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Assessing national-level provision of conservation capacity building: lessons learnt from a case study of Kenya. ORYX 2022. [DOI: 10.1017/s0030605322000345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
As global environmental pressures grow, the need for delivering relevant and sustainable capacity building in conservation has never been greater. Individuals, organizations and communities need the skills, knowledge and information that allow them to address environmental issues at a variety of spatial scales and in diverse contexts. Capacity is currently built through a range of activities, including tertiary education, training courses, online learning, mentoring and continuing professional development. However, a significant proportion of the current capacity-building provision is non-strategic, project-based and reactive. The conservation sector still lacks a coordinated approach to capacity building linked to broader conservation goals. Without an assessment of current capacity-building provision and future capacity needs, the delivery of capacity building in conservation will remain fundamentally ad hoc. The need for strategic conservation capacity building in sub-Saharan Africa has been identified and here we report on the first collation of online material to assess current conservation capacity provision in Kenya (the country with the greatest online capacity-building presence). We reviewed a total of 177 capacity-building initiatives delivered during 2014–2019 and recorded 55 separate metrics for each initiative. We present: (1) a broad overview of the data collation methods developed, (2) examples of data that will support strategic capacity-building strategies, and (3) the lessons learnt from this assessment.
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2
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Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, Lord E, Dehasque M, Stanton DWG, Khoonsari PE, Nystedt B, Dalén L, Díez-Del-Molino D. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. BMC Bioinformatics 2022; 23:228. [PMID: 35698034 PMCID: PMC9195343 DOI: 10.1186/s12859-022-04757-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022] Open
Abstract
Background Many wild species have suffered drastic population size declines over the past centuries, which have led to ‘genomic erosion’ processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses. Results Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode). Conclusions GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04757-0.
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Affiliation(s)
- Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden.
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom van der Valk
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - David W G Stanton
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Payam Emami Khoonsari
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden.
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3
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Hogg CJ, Ottewell K, Latch P, Rossetto M, Biggs J, Gilbert A, Richmond S, Belov K. Threatened Species Initiative: Empowering conservation action using genomic resources. Proc Natl Acad Sci U S A 2022; 119:e2115643118. [PMID: 35042806 PMCID: PMC8795520 DOI: 10.1073/pnas.2115643118] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Kym Ottewell
- Conservation Science Centre, Department of Biodiversity, Conservation, & Attractions, Kensington, WA 6151, Australia
| | - Peter Latch
- Australian Government Department of Agriculture, Water & Environment, Canberra, ACT 2600, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - James Biggs
- Zoo and Aquarium Association Australasia, Mosman, NSW 2088, Australia
| | | | | | - Katherine Belov
- School of Life & Environmental Science, University of Sydney, Sydney, NSW 2006, Australia
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4
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Genomic Approaches for Conservation Management in Australia under Climate Change. Life (Basel) 2021; 11:life11070653. [PMID: 34357024 PMCID: PMC8304512 DOI: 10.3390/life11070653] [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] [Received: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.
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5
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Lima CS, Magalhães RF, Santos FR. Conservation issues using discordant taxonomic and evolutionary units: a case study of the American manatee (Trichechus manatus, Sirenia). WILDLIFE RESEARCH 2021. [DOI: 10.1071/wr20197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The delimitation of evolutionarily significant units (ESUs) frequently results in controversy, but prioritising populations with evolutionary independence is essential for effective in situ conservation management. The American manatee (Trichechus manatus) is distributed along subtropical and tropical coastal waters from Florida (USA) to Alagoas (Brazil), and two subspecies are traditionally recognised, namely, T. m. latirostris, restricted to the Florida peninsula, and T. m. manatus, found in the remaining areas. However, this subspecific classification is not supported by genetic and morphologic evidence, which, rather, recognises two deeply differentiated populations or ESUs called Atlantic (Brazil) and Caribbean (from Venezuela to Florida). In this viewpoint paper, we compare both intraspecific divisions of T. manatus and the conservation implications. First, we used all available mtDNA evidence to test the genealogical clustering of the two American manatee ESUs by using a tree-based coalescent method. Second, we have used different models under a coalescent framework to estimate the historic gene flow among manatee populations. The analysis of the spatial distribution of mtDNA clusters confirmed the existence of the two suggested ESUs, rather than the two claimed subspecies. Furthermore, the best model to explain historic migration indicates that Brazilian manatees belong to an isolated population, whereas Florida and Caribbean populations are connected by more recent gene flow. These results have confirmed that T. manatus of the Caribbean, Gulf of Mexico and Florida belong to the same deme or Caribbean ESU, and the relatively isolated population inhabiting the Atlantic coast of Brazil belongs to the Atlantic ESU. Furthermore, both ESUs are separated by an interspecific hybrid zone (with the Amazonian manatee) located around the mouth of the Amazon River towards the Guianas coastline. The subdivision of two ESUs is also highly supported by karyotypic, morphological and ecological data, and is in clear disagreement with the traditional subspecies designations and the IUCN priorities, which manages Brazilian manatees as part of the Antillean manatee subspecies (T. m. manatus). Rather, Brazilian manatees should be considered as a full priority for conservation and require further taxonomic research; because of their deep history of isolation, they present high genetic and morphologic differentiation from all other American manatees.
