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Langhammer PF, Bull JW, Bicknell JE, Oakley JL, Brown MH, Bruford MW, Butchart SHM, Carr JA, Church D, Cooney R, Cutajar S, Foden W, Foster MN, Gascon C, Geldmann J, Genovesi P, Hoffmann M, Howard-McCombe J, Lewis T, Macfarlane NBW, Melvin ZE, Merizalde RS, Morehouse MG, Pagad S, Polidoro B, Sechrest W, Segelbacher G, Smith KG, Steadman J, Strongin K, Williams J, Woodley S, Brooks TM. The positive impact of conservation action. Science 2024; 384:453-458. [PMID: 38662833 DOI: 10.1126/science.adj6598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 03/14/2024] [Indexed: 05/03/2024]
Abstract
Governments recently adopted new global targets to halt and reverse the loss of biodiversity. It is therefore crucial to understand the outcomes of conservation actions. We conducted a global meta-analysis of 186 studies (including 665 trials) that measured biodiversity over time and compared outcomes under conservation action with a suitable counterfactual of no action. We find that in two-thirds of cases, conservation either improved the state of biodiversity or at least slowed declines. Specifically, we find that interventions targeted at species and ecosystems, such as invasive species control, habitat loss reduction and restoration, protected areas, and sustainable management, are highly effective and have large effect sizes. This provides the strongest evidence to date that conservation actions are successful but require transformational scaling up to meet global targets.
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Affiliation(s)
- Penny F Langhammer
- Re:wild, PO Box 129, Austin, TX 78767, USA
- Arizona State University, School of Life Sciences, PO Box 874501, Tempe, AZ 85287, USA
| | - Joseph W Bull
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury CT2 7NR, UK
- Wild Business Ltd, London, UK
| | - Jake E Bicknell
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury CT2 7NR, UK
| | | | | | - Michael W Bruford
- School of Biosciences and Sustainable Places Research Institute, Cathays Park, Cardiff CF10 3AX, UK
- IUCN SSC Conservation Genetics Specialist Group, 28 rue Mauverney, 1196 Gland, Switzerland
| | - Stuart H M Butchart
- BirdLife International, David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK
- Department of Zoology, University of Cambridge, Downing St., Cambridge CB2 3EJ, UK
| | - Jamie A Carr
- Leverhulme Centre for Anthropocene Biodiversity, University of York, York YO10 15DD, UK
- Department of Environment and Geography, University of York, York YO10 5DD, UK
- IUCN SSC Climate Change Specialist Group, 28 rue Mauverney, 1196 Gland, Switzerland
| | - Don Church
- Re:wild, PO Box 129, Austin, TX 78767, USA
| | - Rosie Cooney
- CEESP/SSC IUCN Sustainable Use and Livelihoods Specialist Group, 28 rue Mauverney, 1196 Gland, Switzerland
- Fenner School of Environment and Society, Australian National University, ACT 2601, Australia
| | | | - Wendy Foden
- IUCN SSC Climate Change Specialist Group, 28 rue Mauverney, 1196 Gland, Switzerland
- South African National Parks, Cape Research Centre, Tokai, Cape Town, 7966, South Africa
- FitzPatrick Institute of African Ornithology, Rondebosch, Cape Town, 7701, South Africa
- Global Change Biology Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Claude Gascon
- The Global Environment Facility, 1818 H Street NW, Washington, DC 20433, USA
| | - Jonas Geldmann
- Department of Zoology, University of Cambridge, Downing St., Cambridge CB2 3EJ, UK
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen E, Denmark
| | - Piero Genovesi
- Institute for Environmental Protection and Research, Via Vitaliano Brancati 48, 00144 Rome, Italy
- IUCN SSC Invasive Species Specialist Group, 00144 Rome, Italy
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Michael Hoffmann
- IUCN Species Survival Commission, 28 rue Mauverney, 1196 Gland, Switzerland
- Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Jo Howard-McCombe
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- RZSS WildGenes, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Tiffany Lewis
- Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85281, USA
| | | | - Zoe E Melvin
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor, Gwynedd, Wales LL57 2UW, UK
| | | | - Meredith G Morehouse
- LLaves: Keys to Bilingual Conservation, LLC, 346 Mayberry Hill Road, Casco, Maine 04015, USA
| | - Shyama Pagad
- University of Auckland, Auckland 1072, New Zealand
| | - Beth Polidoro
- IUCN Species Survival Commission, 28 rue Mauverney, 1196 Gland, Switzerland
- Arizona State University, 4701 W. Thunderbird Rd, Glendale, AZ 85382, USA
| | | | - Gernot Segelbacher
- IUCN SSC Conservation Genetics Specialist Group, 28 rue Mauverney, 1196 Gland, Switzerland
- University Freiburg, Tennenbacher Str. 4, 79106 Freiburg, Germany
| | - Kevin G Smith
- IUCN, The David Attenborough Building, Pembroke St, Cambridge CB2 3QZ, UK
| | - Janna Steadman
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury CT2 7NR, UK
| | - Kyle Strongin
- Arizona State University, 800 S. Cady Mall, Tempe, AZ 85281, USA
| | - Jake Williams
- Imperial College London, Silwood Park, Ascot SL5 7PY, UK
| | - Stephen Woodley
- IUCN World Commission on Protected Areas, 64 Juniper Road, Chelsea, Quebec J9B 1T3, Canada
| | - Thomas M Brooks
- IUCN, 28 rue Mauverney, 1196 Gland, Switzerland
- World Agroforestry Center, University of The Philippines Los Baños, Laguna, Philippines
- Institute for Marine & Antarctic Studies, University of Tasmania, Hobart, Australia
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Wang D, Smith JLD, Accatino F, Ge J, Wang T. Addressing the impact of canine distemper spreading on an isolated tiger population in northeast Asia. Integr Zool 2023; 18:994-1008. [PMID: 36881515 DOI: 10.1111/1749-4877.12712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The continuation of the isolated Amur tiger (Panthera tigris altaica) population living along the China-Russia border is facing serious challenges due to factors such as its small size (including 38 individuals) and canine distemper virus (CDV). We use a population viability analysis metamodel, which consists of a traditional individual-based demographic model linked to an epidemiological model, to assess options for controlling the impact of negative factors through domestic dog management in protected areas, increasing connectivity to the neighboring large population (including more than 400 individuals), and habitat expansion. Without intervention, under inbreeding depression of 3.14, 6.29, and 12.26 lethal equivalents, our metamodel predicted the extinction within 100 years is 64.4%, 90.6%, and 99.8%, respectively. In addition, the simulation results showed that dog management or habitat expansion independently will not ensure tiger population viability for the next 100 years, and connectivity to the neighboring population would only keep the population size from rapidly declining. However, when the above three conservation scenarios are combined, even at the highest level of 12.26 lethal equivalents inbreeding depression, population size will not decline and the probability of extinction will be <5.8%. Our findings highlight that protecting the Amur tiger necessitates a multifaceted synergistic effort. Our key management recommendations for this population underline the importance of reducing CDV threats and expanding tiger occupancy to its former range in China, but re-establishing habitat connectivity to the neighboring population is an important long-term objective.
