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Harika TL, Al-Ghanim KA, Riaz MN, Krishnappa K, Pandiyan J, Govindarajan M. Fishing Cat Scats as a Biomonitoring Tool for Toxic Heavy Metal Contamination in Aquatic Ecosystems. TOXICS 2023; 11:173. [PMID: 36851048 PMCID: PMC9961565 DOI: 10.3390/toxics11020173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Mangrove forest is one of the productive ecosystems that provide essential habitats for various fauna as breeding and feeding drives. However, heavy metal pollution in the mangrove forest has led to severe health problems for several aquatic species. Biomonitoring of metals using a nondestructive method is an emerging technique. Scats of the fishing cat (Prionailurus viverrinus) were collected from five locations in the Godavari estuary mangrove habitats, Coringa Wildlife Sanctuary, Andhra Pradesh, India, to determine the level of various metals. An opportunistic method was applied to collect scats in the mangrove forest. Six scat samples were collected from each of the sampling sites. The following prey species, such as crabs, fishes, birds, rodents, plants, plastics, and unidentifiable prey matters, were found in the scats. Select metals, such as chromium (Cr), copper (Cu), and lead (Pb) were analyzed from the scats of the fishing cat since they intensively influence the physiology and behavior of top predators. The concentration of Cu in fishing cat scats was higher than the other two metals assessed. Metals showed statistically substantial variation across locations (p < 0.05). According to the current study, heavy metals may significantly threaten the fishing cat in the Coringa Wildlife Sanctuary. The fishing cat is a vulnerable species in accordance with the ICUN categories. Due to pollution and other human pressures, the fishing cat may soon be categorized as a threatened or endangered species; the research advises that authorities should prioritize the protection of the vulnerable species of the fishing cat from the Coringa Wildlife Sanctuary, Andhra Pradesh, India.
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Affiliation(s)
- Thirupati Lakshmi Harika
- Department of Zoology and Wildlife Biology, A.V.C. College, Mannampandal, Mayiladuthurai 609 305, Tamil Nadu, India
| | - Khalid A. Al-Ghanim
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Kaliyamoorthy Krishnappa
- Department of Zoology and Wildlife Biology, A.V.C. College, Mannampandal, Mayiladuthurai 609 305, Tamil Nadu, India
| | - Jeganathan Pandiyan
- Department of Zoology and Wildlife Biology, A.V.C. College, Mannampandal, Mayiladuthurai 609 305, Tamil Nadu, India
| | - Marimuthu Govindarajan
- Unit of Mycology and Parasitology, Department of Zoology, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India
- Unit of Natural Products and Nanotechnology, Department of Zoology, Government College for Women (Autonomous), Kumbakonam 612 001, Tamil Nadu, India
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Long-Term Ringing Data on Migrating Passerines Reveal Overall Avian Decline in Europe. DIVERSITY 2022. [DOI: 10.3390/d14110905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The loss of biodiversity is shaping today’s environment. Bird ringing is a citizen science research tool that can determine species population dynamics and trends over a large geographic area. We used a 17-year time series to assess population trends of 74 passerine species based on ringing data from autumn migration in Slovenia (south-central Europe). We defined seven guilds of species according to geographic location, ecological, migratory, breeding, and life-history traits. Almost all guilds showed declining trends, except for the group of species of northeastern European origin, which showed a stable trend. The greatest decline was in low-productivity wetland specialists. Forest birds, seed-eaters, and high-productivity species experienced the smallest declines. The general declines in avifauna across a range of life-history and behavioural traits, and across a range of spatial and ecological scales, suggest widespread environmental change in Europe. Our data indicates that recent trends are toward ecosystem homogeneity, with an impoverished avifauna, including a few species that are increasing in abundance. These are the species with higher productivity and flexible behaviour, such as short-distance migrants, that have the greatest chance of prevailing in the recently rapidly changing environment because of their ability to adapt to changes in a timely manner.