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6
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Cope HR, Peck S, Hobbs R, Keeley T, Izzard S, Yeen-Yap W, White PJ, Hogg CJ, Herbert CA. Contraceptive efficacy and dose-response effects of the gonadotrophin-releasing hormone (GnRH) agonist deslorelin in Tasmanian devils (Sarcophilus harrisii). Reprod Fertil Dev 2020; 31:1473-1485. [PMID: 31046901 DOI: 10.1071/rd18407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/13/2019] [Indexed: 11/23/2022] Open
Abstract
Contraception is increasingly used to manage breeding opportunities in conservation-dependent species. This study aimed to determine the efficacy, duration of effect, optimal dose and potential side effects of Suprelorin contraceptive implants in Tasmanian devils, for use in the conservation breeding program. In our pilot study, Suprelorin was found to effectively suppress oestrous cycles in female devils, yet caused a paradoxical increase in testosterone in males. Therefore, we focussed on females in further trials. Females received one (n=5), two (n=5) or no (n=5) Suprelorin implants, with quarterly gonadotrophin-releasing hormone (GnRH) challenges used to test pituitary responsiveness over two breeding seasons. Both Suprelorin doses suppressed pituitary responsiveness for at least one breeding season, with a reduced effect in the second. There was a dose-response effect on duration rather than magnitude of effect, with high-dose devils remaining suppressed for longer than low-dose animals. There were no apparent negative effects on general health, yet captivity and contraception together may cause weight gain. Suprelorin contraceptive implants are now routinely used in the Save the Tasmanian Devil Program insurance metapopulation to meet the aims of maintaining genetic and behavioural integrity by controlling individual reproductive contributions in group housing situations.
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Affiliation(s)
- Holly R Cope
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, J.D. Stewart Building B01, Camperdown, NSW 2006, Australia
| | - Sarah Peck
- Wildlife Management Branch, Department of Primary Industries, Parks, Water and Environment, Hobart, Tas. 7000, Australia
| | - Rebecca Hobbs
- Taronga Institute of Science and Learning, Taronga Conservation Society, NSW 2088, Australia
| | - Tamara Keeley
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Qld 4343, Australia
| | - Stephen Izzard
- Wildlife Management Branch, Department of Primary Industries, Parks, Water and Environment, Hobart, Tas. 7000, Australia
| | | | - Peter J White
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, R.M.C. Gunn Building B19, Camperdown, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, J.D. Stewart Building B01, Camperdown, NSW 2006, Australia; and Zoo and Aquarium Association Australasia, Mosman, NSW 2088, Australia
| | - Catherine A Herbert
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, J.D. Stewart Building B01, Camperdown, NSW 2006, Australia; and Corresponding author.
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7
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Grueber CE, Peel E, Wright B, Hogg CJ, Belov K. A Tasmanian devil breeding program to support wild recovery. Reprod Fertil Dev 2020; 31:1296-1304. [PMID: 32172782 DOI: 10.1071/rd18152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/01/2018] [Indexed: 01/03/2023] Open
Abstract
Tasmanian devils are threatened in the wild by devil facial tumour disease: a transmissible cancer with a high fatality rate. In response, the Save the Tasmanian Devil Program (STDP) established an 'insurance population' to enable the preservation of genetic diversity and natural behaviours of devils. This breeding program includes a range of institutions and facilities, from zoo-based intensive enclosures to larger, more natural environments, and a strategic approach has been required to capture and maintain genetic diversity, natural behaviours and to ensure reproductive success. Laboratory-based research, particularly genetics, in tandem with adaptive management has helped the STDP reach its goals, and has directly contributed to the conservation of the species in the wild. Here we review this work and show that the Tasmanian devil breeding program is a powerful example of how genetic research can be used to understand and improve reproductive success in a threatened species.