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Affiliation(s)
- Dawei Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Engineering, NFGA Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard & College of Life Sciences, Beijing Normal University, Beijing, China
| | - James L D Smith
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, MN, USA
| | - Francesco Accatino
- UMR SADAPT, INRAE, AgroParisTech, Université Paris-Saclay, PALAISEAU Cedex, France
| | - Jianping Ge
- Ministry of Education Key Laboratory for Biodiversity Science and Engineering, NFGA Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard & College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tianming Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Engineering, NFGA Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard & College of Life Sciences, Beijing Normal University, Beijing, China
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3
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Gilbertson MLJ, Hart SN, VanderWaal K, Onorato D, Cunningham M, VandeWoude S, Craft ME. Seasonal changes in network connectivity and consequences for pathogen transmission in a solitary carnivore. Sci Rep 2023; 13:17802. [PMID: 37853051 PMCID: PMC10584909 DOI: 10.1038/s41598-023-44815-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023] Open
Abstract
Seasonal variation in habitat use and animal behavior can alter host contact patterns with potential consequences for pathogen transmission dynamics. The endangered Florida panther (Puma concolor coryi) has experienced significant pathogen-induced mortality and continues to be at risk of future epidemics. Prior research has found increased panther movement in Florida's dry versus wet seasons, which may affect panther population connectivity and seasonally increase potential pathogen transmission. Our objective was to determine if Florida panthers are more spatially connected in dry seasons relative to wet seasons, and test if identified connectivity differences resulted in divergent predicted epidemic dynamics. We leveraged extensive panther telemetry data to construct seasonal panther home range overlap networks over an 11 year period. We tested for differences in network connectivity, and used observed network characteristics to simulate transmission of a broad range of pathogens through dry and wet season networks. We found that panthers were more spatially connected in dry seasons than wet seasons. Further, these differences resulted in a trend toward larger and longer pathogen outbreaks when epidemics were initiated in the dry season. Our results demonstrate that seasonal variation in behavioral patterns-even among largely solitary species-can have substantial impacts on epidemic dynamics.
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Affiliation(s)
- Marie L J Gilbertson
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, 55108, USA.
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - S Niamh Hart
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, 55108, USA
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, 55108, USA
| | - Dave Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL, 34114, USA
| | - Mark Cunningham
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, 32601, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, 55108, USA
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4
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Wang D, Accatino F, Smith JLD, Wang T. Contributions of distemper control and habitat expansion to the Amur leopard viability. Commun Biol 2022; 5:1153. [PMID: 36310335 PMCID: PMC9618572 DOI: 10.1038/s42003-022-04127-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
The Amur leopard (Panthera pardus orientalis) is a critically endangered top predator that struggles on the brink of extinction due to threats such as canine distemper virus (CDV), habitat loss, and inbreeding depression. Here we develop a viability analysis metamodel that combines a traditional individual-based demographic model with an epidemiological model to assess the benefits of alternative population management actions in response to multiple distinct threats. Our results showed an extinction risk of 10.3%-99.9% if no management actions were taken over 100 years under different levels of inbreeding depression. Reducing the risk of CDV infection in Amur leopards through the low-coverage vaccination of leopards and the management of sympatric domestic dogs could effectively improve the survival probability of the leopard population, and with habitat expansion added to these management measures, the population expanded further. Our findings highlight that protecting the Amur leopard necessitates a multifaceted synergistic effort, and controlling multiple threats together may significantly escalate overall viability of a species, especially for small-isolated threatened population. More broadly, our modeling framework could offer critical perspectives and scientific support for conservation planning, as well as specific adaptive management actions for endangered species around the world. In the absence of management strategies, canine distemper virus threatens the future existence of the endangered Amur leopard.
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5
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Bosse M, van Loon S. Challenges in quantifying genome erosion for conservation. Front Genet 2022; 13:960958. [PMID: 36226192 PMCID: PMC9549127 DOI: 10.3389/fgene.2022.960958] [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: 06/03/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.
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Affiliation(s)
- Mirte Bosse
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mirte Bosse,
| | - Sam van Loon
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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6
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Bled F, Cherry MJ, Garrison EP, Miller KV, Conner LM, Abernathy HN, Ellsworth WH, Margenau LLS, Crawford DA, Engebretsen KN, Kelly BD, Shindle DB, Chandler RB. Balancing carnivore conservation and sustainable hunting of a key prey species: A case study on the Florida panther and white‐tailed deer. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florent Bled
- Warnell School of Forestry and Natural Resources The University of Georgia Athens GA USA
- Florida Fish and Wildlife Conservation Commission St. Petersburg FL USA
| | - Michael J. Cherry
- Caesar Kleberg Wildlife Research Institute Texas A&M University‐Kingsville Kingsville TX USA
| | - Elina P. Garrison
- Florida Fish and Wildlife Conservation Commission Gainesville FL USA
| | - Karl V. Miller
- Warnell School of Forestry and Natural Resources The University of Georgia Athens GA USA
| | | | - Heather N. Abernathy
- Caesar Kleberg Wildlife Research Institute Texas A&M University‐Kingsville Kingsville TX USA
- Department of Fish and Wildlife Conservation Virginia Polytechnic Institute and State University Blacksburg VA USA
| | - W. Hunter Ellsworth
- Department of Fish and Wildlife Conservation Virginia Polytechnic Institute and State University Blacksburg VA USA
| | - Lydia L. S. Margenau
- Warnell School of Forestry and Natural Resources The University of Georgia Athens GA USA
| | - Daniel A. Crawford
- Warnell School of Forestry and Natural Resources The University of Georgia Athens GA USA
| | - Kristin N. Engebretsen
- Warnell School of Forestry and Natural Resources The University of Georgia Athens GA USA
| | - Brian D. Kelly
- Warnell School of Forestry and Natural Resources The University of Georgia Athens GA USA
| | - David B. Shindle
- U.S. Fish and Wildlife Service Florida Ecological Services Field Office Immokalee FL USA
| | - Richard B. Chandler
- Warnell School of Forestry and Natural Resources The University of Georgia Athens GA USA
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Whitacre LK, Wildhaber ML, Johnson GS, Durbin HJ, Rowan TN, Tribe P, Schnabel RD, Mhlanga-Mutangadura T, Tabor VM, Fenner D, Decker JE. Exploring genetic variation and population structure in a threatened species, Noturus placidus, with whole-genome sequence data. G3 (BETHESDA, MD.) 2022; 12:jkac046. [PMID: 35188205 PMCID: PMC8982419 DOI: 10.1093/g3journal/jkac046] [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: 08/26/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The Neosho madtom (Noturus placidus) is a small catfish, generally less than 3 inches in length, unique to the Neosho-Spring River system within the Arkansas River Basin. It was federally listed as threatened in 1990, largely due to habitat loss. For conservation efforts, we generated whole-genome sequence data from 10 Neosho madtom individuals originating from 3 geographically separated populations to evaluate genetic diversity and population structure. A Neosho madtom genome was de novo assembled, and genome size and content were assessed. Single nucleotide polymorphisms were assessed from de Bruijn graphs, and via reference alignment with both the channel catfish (Ictalurus punctatus) reference genome and Neosho madtom reference genome. Principal component analysis and structure analysis indicated weak population structure, suggesting fish from the 3 locations represent a single population. Using a novel method, genome-wide conservation and divergence between the Neosho madtom, channel catfish, and zebrafish (Danio rerio) was assessed by pairwise contig alignment, which demonstrated that genes important to embryonic development frequently had conserved sequences. This research in a threatened species with no previously published genomic resources provides novel genetic information to guide current and future conservation efforts and demonstrates that using whole-genome sequencing provides detailed information of population structure and demography using only a limited number of rare and valuable samples.
