1
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Silver LW, McLennan EA, Beaman J, da Silva KB, Timms P, Hogg CJ, Belov K. Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas. Immunogenetics 2024:10.1007/s00251-024-01356-6. [PMID: 39367971 DOI: 10.1007/s00251-024-01356-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 09/15/2024] [Indexed: 10/07/2024]
Abstract
Conservation genomics can greatly improve conservation outcomes of threatened populations, including those impacted by disease. Understanding diversity within immune gene families, including the major histocompatibility complex (MHC) and toll-like receptors (TLR), is important due to the role they play in disease resilience and susceptibility. With recent advancements in sequencing technologies and bioinformatic tools, the cost of generating high-quality sequence data has significantly decreased and made it possible to investigate diversity across entire gene families in large numbers of individuals compared to investigating only a few genes or a few populations previously. Here, we use the koala as a case study for investigating functional diversity across populations. We utilised previous target enrichment data and 438 whole genomes to firstly, determine the level of sequencing depth required to investigate MHC diversity and, secondly, determine the current level of diversity in MHC genes in koala populations. We determined for low complexity, conserved genes such as TLR genes 10 × sequencing depth is sufficient to reliably genotype more than 90% of variants, whereas for complex genes such as the MHC greater than 20 × and preferably 30 × sequencing depth is required. We used whole genome data to identify 270 biallelic SNPs across 24 MHC genes as well as copy number variation (CNV) within class I and class II genes and conduct supertype analysis. Overall, we have provided a bioinformatic workflow for investigating variation in a complex immune gene family from whole genome sequencing data and determined current levels of diversity within koala MHC genes.
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Affiliation(s)
- Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Elspeth A McLennan
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Julian Beaman
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, 5001, Australia
| | - Karen Burke da Silva
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, 5001, Australia
| | - Peter Timms
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Camperdown, NSW, 2006, Australia.
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Camperdown, NSW, 2006, Australia
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2
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Johnston SD, Hulse L, Keeley T, Mucci A, Seddon J, Maynard S. The Utility of the Koala Scat: A Scoping Review. BIOLOGY 2024; 13:523. [PMID: 39056716 PMCID: PMC11273466 DOI: 10.3390/biology13070523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/21/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024]
Abstract
The use of samples or scats to provide important ecological, genetic, disease and physiology details on free-range populations is gaining popularity as an alternative non-invasive methodology. Koala populations in SE Queensland and NSW have recently been listed as endangered and continue to face anthropomorphic and stochastic environmental impacts that could potentially lead to their extinction. This scoping review examines the current and potential utility of the koala scat to contribute data relevant to the assessment of koala conservation status and decision making. Although we demonstrate that there is great potential for this methodology in providing details for both individual wild animal and population biology (distribution, abundance, sex ratio, immigration/emigration, genetic diversity, evolutionary significant unit, disease epidemiology, nutrition, reproductive status and stress physiology), the calibre of this information is likely to be a function of the quality of the scat that is sampled.
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Affiliation(s)
- Stephen D. Johnston
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
| | - Lyndal Hulse
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
| | - Tamara Keeley
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
| | - Albano Mucci
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
| | - Jennifer Seddon
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
- Research Division, James Cook University, Townsville 4811, Australia
| | - Sam Maynard
- Saunders Havill Group, Bowen Hills 4006, Australia;
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3
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Hui TCY, Tang Q, Ng EYX, Chong JL, Slade EM, Rheindt FE. Small-Mammal Genomics Highlights Viaducts as Potential Dispersal Conduits for Fragmented Populations. Animals (Basel) 2024; 14:426. [PMID: 38338069 PMCID: PMC10854910 DOI: 10.3390/ani14030426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Wildlife crossings are implemented in many countries to facilitate the dispersal of animals among habitats fragmented by roads. However, the efficacy of different types of habitat corridors remains poorly understood. We used a comprehensive sampling regime in two lowland dipterocarp forest areas in peninsular Malaysia to sample pairs of small mammal individuals in three treatment types: (1) viaduct sites, at which sampling locations were separated by a highway but connected by a vegetated viaduct; (2) non-viaduct sites, at which sampling locations were separated by a highway and not connected by a viaduct; and (3) control sites, at which there was no highway fragmenting the forest. For four small mammal species, the common tree shrew Tupaia glis, Rajah's spiny rat Maxomys rajah, Whitehead's spiny rat Maxomys whiteheadi and dark-tailed tree rat Niviventer cremoriventer, we used genome-wide markers to assess genetic diversity, gene flow and genetic structure. The differences in genetic distance across sampling settings among the four species indicate that they respond differently to the presence of highways and viaducts. Viaducts connecting forests separated by highways appear to maintain higher population connectivity than forest fragments without viaducts, at least in M. whiteheadi, but apparently not in the other species.
