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Mijangos JL, Bino G, Hawke T, Kolomyjec SH, Kingsford RT, Sidhu H, Grant T, Day J, Dias KN, Gongora J, Sherwin WB. Fragmentation by major dams and implications for the future viability of platypus populations. Commun Biol 2022; 5:1127. [PMID: 36329312 PMCID: PMC9633709 DOI: 10.1038/s42003-022-04038-9] [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: 03/16/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (FST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; FST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, FST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.
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Affiliation(s)
- Jose L. Mijangos
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia ,grid.1039.b0000 0004 0385 7472Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Gilad Bino
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Tahneal Hawke
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Stephen H. Kolomyjec
- grid.258898.60000 0004 0462 9201College of Science and the Environment, Lake Superior State University, Sault Sainte Marie, USA
| | - Richard T. Kingsford
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Harvinder Sidhu
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia
| | - Tom Grant
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Jenna Day
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Kimberly N. Dias
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Jaime Gongora
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - William B. Sherwin
- grid.1005.40000 0004 4902 0432Evolution & Ecology Research Centre, UNSW, Sydney, Australia
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2
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Pearson RG, Connolly NM, Davis AM, Brodie JE. Fresh waters and estuaries of the Great Barrier Reef catchment: Effects and management of anthropogenic disturbance on biodiversity, ecology and connectivity. MARINE POLLUTION BULLETIN 2021; 166:112194. [PMID: 33690082 DOI: 10.1016/j.marpolbul.2021.112194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/27/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
We review the literature on the ecology, connectivity, human impacts and management of freshwater and estuarine systems in the Great Barrier Reef catchment (424,000 km2), on the Australian east coast. The catchment has high biodiversity, with substantial endemicity (e.g., lungfish). Freshwater and estuarine ecosystems are closely linked to the land and are affected by human disturbance, including climate change, flow management, land clearing, habitat damage, weed invasion, and excessive sediments, nutrients and pesticides. They require holistic integrated management of impacts, interactions, and land-sea linkages. This requirement is additional to land management aimed at reducing pollutant delivery to reef waters. Despite advances in research and management over recent decades, there are substantial deficiencies that need addressing, including understanding of physical and biological processes and impacts in ground waters, large rivers and estuaries; ecological effects of pesticides; management and mitigation for invasive species and climate change; and explicit protection of non-marine waters.
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Affiliation(s)
- Richard G Pearson
- TropWater and College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia.
| | - Niall M Connolly
- Queensland Department of Agriculture and Fisheries, Townsville, Queensland 4814, Australia.
| | - Aaron M Davis
- TropWater, James Cook University, Townsville, Queensland 4811, Australia.
| | - Jon E Brodie
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
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3
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Hardouin EA, Baltazar‐Soares M, Schilling A, Butler H, García‐Rodríguez O, Crowley E, Liang W, Meredith A, Lurz PWW, Forster J, Kenward RE, Hodder KH. Conservation of genetic uniqueness in remaining populations of red squirrels ( Sciurus vulgaris L.) in the South of England. Ecol Evol 2019; 9:6547-6558. [PMID: 31236243 PMCID: PMC6580283 DOI: 10.1002/ece3.5233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 11/21/2022] Open
Abstract
The Eurasian red squirrel (Sciurus vulgaris) is an emblematic species for conservation, and its decline in the British Isles exemplifies the impact that alien introductions can have on native ecosystems. Indeed, red squirrels in this region have declined dramatically over the last 60 years due to the spread of squirrelpox virus following the introduction of the gray squirrel (Sciurus carolinensis). Currently, red squirrel populations in Britain are fragmented and need to be closely monitored in order to assess their viability and the effectiveness of conservation efforts. The situation is even more dramatic in the South of England, where S. vulgaris survives only on islands (Brownsea Island, Furzey Island, and the Isle of Wight). Using the D-loop, we investigated the genetic diversity and putative ancestry of the squirrels from Southern England and compared them to a European dataset composed of 1,016 samples from 54 populations. We found that our three populations were more closely related to other squirrels from the British Isles than squirrels from Europe, showed low genetic diversity, and also harbored several private haplotypes. Our study demonstrates how genetically unique the Southern English populations are in comparison with squirrels from the continental European range. We report the presence of four private haplotypes, suggesting that these populations may potentially harbor distinct genetic lineages. Our results emphasize the importance of preserving these isolated red squirrel populations for the conservation of the species.