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Affiliation(s)
- Lynsey K Whitacre
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
| | - Mark L Wildhaber
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO 65201, USA
| | - Gary S Johnson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Harly J Durbin
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
| | - Troy N Rowan
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
| | - Peoria Tribe
- The Peoria Tribe of Indians of Oklahoma, Miami, OK 74354, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
| | - Tendai Mhlanga-Mutangadura
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Vernon M Tabor
- U.S. Fish and Wildlife Service, Kansas Ecological Services Field Office, Manhattan, KS 66502, USA
| | - Daniel Fenner
- U.S. Fish and Wildlife Service, Oklahoma Ecological Services Field Office, Tulsa, OK 74129, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
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8
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Kearns AM, Campana MG, Slikas B, Berry L, Saitoh T, Cibois A, Fleischer RC. Conservation genomics and systematics of a near-extinct island radiation. Mol Ecol 2022; 31:1995-2012. [PMID: 35119154 DOI: 10.1111/mec.16382] [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: 10/14/2021] [Revised: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
Abstract
Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mtDNA, nuclear SNPs support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographic structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that predate modern anthropogenic threats require further study with denser population sampling. Our study highlights the value conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragments their ranges and contributes to rapid declines in population abundances.
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Affiliation(s)
- Anna M Kearns
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Beth Slikas
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA.,Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Lainie Berry
- Department of Lands and Natural Resources, Commonwealth of the Northern Mariana Islands, Saipan, MP, 96950, USA.,Hawaii Department of Land and Natural Resources-Division of Forestry and Wildlife, Honolulu, HI, 96813, USA
| | - Takema Saitoh
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan
| | - Alice Cibois
- Natural History Museum of Geneva, CP, 6434, 1211, Geneva, Switzerland
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
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OUP accepted manuscript. J Mammal 2022. [DOI: 10.1093/jmammal/gyac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Heckwolf MJ, Morim T, Riccioli F, Baltazar-Soares M. Fresh start after rough rides: understanding patterns of genetic differentiation upon human-mediated translocations. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02605-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Chaudhary V, Oli MK. False dichotomy in population viability analysis quality assessment: reply to Lawson et al. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1686-1688. [PMID: 34405449 DOI: 10.1111/cobi.13819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Vratika Chaudhary
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA
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13
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Location and extent of unoccupied panther (Puma concolor coryi) habitat in Florida: Opportunities for recovery. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Hostetler JA, Martin J, Kosempa M, Edwards HH, Rood KA, Barton SL, Runge MC. Reconstructing population dynamics of a threatened marine mammal using multiple data sets. Sci Rep 2021; 11:2702. [PMID: 33514785 PMCID: PMC7846604 DOI: 10.1038/s41598-021-81478-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Models of marine mammal population dynamics have been used extensively to predict abundance. A less common application of these models is to reconstruct historical population dynamics, filling in gaps in observation data by integrating information from multiple sources. We developed an integrated population model for the Florida manatee (Trichechus manatus latirostris) to reconstruct its population dynamics in the southwest region of the state over the past 20 years. Our model improved precision of key parameter estimates and permitted inference on poorly known parameters. Population growth was slow (averaging 1.02; 95% credible interval 1.01-1.03) but not steady, and an unusual mortality event in 2013 led to an estimated net loss of 332 (217-466) manatees. Our analyses showed that precise estimates of abundance could be derived from estimates of vital rates and a few input estimates of abundance, which may mean costly surveys to estimate abundance don't need to be conducted as frequently. Our study also shows that retrospective analyses can be useful to: (1) model the transient dynamics of age distribution; (2) assess and communicate the conservation status of wild populations; and (3) improve our understanding of environmental effects on population dynamics and thus enhance our ability to forecast.
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Affiliation(s)
- Jeffrey A. Hostetler
- grid.427218.a0000 0001 0556 4516Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL 33701 USA ,grid.462979.70000 0001 2287 7477Present Address: Patuxent Wildlife Research Center, U.S. Fish and Wildlife Service, Laurel, MD 20708 USA
| | - Julien Martin
- grid.2865.90000000121546924Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, FL 32653 USA ,grid.2865.90000000121546924U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL 33701 USA
| | - Michael Kosempa
- grid.427218.a0000 0001 0556 4516Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL 33701 USA
| | - Holly H. Edwards
- grid.427218.a0000 0001 0556 4516Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL 33701 USA
| | - Kari A. Rood
- grid.427218.a0000 0001 0556 4516Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL 33701 USA
| | - Sheri L. Barton
- grid.285683.20000 0000 8907 1788Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236 USA
| | - Michael C. Runge
- grid.2865.90000000121546924Patuxent Wildlife Research Center, U.S. Geological Survey, 12100 Beech Forest Road, Laurel, MD 20708 USA
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15
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Rose C, Prange IS, Landry SM. Extirpated, immigrated, genetically stratified—first demographic assessment of a recovering bobcat (Lynx rufus) population after a century of extinction. MAMMAL RES 2020. [DOI: 10.1007/s13364-019-00462-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Chaudhary V, Oli MK. A critical appraisal of population viability analysis. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:26-40. [PMID: 31435956 DOI: 10.1111/cobi.13414] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/06/2019] [Accepted: 06/04/2019] [Indexed: 06/10/2023]
Abstract
Population viability analysis (PVA) is useful in management of imperiled species. Applications range from research design, threat assessment, and development of management frameworks. Given the importance of PVAs, it is essential that they be rigorous and adhere to widely accepted guidelines; however, the quality of published PVAs is rarely assessed. We evaluated the quality of 160 PVAs of 144 species of birds and mammals published in peer-reviewed journals from 1990 to 2017. We hypothesized that PVA quality would be lower with generic programs than with custom-built programs; be higher for those developed for imperiled species; change over time; and be higher for those published in journals with high impact factors (IFs). Each included study was evaluated based on answers to an evaluation framework containing 32 questions reflecting whether and to what extent the PVA study adhered to published PVA guidelines or contained important PVA components. All measures of PVA quality were generally lower for studies based on generic programs. Conservation status of the species did not affect any measure of PVA quality, but PVAs published in high IF journals were of higher quality. Quality generally declined over time, suggesting the quantitative literacy of PVA practitioners has not increased over time or that PVAs developed by unskilled users are being published in peer-reviewed journals. Only 18.1% of studies were of high quality (score >75%), which is troubling because poor-quality PVAs could misinform conservation decisions. We call for increased scrutiny of PVAs by journal editors and reviewers. Our evaluation framework can be used for this purpose. Because poor-quality PVAs continue to be published, we recommend caution while using PVA results in conservation decision making without thoroughly assessing the PVA quality.