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Affiliation(s)
- C E Grueber
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - E Peel
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - B Wright
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - C J Hogg
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - K Belov
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
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8
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Taft HR, McCoskey DN, Miller JM, Pearson SK, Coleman MA, Fletcher NK, Mittan CS, Meek MH, Barbosa S. Research–management partnerships: An opportunity to integrate genetics in conservation actions. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.218] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
| | | | - Joshua M. Miller
- Department of Biological SciencesUniversity of Alberta Edmonton Alberta Canada
| | - Sarah K. Pearson
- College of Science and EngineeringFlinders University of South Australia Adelaide South Australia Australia
| | - Melinda A. Coleman
- Department of Primary Industries NSW FisheriesNational Marine Science Centre Coffs Harbour New South Wales Australia
- National Marine Science CentreSouthern Cross University Coffs Harbour New South Wales Australia
| | - Nicholas K. Fletcher
- Department of Ecology and Evolutionary BiologyCornell University, Corson Hall Ithaca New York USA
| | - Cinnamon S. Mittan
- Department of Ecology and Evolutionary BiologyCornell University, Corson Hall Ithaca New York USA
| | - Mariah H. Meek
- Department of Integrative BiologyMichigan State University East Lansing Michigan USA
| | - Soraia Barbosa
- Department of Fish and Wildlife SciencesUniversity of Idaho Moscow Idaho USA
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9
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Nyirenda VR, Yambayamba AM, Chisha‐Kasumu E. Influences of seasons and dietary composition on diurnal raptor habitat use in Chembe Bird Sanctuary, Zambia: Implications for conservation. Afr J Ecol 2020. [DOI: 10.1111/aje.12752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vincent R. Nyirenda
- Department of Zoology and Aquatic Sciences School of Natural Resources The Copperbelt University Kitwe Zambia
| | - Arthur M. Yambayamba
- Department of Plant and Environmental Sciences School of Natural Resources The Copperbelt University Kitwe Zambia
| | - Exildah Chisha‐Kasumu
- Department of Plant and Environmental Sciences School of Natural Resources The Copperbelt University Kitwe Zambia
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10
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Bourret V, Albert V, April J, Côté G, Morissette O. Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evol Appl 2020; 13:1420-1434. [PMID: 32684967 PMCID: PMC7359848 DOI: 10.1111/eva.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.
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Affiliation(s)
- Vincent Bourret
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Vicky Albert
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Julien April
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Guillaume Côté
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Olivier Morissette
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
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11
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Brandies P, Peel E, Hogg CJ, Belov K. The Value of Reference Genomes in the Conservation of Threatened Species. Genes (Basel) 2019; 10:E846. [PMID: 31717707 PMCID: PMC6895880 DOI: 10.3390/genes10110846] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Conservation initiatives are now more crucial than ever-over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.
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Affiliation(s)
| | | | | | - Katherine Belov
- School of Life & Environmental Sciences, The University of Sydney, Sydney 2006, Australia; (P.B.); (E.P.); (C.J.H.)
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12
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Wright B, Farquharson KA, McLennan EA, Belov K, Hogg CJ, Grueber CE. From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species. BMC Genomics 2019; 20:453. [PMID: 31159724 PMCID: PMC6547446 DOI: 10.1186/s12864-019-5806-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
Background Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome sequencing data. Here we examine population genetic inferences from two species for which reference-aligned reduced-representation data have been collected. Our two study species are a threatened Australian marsupial (Tasmanian devil Sarcophilus harrisii; declining population) and an Arctic-circle migrant bird (pink-footed goose Anser brachyrhynchus; expanding population). Analyses of these data are compared using Stacks versus two widely-used genomics packages, SAMtools and GATK. We also introduce a custom R script to improve the reliability of single nucleotide polymorphism (SNP) calls in all pipelines and conduct population genetic inferences for non-model species with reference genomes. Results Although we identified orders of magnitude fewer SNPs in our devil dataset than for goose, we found remarkable symmetry between the two species in our assessment of software performance. For both datasets, all three methods were able to delineate population structure, even with varying numbers of loci. For both species, population structure inferences were influenced by the percent of missing data. Conclusions For studies of non-model species with a reference genome, we recommend combining Stacks output with further filtering (as included in our R pipeline) for population genetic studies, paying particular attention to potential impact of missing data thresholds. We recognise SAMtools as a viable alternative for researchers more familiar with this software. We caution against the use of GATK in studies with limited computational resources or time. Electronic supplementary material The online version of this article (10.1186/s12864-019-5806-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Belinda Wright
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Katherine A Farquharson
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Elspeth A McLennan
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Katherine Belov
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Carolyn J Hogg
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Catherine E Grueber
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia. .,San Diego Zoo Global, San Diego, USA.
