlerdsiri
- Faculty of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - J E Griffith
- Faculty of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - J Gongora
- Faculty of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - D P Higgins
- Faculty of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
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29
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Hobbs M, Pavasovic A, King AG, Prentis PJ, Eldridge MDB, Chen Z, Colgan DJ, Polkinghorne A, Wilkins MR, Flanagan C, Gillett A, Hanger J, Johnson RN, Timms P. A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity. BMC Genomics 2014; 15:786. [PMID: 25214207 PMCID: PMC4247155 DOI: 10.1186/1471-2164-15-786] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/03/2014] [Indexed: 11/10/2022] Open
Abstract
Background The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. Results RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. Conclusions This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-786) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 6 College Street, Sydney, NSW 2010, Australia.
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30
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Adams-Hosking C, McAlpine CA, Rhodes JR, Moss PT, Grantham HS. Prioritizing Regions to Conserve a Specialist Folivore: Considering Probability of Occurrence, Food Resources, and Climate Change. Conserv Lett 2014. [DOI: 10.1111/conl.12125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Christine Adams-Hosking
- The University of Queensland; Landscape Ecology and Conservation Group; School of Geography; Planning, and Environmental Management; Brisbane Qld 4072 Australia
- Global Change Institute; The University of Queensland; Brisbane Qld 4072 Australia
- Environmental Decisions Group; The University of Queensland; Brisbane Qld 4072 Australia
| | - Clive A. McAlpine
- The University of Queensland; Landscape Ecology and Conservation Group; School of Geography; Planning, and Environmental Management; Brisbane Qld 4072 Australia
- The University of Queensland; The Ecology Centre; Brisbane Qld 4072 Australia
- Environmental Decisions Group; The University of Queensland; Brisbane Qld 4072 Australia
| | - Jonathan R. Rhodes
- The University of Queensland; Landscape Ecology and Conservation Group; School of Geography; Planning, and Environmental Management; Brisbane Qld 4072 Australia
- The University of Queensland; The Ecology Centre; Brisbane Qld 4072 Australia
- ARC Centre of Excellence for Environmental Decisions; The University of Queensland; Brisbane Qld 4072 Australia
- Environmental Decisions Group; The University of Queensland; Brisbane Qld 4072 Australia
| | - Patrick T. Moss
- The University of Queensland; Landscape Ecology and Conservation Group; School of Geography; Planning, and Environmental Management; Brisbane Qld 4072 Australia
| | - Hedley S. Grantham
- The University of Queensland; The Ecology Centre; Brisbane Qld 4072 Australia
- Conservation International; 2011 Crystal Drive Suite 500 Arlington VA USA
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31
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Sequeira AMM, Roetman PEJ, Daniels CB, Baker AK, Bradshaw CJA. Distribution models for koalas in South Australia using citizen science-collected data. Ecol Evol 2014; 4:2103-14. [PMID: 25360252 PMCID: PMC4201425 DOI: 10.1002/ece3.1094] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/03/2014] [Accepted: 04/05/2014] [Indexed: 11/06/2022] Open
Abstract
The koala (Phascolarctos cinereus) occurs in the eucalypt forests of eastern and southern Australia and is currently threatened by habitat fragmentation, climate change, sexually transmitted diseases, and low genetic variability throughout most of its range. Using data collected during the Great Koala Count (a 1-day citizen science project in the state of South Australia), we developed generalized linear mixed-effects models to predict habitat suitability across South Australia accounting for potential errors associated with the dataset. We derived spatial environmental predictors for vegetation (based on dominant species of Eucalyptus or other vegetation), topographic water features, rain, elevation, and temperature range. We also included predictors accounting for human disturbance based on transport infrastructure (sealed and unsealed roads). We generated random pseudo-absences to account for the high prevalence bias typical of citizen-collected data. We accounted for biased sampling effort along sealed and unsealed roads by including an offset for distance to transport infrastructures. The model with the highest statistical support (wAIC c ∼ 1) included all variables except rain, which was highly correlated with elevation. The same model also explained the highest deviance (61.6%), resulted in high R (2)(m) (76.4) and R (2)(c) (81.0), and had a good performance according to Cohen's κ (0.46). Cross-validation error was low (∼ 0.1). Temperature range, elevation, and rain were the best predictors of koala occurrence. Our models predict high habitat suitability in Kangaroo Island, along the Mount Lofty Ranges, and at the tips of the Eyre, Yorke and Fleurieu Peninsulas. In the highest-density region (5576 km(2)) of the Adelaide-Mount Lofty Ranges, a density-suitability relationship predicts a population of 113,704 (95% confidence interval: 27,685-199,723; average density = 5.0-35.8 km(-2)). We demonstrate the power of citizen science data for predicting species' distributions provided that the statistical approaches applied account for some uncertainties and potential biases. A future improvement to citizen science surveys to provide better data on search effort is that smartphone apps could be activated at the start of the search. The results of our models provide preliminary ranges of habitat suitability and population size for a species for which previous data have been difficult or impossible to gather otherwise.
