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von Takach B, Sargent H, Penton CE, Rick K, Murphy BP, Neave G, Davies HF, Hill BM, Banks SC. Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia. Heredity (Edinb) 2023; 130:278-288. [PMID: 36899176 PMCID: PMC10162988 DOI: 10.1038/s41437-023-00601-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 03/12/2023] Open
Abstract
Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.
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Affiliation(s)
- Brenton von Takach
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.,Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Holly Sargent
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Cara E Penton
- Warddeken Land Management Ltd, Darwin, NT, Australia
| | - Kate Rick
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Brett P Murphy
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Georgina Neave
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Hugh F Davies
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Brydie M Hill
- Flora and Fauna Division, Department of Environment, Parks and Water Security, Northern Territory Government, Berrimah, NT, 0831, Australia
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia.
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2
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Roycroft E, Moritz C, Rowe KC, Moussalli A, Eldridge MDB, Portela Miguez R, Piggott MP, Potter S. Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.931644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.
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Cremona T, Baker AM, Cooper SJB, Montague-Drake R, Stobo-Wilson AM, Carthew SM. Integrative taxonomic investigation of Petaurus breviceps (Marsupialia: Petauridae) reveals three distinct species. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Australian sugar glider, Petaurus breviceps s.l., is widely distributed across eastern and northern Australia. Examination of historical and contemporary collections of Petaurus specimens and phylogenetic analyses have revealed considerable taxonomic diversity within the genus. We aimed to utilize an integrative taxonomic approach, combining genetic and morphological evidence, to resolve the taxonomy of Australian gliders currently recognized as Petaurus breviceps. Herein, we confirm the existence of three distinct species: P. breviceps, P. notatus comb. nov. and P. ariel comb. nov.. Petaurus breviceps and P. notatus are each represented by major mtDNA lineages in P. breviceps, while P. ariel forms a sister-lineage to P. norfolcensis and P. gracilis. Subtle morphological differences distinguish P. breviceps from the closely related P. notatus, while the morphological distinctions between P. ariel and its genetically similar sister-taxa, P. norfolcensis and P. gracilis, are more obvious. Given the purported broad geographic distribution of the taxon, P. breviceps s.l. was not listed as threatened, but dividing this taxon into three species has important conservation implications for all taxa in the group, particularly given the lamentable record for mammal extinctions in Australia. Concerted and targeted conservation efforts are necessary to preserve these distinct, newly described species.
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Affiliation(s)
- Teigan Cremona
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Natural Environments Program, Queensland Museum, South Brisbane, QLD, Australia
| | - Steven J B Cooper
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA, Australia
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | | | - Alyson M Stobo-Wilson
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Susan M Carthew
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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Eldridge MDB, Beck RMD, Croft DA, Travouillon KJ, Fox BJ. An emerging consensus in the evolution, phylogeny, and systematics of marsupials and their fossil relatives (Metatheria). J Mammal 2019. [DOI: 10.1093/jmammal/gyz018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Robin M D Beck
- School of Environment and Life Sciences, University of Salford, Manchester, United Kingdom
| | - Darin A Croft
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Barry J Fox
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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5
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Eldridge MDB, Potter S. Taxonomy of rock-wallabies, Petrogale (Marsupialia : Macropodidae). V. A description of two new subspecies of the black-footed rock-wallaby (Petrogale lateralis). AUST J ZOOL 2019. [DOI: 10.1071/zo19063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The black-footed rock-wallaby (Petrogale lateralis) is the most widespread member of the endemic Australian macropodid genus Petrogale. Considerable morphological and genetic diversity within this species has long been recognised and P. lateralis is currently divided into three described subspecies (P. lateralis lateralis, P. l. pearsoni, P. l. hacketti) and two undescribed forms (MacDonnell Ranges race, West Kimberley race). Chromosomal, morphological, genic and genomic studies have demonstrated that these five taxa are closely related but distinguishable. Here, we formally name the MacDonnell Ranges race and the West Kimberley race as subspecies of P. lateralis.
