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Sévêque A, Lonsinger RC, Waits LP, Brzeski KE, Komoroske LM, Ott-Conn CN, Mayhew SL, Norton DC, Petroelje TR, Swenson JD, Morin DJ. Sources of bias in applying close-kin mark-recapture to terrestrial game species with different life histories. Ecology 2024; 105:e4244. [PMID: 38272487 DOI: 10.1002/ecy.4244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/18/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024]
Abstract
Close-kin mark-recapture (CKMR) is a method analogous to traditional mark-recapture but without requiring recapture of individuals. Instead, multilocus genotypes (genetic marks) are used to identify related individuals in one or more sampling occasions, which enables the opportunistic use of samples from harvested wildlife. To apply the method accurately, it is important to build appropriate CKMR models that do not violate assumptions linked to the species' and population's biology and sampling methods. In this study, we evaluated the implications of fitting overly simplistic CKMR models to populations with complex reproductive success dynamics or selective sampling. We used forward-in-time, individual-based simulations to evaluate the accuracy and precision of CKMR abundance and survival estimates in species with different longevities, mating systems, and sampling strategies. Simulated populations approximated a range of life histories among game species of North America with lethal sampling to evaluate the potential of using harvested samples to estimate population size. Our simulations show that CKMR can yield nontrivial biases in both survival and abundance estimates, unless influential life history traits and selective sampling are explicitly accounted for in the modeling framework. The number of kin pairs observed in the sample, in combination with the type of kinship used in the model (parent-offspring pairs and/or half-sibling pairs), can affect the precision and/or accuracy of the estimates. CKMR is a promising method that will likely see an increasing number of applications in the field as costs of genetic analysis continue to decline. Our work highlights the importance of applying population-specific CKMR models that consider relevant demographic parameters, individual covariates, and the protocol through which individuals were sampled.
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Affiliation(s)
- Anthony Sévêque
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Mississippi, USA
| | - Robert C Lonsinger
- U.S. Geological Survey, Oklahoma Cooperative Fish and Wildlife Research Unit, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Resources, University of Idaho, Moscow, Idaho, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Caitlin N Ott-Conn
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - Sarah L Mayhew
- Wildlife Division, Michigan Department of Natural Resources, Lansing, Michigan, USA
| | - D Cody Norton
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - Tyler R Petroelje
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - John D Swenson
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Dana J Morin
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Mississippi, USA
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2
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Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
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Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
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3
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Rosenbaum SW, May SA, Shedd KR, Cunningham CJ, Peterson RL, Elliot BW, McPhee MV. Reliability of trans-generational genetic mark-recapture (tGMR) for enumerating Pacific salmon. Evol Appl 2024; 17:e13647. [PMID: 38333554 PMCID: PMC10848877 DOI: 10.1111/eva.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
As Pacific salmon (Oncorhynchus spp.) decline across much of their range, it is imperative to further develop minimally invasive tools to quantify population abundance. One such advancement, trans-generational genetic mark-recapture (tGMR), uses parentage analysis to estimate the size of wild populations. Our study examined the precision and accuracy of tGMR through a comparison to a traditional mark-recapture estimate for Chilkat River Chinook salmon (O. tshawytscha) in Southeast Alaska. We examined how adult sampling location and timing impact tGMR by comparing estimates derived using samples collected in the lower river mainstem to those using samples obtained in upriver spawning tributaries. Results indicated that tGMR estimates using a representative sample of mainstem adults were most concordant with, and 3% more precise than, the traditional mark-recapture estimate for this stock. Importantly, the timing and location of adult sampling were found to impact abundance estimates, depending on what proportion of the population dies or moves to unsampled areas between downriver and upriver sampling events. Additionally, we identified potential sources of bias in tGMR arising from violations of key assumptions using a novel individual-based modeling framework, parameterized with empirical values from the Chilkat River. Simulations demonstrated that increased reproductive success and sampling selectivity of older, larger individuals, introduced negative bias into tGMR estimates. Our individual-based model offers a customizable and accessible method to identify and quantify these biases in tGMR applications (https://github.com/swrosenbaum/tGMR_simulations). We underscore the critical role of system-specific sampling design considerations in ensuring the precision and accuracy of tGMR projects. This study validates tGMR as a potentially useful tool for improved population enumeration in semelparous species.