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Affiliation(s)
- Ana M M Sequeira
- The Environment Institute and School of Earth and Environmental Sciences, The University of Adelaide Adelaide, South Australia, 5005, Australia
| | - Philip E J Roetman
- Barbara Hardy Institute, University of South Australia GPO Box 2471, Adelaide, South Australia, 5001, Australia
| | - Christopher B Daniels
- Barbara Hardy Institute, University of South Australia GPO Box 2471, Adelaide, South Australia, 5001, Australia
| | - Andrew K Baker
- CSIRO Land and Water Private Bag No. 2, Glen Osmond, South Australia, 5064, Australia
| | - Corey J A Bradshaw
- The Environment Institute and School of Earth and Environmental Sciences, The University of Adelaide Adelaide, South Australia, 5005, Australia
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32
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Reumer JWF, Ten Broek CMA, Galis F. Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths. PeerJ 2014; 2:e318. [PMID: 24711969 PMCID: PMC3970796 DOI: 10.7717/peerj.318] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/03/2014] [Indexed: 11/26/2022] Open
Abstract
The number of cervical vertebrae in mammals is highly conserved at seven. We have shown that changes of this number are selected against due to a coupling with major congenital abnormalities (pleiotropic effects). Here we show that the incidence of abnormal cervical vertebral numbers in Late Pleistocene mammoths from the North Sea is high (33.3%) and approximately 10 times higher than that of extant elephants (3.6%). Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, which we deduced from the presence of rib articulation facets on sixth (posterior side) and seventh (anterior side) cervical vertebrae. The incidence of abnormal cervical vertebral numbers in mammoths appears to be much higher than in other mammalian species, apart from exceptional sloths, manatees and dugongs and indicates a vulnerable condition. We argue that the increased incidence of cervical ribs in mammoths is probably caused by inbreeding and adverse conditions that impact early pregnancies in declining populations close to extinction in the Late Pleistocene.
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Affiliation(s)
- Jelle W F Reumer
- Natural History Museum , Rotterdam , The Netherlands ; Faculty of Geosciences, Utrecht University , Utrecht , The Netherlands
| | - Clara M A Ten Broek
- Naturalis Biodiversity Center, Terrestrial Zoology/Geology , Leiden , The Netherlands ; University Antwerp, Evolutionary Ecology Group , Antwerp , Belgium
| | - Frietson Galis
- Naturalis Biodiversity Center, Terrestrial Zoology/Geology , Leiden , The Netherlands
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33
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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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34
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Sontakke SD, Kandukuri LR, Umapathy G, Kulashekaran KM, Venkata PO, Shivaji S, Singh L. The 34,XY1,der(13) chromosome constitution with loss of Y2 is associated with unilateral testicular hypoplasia in the endangered Indian blackbuck antelope (Antilope cervicapra). Sex Dev 2012; 6:240-6. [PMID: 22846804 DOI: 10.1159/000339898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2012] [Indexed: 11/19/2022] Open
Abstract
The present study is the first report of unilateral testicular hypoplasia in 3 of 15 (20%) Indian blackbuck antelopes (Antilope cervicapra). Interestingly, the condition was restricted to only the right testis in all cases. Cytogenetic analysis revealed chromosomal aneuploidy in the affected individuals which had a 34,XY(1),der(13) karyotype with loss of the acrocentric (autosomal) Y(2) and an aberrant chromosome 13. We further determined that the semen output and the circulating testosterone levels were markedly low in the males with hypoplastic testes as compared to fertile males.