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Affiliation(s)
- Vratika Chaudhary
- Department of Wildlife Ecology and Conservation, Newins-Zeigler Hall, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, Newins-Zeigler Hall, University of Florida, Gainesville, FL, 32611, U.S.A
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17
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Kerk M, Onorato DP, Hostetler JA, Bolker BM, Oli MK. Dynamics, Persistence, and Genetic Management of the Endangered Florida Panther Population. WILDLIFE MONOGRAPHS 2019. [DOI: 10.1002/wmon.1041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Madelon Kerk
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
| | - David P. Onorato
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 298 Sabal Palm Road Naples FL 34114 USA
| | - Jeffrey A. Hostetler
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 100 8th Avenue SE St. Petersburg FL 33701 USA
| | - Benjamin M. Bolker
- Departments of Mathematics and Statistics and Biology McMaster University 314 Hamilton Hall Hamilton ON L8S 4K1 Canada
| | - Madan K. Oli
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
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18
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Grueber CE, Fox S, McLennan EA, Gooley RM, Pemberton D, Hogg CJ, Belov K. Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild. Evol Appl 2019; 12:280-291. [PMID: 30697339 PMCID: PMC6346650 DOI: 10.1111/eva.12715] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 08/15/2018] [Accepted: 09/04/2018] [Indexed: 12/18/2022] Open
Abstract
For bottlenecked populations of threatened species, supplementation often leads to improved population metrics (genetic rescue), provided that guidelines can be followed to avoid negative outcomes. In cases where no "ideal" source populations exist, or there are other complicating factors such as prevailing disease, the benefit of supplementation becomes uncertain. Bringing multiple data and analysis types together to plan genetic management activities can help. Here, we consider three populations of Tasmanian devil, Sarcophilus harrisii, as candidates for genetic rescue. Since 1996, devil populations have been severely impacted by devil facial tumour disease (DFTD), causing significant population decline and fragmentation. Like many threatened species, the key threatening process for devils cannot currently be fully mitigated, so species management requires a multifaceted approach. We examined diversity of 31 putatively neutral and 11 MHC-linked microsatellite loci of three remnant wild devil populations (one sampled at two time-points), alongside computational diversity projections, parameterized by field data from DFTD-present and DFTD-absent sites. Results showed that populations had low diversity, connectivity was poor, and diversity has likely decreased over the last decade. Stochastic simulations projected further diversity losses. For a given population size, the effects of DFTD on population demography (including earlier age at death and increased female productivity) did not impact diversity retention, which was largely driven by final population size. Population sizes ≥500 (depending on the number of founders) were necessary for maintaining diversity in otherwise unmanaged populations, even if DFTD is present. Models indicated that smaller populations could maintain diversity with ongoing immigration. Taken together, our results illustrate how multiple analysis types can be combined to address complex population genetic challenges.
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Affiliation(s)
- Catherine E. Grueber
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- San Diego Zoo GlobalSan DiegoCalifornia
| | - Samantha Fox
- Save the Tasmanian Devil ProgramDPIPWEHobartTasmaniaAustralia
- Toledo ZooToledoOhio
| | - Elspeth A. McLennan
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Rebecca M. Gooley
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - David Pemberton
- Save the Tasmanian Devil ProgramDPIPWEHobartTasmaniaAustralia
| | - Carolyn J. Hogg
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Zoo and Aquarium Association AustralasiaMosmanNew South WalesAustralia
| | - Katherine Belov
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
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19
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Acosta AL, d'Albertas F, de Souza Leite M, Saraiva AM, Walter Metzger JP. Gaps and limitations in the use of restoration scenarios: a review. Restor Ecol 2018. [DOI: 10.1111/rec.12882] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Andre L. Acosta
- Department of Ecology, Biosciences Institute; Universidade de São Paulo - Rua do Matão; Travessa 14, No. 321, 05508-090, São Paulo SP Brazil
- Research Center on Biodiversity and Computing; Universidade de São Paulo - Av. Prof. Luciano Gualberto; Travessa 3, No. 158, 05508-900, São Paulo SP Brazil
- Biodiversity and Ecosystem Scenarios Network (ScenNet-FAPESP and Belmont Forum); Brazil Headquarter: Biosciences Institute, Universidade de São Paulo - Rua do Matão; Travessa 14, No. 321, 05508-090, São Paulo SP Brazil
| | - Francisco d'Albertas
- Department of Ecology, Biosciences Institute; Universidade de São Paulo - Rua do Matão; Travessa 14, No. 321, 05508-090, São Paulo SP Brazil
- Biodiversity and Ecosystem Scenarios Network (ScenNet-FAPESP and Belmont Forum); Brazil Headquarter: Biosciences Institute, Universidade de São Paulo - Rua do Matão; Travessa 14, No. 321, 05508-090, São Paulo SP Brazil
| | - Melina de Souza Leite
- Department of Ecology, Biosciences Institute; Universidade de São Paulo - Rua do Matão; Travessa 14, No. 321, 05508-090, São Paulo SP Brazil
| | - Antonio M. Saraiva
- Research Center on Biodiversity and Computing; Universidade de São Paulo - Av. Prof. Luciano Gualberto; Travessa 3, No. 158, 05508-900, São Paulo SP Brazil
- Department of Computing and Digital Systems Engineering; Polytechnic School, Universidade de São Paulo - Av. Prof. Luciano Gualberto; No. 380, 05508-970, São Paulo SP Brazil
- Biodiversity and Ecosystem Scenarios Network (ScenNet-FAPESP and Belmont Forum); Brazil Headquarter: Biosciences Institute, Universidade de São Paulo - Rua do Matão; Travessa 14, No. 321, 05508-090, São Paulo SP Brazil
| | - Jean P. Walter Metzger
- Department of Ecology, Biosciences Institute; Universidade de São Paulo - Rua do Matão; Travessa 14, No. 321, 05508-090, São Paulo SP Brazil
- Biodiversity and Ecosystem Scenarios Network (ScenNet-FAPESP and Belmont Forum); Brazil Headquarter: Biosciences Institute, Universidade de São Paulo - Rua do Matão; Travessa 14, No. 321, 05508-090, São Paulo SP Brazil
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20
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Zubillaga M, Skewes O, Soto N, Rabinovich JE. How density-dependence and climate affect guanaco population dynamics. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Mathieu-Bégné E, Loot G, Chevalier M, Paz-Vinas I, Blanchet S. Demographic and genetic collapses in spatially structured populations: insights from a long-term survey in wild fish metapopulations. OIKOS 2018. [DOI: 10.1111/oik.05511] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eglantine Mathieu-Bégné
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
| | - Géraldine Loot
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
- Inst. Universitaire de France; Paris France
| | - Mathieu Chevalier
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
| | - Ivan Paz-Vinas
- Univ. de Lyon, Ecole Nationale des Travaux Publics de l'Etat (ENTPE), CNRS; UMR5023, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés; Villeurbanne France
- UPS, INP, CNRS, Univ. de Toulouse, UMR 5245 Laboratoire Écologie Fonctionnelle et Environnement; Ecolab Toulouse France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
- CNRS, UPS; UMR5321, Station d'Ecologie Théorique et Expérimentale; Moulis France
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22
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Criffield M, van de Kerk M, Leone E, Cunningham MW, Lotz M, Oli MK, Onorato DP. Assessing impacts of intrinsic and extrinsic factors on Florida panther movements. J Mammal 2018. [DOI: 10.1093/jmammal/gyy025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marc Criffield
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL, USA
| | - Madelon van de Kerk
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Erin Leone
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, USA
| | - Mark W Cunningham
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, USA
| | - Mark Lotz
- Division of Habitat and Species Conservation, Florida Fish and Wildlife Conservation Commission, Naples, FL, USA
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Dave P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL, USA
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23
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Manlik O, Lacy RC, Sherwin WB. Applicability and limitations of sensitivity analyses for wildlife management. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.13044] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oliver Manlik
- School of Biological, Earth and Environmental Sciences; Evolution and Ecology Research Centre; University of New South Wales; Sydney NSW Australia
| | | | - William B. Sherwin
- School of Biological, Earth and Environmental Sciences; Evolution and Ecology Research Centre; University of New South Wales; Sydney NSW Australia