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Mink (Neovison vison) fecal microbiomes are influenced by sex, temperature, and time postdefecation. J Mammal 2022. [DOI: 10.1093/jmammal/gyab140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Gut microbiomes encode myriad metabolic functions critical to mammalian ecology and evolution. While fresh fecal samples provide an efficient, noninvasive method of sampling gut microbiomes, collecting fresh feces from elusive species is logistically challenging. Nonfresh feces, however, may not accurately represent the gut microbiome of the host due to succession of gut microbial consortia postdefecation as well as colonization by microbes from the surrounding environment. Using American mink (Neovison vison) as a model species, we examined postdefecation microbial community succession to learn how ambient temperature and temporal sampling constraints influence the reliability of nonfresh feces to represent host gut microbiomes. To achieve our goal, we analyzed fresh mink feces (n = 5 females; n = 5 males) collected at the time of defecation from captive mink at a farm in the Upper Peninsula of Michigan and we subsequently subsampled each fecal specimen to investigate microbial community succession over five days, under both warm (21°C) and cold (–17°C to –1°C) temperature treatments. We found that both temperature and time influenced fecal microbiome composition; and we also detected significant sexual dimorphism in microbial community structures, with female mink microbiomes exhibiting significantly greater variation than males’ when exposed to the warm temperature treatment. Our results demonstrate that feces from unknown individuals can be a powerful tool for examining carnivore gut microbiomes, though rigorous study design is required because sex, ambient temperature, and time since defecation drive significant microbial variation and the sample size requirements necessary for detecting statistically significant differences between target populations is an important consideration for future ecologically meaningful research.
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Pugesek G, Mumma MA, Mahoney SP, Waits LP. Molecular evaluation of American black bear prey consumption following diversionary feeding. URSUS 2021. [DOI: 10.2192/ursus-d-20-00027.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Genevieve Pugesek
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID 83844, USA
| | - Matthew A. Mumma
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID 83844, USA
| | - Shane P. Mahoney
- Department of Environment and Conservation, Government of Newfoundland and Labrador, St. John's, Newfoundland A1B 4J6, Canada
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID 83844, USA
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Scarpulla E, Boattini A, Cozzo M, Giangregorio P, Ciucci P, Mucci N, Randi E, Davoli F. First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach. BMC Genomics 2021; 22:623. [PMID: 34407764 PMCID: PMC8371798 DOI: 10.1186/s12864-021-07915-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/28/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears (Ursus arctos marsicanus), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes. RESULTS We examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping. CONCLUSIONS The proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies.
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Affiliation(s)
- Erminia Scarpulla
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Mario Cozzo
- Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca' Fornacetta, 9 - 40064 Ozzano dell'Emilia, Bologna, Italy
| | - Patrizia Giangregorio
- Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca' Fornacetta, 9 - 40064 Ozzano dell'Emilia, Bologna, Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnology "Charles Darwin" (BBCD), Sapienza University of Rome, Rome, Italy
| | - Nadia Mucci
- Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca' Fornacetta, 9 - 40064 Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Faculty of Engineering and Science, Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | - Francesca Davoli
- Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca' Fornacetta, 9 - 40064 Ozzano dell'Emilia, Bologna, Italy.
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Tattoni C, Bragalanti N, Ciolli M, Groff C, Rovero F. Behavior of the European brown bear at rub trees. URSUS 2021. [DOI: 10.2192/ursus-d-20-00022.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Clara Tattoni
- Forest Ecology Laboratory, DICAM, University of Trento, via Mesiano 77 Trento, Italy
| | - Natalia Bragalanti
- Servizio Foreste e Fauna, Provincia Autonoma di Trento, Via Trener 3, Trento, Italy
| | - Marco Ciolli
- Forest Ecology Laboratory, DICAM, University of Trento, via Mesiano 77 Trento, Italy
| | - Claudio Groff
- Servizio Foreste e Fauna, Provincia Autonoma di Trento, Via Trener 3, Trento, Italy
| | - Francesco Rovero
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
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Sun CC, Hurst JE, Fuller AK. Citizen Science Data Collection for Integrated Wildlife Population Analyses. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.682124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Citizen science, or community science, has emerged as a cost-efficient method to collect data for wildlife monitoring. To inform research and conservation, citizen science sampling designs should collect data that match the robust statistical analyses needed to quantify species and population patterns. Further increasing the contributions of citizen science, integrating citizen science data with other datasets and datatypes can improve population estimates and expand the spatiotemporal extent of inference. We demonstrate these points with a citizen science program called iSeeMammals developed in New York state in 2017 to supplement costly systematic spatial capture-recapture sampling by collecting opportunistic data from one-off observations, hikes, and camera traps. iSeeMammals has initially focused on the growing population of American black bear (Ursus americanus), with integrated analysis of iSeeMammals camera trap data with systematic data for a region with a growing bear population. The triumvirate of increased spatial and temporal coverage by at least twofold compared to systematic sampling, an 83% reduction in annual sampling costs, and improved density estimates when integrated with systematic data highlight the benefits of collecting presence-absence data in citizen science programs for estimating population patterns. Additional opportunities will come from applying presence-only data, which are oftentimes more prevalent than presence-absence data, to integrated models. Patterns in data submission and filtering also emphasize the importance of iteratively evaluating patterns in engagement, usability, and accessibility, especially focusing on younger adult and teenage demographics, to improve data quality and quantity. We explore how the development and use of integrated models may be paired with citizen science project design in order to facilitate repeated use of datasets in standalone and integrated analyses for supporting wildlife monitoring and informing conservation.