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Affiliation(s)
- Tabitha C. Y. Hui
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Elize Y. X. Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Hobart, TAS 7005, Australia
| | - Ju Lian Chong
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Terengganu, Malaysia;
| | - Eleanor M. Slade
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
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4
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Martchenko D, Shafer ABA. Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study. Heredity (Edinb) 2023; 131:273-281. [PMID: 37532838 PMCID: PMC10539292 DOI: 10.1038/s41437-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023] Open
Abstract
Genomes capture the adaptive and demographic history of a species, but the choice of sequencing strategy and sample size can impact such inferences. We compared whole genome and reduced representation sequencing approaches to study the population demographic and adaptive signals of the North American mountain goat (Oreamnos americanus). We applied the restriction site-associated DNA sequencing (RADseq) approach to 254 individuals and whole genome resequencing (WGS) approach to 35 individuals across the species range at mid-level coverage (9X) and to 5 individuals at high coverage (30X). We used ANGSD to estimate the genotype likelihoods and estimated the effective population size (Ne), population structure, and explicitly modelled the demographic history with δaδi and MSMC2. The data sets were overall concordant in supporting a glacial induced vicariance and extremely low Ne in mountain goats. We evaluated a set of climatic variables and geographic location as predictors of genetic diversity using redundancy analysis. A moderate proportion of total variance (36% for WGS and 21% for RADseq data sets) was explained by geography and climate variables; both data sets support a large impact of drift and some degree of local adaptation. The empirical similarities of WGS and RADseq presented herein reassuringly suggest that both approaches will recover large demographic and adaptive signals in a population; however, WGS offers several advantages over RADseq, such as inferring adaptive processes and calculating runs-of-homozygosity estimates. Considering the predicted climate-induced changes in alpine environments and the genetically depauperate mountain goat, the long-term adaptive capabilities of this enigmatic species are questionable.
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Affiliation(s)
- Daria Martchenko
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
- Department of Forensics & Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
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Lane MR, Lowe A, Vukcevic J, Clark RG, Madani G, Higgins DP, Silver L, Belov K, Hogg CJ, Marsh KJ. Health Assessments of Koalas after Wildfire: A Temporal Comparison of Rehabilitated and Non-Rescued Resident Individuals. Animals (Basel) 2023; 13:2863. [PMID: 37760263 PMCID: PMC10525633 DOI: 10.3390/ani13182863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/25/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Many koalas (Phascolarctos cinereus) required rehabilitation after the 2019/20 Australian megafires. Little is known about how the post-release health of rehabilitated koalas compares to non-rescued resident koalas. We evaluated health parameters in rehabilitated koalas and resident koalas in burnt and unburnt habitat in southern New South Wales, Australia. Health checks were undertaken within six weeks of fire (rehabilitated group), 5-9 months post-fire and 12-16 months post-fire. Body condition improved significantly over time in rehabilitated koalas, with similar condition between all groups at 12-16 months. Rehabilitated koalas therefore gained body condition at similar rates to koalas who remained and survived in the wild. The prevalence of Chlamydia pecorum was also similar between groups and timepoints, suggesting wildfire and rehabilitation did not exacerbate disease in this population. While there was some variation in measured serum biochemistry and haematology parameters between groups and timepoints, most were within normal reference ranges. Our findings show that koalas were generally healthy at the time of release and when recaptured nine months later. Landscapes in the Monaro region exhibiting a mosaic of burn severity can support koalas, and rehabilitated koala health is not compromised by returning them to burnt habitats 4-6 months post-fire.
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Affiliation(s)
- Murraya R. Lane
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia;
| | - Arianne Lowe
- Stromlo Veterinary Services, P.O. Box 3963, Weston, ACT 2611, Australia;
| | | | - Robert G. Clark
- Research School of Finance, Actuarial Studies and Statistics, The Australian National University, Canberra, ACT 2601, Australia;
| | - George Madani
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia;
| | - Damien P. Higgins
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Luke Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (L.S.); (K.B.); (C.J.H.)
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (L.S.); (K.B.); (C.J.H.)
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (L.S.); (K.B.); (C.J.H.)
| | - Karen J. Marsh
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia;
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6
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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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7
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Ng EYX, Li S, Zhang D, Garg KM, Song G, Martinez J, Hung LM, Tu VT, Fuchs J, Dong L, Olsson U, Huang Y, Alström P, Rheindt FE, Lei F. Genome‐wide
SNPs
confirm plumage polymorphism and hybridisation within a
Cyornis
flycatcher species complex. ZOOL SCR 2022. [DOI: 10.1111/zsc.12568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Elize Y. X. Ng
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Discipline of Biological Science, School of Natural Sciences University of Tasmania Hobart Tasmania Australia
| | - Siqi Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences Shaanxi Normal University Xi'an China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Kritika M. Garg
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Centre for Interdisciplinary Archaeological Research Ashoka University Sonipat India
- Department of Biology Ashoka University Sonipat India
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | | | - Le Manh Hung
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle CNRS, 22 S U, EPHE, UA CP51 Paris France
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences Beijing Normal University Beijing China
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Center Göteborg Sweden
| | - Yuan Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Frank E. Rheindt
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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8
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Hohwieler KR, Villiers DL, Cristescu RH, Frere CH. Genetic erosion detected in a specialist mammal living in a fast‐developing environment. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Katrin R. Hohwieler
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | | | - Romane H. Cristescu
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | - Celine H. Frere
- School of Biological Sciences University of Queensland St Lucia QLD Australia
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9
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Lott MJ, Wright BR, Neaves LE, Frankham GJ, Dennison S, Eldridge MDB, Potter S, Alquezar-Planas DE, Hogg CJ, Belov K, Johnson RN. Future-proofing the koala: synergising genomic and environmental data for effective species management. Mol Ecol 2022; 31:3035-3055. [PMID: 35344635 DOI: 10.1111/mec.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/19/2022] [Accepted: 03/04/2022] [Indexed: 11/30/2022]
Abstract
Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250 specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial divergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (∼ 430-300 kya), a major climatic reorganization that increased the amplitude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of threatened populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g. guiding translocations), as existing management divisions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.