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24
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Ochoa A, Onorato DP, Fitak RR, Roelke-Parker ME, Culver M. Evolutionary and Functional Mitogenomics Associated With the Genetic Restoration of the Florida Panther. J Hered 2017; 108:449-455. [PMID: 28204600 DOI: 10.1093/jhered/esx015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/14/2017] [Indexed: 01/02/2023] Open
Abstract
Florida panthers are endangered pumas that currently persist in reduced patches of habitat in South Florida, USA. We performed mitogenome reference-based assemblies for most parental lines of the admixed Florida panthers that resulted from the introduction of female Texas pumas into South Florida in 1995. With the addition of 2 puma mitogenomes, we characterized 174 single nucleotide polymorphisms (SNPs) across 12 individuals. We defined 5 haplotypes (Pco1-Pco5), one of which (Pco1) had a geographic origin exclusive to Costa Rica and Panama and was possibly introduced into the Everglades National Park, Florida, prior to 1995. Haplotype Pco2 was native to Florida. Haplotypes Pco3 and Pco4 were exclusive to Texas, whereas haplotype Pco5 had an undetermined geographic origin. Phylogenetic inference suggests that haplotypes Pco1-Pco4 diverged ~202000 (95% HPDI = 83000-345000) years ago and that haplotypes Pco2-Pco4 diverged ~61000 (95% HPDI = 9000-127000) years ago. These results are congruent with a south-to-north continental expansion and with a recent North American colonization by pumas. Furthermore, pumas may have migrated from Texas to Florida no earlier than ~44000 (95% HPDI = 2000-98000) years ago. Synonymous mutations presented a greater mean substitution rate than other mitochondrial functional regions: nonsynonymous mutations, tRNAs, rRNAs, and control region. Similarly, all protein-coding genes were under predominant negative selection constraints. We directly and indirectly assessed the presence of potential deleterious SNPs in the ND2 and ND5 genes in Florida panthers prior to and as a consequence of the introduction of Texas pumas. Screenings for such variants are recommended in extant Florida panthers.
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Affiliation(s)
- Alexander Ochoa
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
| | - David P Onorato
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
| | - Robert R Fitak
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
| | - Melody E Roelke-Parker
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
| | - Melanie Culver
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
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25
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Romero MA, Grandi MF, Koen-Alonso M, Svendsen G, Ocampo Reinaldo M, García NA, Dans SL, González R, Crespo EA. Analysing the natural population growth of a large marine mammal after a depletive harvest. Sci Rep 2017; 7:5271. [PMID: 28706228 PMCID: PMC5509669 DOI: 10.1038/s41598-017-05577-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/30/2017] [Indexed: 11/25/2022] Open
Abstract
An understanding of the underlying processes and comprehensive history of population growth after a harvest-driven depletion is necessary when assessing the long-term effectiveness of management and conservation strategies. The South American sea lion (SASL), Otaria flavescens, is the most conspicuous marine mammal along the South American coasts, where it has been heavily exploited. As a consequence of this exploitation, many of its populations were decimated during the early 20th century but currently show a clear recovery. The aim of this study was to assess SASL population recovery by applying a Bayesian state-space modelling framework. We were particularly interested in understanding how the population responds at low densities, how human-induced mortality interplays with natural mechanisms, and how density-dependence may regulate population growth. The observed population trajectory of SASL shows a non-linear relationship with density, recovering with a maximum increase rate of 0.055. However, 50 years after hunting cessation, the population still represents only 40% of its pre-exploitation abundance. Considering that the SASL population in this region represents approximately 72% of the species abundance within the Atlantic Ocean, the present analysis provides insights into the potential mechanisms regulating the dynamics of SASL populations across the global distributional range of the species.
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Affiliation(s)
- M A Romero
- Instituto de Biología Marina y Pesquera Almirante Storni, Escuela Superior de Ciencias Marinas - Universidad Nacional del Comahue, San Martín 247, 8520, San Antonio, Oeste (RN), Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - M F Grandi
- Laboratorio de Mamíferos Marinos, Centro para el Estudio de Sistemas Marinos (CESIMAR) CCT-CENPAT-CONICET, Bvd. Brown 2915, 9120, Puerto Madryn, Chubut, Argentina
| | - M Koen-Alonso
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, A1C 5X1, Newfoundland and Labrador, Canada
| | - G Svendsen
- Instituto de Biología Marina y Pesquera Almirante Storni, Escuela Superior de Ciencias Marinas - Universidad Nacional del Comahue, San Martín 247, 8520, San Antonio, Oeste (RN), Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Ocampo Reinaldo
- Instituto de Biología Marina y Pesquera Almirante Storni, Escuela Superior de Ciencias Marinas - Universidad Nacional del Comahue, San Martín 247, 8520, San Antonio, Oeste (RN), Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - N A García
- Laboratorio de Mamíferos Marinos, Centro para el Estudio de Sistemas Marinos (CESIMAR) CCT-CENPAT-CONICET, Bvd. Brown 2915, 9120, Puerto Madryn, Chubut, Argentina
| | - S L Dans
- Laboratorio de Mamíferos Marinos, Centro para el Estudio de Sistemas Marinos (CESIMAR) CCT-CENPAT-CONICET, Bvd. Brown 2915, 9120, Puerto Madryn, Chubut, Argentina
- Universidad Nacional de la Patagonia San Juan Bosco, Bvd. Brown 3051, 9120, Puerto Madryn, Chubut, Argentina
| | - R González
- Instituto de Biología Marina y Pesquera Almirante Storni, Escuela Superior de Ciencias Marinas - Universidad Nacional del Comahue, San Martín 247, 8520, San Antonio, Oeste (RN), Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - E A Crespo
- Laboratorio de Mamíferos Marinos, Centro para el Estudio de Sistemas Marinos (CESIMAR) CCT-CENPAT-CONICET, Bvd. Brown 2915, 9120, Puerto Madryn, Chubut, Argentina
- Universidad Nacional de la Patagonia San Juan Bosco, Bvd. Brown 3051, 9120, Puerto Madryn, Chubut, Argentina
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26
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Trask AE, Bignal EM, McCracken DI, Piertney SB, Reid JM. Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity. J Anim Ecol 2017; 86:1082-1093. [PMID: 28543048 DOI: 10.1111/1365-2656.12703] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/05/2017] [Indexed: 01/25/2023]
Abstract
A population's effective size (Ne ) is a key parameter that shapes rates of inbreeding and loss of genetic diversity, thereby influencing evolutionary processes and population viability. However, estimating Ne , and identifying key demographic mechanisms that underlie the Ne to census population size (N) ratio, remains challenging, especially for small populations with overlapping generations and substantial environmental and demographic stochasticity and hence dynamic age-structure. A sophisticated demographic method of estimating Ne /N, which uses Fisher's reproductive value to account for dynamic age-structure, has been formulated. However, this method requires detailed individual- and population-level data on sex- and age-specific reproduction and survival, and has rarely been implemented. Here, we use the reproductive value method and detailed demographic data to estimate Ne /N for a small and apparently isolated red-billed chough (Pyrrhocorax pyrrhocorax) population of high conservation concern. We additionally calculated two single-sample molecular genetic estimates of Ne to corroborate the demographic estimate and examine evidence for unobserved immigration and gene flow. The demographic estimate of Ne /N was 0.21, reflecting a high total demographic variance (σ2dg) of 0.71. Females and males made similar overall contributions to σ2dg. However, contributions varied among sex-age classes, with greater contributions from 3 year-old females than males, but greater contributions from ≥5 year-old males than females. The demographic estimate of Ne was ~30, suggesting that rates of increase of inbreeding and loss of genetic variation per generation will be relatively high. Molecular genetic estimates of Ne computed from linkage disequilibrium and approximate Bayesian computation were approximately 50 and 30, respectively, providing no evidence of substantial unobserved immigration which could bias demographic estimates of Ne . Our analyses identify key sex-age classes contributing to demographic variance and thus decreasing Ne /N in a small age-structured population inhabiting a variable environment. They thereby demonstrate how assessments of Ne can incorporate stochastic sex- and age-specific demography and elucidate key demographic processes affecting a population's evolutionary trajectory and viability. Furthermore, our analyses show that Ne for the focal chough population is critically small, implying that management to re-establish genetic connectivity may be required to ensure population viability.