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Affiliation(s)
- Emilie A. Hardouin
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Miguel Baltazar‐Soares
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Anna‐Katarina Schilling
- Royal (Dick) School of Veterinary Sciences, Easter Bush CampusUniversity of EdinburghMidlothianUK
- Moredun Research InstitutePentlands Science ParkPenicuikUK
| | | | - Oxala García‐Rodríguez
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Eloise Crowley
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Wei‐Jun Liang
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Anna Meredith
- Royal (Dick) School of Veterinary Sciences, Easter Bush CampusUniversity of EdinburghMidlothianUK
- Faculty of Veterinary and Agricultural Sciences, Parkville CampusThe University of MelbourneMelbourneVictoriaAustralia
| | - Peter W. W. Lurz
- Royal (Dick) School of Veterinary Sciences, Easter Bush CampusUniversity of EdinburghMidlothianUK
| | - Jane Forster
- WISH Lab, Academic Unit of Cancer Sciences, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | | | - Kathy H. Hodder
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
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4
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Bino G, Kingsford RT, Archer M, Connolly JH, Day J, Dias K, Goldney D, Gongora J, Grant T, Griffiths J, Hawke T, Klamt M, Lunney D, Mijangos L, Munks S, Sherwin W, Serena M, Temple-Smith P, Thomas J, Williams G, Whittington C. The platypus: evolutionary history, biology, and an uncertain future. J Mammal 2019; 100:308-327. [PMID: 31043761 PMCID: PMC6479513 DOI: 10.1093/jmammal/gyz058] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/25/2019] [Indexed: 12/21/2022] Open
Abstract
The platypus (Ornithorhynchus anatinus) is one of the world's most evolutionarily distinct mammals, one of five extant species of egg-laying mammals, and the only living species within the family Ornithorhynchidae. Modern platypuses are endemic to eastern mainland Australia, Tasmania, and adjacent King Island, with a small introduced population on Kangaroo Island, South Australia, and are widely distributed in permanent river systems from tropical to alpine environments. Accumulating knowledge and technological advancements have provided insights into many aspects of its evolutionary history and biology but have also raised concern about significant knowledge gaps surrounding distribution, population sizes, and trends. The platypus' distribution coincides with many of Australia's major threatening processes, including highly regulated and disrupted rivers, intensive habitat destruction, and fragmentation, and they were extensively hunted for their fur until the early 20th century. Emerging evidence of local population declines and extinctions identifies that ecological thresholds have been crossed in some populations and, if threats are not addressed, the species will continue to decline. In 2016, the IUCN Red Listing for the platypus was elevated to "Near Threatened," but the platypus remains unlisted on threatened species schedules of any Australian state, apart from South Australia, or nationally. In this synthesis, we review the evolutionary history, genetics, biology, and ecology of this extraordinary mammal and highlight prevailing threats. We also outline future research directions and challenges that need to be met to help conserve the species.
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Affiliation(s)
- Gilad Bino
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard T Kingsford
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Archer
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Joanne H Connolly
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, New South Wales, Australia
| | - Jenna Day
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Kimberly Dias
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - David Goldney
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Tom Grant
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Tahneal Hawke
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa Klamt
- Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Daniel Lunney
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,Office of Environment and Heritage, Hurstville, New South Wales, Australia
| | - Luis Mijangos
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sarah Munks
- School of Biological Sciences, University of Tasmania, Tasmania, Australia.,Forest Practices Authority, Hobart, Tasmania, Australia
| | - William Sherwin
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Melody Serena
- Australian Platypus Conservancy, Wiseleigh, Victoria, Australia
| | - Peter Temple-Smith
- Department of Obstetrics and Gynaecology, Southern Clinical School, Monash University, Clayton, Victoria, Australia
| | | | - Geoff Williams
- Australian Platypus Conservancy, Wiseleigh, Victoria, Australia
| | - Camilla Whittington
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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5
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Martin HC, Batty EM, Hussin J, Westall P, Daish T, Kolomyjec S, Piazza P, Bowden R, Hawkins M, Grant T, Moritz C, Grutzner F, Gongora J, Donnelly P. Insights into Platypus Population Structure and History from Whole-Genome Sequencing. Mol Biol Evol 2018; 35:1238-1252. [PMID: 29688544 PMCID: PMC5913675 DOI: 10.1093/molbev/msy041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.