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13
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Genetic evaluation of the Iberian lynx ex situ conservation programme. Heredity (Edinb) 2019; 123:647-661. [PMID: 30952964 DOI: 10.1038/s41437-019-0217-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 11/09/2022] Open
Abstract
Ex situ programmes have become critical for improving the conservation of many threatened species, as they establish backup populations and provide individuals for reintroduction and reinforcement of wild populations. The Iberian lynx was considered the most threatened felid species in the world in the wake of a dramatic decline during the second half of the 20th century that reduced its numbers to around only 100 individuals. An ex situ conservation programme was established in 2003 with individuals from the two well-differentiated, remnant populations, with great success from a demographic point of view. Here, we evaluate the genetic status of the Iberian lynx captive population based on molecular data from 36 microsatellites, including patterns of relatedness and representativeness of the two remnant genetic backgrounds among founders, the evolution of diversity and inbreeding over the years, and genetic differentiation among breeding facilities. In general terms, the ex situ population harbours most of the genetic variability found in the two wild populations and has been able to maintain reasonably low levels of inbreeding and high diversity, thus validating the applied management measures and potentially representing a model for other species in need of conservation.
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14
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Norman AJ, Putnam AS, Ivy JA. Use of molecular data in zoo and aquarium collection management: Benefits, challenges, and best practices. Zoo Biol 2018; 38:106-118. [PMID: 30465726 DOI: 10.1002/zoo.21451] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 10/05/2018] [Accepted: 10/12/2018] [Indexed: 01/06/2023]
Abstract
The global zoo and aquarium community widely recognizes that its animal collections and cooperative breeding programs are facing a sustainability crisis. It has become commonly accepted that numerous priority species cannot be maintained unless new management strategies are adopted. While molecular data have the potential to greatly improve management across a range of scenarios, they have been generally underutilized by the zoo and aquarium community. This failure to effectively apply molecular data to collection management has been due, in part, to a paucity of resources within the community on which to base informed decisions about when the use of such data is appropriate and what steps are necessary to successfully integrate data into management. Here, we identify three broad areas of inquiry where molecular data can inform management: 1) taxonomic identification; 2) incomplete or unknown pedigrees; and 3) hereditary disease. Across these topics, we offer a discussion of the advantages, limitations, and considerations for applying molecular data to ex situ animal populations in a style accessible to zoo and aquarium professionals. Ultimately, we intend for this compiled information to serve as a resource for the community to help ensure that molecular projects directly and effectively benefit the long-term persistence of ex situ populations.
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Affiliation(s)
- Anita J Norman
- Department of Life Sciences, San Diego Zoo Global, San Diego, California
| | - Andrea S Putnam
- Department of Life Sciences, San Diego Zoo Global, San Diego, California
| | - Jamie A Ivy
- Department of Life Sciences, San Diego Zoo Global, San Diego, California
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Rout TM, Baker CM, Huxtable S, Wintle BA. Monitoring, imperfect detection, and risk optimization of a Tasmanian devil insurance population. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:267-275. [PMID: 28657164 DOI: 10.1111/cobi.12975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 04/13/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
Most species are imperfectly detected during biological surveys, which creates uncertainty around their abundance or presence at a given location. Decision makers managing threatened or pest species are regularly faced with this uncertainty. Wildlife diseases can drive species to extinction; thus, managing species with disease is an important part of conservation. Devil facial tumor disease (DFTD) is one such disease that led to the listing of the Tasmanian devil (Sarcophilus harrisii) as endangered. Managers aim to maintain devils in the wild by establishing disease-free insurance populations at isolated sites. Often a resident DFTD-affected population must first be removed. In a successful collaboration between decision scientists and wildlife managers, we used an accessible population model to inform monitoring decisions and facilitate the establishment of an insurance population of devils on Forestier Peninsula. We used a Bayesian catch-effort model to estimate population size of a diseased population from removal and camera trap data. We also analyzed the costs and benefits of declaring the area disease-free prior to reintroduction and establishment of a healthy insurance population. After the monitoring session in May-June 2015, the probability that all devils had been successfully removed was close to 1, even when we accounted for a possible introduction of a devil to the site. Given this high probability and the baseline cost of declaring population absence prematurely, we found it was not cost-effective to carry out any additional monitoring before introducing the insurance population. Considering these results within the broader context of Tasmanian devil management, managers ultimately decided to implement an additional monitoring session before the introduction. This was a conservative decision that accounted for uncertainty in model estimates and for the broader nonmonetary costs of mistakenly declaring the area disease-free.
