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Bell KL, Campos M, Hoffmann BD, Encinas-Viso F, Hunter GC, Webber BL. Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171810. [PMID: 38513869 DOI: 10.1016/j.scitotenv.2024.171810] [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: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.
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Affiliation(s)
- Karen L Bell
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Mariana Campos
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Francisco Encinas-Viso
- CSIRO Centre of Australian National Biodiversity Research, Black Mountain, Australian Capital Territory 2601, Australia
| | - Gavin C Hunter
- CSIRO Health & Biosecurity, Black Mountain, Australian Capital Territory 2601, Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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Patterson CR, Lustig A, Seddon PJ, Wilson DJ, van Heezik Y. Eradicating an invasive mammal requires local elimination and reduced reinvasion from an urban source population. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2949. [PMID: 38442922 DOI: 10.1002/eap.2949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/19/2023] [Accepted: 12/20/2023] [Indexed: 03/07/2024]
Abstract
Invasive mammal eradications are increasingly attempted across large, complex landscapes. Sequentially controlled management zones can be at risk of reinvasion from adjacent uncontrolled areas, and managers must weigh the relative benefits of ensuring complete elimination from a zone or minimizing reinvasion risk. This is complicated in urban areas, where habitat heterogeneity and a lack of baseline ecological knowledge increase uncertainty. We applied a spatial agent-based model to predict the reinvasion of a well-studied species, the brushtail possum (Trichosurus vulpecula), across an urban area onto a peninsula that is the site of an elimination campaign in Aotearoa New Zealand. We represented fine-scale urban habitat heterogeneity in a land cover layer and tested management scenarios that varied four factors: the density of possums remaining following an elimination attempt, the maintenance trap density on the peninsula, and effort expended toward preventing reinvasion by means of a high-density trap buffer at the peninsula isthmus or control of the source population adjacent to the peninsula. We found that achieving complete elimination on the peninsula was crucial to avoid rapid repopulation. The urban isthmus was predicted to act as a landscape barrier and restrict immigration onto the peninsula, but reliance on this barrier alone would fail to prevent repopulation. In combination, complete elimination, buffer zone, and source population control could reduce the probability of possum repopulation to near zero. Our findings support urban landscape barriers as one tool for sequential invasive mammal elimination but reaffirm that novel methods to expose residual individuals to control will be necessary to secure elimination in management zones. Work to characterize the urban ecology of many invasive mammals is still needed.
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Affiliation(s)
| | - Audrey Lustig
- Manaaki Whenua-Landcare Research, Lincoln, New Zealand
- Te Pūnaha Matatini: The Centre for Complex Systems and Networks, Auckland, New Zealand
| | - Philip J Seddon
- Department of Zoology, University of Otago, Dunedin, New Zealand
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The tails of two invasive species: genetic responses to acute and chronic bottlenecks. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractGenetic diversity can affect population viability and can be reduced by both acute and chronic mechanisms. Using the history of the establishment and management of two invasive rat species on Tetiaroa atoll, French Polynesia, we investigated the intensity and longevity of contrasting population bottleneck mechanisms on genetic diversity and bottleneck signal. Using microsatellite loci we show how both a chronic reduction over approximately 50 years of a Rattus exulans population caused by the arrival of its competitor R. rattus, and an acute reduction in a R. rattus population caused by a failed eradication approximately 10 years ago, caused similar magnitudes of genetic diversity loss. Furthermore, these strong bottleneck signals were in addition to the lasting signal from initial colonisation by each species many decades to centuries earlier, characterising a genetic paradox of biological invasion. These findings have implications for the study of population genetics of invasive species, and underscore how important historical context of population dynamics is when interpreting snapshots of genetic diversity.
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Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands. Commun Biol 2022; 5:223. [PMID: 35273319 PMCID: PMC8913846 DOI: 10.1038/s42003-022-03159-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/14/2022] [Indexed: 11/08/2022] Open
Abstract
Invasive mammals represent a critical threat to island biodiversity; eradications can result in ecological restoration yet may fail in the absence of key population parameters. Over-browsing by invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) is causing severe ecological and cultural impacts across the Haida Gwaii archipelago (Canada). Previous eradication attempts demonstrate forest regeneration upon deer removal, but reinvasion reverses conservation gains. Here we use restriction-site associated DNA sequencing (12,947 SNPs) to investigate connectivity and gene flow of invasive deer (n = 181) across 15 islands, revealing little structure throughout Haida Gwaii and identifying the large, central island of Moresby (>2600 km2) as the greatest source of migrants. As a result, the archipelago itself should be considered the primary eradication unit, with the exception of geographically isolated islands like SGang Gwaay. Thus, limiting eradications to isolated islands combined with controlled culling and enhanced biosecurity may be the most effective strategies for achieving ecological restoration goals. Genomic data presented in this study provide clues about why previous attempts to eradicate the invasive Sitka black-tailed deer from the Haida Gwaii archipelago in Canada have been incomplete. The authors find substantial gene flow between islands, with the exception of the remote island of SGang Gwaay, which they argue is a viable option for near-term eradication efforts.