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Affiliation(s)
- Amanda E Trask
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Eric M Bignal
- Scottish Chough Study Group, Isle of Islay, Argyll, UK
| | | | - Stuart B Piertney
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Jane M Reid
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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27
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Mussmann SM, Douglas MR, Anthonysamy WJB, Davis MA, Simpson SA, Louis W, Douglas ME. Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160736. [PMID: 28386428 PMCID: PMC5367285 DOI: 10.1098/rsos.160736] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/25/2017] [Indexed: 06/07/2023]
Abstract
A central question in conservation is how best to manage biodiversity, despite human domination of global processes (= Anthropocene). Common responses (i.e. translocations, genetic rescue) forestall potential extirpations, yet have an uncertain duration. A textbook example is the greater prairie chicken (GRPC: Tympanuchus cupido pinnatus), where translocations (1992-1998) seemingly rescued genetically depauperate Illinois populations. We re-evaluated this situation after two decades by genotyping 21 microsatellite loci from 1831 shed feathers across six leks in two counties over 4 years (2010-2013). Low migration rates (less than 1%) established each county as demographically independent, but with declining-population estimates (4 year average N = 79). Leks were genetically similar and significantly bottlenecked, with low effective population sizes (average Ne = 13.1; 4 year Ne/N = 0.166). Genetic structure was defined by 12 significantly different family groups, with relatedness r = 0.31 > half-sib r = 0.25. Average heterozygosity, indicating short-term survival, did not differ among contemporary, pre- and post-translocated populations, whereas allelic diversity did. Our results, the natural history of GRPC (i.e. few leks, male dominance hierarchies) and its controlled immigration suggest demographic expansion rather than genetic rescue. Legal protection under the endangered species act (ESA) may enhance recovery, but could exacerbate political-economic concerns on how best to manage 'conservation-reliant' species, for which GRPC is now an exemplar.
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Affiliation(s)
- S. M. Mussmann
- Biological Sciences, University of Arkansas, Fayetteville, AR, USA
- Illinois Natural History Survey, University of Illinois, Champaign, IL, USA
| | - M. R. Douglas
- Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | | | - M. A. Davis
- Illinois Natural History Survey, University of Illinois, Champaign, IL, USA
| | - S. A. Simpson
- Illinois Department of Natural Resources, Prairie Ridge State Natural Area, Newton, IL, USA
| | - W. Louis
- Illinois Department of Natural Resources, Gibson City, IL, USA
| | - M. E. Douglas
- Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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Fulgione D, Rippa D, Buglione M, Trapanese M, Petrelli S, Maselli V. Unexpected but welcome. Artificially selected traits may increase fitness in wild boar. Evol Appl 2016; 9:769-76. [PMID: 27330553 PMCID: PMC4908463 DOI: 10.1111/eva.12383] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/12/2016] [Indexed: 01/13/2023] Open
Abstract
Artificial selection affects phenotypes differently by natural selection. Domestic traits, which pass into the wild, are usually negatively selected. Yet, exceptionally, this axiom may fail to apply if genes, from the domestic animals, increase fertility in the wild. We studied a rare case of a wild boar population under the framework of Wright's interdemic selection model, which could explain gene flow between wild boar and pig, both considered as demes. We analysed the MC1R gene and microsatellite neutral loci in 62 pregnant wild boars as markers of hybridization, and we correlated nucleotide mutations on MC1R (which are common in domestic breeds) to litter size, as an evaluation of fitness in wild sow. Regardless of body size and phyletic effects, wild boar sows bearing nonsynonymous MC1R mutations produced larger litters. This directly suggests that artificially selected traits reaching wild populations, through interdemic gene flow, could bypass natural selection if and only if they increase the fitness in the wild.
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Affiliation(s)
| | - Daniela Rippa
- Department of Biology University of Naples Federico II Naples Italy
| | - Maria Buglione
- Department of Biology University of Naples Federico II Naples Italy
| | | | - Simona Petrelli
- Department of Biology University of Naples Federico II Naples Italy
| | - Valeria Maselli
- Department of Biology University of Naples Federico II Naples Italy
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Miller JM, Hamilton JA. Interspecies hybridization in the conservation toolbox: response to Kovach et al. (2016). CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:431-433. [PMID: 26918380 DOI: 10.1111/cobi.12677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 12/30/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem St. New Haven, CT, 06520, U.S.A
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58102, U.S.A
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Hamilton JA, Miller JM. Adaptive introgression as a resource for management and genetic conservation in a changing climate. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:33-41. [PMID: 26096581 DOI: 10.1111/cobi.12574] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 05/22/2023]
Abstract
Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species' and populations' ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species' ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced-generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate.
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Affiliation(s)
- Jill A Hamilton
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, U.S.A..
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58102, U.S.A..