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Affiliation(s)
- Matthew J Lott
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Belinda R Wright
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia.,Sydney School of Veterinary Sciences, Faculty of Science, the University of Sydney, 2006, New South Wales, Australia
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,Fenner School of Environment and Society, the Australian National University, Canberra, Australian Capital Territory, 2600, Australia
| | - Greta J Frankham
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Siobhan Dennison
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Sally Potter
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,Division of Ecology & Evolution, Research School of Biology, the Australian National University, Australian Capital Territory, Canberra, 2600, Australia
| | - David E Alquezar-Planas
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,National Museum of Natural History, District of Columbia, Washington, 20560, United States
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10
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Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAustralian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.
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11
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Littleford-Colquhoun BL, Weyrich LS, Hohwieler K, Cristescu R, Frère CH. How microbiomes can help inform conservation: landscape characterisation of gut microbiota helps shed light on additional population structure in a specialist folivore. Anim Microbiome 2022; 4:12. [PMID: 35101152 PMCID: PMC8802476 DOI: 10.1186/s42523-021-00122-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progressive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite this, very little is known about the landscape variability and factors affecting koala gut microbial community dynamics. We used large scale field surveys to evaluate the variation and diversity of koala gut microbiotas and compared these diversity patterns to those detected using a population genetics approach. Scat samples were collected from five locations across South East Queensland with microbiota analysed using 16S rRNA gene amplicon sequencing. RESULTS Across the landscape koala gut microbial profiles showed large variability, with location having a large effect on bacterial community composition and bacterial diversity. Certain bacteria were found to be significantly differentially abundant amongst locations; koalas from Noosa showed a depletion in two bacterial orders (Gastranaerophilales and Bacteroidales) which have been shown to provide beneficial properties to their host. Koala gut microbial patterns were also not found to mirror population genetic patterns, a molecular tool often used to design conservation initiatives. CONCLUSIONS Our data shows that koala gut microbiotas are extremely variable across the landscape, displaying complex micro- and macro- spatial variation. By detecting locations which lack certain bacteria we identified koala populations that may be under threat from future microbial imbalance or dysbiosis. Additionally, the mismatching of gut microbiota and host population genetic patterns exposed important population structure that has previously gone undetected across South East Queensland. Overall, this baseline data highlights the importance of integrating microbiota research into conservation biology in order to guide successful conservation programs such as species translocation and the implementation of faecal inoculations.
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Affiliation(s)
- B. L. Littleford-Colquhoun
- Global Change Ecology, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556 Australia
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912 USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI 02912 USA
| | - L. S. Weyrich
- Department of Anthropology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802 USA
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - K. Hohwieler
- Global Change Ecology, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556 Australia
| | - R. Cristescu
- Global Change Ecology, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556 Australia
| | - C. H. Frère
- Global Change Ecology, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556 Australia
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12
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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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Ferrante JA, Smith CH, Thompson LM, Hunter ME. Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01402-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractGenome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.
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Dissanayake RB, Giorgi E, Stevenson M, Allavena R, Henning J. Estimating koala density from incidental koala sightings in South-East Queensland, Australia (1997-2013), using a self-exciting spatio-temporal point process model. Ecol Evol 2021; 11:13805-13814. [PMID: 34707819 PMCID: PMC8525080 DOI: 10.1002/ece3.8082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 07/15/2021] [Accepted: 08/17/2021] [Indexed: 11/26/2022] Open
Abstract
The koala, Phascolarctos cinereus, is an iconic Australian wildlife species facing a rapid decline in South-East Queensland (SEQLD). For conservation planning, the ability to estimate the size of koala populations is crucial. Systematic surveys are the most common approach to estimate koala populations but because of their cost they are often restricted to small geographic areas and are conducted infrequently. Public interest and participation in the collection of koala sighting data is increasing in popularity, but such data are generally not used for population estimation. We modeled monthly sightings of koalas reported by members of the public from 1997 to 2013 in SEQLD by developing a self-exciting spatio-temporal point process model. This allowed us to account for characteristics that are associated with koala presence (which vary over both space and time) while accounting for detection bias in the koala sighting process and addressing spatial clustering of observations. The density of koalas varied spatially due to the heterogeneous nature of koala habitat in SEQLD, with a mean density of 0.0019 koalas per km2 over the study period. The percentage of land areas with very low densities (0-0.0005 koalas per km2) remained similar throughout the study period representing, on average, 66% of the total study area. The approach described in this paper provides a useful starting point to allow greater use to be made of incidental koala sighting data. We propose that the model presented here could be used to combine systematic koala survey data (which is spatially restricted, but more precise) with koala sighting data (which is incidental and often biased by nature, but often collected over large geographical areas). Our approach could also be adopted for modeling the density of other wildlife species where data is collected in the same manner.