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Affiliation(s)
- S D Sontakke
- Laboratory for the Conservation of Endangered Species Annexe I and Chromosome Diagnostics Facility, Clinical Research Facility-Medical Biotechnology Annexe II, Centre for Cellular and Molecular Biology (CSIR), Hyderabad, India
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Lee T, Zenger KR, Close RL, Phalen DN. Genetic analysis reveals a distinct and highly diverse koala (Phascolarctos cinereus) population in South Gippsland, Victoria, Australia. AUSTRALIAN MAMMALOGY 2012. [DOI: 10.1071/am10035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Population genetics can reveal otherwise hidden information involving a species’ history in a given region. Koalas were thought to have been virtually exterminated from the Australian state of Victoria during the koala fur trade of the late 1800s. Koalas in the South Gippsland region of Victoria were examined using microsatellite markers to infer population structure and gene flow and to locate a possible remnant gene pool. The results indicate that the South Gippsland koala population had higher genetic diversity (A = 5.97, HO = 0.564) than other published Victorian populations, and was genetically distinct from other koala populations examined. South Gippsland koalas, therefore, may have survived the population reductions of the koala fur trade and now represent a remnant Victorian gene pool that has been largely lost from the remainder of Victoria. This paper illustrates that historic anthropogenic impacts have had little effect on reducing the genetic diversity of a population in the South Gippsland region. However, the South Gippsland population is now subject to threats such as logging and loss of habitat from housing and agriculture expansion. Our results suggest that the South Gippsland koalas require an alternative conservation management program.
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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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Adams-Hosking C, Grantham HS, Rhodes JR, McAlpine C, Moss PT. Modelling climate-change-induced shifts in the distribution of the koala. WILDLIFE RESEARCH 2011. [DOI: 10.1071/wr10156] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
The impacts of climate change on the climate envelopes, and hence, distributions of species, are of ongoing concern for biodiversity worldwide. Knowing where climate refuge habitats will occur in the future is essential to conservation planning. The koala (Phascolarctos cinereus) is recognised by the International Union for Conservation of Nature (IUCN) as a species highly vulnerable to climate change. However, the impact of climate change on its distribution is poorly understood.
Aims
We aimed to predict the likely shifts in the climate envelope of the koala throughout its natural distribution under various climate change scenarios and identify potential future climate refugia.
Methods
To predict possible future koala climate envelopes we developed bioclimatic models using Maxent, based on a substantial database of locality records and several climate change scenarios.
Key results
The predicted current koala climate envelope was concentrated in south-east Queensland, eastern New South Wales and eastern Victoria, which generally showed congruency with their current known distribution. Under realistic projected future climate change, with the climate becoming increasingly drier and warmer, the models showed a significant progressive eastward and southward contraction in the koala’s climate envelope limit in Queensland, New South Wales and Victoria. The models also indicated novel potentially suitable climate habitat in Tasmania and south-western Australia.
Conclusions
Under a future hotter and drier climate, current koala distributions, based on their climate envelope, will likely contract eastwards and southwards to many regions where koala populations are declining due to additional threats of high human population densities and ongoing pressures from habitat loss, dog attacks and vehicle collisions. In arid and semi-arid regions such as the Mulgalands of south-western Queensland, climate change is likely to compound the impacts of habitat loss, resulting in significant contractions in the distribution of this species.
Implications
Climate change pressures will likely change priorities for allocating conservation efforts for many species. Conservation planning needs to identify areas that will provide climatically suitable habitat for a species in a changing climate. In the case of the koala, inland habitats are likely to become climatically unsuitable, increasing the need to protect and restore the more mesic habitats, which are under threat from urbanisation. National and regional koala conservation policies need to anticipate these changes and synergistic threats. Therefore, a proactive approach to conservation planning is necessary to protect the koala and other species that depend on eucalypt forests.
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Whisson DA, Carlyon K. Temporal variation in reproductive characteristics of an introduced and abundant island population of koalas. J Mammal 2010. [DOI: 10.1644/09-mamm-a-384.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Hunter ME, Auil-Gomez NE, Tucker KP, Bonde RK, Powell J, McGuire PM. Low genetic variation and evidence of limited dispersal in the regionally important Belize manatee. Anim Conserv 2010. [DOI: 10.1111/j.1469-1795.2010.00383.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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Detecting bottlenecks using BOTTLENECK 1.2.02 in wild populations: the importance of the microsatellite structure. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9949-2] [Citation(s) in RCA: 35] [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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