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Hogg CJ, Edwards RJ, Farquharson KA, Silver LW, Brandies P, Peel E, Escalona M, Jaya FR, Thavornkanlapachai R, Batley K, Bradford TM, Chang JK, Chen Z, Deshpande N, Dziminski M, Ewart KM, Griffith OW, Marin Gual L, Moon KL, Travouillon KJ, Waters P, Whittington CM, Wilkins MR, Helgen KM, Lo N, Ho SYW, Ruiz Herrera A, Paltridge R, Marshall Graves JA, Renfree M, Shapiro B, Ottewell K, Belov K. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 2024; 8:1311-1326. [PMID: 38945974 PMCID: PMC11239497 DOI: 10.1038/s41559-024-02436-2] [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: 12/08/2023] [Accepted: 05/03/2024] [Indexed: 07/02/2024]
Abstract
Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.
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Affiliation(s)
- Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
| | - Richard J Edwards
- Minderoo OceanOmics Centre at UWA, Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Katherine A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Merly Escalona
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Frederick R Jaya
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rujiporn Thavornkanlapachai
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kimberley Batley
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Tessa M Bradford
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - J King Chang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Nandan Deshpande
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Martin Dziminski
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Oliver W Griffith
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Laia Marin Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kenny J Travouillon
- Collections and Research, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Paul Waters
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Camilla M Whittington
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Aurora Ruiz Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Rachel Paltridge
- Indigenous Desert Alliance, Alice Springs, Northern Territory, Australia
| | | | - Marilyn Renfree
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
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Taylor MC, Travouillon KJ, Andrew ME, Fleming PA, Warburton NM. Keeping an ear out: size relationship of the tympanic bullae and pinnae in bandicoots and bilbies (Marsupialia: Peramelemorphia). Curr Zool 2021; 68:251-264. [PMID: 35592340 PMCID: PMC9113346 DOI: 10.1093/cz/zoab055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/05/2021] [Indexed: 11/21/2022] Open
Abstract
Bandicoots and bilbies (Order Peramelemorphia) occupy a broad range of habitats across Australia and New Guinea, from open, arid deserts to dense forests. This once diverse group has been particularly vulnerable to habitat loss and introduced eutherian predators, and numerous species extinctions and range retractions have occurred. Understanding reasons for this loss requires greater understanding of their biology. Morphology of the pinnae and tympanic bullae varies markedly among species. As hearing is important for both predator avoidance and prey location, the variability in ear morphology could reflect specialization and adaptation to specific environments, and therefore be of conservation relevance. We measured 798 museum specimens representing 29 species of Peramelemorphia. Controlling for phylogenetic relatedness and head length, pinna surface area was weakly negatively correlated with average precipitation (rainfall being our surrogate measure of vegetation productivity/complexity), and there were no environmental correlates with effective diameter (pinna width). Controlling for phylogenetic relatedness and skull length, tympanic bulla volume was negatively correlated with precipitation. Species that inhabited drier habitats, which would be open and allow sound to carry further with less obstruction, had relatively larger pinnae and tympanic bullae. In contrast, species from higher rainfall habitats, where sounds would be attenuated and diffused by dense vegetation, had the smallest pinnae and bullae, suggesting that low-frequency hearing is not as important in these habitats. Associations with temperature did not reach statistical significance. These findings highlight linkages between hearing traits and habitat that can inform conservation and management strategies for threatened species.
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Affiliation(s)
- Melissa C Taylor
- Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South St, Murdoch, WA 6150, Australia
- Collections and Research, Western Australian Museum, Welshpool, WA 6106, Australia
| | - Kenny J Travouillon
- Collections and Research, Western Australian Museum, Welshpool, WA 6106, Australia
| | - Margaret E Andrew
- Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South St, Murdoch, WA 6150, Australia
| | - Patricia A Fleming
- Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South St, Murdoch, WA 6150, Australia
| | - Natalie M Warburton
- Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South St, Murdoch, WA 6150, Australia
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Stannard HJ, Dennington K, Old JM. The external ear morphology and presence of tragi in Australian marsupials. Ecol Evol 2020; 10:9853-9866. [PMID: 33005349 PMCID: PMC7520188 DOI: 10.1002/ece3.6634] [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: 01/29/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 11/29/2022] Open
Abstract
Multiple studies have described the anatomy and function of the external ear (pinna) of bats, and other placental mammals, however, studies of marsupial pinna are largely absent. In bats, the tragus appears to be especially important for locating and capturing insect prey. In this study, we aimed to investigate the pinnae of Australian marsupials, with a focus on the presence/absence of tragi and how they may relate to diet. We investigated 23 Australian marsupial species with varying diets. The pinnae measurements (scapha width, scapha length) and tragi (where present) were measured. The interaural distance and body length were also recorded for each individual. Results indicated that all nectarivorous, carnivorous, and insectivorous species had tragi with the exception of the insectivorous striped possum (Dactylopsila trivirgata), numbat (Myrmecobius fasciatus), and nectarivorous sugar glider (Petaurus breviceps). No herbivorous or omnivorous species had tragi. Based on the findings in this study, and those conducted on placental mammals, we suggest marsupials use tragi in a similar way to placentals to locate and target insectivorous prey. The Tasmanian devil (Sarcophilus harrisii) displayed the largest interaural distance that likely aids in better localization and origin of noise associated with prey detection. In contrast, the smallest interaural distance was exhibited by a macropod. Previous studies have suggested the hearing of macropods is especially adapted to detect warnings of predators made by conspecifics. While the data in this study demonstrate a diversity in pinnae among marsupials, including presence and absence of tragi, it suggests that there is a correlation between pinna structure and diet choice among marsupials. A future study should investigate a larger number of individuals and species and include marsupials from Papua New Guinea, and Central and South America as a comparison.
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Affiliation(s)
- Hayley J. Stannard
- School of Animal and Veterinary SciencesCharles Sturt UniversityWagga WaggaNSWAustralia
| | - Kathryn Dennington
- School of Science and HealthHawkesbury CampusWestern Sydney UniversityPenrithNSWAustralia
| | - Julie M. Old
- School of Science and HealthHawkesbury CampusWestern Sydney UniversityPenrithNSWAustralia
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Cramer VA, Dziminski MA, Southgate R, Carpenter FM, Ellis RJ, van Leeuwen S. A conceptual framework for habitat use and research priorities for the greater bilby (Macrotis lagotis) in the north of Western Australia. AUSTRALIAN MAMMALOGY 2017. [DOI: 10.1071/am16009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Little is known of the area of occupancy, extent of occurrence, abundance, density or habitat use of the greater bilby (Macrotis lagotis) in the north of Western Australia. To seek broad collaborative agreement on a research agenda, the Western Australian Department of Parks and Wildlife hosted a workshop where research priorities were identified through a facilitated process. Five key areas for future research effort were identified: (1) refine survey methods, (2) improve understanding of habitat use, (3) improve understanding of the genetic structure of (meta)populations, (4) improve understanding of the threat posed by introduced predators and herbivores, and (5) improve understanding of how fire regimes affect bilby conservation. A conceptual model describing the main landscape components thought to be influencing distribution is used to reconcile existing knowledge, link research priorities for the bilby in the north of Western Australia, and guide the development of an integrated program of research. The broad nature of the priorities reflects the limited knowledge of bilbies in the north of the state; however, this research program provides an opportunity to increase knowledge to enact both species- and ecosystem-focused approaches to conservation, and potentially contributes towards the implementation of more dynamic conservation approaches for mobile species.
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