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Burgess BT, Irvine RL, Howald GR, Russello MA. The Promise of Genetics and Genomics for Improving Invasive Mammal Management on Islands. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.704809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Invasive species are major contributors to global biodiversity decline. Invasive mammalian species (IMS), in particular, have profound negative effects in island systems that contain disproportionally high levels of species richness and endemism. The eradication and control of IMS have become important conservation tools for managing species invasions on islands, yet these management operations are often subject to failure due to knowledge gaps surrounding species- and system-specific characteristics, including invasion pathways and contemporary migration patterns. Here, we synthesize the literature on ways in which genetic and genomic tools have effectively informed IMS management on islands, specifically associated with the development and modification of biosecurity protocols, and the design and implementation of eradication and control programs. In spite of their demonstrated utility, we then explore the challenges that are preventing genetics and genomics from being implemented more frequently in IMS management operations from both academic and non-academic perspectives, and suggest possible solutions for breaking down these barriers. Finally, we discuss the potential application of genome editing to the future management of invasive species on islands, including the current state of the field and why islands may be effective targets for this emerging technology.
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Samaniego A, Kappes P, Broome K, Cranwell S, Griffiths R, Harper G, McClelland P, Palmer R, Rocamora G, Springer K, Will D, Siers S. Factors leading to successful island rodent eradications following initial failure. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Peter Kappes
- USDA APHIS Wildlife Services, National Wildlife Research Center Hilo Hawaii USA
- Coastal Research and Extension Center Mississippi State University Biloxi Mississippi USA
| | - Keith Broome
- New Zealand Department of Conservation Wellington New Zealand
| | | | | | - Grant Harper
- Biodiversity Restoration Specialists Murchison New Zealand
| | | | - Russell Palmer
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions Kensington Western Australia Australia
| | - Gérard Rocamora
- Island Biodiversity & Conservation Centre University of Seychelles Mahé Seychelles
| | | | - David Will
- Island Conservation Santa Cruz California USA
| | - Shane Siers
- USDA APHIS Wildlife Services, National Wildlife Research Center Hilo Hawaii USA
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Pichlmueller F, Murphy EC, MacKay JWB, Henderson J, Fewster RM, Russell JC. Island invasion and reinvasion: Informing invasive species management with genetic measures of connectivity. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Pichlmueller
- School of Biological Sciences University of Auckland Auckland New Zealand
- School of Biomedical Sciences University of Otago Dunedin New Zealand
| | | | - Jamie W. B. MacKay
- School of Biological Sciences University of Auckland Auckland New Zealand
- Wildland Consultants Ltd Auckland New Zealand
| | | | - Rachel M. Fewster
- Department of Statistics University of Auckland Auckland New Zealand
| | - James C. Russell
- School of Biological Sciences University of Auckland Auckland New Zealand
- Department of Statistics University of Auckland Auckland New Zealand
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Hansen N, Hughes NK, Byrom AE, Banks PB. Population recovery of alien black rats
Rattus rattus
: A test of reinvasion theory. AUSTRAL ECOL 2020. [DOI: 10.1111/aec.12855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Nicole Hansen
- School of Biological, Earth and Environmental Sciences University of New South Wales Sydney 2052Australia
| | | | | | - Peter B. Banks
- School of Biological, Earth and Environmental Sciences University of New South Wales Sydney 2052Australia
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
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Peltzer DA, Bellingham PJ, Dickie IA, Houliston G, Hulme PE, Lyver PO, McGlone M, Richardson SJ, Wood J. Scale and complexity implications of making New Zealand predator-free by 2050. J R Soc N Z 2019. [DOI: 10.1080/03036758.2019.1653940] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | | | - Ian A. Dickie
- Bio-Protection Research Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Philip E. Hulme
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
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