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Affiliation(s)
- Hilary C Martin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elizabeth M Batty
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Julie Hussin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Portia Westall
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Tasman Daish
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Stephen Kolomyjec
- School of Biological Sciences, Lake Superior State University, Sault Sainte Marie, MI
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Medicine, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Tom Grant
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Acton, ACT, Australia
| | - Frank Grutzner
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jaime Gongora
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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6
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Integration of genetic and demographic data to assess population risk in a continuously distributed species. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0885-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Weeks AR, Stoklosa J, Hoffmann AA. Conservation of genetic uniqueness of populations may increase extinction likelihood of endangered species: the case of Australian mammals. Front Zool 2016; 13:31. [PMID: 27398088 PMCID: PMC4939060 DOI: 10.1186/s12983-016-0163-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/28/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND As increasingly fragmented and isolated populations of threatened species become subjected to climate change, invasive species and other stressors, there is an urgent need to consider adaptive potential when making conservation decisions rather than focussing on past processes. In many cases, populations identified as unique and currently managed separately suffer increased risk of extinction through demographic and genetic processes. Other populations currently not at risk are likely to be on a trajectory where declines in population size and fitness soon appear inevitable. RESULTS Using datasets from natural Australian mammal populations, we show that drift processes are likely to be driving uniqueness in populations of many threatened species as a result of small population size and fragmentation. Conserving and managing such remnant populations separately will therefore often decrease their adaptive potential and increase species extinction risk. CONCLUSIONS These results highlight the need for a paradigm shift in conservation biology practise; strategies need to focus on the preservation of genetic diversity at the species level, rather than population, subspecies or evolutionary significant unit. The introduction of new genetic variants into populations through in situ translocation needs to be considered more broadly in conservation programs as a way of decreasing extinction risk by increasing neutral genetic diversity which may increase the adaptive potential of populations if adaptive variation is also increased.
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Affiliation(s)
- Andrew R. Weeks
- />School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Jakub Stoklosa
- />School of Mathematics & Statistics and Evolution & Ecology Research Centre, The University of New South Wales, Kensington, NSW 2052 Australia
| | - Ary A. Hoffmann
- />School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010 Australia
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8
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Bino G, Grant TR, Kingsford RT. Life history and dynamics of a platypus (Ornithorhynchus anatinus) population: four decades of mark-recapture surveys. Sci Rep 2015; 5:16073. [PMID: 26536832 PMCID: PMC4633588 DOI: 10.1038/srep16073] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/07/2015] [Indexed: 12/31/2022] Open
Abstract
Knowledge of the life-history and population dynamics of Australia's iconic and evolutionarily distinct platypus (Ornithorhynchus anatinus) remains poor. We marked-recaptured 812 unique platypuses (total 1,622 captures), over four decades (1973-2014) in the Shoalhaven River, Australia. Strong sex-age differences were observed in life-history, including morphology and longevity. Apparent survival of adult females (Φ = 0.76) were higher than adult males (Φ = 0.57), as in juveniles: females Φ = 0.27, males Φ = 0.13. Females were highly likely to remain in the same pool (adult: P = 0.85, juvenile: P = 0.88), while residency rates were lower for males (adult: P = 0.74, juvenile: P = 0.46). We combined survival, movement and life-histories to develop population viability models and test the impact of a range of life-history parameters. While using estimated apparent survival produced unviable populations (mean population growth rate r = -0.23, extinction within 20 years), considering residency rates to adjust survival estimates, indicated more stable populations (r = 0.004, p = 0.04 of 100-year extinction). Further sensitivity analyses highlighted adult female survival and overall success of dispersal as most affecting viability. Findings provide robust life-history and viability estimates for a difficult study species. These could support developing large-scale population dynamics models required to underpin a much needed national risk assessment for the platypus, already declining in parts of its current distribution.
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Affiliation(s)
- Gilad Bino
- Centre for Ecosystem Science, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney 2052 NSW, Australia
| | - Tom R. Grant
- Centre for Ecosystem Science, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney 2052 NSW, Australia
| | - Richard T. Kingsford
- Centre for Ecosystem Science, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney 2052 NSW, Australia
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