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Affiliation(s)
- Samuel W. Rosenbaum
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
| | - Samuel A. May
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
| | | | - Curry J. Cunningham
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
| | | | | | - Megan V. McPhee
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
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Swenson JD, Brooks EN, Kacev D, Boyd C, Kinney MJ, Marcy‐Quay B, Sévêque A, Feldheim KA, Komoroske LM. Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments. Ecol Evol 2024; 14:e10854. [PMID: 38327683 PMCID: PMC10847890 DOI: 10.1002/ece3.10854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 01/01/2024] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve the monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding the application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.
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Affiliation(s)
- John D. Swenson
- Department of Environmental ConservationThe University of Massachusetts AmherstAmherstMassachusettsUSA
| | - Elizabeth N. Brooks
- Population Dynamics Branch, Northeast Fisheries Science Center, National Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationWoods HoleMassachusettsUSA
| | - Dovi Kacev
- Marine Biology Research DivisionScripps Institution of OceanographySan DiegoCaliforniaUSA
| | - Charlotte Boyd
- International Union for Conservation of NatureNorth America OfficeWashington DCMarylandUSA
| | - Michael J. Kinney
- NOAA FisheriesPacific Island Fisheries Science CenterHonoluluHawaiiUSA
| | - Benjamin Marcy‐Quay
- Rubenstein Ecosystem Science LaboratoryUniversity of VermontBurlingtonVermontUSA
| | - Anthony Sévêque
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and EvolutionThe Field MuseumChicagoIllinoisUSA
| | - Lisa M. Komoroske
- Department of Environmental ConservationThe University of Massachusetts AmherstAmherstMassachusettsUSA
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5
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Grant MI, Kyne PM, James J, Hu Y, Mukherji S, Amepou Y, Baje L, Chin A, Johnson G, Lee T, Mahan B, Wurster C, White WT, Simpfendorfer CA. Elemental analysis of vertebrae discerns diadromous movements of threatened non-marine elasmobranchs. JOURNAL OF FISH BIOLOGY 2023; 103:1357-1373. [PMID: 37632330 DOI: 10.1111/jfb.15537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
River sharks (Glyphis spp.) and some sawfishes (Pristidae) inhabit riverine environments, although their long-term habitat use patterns are poorly known. We investigated the diadromous movements of the northern river shark (Glyphis garricki), speartooth shark (Glyphis glyphis), narrow sawfish (Anoxypristis cuspidata), and largetooth sawfish (Pristis pristis) using in situ laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) on vertebrae to recover elemental ratios over each individual's lifetime. We also measured elemental ratios for the bull shark (Carcharhinus leucas) and a range of inshore and offshore stenohaline marine species to assist in interpretation of results. Barium (Ba) was found to be an effective indicator of freshwater use, whereas lithium (Li) and strontium (Sr) were effective indicators of marine water use. The relationships between Ba and Li and Ba and Sr were negatively correlated, whereas the relationship between Li and Sr was positively correlated. Both river shark species had elemental signatures indicative of prolonged use of upper-estuarine environments, whereas adults appear to mainly use lower-estuarine environments rather than marine environments. Decreases in Li:Ba and Sr:Ba at the end of the prenatal growth zone of P. pristis samples indicated that parturition likely occurs in fresh water. There was limited evidence of prolonged riverine habitat use for A. cuspidata. The results of this study support elemental-environment relationships observed in teleost otoliths and indicate that in situ LA-ICP-MS elemental characterization is applicable to a wide range of elasmobranch species as a discriminator for use and movement across salinity gradients. A greater understanding of processes that lead to element incorporation in vertebrae, and relative concentrations in vertebrae with respect to the ambient environment, will improve the applicability of elemental analysis to understand movements across the life history of elasmobranchs into the future.