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Affiliation(s)
- Tracy M Rout
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia
- Centre for Biodiversity and Conservation Science & School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher M Baker
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
- CSIRO Ecosystem Sciences, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Stewart Huxtable
- Save the Tasmanian Devil Program, Department of Primary Industries, Parks, Water and Environment, 134 Macquarie Street, Hobart, TAS 7000, Australia
| | - Brendan A Wintle
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia
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Cope HR, Hogg CJ, Fagg K, Barnard O, White PJ, Herbert CA. Effects of deslorelin implants on reproduction and feeding behavior in Tasmanian devils (Sarcophilus harrisii) housed in free-range enclosures. Theriogenology 2017; 107:134-141. [PMID: 29149677 DOI: 10.1016/j.theriogenology.2017.10.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/30/2017] [Accepted: 10/30/2017] [Indexed: 11/19/2022]
Abstract
In captive breeding programs, it is becoming increasingly important to maximize the retention of genetic diversity by managing the reproductive contribution of each individual, which can be facilitated through the use of selective contraception. This becomes critical when captive populations are held for several generations, and managers must prevent the confines of housing space and financial support from compromising genetic integrity. For example, the Tasmanian devil insurance population, established in 2006, is strategically managed to equalize founder representation. This becomes difficult when devils are housed in large groups in free-range enclosures (FREs). This study examined the efficacy, duration and potential side effects of Suprelorin® contraceptive implants (containing 4.7 mg of deslorelin) on Tasmanian devils housed in FREs. Females were monitored to assess post-treatment reproductive rates, feeding behavior and weight changes. Suprelorin® successfully prevented reproduction in all treated females (P < 0.001) for at least one breeding season. For one year after contraception, there was no difference in proportion of time spent feeding between contraception and control groups (P > 0.05) and there was no effect of contraception on order of arrival at food (P = 0.632), suggesting no alterations to social structure. Devils with pouch young spent more time feeding than those without (P < 0.001). Treatment and month had an interactive effect on weight (P < 0.001), yet contracepted females were only heavier than controls in one season, indicating no overall excessive weight gain. Suprelorin® implants inhibit reproduction for at least one breeding season, with no apparent negative effects on feeding behavior or social dynamic. Selective contraception has the potential to become an important tool for conservation managers, to meet multiple reproductive, genetic and behavioral goals for this species.
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Affiliation(s)
- Holly R Cope
- The University of Sydney, Faculty of Science, SOLES, J.D. Stewart Building B01, Camperdown, 2006, NSW, Australia
| | - Carolyn J Hogg
- The University of Sydney, Faculty of Science, SOLES, J.D. Stewart Building B01, Camperdown, 2006, NSW, Australia; Zoo and Aquarium Association Australasia, Mosman, 2088, NSW, Australia
| | - Karen Fagg
- Save the Tasmanian Devil Program, Captive Management and Translocation Section, Wildlife Management Branch, Department of Primary Industries, Parks, Water and Environment, Australia
| | - Olivia Barnard
- Save the Tasmanian Devil Program, Captive Management and Translocation Section, Wildlife Management Branch, Department of Primary Industries, Parks, Water and Environment, Australia
| | - Peter J White
- The University of Sydney, Faculty of Science, SSVS, R.M.C. Gunn Building B19, Camperdown, 2006, NSW, Australia
| | - Catherine A Herbert
- The University of Sydney, Faculty of Science, SOLES, J.D. Stewart Building B01, Camperdown, 2006, NSW, Australia.