Taxonomic registration: (LSID publication) http://zoobank.org/urn:lsid:zoobank.org:pub:71C3B7CE-CE3D-4A78-83A6-5EB50FBBA810
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Afonso Silva AC, Bragg JG, Potter S, Fernandes C, Coelho MM, Moritz C. Tropical specialist vs. climate generalist: Diversification and demographic history of sister species of
Carlia
skinks from northwestern Australia. Mol Ecol 2017; 26:4045-4058. [DOI: 10.1111/mec.14185] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 04/29/2016] [Accepted: 05/02/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Ana C. Afonso Silva
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Jason G. Bragg
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
- Royal Botanic Garden Sydney NSW Australia
| | - Sally Potter
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
| | - Carlos Fernandes
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Maria Manuela Coelho
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
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Moritz C, Fujita MK, Rosauer D, Agudo R, Bourke G, Doughty P, Palmer R, Pepper M, Potter S, Pratt R, Scott M, Tonione M, Donnellan S. Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia. Mol Ecol 2016; 25:1354-66. [DOI: 10.1111/mec.13511] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/16/2015] [Accepted: 11/24/2015] [Indexed: 11/30/2022]
Affiliation(s)
- C. Moritz
- Research School of Biology; The Australian National University; Acton ACT 2601 Australia
- Centre for Biodiversity Analysis; Acton ACT 2601 Australia
| | - M. K. Fujita
- Department of Biology; University of Texas at Arlington; Arlington TX 76019 USA
| | - D. Rosauer
- Research School of Biology; The Australian National University; Acton ACT 2601 Australia
- Centre for Biodiversity Analysis; Acton ACT 2601 Australia
| | - R. Agudo
- Research School of Biology; The Australian National University; Acton ACT 2601 Australia
- Centre for Biodiversity Analysis; Acton ACT 2601 Australia
| | - G. Bourke
- Research School of Biology; The Australian National University; Acton ACT 2601 Australia
- Centre for Biodiversity Analysis; Acton ACT 2601 Australia
| | - P. Doughty
- Western Australian Museum; Welshpool WA 6986 Australia
| | - R. Palmer
- Science & Conservation Division; Department of Parks and Wildlife; Woodvale WA 6026 Australia
| | - M. Pepper
- Research School of Biology; The Australian National University; Acton ACT 2601 Australia
- Centre for Biodiversity Analysis; Acton ACT 2601 Australia
| | - S. Potter
- Research School of Biology; The Australian National University; Acton ACT 2601 Australia
- Centre for Biodiversity Analysis; Acton ACT 2601 Australia
| | - R. Pratt
- Research School of Biology; The Australian National University; Acton ACT 2601 Australia
- Centre for Biodiversity Analysis; Acton ACT 2601 Australia
| | - M. Scott
- Research School of Biology; The Australian National University; Acton ACT 2601 Australia
- Centre for Biodiversity Analysis; Acton ACT 2601 Australia
| | - M. Tonione
- Museum of Vertebrate Zoology; University of California; Berkeley CA 94720-3102 USA
| | - S. Donnellan
- South Australian Museum; Adelaide SA 5000 Australia
- School of Biological Sciences; The University of Adelaide; Adelaide SA 5000 Australia
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Vermeulen ET, Power ML, Nipperess DA, Beveridge I, Eldridge MDB. Biodiversity of parasite assemblages in the genus Petrogale and its relation to the phylogeny and biogeography of their hosts. AUST J ZOOL 2016. [DOI: 10.1071/zo16023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Parasites form an integral part of overall biodiversity although they are often overlooked in conservation management, where emphasis is primarily directed towards the host. Parasites are often highly specialised to particular hosts, and thus may be just as threatened as the host they inhabit. For many of Australia’s wildlife species, little is known about their associated parasite communities. To begin to address this knowledge gap, we documented the parasite fauna described in the genetically diverse marsupial genus Petrogale, which contains seven species of conservation concern. The literature evaluation showed parasites of Petrogale to be highly diverse, with 17 species of protozoa, 8 species of cestodes, 102 species of nematodes and 30 species of ectoparasites identified in 16 of 17 Petrogale host species. A comparison of the parasite communities amongst Petrogale host species indicated a highly significant correlation between the parasite community similarity, and the phylogeny (P = 0.008) and biogeography (P = 0.0001) of their Petrogale hosts, suggesting high host specificity within their associated parasite assemblages. Five Petrogale species have established species recovery programs and their parasite communities should also be considered threatened, and management of parasite diversity required as part of these conservation programs.
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