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
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Schregel J, Eiken HG, Grøndahl FA, Hailer F, Aspi J, Kojola I, Tirronen K, Danilov P, Rykov A, Poroshin E, Janke A, Swenson JE, Hagen SB. Y chromosome haplotype distribution of brown bears (Ursus arctos
) in Northern Europe provides insight into population history and recovery. Mol Ecol 2015; 24:6041-60. [DOI: 10.1111/mec.13448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 10/17/2015] [Accepted: 10/26/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Julia Schregel
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
| | | | - Frank Hailer
- School of Biosciences; Cardiff University; Cardiff CF10 3AX Wales UK
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Jouni Aspi
- Department of Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Ilpo Kojola
- Natural Resources Institute; P.O. Box 16 96301 Rovaniemi Finland
| | - Konstantin Tirronen
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Piotr Danilov
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Alexander Rykov
- Pinezhsky Strict Nature Reserve; Pervomayskaja 123a 164610 Pinega Russian Federation
| | - Eugene Poroshin
- Institute of Biology; Komi Research Centre of the Russian Academy of Science; 016761 Syktvkar Russian Federation
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
- Goethe University Frankfurt; Institute for Ecology; Evolution & Diversity; 60438 Frankfurt am Main Germany
| | - Jon E. Swenson
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
- Norwegian Institute for Nature Research; 7485 Trondheim Norway
| | - Snorre B. Hagen
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
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33
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Wisely SM, Ryder OA, Santymire RM, Engelhardt JF, Novak BJ. A Road Map for 21st Century Genetic Restoration: Gene Pool Enrichment of the Black-Footed Ferret. J Hered 2015; 106:581-92. [PMID: 26304983 PMCID: PMC4567841 DOI: 10.1093/jhered/esv041] [Citation(s) in RCA: 27] [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] [Received: 01/23/2015] [Accepted: 06/07/2015] [Indexed: 12/15/2022] Open
Abstract
Interspecies somatic cell nuclear transfer (iSCNT) could benefit recovery programs of critically endangered species but must be weighed with the risks of failure. To weigh the risks and benefits, a decision-making process that evaluates progress is needed. Experiments that evaluate the efficiency and efficacy of blastocyst, fetal, and post-parturition development are necessary to determine the success or failure or species-specific iSCNT programs. Here, we use the black-footed ferret (Mustela nigripes) as a case study for evaluating this emerging biomedical technology as a tool for genetic restoration. The black-footed ferret has depleted genetic variation yet genome resource banks contain genetic material of individuals not currently represented in the extant lineage. Thus, genetic restoration of the species is in theory possible and could help reduce the persistent erosion of genetic diversity from drift. Extensive genetic, genomic, and reproductive science tools have previously been developed in black-footed ferrets and would aid in the process of developing an iSCNT protocol for this species. Nonetheless, developing reproductive cloning will require years of experiments and a coordinated effort among recovery partners. The information gained from a well-planned research effort with the goal of genetic restoration via reproductive cloning could establish a 21st century model for evaluating and implementing conservation breeding that would be applicable to other genetically impoverished species.
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Affiliation(s)
- Samantha M Wisely
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak).
| | - Oliver A Ryder
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - Rachel M Santymire
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - John F Engelhardt
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - Ben J Novak
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
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Vickers TW, Sanchez JN, Johnson CK, Morrison SA, Botta R, Smith T, Cohen BS, Huber PR, Ernest HB, Boyce WM. Survival and Mortality of Pumas (Puma concolor) in a Fragmented, Urbanizing Landscape. PLoS One 2015; 10:e0131490. [PMID: 26177290 PMCID: PMC4503643 DOI: 10.1371/journal.pone.0131490] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/01/2015] [Indexed: 12/02/2022] Open
Abstract
Wide-ranging large carnivores pose myriad challenges for conservation, especially in highly fragmented landscapes. Over a 13-year period, we combined monitoring of radio collared pumas (Puma concolor) with complementary multi-generational genetic analyses to inform puma conservation in southern California, USA. Our goals were to generate survivorship estimates, determine causes of mortality, identify barriers to movement, and determine the genetic and demographic challenges to puma persistence among >20,000,000 people and extensive urban, suburban, and exurban development. Despite protection from hunting, annual survival for radio collared pumas was surprisingly low (55.8%), and humans caused the majority of puma deaths. The most common sources of mortality were vehicle collisions (28% of deaths), and mortalities resulting from depredation permits issued after pumas killed domestic animals (17% of deaths). Other human-caused mortalities included illegal shootings, public safety removals, and human-caused wildfire. An interstate highway (I-15) bisecting this study area, and associated development, have created a nearly impermeable barrier to puma movements, resulting in severe genetic restriction and demographic isolation of the small puma population (n ~ 17-27 adults) in the Santa Ana Mountains west of I-15. Highways that bisect habitat or divide remaining "conserved" habitat, and associated ongoing development, threaten to further subdivide this already fragmented puma population and increase threats to survival. This study highlights the importance of combining demographic and genetic analyses, and illustrates that in the absence of effective measures to reduce mortality and enhance safe movement across highways, translocation of pumas, such as was done with the endangered Florida panther (P. c. coryi), may ultimately be necessary to prevent further genetic decline and ensure persistence of the Santa Ana Mountains population.
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Affiliation(s)
- T. Winston Vickers
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Jessica N. Sanchez
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Christine K. Johnson
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Scott A. Morrison
- The Nature Conservancy, San Francisco, California, United States of America
| | - Randy Botta
- California Department of Fish and Wildlife, Valley Center, California, United States of America
| | - Trish Smith
- The Nature Conservancy, San Francisco, California, United States of America
| | - Brian S. Cohen
- The Nature Conservancy, San Francisco, California, United States of America
| | - Patrick R. Huber
- Information Center for the Environment, University of California Davis, Davis, California, United States of America
| | - Holly B. Ernest
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Walter M. Boyce
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
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35
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Hostetler JA, Chandler RB. Improved state-space models for inference about spatial and temporal variation in abundance from count data. Ecology 2015. [DOI: 10.1890/14-1487.1] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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36
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Pierson JC, Beissinger SR, Bragg JG, Coates DJ, Oostermeijer JGB, Sunnucks P, Schumaker NH, Trotter MV, Young AG. Incorporating evolutionary processes into population viability models. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:755-764. [PMID: 25494697 DOI: 10.1111/cobi.12431] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/03/2014] [Indexed: 06/04/2023]
Abstract
We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence.
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Affiliation(s)
| | - Steven R Beissinger
- Department of Environmental Science, Policy and Management, and Museum of Vertebrate Zoology, UC Berkeley, Berkeley, CA, 94720, U.S.A
| | - Jason G Bragg
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - David J Coates
- Plant Science and Herbarium Program, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, Bentley, WA, 6983, Australia
| | - J Gerard B Oostermeijer
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, VIC, 3800, Australia
| | - Nathan H Schumaker
- Western Ecology Division, Environmental Protection Agency, Corvallis, OR, 97333, U.S.A
| | | | - Andrew G Young
- CSIRO Plant Industry, P.O. Box 1600, Canberra, ACT, 2601, Australia
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37
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Hoffmann A, Griffin P, Dillon S, Catullo R, Rane R, Byrne M, Jordan R, Oakeshott J, Weeks A, Joseph L, Lockhart P, Borevitz J, Sgrò C. A framework for incorporating evolutionary genomics into biodiversity conservation and management. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40665-014-0009-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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38
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Jachowski DS, Kesler DC, Steen DA, Walters JR. Redefining baselines in endangered species recovery. J Wildl Manage 2014. [DOI: 10.1002/jwmg.800] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- David S. Jachowski
- School of Agricultural, Forest, and Environmental Sciences; Clemson University; 258 Lehotsky Hall Clemson SC 29634 USA
| | - Dylan C. Kesler
- Department of Fisheries and Wildlife Sciences; University of Missouri; 302 Natural Resources Building Columbia MO 65211 USA
| | - David A. Steen
- Alabama Natural Heritage Program; Department of Biological Sciences; Auburn University; 1090 South Donahue Drive Auburn AL 36849 USA
| | - Jeffrey R. Walters
- Department of Biological Sciences; Virginia Tech, Blacksburg; 1405 Perry Street VA 24061 USA
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39
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Stelkens RB, Brockhurst MA, Hurst GDD, Greig D. Hybridization facilitates evolutionary rescue. Evol Appl 2014; 7:1209-17. [PMID: 25558281 PMCID: PMC4275092 DOI: 10.1111/eva.12214] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/05/2014] [Indexed: 12/23/2022] Open
Abstract
The resilience of populations to rapid environmental degradation is a major concern for biodiversity conservation. When environments deteriorate to lethal levels, species must evolve to adapt to the new conditions to avoid extinction. Here, we test the hypothesis that evolutionary rescue may be enabled by hybridization, because hybridization increases genetic variability. Using experimental evolution, we show that interspecific hybrid populations of Saccharomyces yeast adapt to grow in more highly degraded environments than intraspecific and parental crosses, resulting in survival rates far exceeding those of their ancestors. We conclude that hybridization can increase evolutionary responsiveness and that taxa able to exchange genes with distant relatives may better survive rapid environmental change.