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Affiliation(s)
| | | | - Mark Stevenson
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVic.Australia
| | - Rachel Allavena
- School of Veterinary ScienceThe University of QueenslandGattonQldAustralia
| | - Joerg Henning
- School of Veterinary ScienceThe University of QueenslandGattonQldAustralia
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15
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Koala Retrovirus in Northern Australia Shows a Mixture of Stable Endogenization and Exogenous Lineage Diversification within Fragmented Koala Populations. J Virol 2021; 95:JVI.02084-20. [PMID: 33472936 PMCID: PMC8092702 DOI: 10.1128/jvi.02084-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The koala population in northern Australia has become increasingly fragmented due to natural and man-made barriers and interventions. This situation has created a unique opportunity to study both endogenous and exogenous koala retrovirus (KoRV). To determine the impact that population isolation has had on KoRV diversity in Queensland, 272 koalas from six fragmented koala populations were profiled for their KoRV provirus across two natural biogeographical barriers (the St Lawrence Gap and the Brisbane Valley Barrier), one man-made geographical barrier (the city of Brisbane) and two translocation events (the single movement of koalas to an island and the repeated movement of koalas into a koala sanctuary). Analysis revealed that all koalas tested were KoRV-A positive, with 90 - 96% of the detected KoRV provirus from each koala representing a single, likely endogenous, KoRV-A strain. The next most abundant proviral sequence was a defective variant of the dominant KoRV-A strain, accounting for 3 - 10% of detected provirus. The remaining KoRV provirus represented expected exogenous strains of KoRV and included geographically localized patterns of KoRV-B, -C, -D, -F, -G, and -I. These results indicate that lineage diversification of exogenous KoRV is actively ongoing. In addition, comparison of KoRV provirus within known dam-sire-joey family groups from the koala sanctuary revealed that joeys consistently had KoRV proviral patterns more similar to their dams than their sires in KoRV-B, -C and -D provirus composition. Collectively, this study highlights both the consistency of endogenous KoRV and the diversity of exogenous KoRV across the fragmented koala populations in northern Australia.IMPORTANCE KoRV infection has become a permanent part of koalas in northern Australia. With KoRV presence and abundance linked to more severe chlamydial disease and neoplasia in these koalas, understanding how KoRV exists throughout an increasingly fragmented koala population is a key first step in designing conservation and management strategies. This survey of KoRV provirus in Queensland koalas indicates that endogenous KoRV provirus is ubiquitous and consistent throughout the state while exogenous KoRV provirus is diverse and distinct in fragmented koala populations. Understanding the prevalence and impact of both endogenous and exogenous KoRV will be needed to ensure a future for all koala populations.
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16
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Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Mol Genet Genomics 2021; 296:457-471. [PMID: 33469716 DOI: 10.1007/s00438-020-01756-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.
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17
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Cros E, Ng EYX, Oh RRY, Tang Q, Benedick S, Edwards DP, Tomassi S, Irestedt M, Ericson PGP, Rheindt FE. Fine-scale barriers to connectivity across a fragmented South-East Asian landscape in six songbird species. Evol Appl 2020; 13:1026-1036. [PMID: 32431750 PMCID: PMC7232758 DOI: 10.1111/eva.12918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/10/2019] [Accepted: 12/08/2019] [Indexed: 12/28/2022] Open
Abstract
Habitat fragmentation is a major extinction driver. Despite dramatically increasing fragmentation across the globe, its specific impacts on population connectivity across species with differing life histories remain difficult to characterize, let alone quantify. Here, we investigate patterns of population connectivity in six songbird species from Singapore, a highly fragmented tropical rainforest island. Using massive panels of genome-wide single nucleotide polymorphisms across dozens of samples per species, we examined population genetic diversity, inbreeding, gene flow and connectivity among species along a spectrum of ecological specificities. We found a higher resilience to habitat fragmentation in edge-tolerant and forest-canopy species as compared to forest-dependent understorey insectivores. The latter exhibited levels of genetic diversity up to three times lower in Singapore than in populations from contiguous forest elsewhere. Using dense genomic and geographic sampling, we identified individual barriers such as reservoirs that effectively minimize gene flow in sensitive understorey birds, revealing that terrestrial forest species may exhibit levels of sensitivity to fragmentation far greater than previously expected. This study provides a blueprint for conservation genomics at small scales with a view to identifying preferred locations for habitat corridors, flagging candidate populations for restocking with translocated individuals and improving the design of future reserves.