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Torres-Florez JP, Johnson WE, Nery MF, Eizirik E, Oliveira-Miranda MA, Galetti PM. The coming of age of conservation genetics in Latin America: what has been achieved and what needs to be done. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1006-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Hayes DA, Kunde DA, Taylor RL, Pyecroft SB, Sohal SS, Snow ET. ERBB3: A potential serum biomarker for early detection and therapeutic target for devil facial tumour 1 (DFT1). PLoS One 2017; 12:e0177919. [PMID: 28591206 PMCID: PMC5462353 DOI: 10.1371/journal.pone.0177919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/05/2017] [Indexed: 12/13/2022] Open
Abstract
Devil Facial Tumour 1 (DFT1) is one of two transmissible neoplasms of Tasmanian devils (Sarcophilus harrisii) predominantly affecting their facial regions. DFT1's cellular origin is that of Schwann cell lineage where lesions are evident macroscopically late in the disease. Conversely, the pre-clinical timeframe from cellular transmission to appearance of DFT1 remains uncertain demonstrating the importance of an effective pre-clinical biomarker. We show that ERBB3, a marker expressed normally by the developing neural crest and Schwann cells, is immunohistohemically expressed by DFT1, therefore the potential of ERBB3 as a biomarker was explored. Under the hypothesis that serum ERBB3 levels may increase as DFT1 invades local and distant tissues our pilot study determined serum ERBB3 levels in normal Tasmanian devils and Tasmanian devils with DFT1. Compared to the baseline serum ERBB3 levels in unaffected Tasmanian devils, Tasmanian devils with DFT1 showed significant elevation of serum ERBB3 levels. Interestingly Tasmanian devils with cutaneous lymphoma (CL) also showed elevation of serum ERBB3 levels when compared to the baseline serum levels of Tasmanian devils without DFT1. Thus, elevated serum ERBB3 levels in otherwise healthy looking devils could predict possible DFT1 or CL in captive or wild devil populations and would have implications on the management, welfare and survival of Tasmanian devils. ERBB3 is also a therapeutic target and therefore the potential exists to consider modes of administration that may eradicate DFT1 from the wild.
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Affiliation(s)
- Dane A. Hayes
- Department of Primary Industries, Parks Water and Environment, Animal Health Laboratory, Launceston, Tasmania, Australia
- Save the Tasmanian Devil Program, University of Tasmania, Hobart, Tasmania, Australia
- School of Health Sciences, Faculty of Health, University of Tasmania, Launceston, Tasmania, Australia
| | - Dale A. Kunde
- School of Health Sciences, Faculty of Health, University of Tasmania, Launceston, Tasmania, Australia
| | - Robyn L. Taylor
- Save the Tasmanian Devil Program, University of Tasmania, Hobart, Tasmania, Australia
- Department of Primary Industries, Parks Water and Environment, Resource Management and Conservation, Hobart, Tasmania, Australia
| | - Stephen B. Pyecroft
- School of Animal & Veterinary Sciences, Faculty of Science, University of Adelaide, Roseworthy Campus, Roseworthy, South Australia
| | - Sukhwinder Singh Sohal
- School of Health Sciences, Faculty of Health, University of Tasmania, Launceston, Tasmania, Australia
| | - Elizabeth T. Snow
- School of Health Sciences, Faculty of Health, University of Tasmania, Launceston, Tasmania, Australia
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Hogg CJ, Lee AV, Srb C, Hibbard C. Metapopulation management of an Endangered species with limited genetic diversity in the presence of disease: the Tasmanian devilSarcophilus harrisii. ACTA ACUST UNITED AC 2016. [DOI: 10.1111/izy.12144] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- C. J. Hogg
- School of Environmental and Life Sciences; University of Sydney; Sydney NSW 2006 Australia
- Zoo and Aquarium Association Australasia; Mosman NSW 2088 Australia
| | - A. V. Lee
- Save the Tasmanian Devil Program; DPIPWE; Hobart Tasmania 7001 Australia
| | - C. Srb
- Healesville Sanctuary; Healesville VIC 3777 Australia
| | - C. Hibbard
- Zoo and Aquarium Association Australasia; Mosman NSW 2088 Australia
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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