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Affiliation(s)
- Rike B Stelkens
- Institute of Integrative Biology, University of Liverpool Liverpool, UK
| | | | - Gregory D D Hurst
- Institute of Integrative Biology, University of Liverpool Liverpool, UK
| | - Duncan Greig
- Max Planck Institute for Evolutionary Biology Plön, Germany ; The Galton Laboratory, Department of Genetics, Evolution, and Environment, University College London London, UK
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40
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Mowry RA, Schneider TM, Latch EK, Gompper ME, Beringer J, Eggert LS. Genetics and the successful reintroduction of the Missouri river otter. Anim Conserv 2014. [DOI: 10.1111/acv.12159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. A. Mowry
- Division of Biological Sciences; University of Missouri; Columbia MO USA
| | - T. M. Schneider
- Division of Biology; Kansas State University; Manhattan KS USA
| | - E. K. Latch
- Department of Biological Sciences; University of Wisconsin; Milwaukee WI USA
| | - M. E. Gompper
- Department of Fisheries and Wildlife Science; University of Missouri; Columbia MO USA
| | - J. Beringer
- Missouri Department of Conservation; Resource Science Center; Columbia MO USA
| | - L. S. Eggert
- Division of Biological Sciences; University of Missouri; Columbia MO USA
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41
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Conclusions: Environmental Change, Wildlife Conservation and Reproduction. REPRODUCTIVE SCIENCES IN ANIMAL CONSERVATION 2014; 753:503-14. [DOI: 10.1007/978-1-4939-0820-2_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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42
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Dowling TE, Turner TF, Carson EW, Saltzgiver MJ, Adams D, Kesner B, Marsh PC. Time-series analysis reveals genetic responses to intensive management of razorback sucker (Xyrauchen texanus). Evol Appl 2013; 7:339-54. [PMID: 24665337 PMCID: PMC3962295 DOI: 10.1111/eva.12125] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 09/26/2013] [Indexed: 11/30/2022] Open
Abstract
Time-series analysis is used widely in ecology to study complex phenomena and may have considerable potential to clarify relationships of genetic and demographic processes in natural and exploited populations. We explored the utility of this approach to evaluate population responses to management in razorback sucker, a long-lived and fecund, but declining freshwater fish species. A core population in Lake Mohave (Arizona-Nevada, USA) has experienced no natural recruitment for decades and is maintained by harvesting naturally produced larvae from the lake, rearing them in protective custody, and repatriating them at sizes less vulnerable to predation. Analyses of mtDNA and 15 microsatellites characterized for sequential larval cohorts collected over a 15-year time series revealed no changes in geographic structuring but indicated significant increase in mtDNA diversity for the entire population over time. Likewise, ratios of annual effective breeders to annual census size (N b /N a) increased significantly despite sevenfold reduction of N a. These results indicated that conservation actions diminished near-term extinction risk due to genetic factors and should now focus on increasing numbers of fish in Lake Mohave to ameliorate longer-term risks. More generally, time-series analysis permitted robust testing of trends in genetic diversity, despite low precision of some metrics.
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Affiliation(s)
- Thomas E Dowling
- School of Life Sciences, Arizona State University Tempe, AZ, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico Albuquerque, NM, USA
| | - Evan W Carson
- Department of Biology and Museum of Southwestern Biology, University of New Mexico Albuquerque, NM, USA
| | | | - Deborah Adams
- School of Life Sciences, Arizona State University Tempe, AZ, USA
| | | | - Paul C Marsh
- School of Life Sciences, Arizona State University Tempe, AZ, USA ; Marsh & Associates Tempe, AZ, USA
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43
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van de Kerk M, de Kroon H, Conde DA, Jongejans E. Carnivora population dynamics are as slow and as fast as those of other mammals: implications for their conservation. PLoS One 2013; 8:e70354. [PMID: 23950922 PMCID: PMC3741307 DOI: 10.1371/journal.pone.0070354] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 06/18/2013] [Indexed: 11/25/2022] Open
Abstract
Of the 285 species of Carnivora 71 are threatened, while many of these species fulfill important ecological roles in their ecosystems as top or meso-predators. Population transition matrices make it possible to study how age-specific survival and fecundity affect population growth, extinction risks, and responses to management strategies. Here we review 38 matrix models from 35 studies on 27 Carnivora taxa, covering 11% of the threatened Carnivora species. We show that the elasticity patterns (i.e. distribution over fecundity, juvenile survival and adult survival) in Carnivora cover the same range in triangular elasticity plots as those of other mammal species, despite the specific place of Carnivora in the food chain. Furthermore, reproductive loop elasticity analysis shows that the studied species spread out evenly over a slow-fast continuum, but also quantifies the large variation in the duration of important life cycles and their contributions to population growth rate. These general elasticity patterns among species, and their correlation with simple life history characteristics like body mass, age of first reproduction and life span, enables the extrapolation of population dynamical properties to unstudied species. With several examples we discuss how this slow-fast continuum, and related patterns of variation in reproductive loop elasticity, can be used in the formulation of tentative management plans for threatened species that cannot wait for the results of thorough demographic studies. We argue, however, that such management programs should explicitly include a plan for learning about the key demographic rates and how these are affected by environmental drivers and threats.
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Affiliation(s)
- Madelon van de Kerk
- Radboud University Nijmegen, Institute for Water and Wetlands Research, Department of Experimental Plant Ecology, Nijmegen, The Netherlands
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America
| | - Hans de Kroon
- Radboud University Nijmegen, Institute for Water and Wetlands Research, Department of Experimental Plant Ecology, Nijmegen, The Netherlands
| | - Dalia A. Conde
- Max Planck Odense Center of Evolutionary Demography, Institute of Biology, University of Southern Denmark, Odense, Denmark
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Eelke Jongejans
- Radboud University Nijmegen, Institute for Water and Wetlands Research, Department of Animal Ecology and Ecophysiology, Nijmegen, The Netherlands
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