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Affiliation(s)
- Emilie Cros
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Elize Y. X. Ng
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Rachel R. Y. Oh
- Centre for Urban Greenery and EcologyNational Parks BoardSingaporeSingapore
- School of Biological SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Qian Tang
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Suzan Benedick
- Sustainable Agriculture SchoolUniversiti Malaysia SabahSabahMalaysia
| | - David P. Edwards
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Suzanne Tomassi
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Martin Irestedt
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Per G. P. Ericson
- Department of ZoologySwedish Museum of Natural HistoryStockholmSweden
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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18
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Fabijan J, Sarker N, Speight N, Owen H, Meers J, Simmons G, Seddon J, Emes RD, Tarlinton R, Hemmatzadeh F, Woolford L, Trott DJ. Pathological Findings in Koala Retrovirus-positive Koalas (Phascolarctos cinereus) from Northern and Southern Australia. J Comp Pathol 2020; 176:50-66. [PMID: 32359636 DOI: 10.1016/j.jcpa.2020.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 01/05/2023]
Abstract
Koala retrovirus (KoRV) infection shows differences in prevalence and load between northern and southern Australian koala populations; however, the effect of this on diseases such as lymphoma and chlamydial disease is unclear. This study compared clinicopathological findings, haematology and splenic lymphoid area of KoRV-positive koalas from northern (Queensland [Qld], n = 67) and southern (South Australia [SA], n = 92) populations in order to provide further insight into KoRV pathogenesis. Blood was collected for routine haematology and for measurement of KoRV proviral load by quantitative polymerase chain reaction (qPCR). Plasma samples were assessed for KoRV viral load by reverse transcriptase qPCR and conjunctival and cloacal swabs were collected for measurement of the load of Chlamydia pecorum (qPCR). During necropsy examination, spleen was collected for lymphoid area analysis. Lymphoma was morphologically similar between the populations and occurred in koalas with the highest KoRV proviral and viral loads. Severe ocular chlamydial disease was observed in both populations, but urinary tract disease was more severe in Qld, despite similar C. pecorum loads. No associations between KoRV and chlamydial disease severity or load were observed, except in SA where viral load correlated positively with chlamydial disease severity. In both populations, proviral and viral loads correlated positively with lymphocyte and metarubricyte counts and correlated negatively with erythrocyte and neutrophil counts. Splenic lymphoid area was correlated positively with viral load. This study has shown further evidence for KoRV-induced oncogenesis and highlighted that lymphocytes and splenic lymphoid tissue may be key sites for KoRV replication. However, KoRV infection appears to be highly complex and continued investigation is required to fully understand its pathogenesis.
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Affiliation(s)
- J Fabijan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia.
| | - N Sarker
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - N Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - H Owen
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - J Meers
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - G Simmons
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - J Seddon
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - R Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - F Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - L Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - D J Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
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D’Urban Jackson J, Bruford MW, Székely T, DaCosta JM, Sorenson MD, Russo IRM, Maher KH, Cruz-López M, Galindo-Espinosa D, Palacios E, De Sucre-Medrano AE, Cavitt J, Pruner R, Morales AL, Gonzalez O, Burke T, Küpper C. Population differentiation and historical demography of the threatened snowy plover Charadrius nivosus (Cassin, 1858). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01256-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractDelineating conservation units is a complex and often controversial process that is particularly challenging for highly vagile species. Here, we reassess population genetic structure and identify those populations of highest conservation value in the threatened snowy plover (Charadrius nivosus, Cassin, 1858), a partial migrant shorebird endemic to the Americas. We use four categories of genetic data—mitochondrial DNA (mtDNA), microsatellites, Z-linked and autosomal single nucleotide polymorphisms (SNPs)—to: (1) assess subspecies delineation and examine population structure (2) compare the sensitivity of the different types of genetic data to detect spatial genetic patterns, and (3) reconstruct demographic history of the populations analysed. Delineation of two traditionally recognised subspecies was broadly supported by all data. In addition, microsatellite and SNPs but not mtDNA supported the recognition of Caribbean snowy plovers (C. n. tenuirostris) and Floridian populations (eastern C. n. nivosus) as distinct genetic lineage and deme, respectively. Low migration rates estimated from autosomal SNPs (m < 0.03) reflect a general paucity of exchange between genetic lineages. In contrast, we detected strong unidirectional migration (m = 0.26) from the western into the eastern nivosus deme. Within western nivosus, we found no genetic differentiation between coastal Pacific and inland populations. The correlation between geographic and genetic distances was weak but significant for all genetic data sets. All demes showed signatures of bottlenecks occurring during the past 1000 years. We conclude that at least four snowy plover conservation units are warranted: in addition to subspecies nivosus and occidentalis, a third unit comprises the Caribbean tenuirostris lineage and a fourth unit the distinct eastern nivosus deme.
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20
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Fabijan J, Speight N, Boardman W, Hemmatzadeh F, Trott DJ, Woolford L. Haematological reference intervals of wild southern Australian koalas (Phascolarctos cinereus). Aust Vet J 2020; 98:207-215. [PMID: 32037511 DOI: 10.1111/avj.12923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/21/2019] [Accepted: 01/06/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Current haematology reference intervals (RIs) for koalas were developed in northern Australian koalas, using low numbers and/or individuals of unknown Chlamydia pecorum and koala retrovirus (KoRV) status. This study developed haematological RIs for wild, clinically healthy southern Australian koalas of known C. pecorum and KoRV infection status and investigated the effects of population, age and sex. METHODS Haematological RIs were determined for 138 clinically healthy South Australian koalas (Mount Lofty Ranges [MLR], n = 68; Kangaroo Island, n = 70) examined in April 2016 and February 2017, respectively. C. pecorum and KoRV status were determined by PCR. RESULTS RIs for southern koala haematological parameters were established for all koalas based on the finding that there were limited differences in haematological values in koalas with subclinical C. pecorum or KoRV infections (P > 0.05), except KoRV-infected koalas had a lower haematocrit than noninfected koalas. MLR koalas had significantly lower erythrocyte mass and leucocyte counts than Kangaroo Island koalas. Young koalas had significantly lower haemoglobin, haematocrit and higher mean cellular haemoglobin concentration and lymphocyte counts than adult koalas. MLR male koalas had elevated erythrocyte, leucocyte and neutrophil counts compared with MLR females. CONCLUSION The haematological RIs developed in this study are based on a large number of clinically healthy koalas, where subclinical C. pecorum and KoRV infections had no effect on haematological values and will be a valuable tool during clinical examination and disease investigation by veterinarians and researchers Australia-wide.