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Affiliation(s)
- Michael I Grant
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Piku Biodiversity Network, National Research Institute, Port Moresby, Papua New Guinea
| | - Peter M Kyne
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Julie James
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Yi Hu
- Advanced Analytical Centre, James Cook University, Townsville, Queensland, Australia
| | - Sushmita Mukherji
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Yolarnie Amepou
- Piku Biodiversity Network, National Research Institute, Port Moresby, Papua New Guinea
| | - Leontine Baje
- National Oceanic Resource Management Authority, Palikir, Pohnpei State, Federated States of Micronesia
| | - Andrew Chin
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Grant Johnson
- Fisheries Division, Northern Territory Department of Industry, Tourism and Trade, Berrimah, Northern Territory, Australia
| | - Tegan Lee
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Perth, Western Australia, Australia
| | - Brandon Mahan
- IsoTropics Geochemistry Laboratory, James Cook University, Townsville, Queensland, Australia
| | - Christopher Wurster
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - William T White
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania, Australia
- Australian National Fish Collection, CSIRO National Research Collections Australia, Hobart, Tasmania, Australia
| | - Colin A Simpfendorfer
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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6
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Lloyd-Jones LR, Bravington MV, Armstrong KN, Lawrence E, Feutry P, Todd CM, Dorrestein A, Welbergen JA, Martin JM, Rose K, Hall J, Phalen DN, Peters I, Baylis SM, Macgregor NA, Westcott DA. Close-kin mark-recapture informs critically endangered terrestrial mammal status. Sci Rep 2023; 13:12512. [PMID: 37532795 PMCID: PMC10397353 DOI: 10.1038/s41598-023-38639-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/12/2023] [Indexed: 08/04/2023] Open
Abstract
Reliable information on population size is fundamental to the management of threatened species. For wild species, mark-recapture methods are a cornerstone of abundance estimation. Here, we show the first application of the close-kin mark-recapture (CKMR) method to a terrestrial species of high conservation value; the Christmas Island flying-fox (CIFF). The CIFF is the island's last remaining native terrestrial mammal and was recently listed as critically endangered. CKMR is a powerful tool for estimating the demographic parameters central to CIFF management and circumvents the complications arising from the species' cryptic nature, mobility, and difficult-to-survey habitat. To this end, we used genetic data from 450 CIFFs captured between 2015 and 2019 to detect kin pairs. We implemented a novel CKMR model that estimates sex-specific abundance, trend, and mortality and accommodates observations from the kin-pair distribution of male reproductive skew and mate persistence. CKMR estimated CIFF total adult female abundance to be approximately 2050 individuals (95% CI (950, 4300)). We showed that on average only 23% of the adult male population contributed to annual reproduction and strong evidence for between-year mate fidelity, an observation not previously quantified for a Pteropus species in the wild. Critically, our population estimates provide the most robust understanding of the status of this critically endangered population, informing immediate and future conservation initiatives.
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Affiliation(s)
- Luke R Lloyd-Jones
- Commonwealth Scientific and Industrial Research Organisation, Data61, Brisbane, QLD, 4072, Australia.