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Affiliation(s)
- J Fabijan
- School of Animal and Veterinary Sciences, the University of Adelaide, Roseworthy, South Australia, Australia
| | - N Speight
- School of Animal and Veterinary Sciences, the University of Adelaide, Roseworthy, South Australia, Australia
| | - Wsj Boardman
- School of Animal and Veterinary Sciences, the University of Adelaide, Roseworthy, South Australia, Australia
| | - F Hemmatzadeh
- School of Animal and Veterinary Sciences, the University of Adelaide, Roseworthy, South Australia, Australia
| | - D J Trott
- School of Animal and Veterinary Sciences, the University of Adelaide, Roseworthy, South Australia, Australia
| | - L Woolford
- School of Animal and Veterinary Sciences, the University of Adelaide, Roseworthy, South Australia, Australia
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21
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Koala retrovirus viral load and disease burden in distinct northern and southern koala populations. Sci Rep 2020; 10:263. [PMID: 31937823 PMCID: PMC6959342 DOI: 10.1038/s41598-019-56546-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/13/2019] [Indexed: 11/09/2022] Open
Abstract
Koala retrovirus (KoRV) displays features of both an endogenous and exogenous virus and is linked to neoplasia and immunosuppression in koalas. This study explores the apparent differences in the nature and impact of KoRV infection between geographically and genetically separated "northern" and "southern" koala populations, by investigating the disease status, completeness of the KoRV genome and the proviral (DNA) and viral (RNA) loads of 71 northern and 97 southern koalas. All northern animals were positive for all KoRV genes (gag, pro-pol and env) in both DNA and RNA forms, whereas many southern animals were missing one or more KoRV genes. There was a significant relationship between the completeness of the KoRV genome and clinical status in this population. The proviral and viral loads of the northern population were significantly higher than those of the southern population (P < 0.0001), and many provirus-positive southern animals failed to express any detectable KoRV RNA. Across both populations there was a positive association between proviral load and neoplasia (P = 0.009). Potential reasons for the differences in the nature of KoRV infection between the two populations are discussed.
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23
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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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24
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Li YL, Xue DX, Zhang BD, Liu JX. Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus. Genome Biol Evol 2019; 11:1751-1764. [PMID: 31173074 PMCID: PMC6601870 DOI: 10.1093/gbe/evz118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
Understanding the patterns of genetic diversity and adaptation across species' range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small catadromous fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.
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Affiliation(s)
- Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Dong-Xiu Xue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Bai-Dong Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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25
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Petrou EL, Drinan DP, Kopperl R, Lepofsky D, Yang D, Moss ML, Hauser L. Intraspecific DNA contamination distorts subtle population structure in a marine fish: Decontamination of herring samples before restriction-site associated sequencing and its effects on population genetic statistics. Mol Ecol Resour 2019; 19:1131-1143. [PMID: 30561168 DOI: 10.1111/1755-0998.12978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 02/04/2023]
Abstract
Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (a) the efficacy of bleach decontamination, (b) the effect of decontamination on RAD genotypes and (c) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and nonspawning (uncontaminated) herring. Samples were soaked for 10 min in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction site-associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data and can impact downstream analyses.
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Affiliation(s)
- Eleni L Petrou
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington
| | - Daniel P Drinan
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington
| | - Robert Kopperl
- Willamette Cultural Resources Associates Ltd., Seattle, Washington
| | - Dana Lepofsky
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Dongya Yang
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Madonna L Moss
- Department of Anthropology, University of Oregon, Eugene, Oregon
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington
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Kjeldsen SR, Raadsma HW, Leigh KA, Tobey JR, Phalen D, Krockenberger A, Ellis WA, Hynes E, Higgins DP, Zenger KR. Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments. Heredity (Edinb) 2019; 122:525-544. [PMID: 30209291 PMCID: PMC6461856 DOI: 10.1038/s41437-018-0144-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/07/2018] [Accepted: 08/01/2018] [Indexed: 02/05/2023] Open
Abstract
The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHecorr=0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene flow and adapt across divergent environments as long as the required food source is available.
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Affiliation(s)
- Shannon R Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia.
| | - Herman W Raadsma
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia
| | - Kellie A Leigh
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia
- Science for Wildlife, PO Box 286, Cammeray, NSW, 2062, Australia
| | - Jennifer R Tobey
- San Diego Zoo Institute for Conservation Research, Escondido, CA, 92027, USA
| | - David Phalen
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia
| | - Andrew Krockenberger
- Centre for Tropical Biodiversity and Climate Change, Division of Research and Innovation, James Cook University, Cairns, QLD, 4878, Australia
| | - William A Ellis
- School of Agriculture and Food Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Emily Hynes
- Ecoplan Australia, PO Box 968, Torquay, VIC, 3228, Australia
| | - Damien P Higgins
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
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Al-Breiki RD, Kjeldsen SR, Afzal H, Al Hinai MS, Zenger KR, Jerry DR, Al-Abri MA, Delghandi M. Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline. BMC Genomics 2018; 19:690. [PMID: 30231936 PMCID: PMC6146514 DOI: 10.1186/s12864-018-5044-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. RESULTS After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. CONCLUSIONS Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.