| | - Mark V Bravington
- Commonwealth Scientific and Industrial Research Organisation, Data61, Hobart, TAS, 7000, Australia
| | - Kyle N Armstrong
- Environment Institute, University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia
| | - Emma Lawrence
- Commonwealth Scientific and Industrial Research Organisation, Data61, Brisbane, QLD, 4072, Australia
| | - Pierre Feutry
- Commonwealth Scientific and Industrial Research Organisation, Oceans and Atmosphere, Hobart, TAS, 7000, Australia
| | - Christopher M Todd
- The Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Annabel Dorrestein
- The Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Justin A Welbergen
- The Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - John M Martin
- The Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Bradleys Head Road, Mosman, NSW, 2088, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Bradleys Head Road, Mosman, NSW, 2088, Australia
| | - Jane Hall
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Bradleys Head Road, Mosman, NSW, 2088, Australia
| | - David N Phalen
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Isabel Peters
- School of Mathematics and Physics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shane M Baylis
- Commonwealth Scientific and Industrial Research Organisation, Oceans and Atmosphere, Hobart, TAS, 7000, Australia
| | - Nicholas A Macgregor
- Parks Australia, Canberra, ACT, 2601, Australia
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury, CT2 7NR, Kent, UK
| | - David A Westcott
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Atherton, QLD, 4883, Australia
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Lloyd‐Jones LR, Brien ML, Feutry P, Lawrence E, Beri P, Booth S, Coulson S, Baylis SM, Villiers K, Taplin LE, Westcott DA. Implications of past and present genetic connectivity for management of the saltwater crocodile ( Crocodylus porosus). Evol Appl 2023; 16:911-935. [PMID: 37124084 PMCID: PMC10130557 DOI: 10.1111/eva.13545] [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: 08/17/2022] [Revised: 02/17/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life-history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long-distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey≈ 3000 high-quality genome-wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present-day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second-degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state-wide scales.
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Affiliation(s)
- Luke R. Lloyd‐Jones
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Matthew L. Brien
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Pierre Feutry
- Commonwealth Scientific and Industrial Research OrganisationOceans and AtmosphereHobartTasmania7000Australia
| | - Emma Lawrence
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Paul Beri
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Simon Booth
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Steven Coulson
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Shane M. Baylis
- Commonwealth Scientific and Industrial Research OrganisationOceans and AtmosphereHobartTasmania7000Australia
| | - Kira Villiers
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Laurence E. Taplin
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - David A. Westcott
- Commonwealth Scientific and Industrial Research OrganisationLand and WaterAthertonQueensland4883Australia
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Larroque J, Balkenhol N. A simulation-based evaluation of methods for estimating census population size of terrestrial game species from genetically-identified parent-offspring pairs. PeerJ 2023; 11:e15151. [PMID: 37070094 PMCID: PMC10105560 DOI: 10.7717/peerj.15151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/09/2023] [Indexed: 04/19/2023] Open
Abstract
Estimates of wildlife population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples, particularly parent-offspring pairs. While these methods are similar to traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals are considered recaptured if a sample contains one or more close relatives. This makes methods based on genetically-identified parent-offspring pairs particularly interesting for species for which releasing marked animals back into the population is not desirable or not possible (e.g., harvested fish or game species). However, while these methods have successfully been applied in commercially important fish species, in the absence of life-history data, they are making several assumptions unlikely to be met for harvested terrestrial species. They assume that a sample contains only one generation of parents and one generation of juveniles of the year, while more than two generations can coexist in the hunting bags of long-lived species, or that the sampling probability is the same for each individual, an assumption that is violated when fecundity and/or survival depend on sex or other individual traits. In order to assess the usefulness of kin-based methods to estimate population sizes of terrestrial game species, we simulated population pedigrees of two different species with contrasting demographic strategies (wild boar and red deer), applied four different methods and compared the accuracy and precision of their estimates. We also performed a sensitivity analysis, simulating population pedigrees with varying fecundity characteristics and various levels of harvesting to identify optimal conditions of applicability of each method. We showed that all these methods reached the required levels of accuracy and precision to be effective in wildlife management under simulated circumstances (i.e., for species within a given range of fecundity and for a given range of sampling intensity), while being robust to fecundity variation. Despite the potential usefulness of the methods for terrestrial game species, care is needed as several biases linked to hunting practices still need to be investigated (e.g., when hunting bags are biased toward a particular group of individuals).
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Affiliation(s)
- Jeremy Larroque
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
| | - Niko Balkenhol
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
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