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Affiliation(s)
- Rufaida Dhuhai Al-Breiki
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
- College of Agriculture and Marine Sciences, Department of Marine Sciences and Fisheries, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Shannon R. Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Hasifa Afzal
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Manal Saif Al Hinai
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Mohammed Ali Al-Abri
- College of Agriculture and Marine Sciences, Department of Animal and Veterinary Sciences and Technology, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Madjid Delghandi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
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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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29
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Boyle JH, Martins DJ, Pelaez J, Musili PM, Kibet S, Ndung'u SK, Kenfack D, Pierce NE. Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant-plant, Acacia ( Vachellia) drepanolobium. Ecol Evol 2018; 8:1441-1450. [PMID: 29435223 PMCID: PMC5792509 DOI: 10.1002/ece3.3752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/15/2017] [Accepted: 11/26/2017] [Indexed: 11/12/2022] Open
Abstract
The Acacia drepanolobium (also known as Vachellia drepanolobium) ant-plant symbiosis is considered a classic case of species coexistence, in which four species of tree-defending ants compete for nesting space in a single host tree species. Coexistence in this system has been explained by trade-offs in the ability of the ant associates to compete with each other for occupied trees versus the ability to colonize unoccupied trees. We seek to understand the proximal reasons for how and why the ant species vary in competitive or colonizing abilities, which are largely unknown. In this study, we use RADseq-derived SNPs to identify relatedness of workers in colonies to test the hypothesis that competitively dominant ants reach large colony sizes due to polygyny, that is, the presence of multiple egg-laying queens in a single colony. We find that variation in polygyny is not associated with competitive ability; in fact, the most dominant species, unexpectedly, showed little evidence of polygyny. We also use these markers to investigate variation in mating behavior among the ant species and find that different species vary in the number of males fathering the offspring of each colony. Finally, we show that the nature of polygyny varies between the two commonly polygynous species, Crematogaster mimosae and Tetraponera penzigi: in C. mimosae, queens in the same colony are often related, while this is not the case for T. penzigi. These results shed light on factors influencing the evolution of species coexistence in an ant-plant mutualism, as well as demonstrating the effectiveness of RADseq-derived SNPs for parentage analysis.
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Affiliation(s)
- John H. Boyle
- Department of Organismic and Evolutionary Biology, and Museum of Comparative ZoologyHarvard UniversityCambridgeMAUSA
- Department of BiologyThe College of William and MaryWilliamsburgVAUSA
| | - Dino J. Martins
- Department of Organismic and Evolutionary Biology, and Museum of Comparative ZoologyHarvard UniversityCambridgeMAUSA
- Mpala Research CentreNanyukiKenya
- Turkana Basin InstituteStony Brook UniversityStony BrookNYUSA
| | - Julianne Pelaez
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCAUSA
| | - Paul M. Musili
- East African Herbarium, Botany DepartmentNational Museums of KenyaNairobiKenya
| | - Staline Kibet
- Department of Land Resource Management and Agricultural TechnologyUniversity of NairobiNairobiKenya
| | | | - David Kenfack
- CTFS‐ForestGEOSmithsonian Tropical Research InstituteWashingtonDCUSA
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, and Museum of Comparative ZoologyHarvard UniversityCambridgeMAUSA
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30
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Bourgeois S, Senn H, Kaden J, Taggart JB, Ogden R, Jeffery KJ, Bunnefeld N, Abernethy K, McEwing R. Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant. Ecol Evol 2018; 8:2207-2217. [PMID: 29468037 PMCID: PMC5817121 DOI: 10.1002/ece3.3854] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/17/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single-nucleotide polymorphisms (SNPs) are particularly cost-effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next-generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in nonmodel species. Here, we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double-digest restriction-site-associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1,365 high-quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step-change in conservation policies for this elusive species.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs NationauxLibrevilleGabon
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Helen Senn
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - Jenny Kaden
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - John B. Taggart
- Aquaculture Pathfoot BuildingUniversity of StirlingStirlingUK
| | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies & The Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs NationauxLibrevilleGabon
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
| | - Nils Bunnefeld
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Katharine Abernethy
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
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31
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Attard CRM, Beheregaray LB, Möller LM. Genotyping‐by‐sequencing for estimating relatedness in nonmodel organisms: Avoiding the trap of precise bias. Mol Ecol Resour 2018; 18:381-390. [DOI: 10.1111/1755-0998.12739] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Catherine R. M. Attard
- Molecular Ecology Lab College of Science and Engineering Flinders University Adelaide SA Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Lab College of Science and Engineering Flinders University Adelaide SA Australia
| | - Luciana M. Möller
- Molecular Ecology Lab College of Science and Engineering Flinders University Adelaide SA Australia
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32
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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33
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A Bigger Toolbox: Biotechnology in Biodiversity Conservation. Trends Biotechnol 2017; 35:55-65. [DOI: 10.1016/j.tibtech.2016.06.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 01/08/2023]
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Shafer ABA, Peart CR, Tusso S, Maayan I, Brelsford A, Wheat CW, Wolf JBW. Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12700] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Aaron B. A. Shafer
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
- Forensic Science and Environmental & Life Sciences Trent University 2014 East Bank Dr K9J 7B8 Peterborough Canada
| | - Claire R. Peart
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
| | - Sergio Tusso
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
| | - Inbar Maayan
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
| | - Alan Brelsford
- Department of Ecology and Evolution University of Lausanne CH‐1015 Lausanne Switzerland
| | | | - Jochen B. W. Wolf
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
- Division of Evolutionary Biology Faculty of Biology Ludwig‐Maximilians University of Munich Grosshaderner Str. 2 82152 Planegg‐Martinsried Germany
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35
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Neaves LE, Frankham GJ, Dennison S, FitzGibbon S, Flannagan C, Gillett A, Hynes E, Handasyde K, Helgen KM, Tsangaras K, Greenwood AD, Eldridge MDB, Johnson RN. Phylogeography of the Koala, (Phascolarctos cinereus), and Harmonising Data to Inform Conservation. PLoS One 2016; 11:e0162207. [PMID: 27588685 PMCID: PMC5010259 DOI: 10.1371/journal.pone.0162207] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/18/2016] [Indexed: 11/18/2022] Open
Abstract
The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus), one of Australia’s most iconic species, was historically widely distributed throughout much of eastern Australia but currently represents a complex conservation challenge. To better understand the challenges to koala genetic health, we assessed the phylogeographic history of the koala. Variation in the maternally inherited mitochondrial DNA (mtDNA) Control Region (CR) was examined in 662 koalas sampled throughout their distribution. In addition, koala CR haplotypes accessioned to Genbank were evaluated and consolidated. A total of 53 unique CR haplotypes have been isolated from koalas to date (including 15 haplotypes novel to this study). The relationships among koala CR haplotypes were indicative of a single Evolutionary Significant Unit and do not support the recognition of subspecies, but were separated into four weakly differentiated lineages which correspond to three geographic clusters: a central lineage, a southern lineage and two northern lineages co-occurring north of Brisbane. The three geographic clusters were separated by known Pleistocene biogeographic barriers: the Brisbane River Valley and Clarence River Valley, although there was evidence of mixing amongst clusters. While there is evidence for historical connectivity, current koala populations exhibit greater structure, suggesting habitat fragmentation may have restricted female-mediated gene flow. Since mtDNA data informs conservation planning, we provide a summary of existing CR haplotypes, standardise nomenclature and make recommendations for future studies to harmonise existing datasets. This holistic approach is critical to ensuring management is effective and small scale local population studies can be integrated into a wider species context.
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Affiliation(s)
- Linda E. Neaves
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, United Kingdom
- * E-mail:
| | - Greta J. Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
| | - Siobhan Dennison
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
| | - Sean FitzGibbon
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Cheyne Flannagan
- Koala Hospital Port Macquarie, PO Box 236, Port Macquarie, NSW, 2444, Australia
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, Queensland, 4519, Australia
| | - Emily Hynes
- Ecoplan Australia Pty Ltd, PO Box 968 Torquay, Victoria, 3228, Australia
| | - Kathrine Handasyde
- School of BioSciences, The University of Melbourne, Victoria, 3010, Australia
| | - Kristofer M. Helgen
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Kyriakos Tsangaras
- Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, 6 International Airport Ave., 2370 Nicosia, Cyprus
| | - Alex D. Greenwood
- Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Mark D. B. Eldridge
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
| | - Rebecca N. Johnson
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales, 2010, Australia
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Ruiz-Rodriguez CT, Ishida Y, Murray ND, O'Brien SJ, Graves JAM, Greenwood AD, Roca AL. Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria. J Hered 2016; 107:573-580. [PMID: 27515769 PMCID: PMC5063317 DOI: 10.1093/jhered/esw049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/04/2016] [Indexed: 11/12/2022] Open
Abstract
The koala (Phascolarctos cinereus) suffered population declines and local extirpation due to hunting in the early 20th century, especially in southern Australia. Koalas were subsequently reintroduced to the Brisbane Ranges (BR) and Stony Rises (SR) by translocating individuals from a population on French Island descended from a small number of founders. To examine genetic diversity and north-south differentiation, we genotyped 13 microsatellite markers in 46 wild koalas from the BR and SR, and 27 Queensland koalas kept at the US zoos. The Queensland koalas displayed much higher heterozygosity (H O = 0.73) than the 2 southern Australian koala populations examined: H O = 0.49 in the BR, whereas H O = 0.41 in the SR. This is consistent with the historical accounts of bottlenecks and founder events affecting the southern populations and contrasts with reports of high genetic diversity in some southern populations. The 2 southern Australian koala populations were genetically similar (F ST = 0.018, P = 0.052). By contrast, northern and southern Australian koalas were highly differentiated (F ST = 0.27, P < 0.001), thereby suggesting that geographic structuring should be considered in the conservation management of koalas. Sequencing of 648bp of the mtDNA control region in Queensland koalas found 8 distinct haplotypes, one of which had not been previously detected among koalas. Queensland koalas displayed high mitochondrial haplotype diversity (H = 0.753) and nucleotide diversity (π = 0.0072), indicating along with the microsatellite data that North American zoos have maintained high levels of genetic diversity among their Queensland koalas.
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Affiliation(s)
- Christina T Ruiz-Rodriguez
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Yasuko Ishida
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Neil D Murray
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Stephen J O'Brien
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Jennifer A M Graves
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Alex D Greenwood
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca)
| | - Alfred L Roca
- From the Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL (Ruiz-Rodriguez, Ishida, Roca); Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia (Murray); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL (O'Brien); School of Life Sciences, La Trobe University, Melbourne Victoria, Australia (Graves); Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (Greenwood); Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany (Greenwood); and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL (Roca).
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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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