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Ebert C, Sandrini J, Welter B, Thiele B, Hohmann U. Estimating red deer (Cervus elaphus) population size based on non-invasive genetic sampling. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01456-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractSome deer species are of conservation concern; others are officially managed as a food source or for their trophies, whereas in many regions, deer are regarded as overabundant or even as a nuisance causing damages. Regardless of local management issues, in most cases, reliable data on deer population sizes and sex ratios are lacking. Non-invasive genetic approaches are promising tools for the estimation of population size and structure. We developed and tested a non-invasive genetic approach for red deer (Cervus elaphus) population size and density estimation based on faeces collected from three free-ranging red deer populations in south-western Germany. Altogether, we genotyped 2762 faecal samples, representing 1431 different individuals. We estimated population density for both sexes separately using two different approaches: spatially explicit capture-recapture (SECR) approach and a single-session urn model (CAPWIRE). The estimated densities of both approaches were similar for all three study areas, ranging between total densities of 3.3 (2.5–4.4) and 8.5 (6.4–11.3) red deer/km2. The estimated sex ratios differed significantly between the studied populations (ranging between 1:1.1 and 1:1.7), resulting in considerable consequences for management. In further research, the issues of population closure and approximation of the effectively sampled area for density estimation should be addressed. The presented approach can serve as a valuable tool for the management of deer populations, and to our knowledge, it represents the only sex-specific approach for estimation of red deer population size and density.
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Sentilles J, Vanpé C, Quenette PY. Benefits of incorporating a scat-detection dog into wildlife monitoring: a case study of Pyrenean brown bear. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.20096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jérôme Sentilles
- Office Français de la Biodiversité (OFB), Direction de la Recherche et de l'Appui Scientifique, Unité Prédateurs et Animaux Déprédateurs et Exotiques, Equipe ours, Impasse de la Chapelle, Villeneuve-de-Rivière, France; e-mail:
| | - Cécile Vanpé
- Office Français de la Biodiversité (OFB), Direction de la Recherche et de l'Appui Scientifique, Unité Prédateurs et Animaux Déprédateurs et Exotiques, Equipe ours, Impasse de la Chapelle, Villeneuve-de-Rivière, France; e-mail:
| | - Pierre-Yves Quenette
- Office Français de la Biodiversité (OFB), Direction de la Recherche et de l'Appui Scientifique, Unité Prédateurs et Animaux Déprédateurs et Exotiques, Equipe ours, Impasse de la Chapelle, Villeneuve-de-Rivière, France; e-mail:
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10
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Fontsere C, Alvarez-Estape M, Lester J, Arandjelovic M, Kuhlwilm M, Dieguez P, Agbor A, Angedakin S, Ayuk Ayimisin E, Bessone M, Brazzola G, Deschner T, Eno-Nku M, Granjon AC, Head J, Kadam P, Kalan AK, Kambi M, Langergraber K, Lapuente J, Maretti G, Jayne Ormsby L, Piel A, Robbins MM, Stewart F, Vergnes V, Wittig RM, Kühl HS, Marques-Bonet T, Hughes DA, Lizano E. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments. Mol Ecol Resour 2020; 21:745-761. [PMID: 33217149 DOI: 10.1111/1755-0998.13300] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/15/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022]
Abstract
Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.
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Affiliation(s)
- Claudia Fontsere
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Marina Alvarez-Estape
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Jack Lester
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Parag Kadam
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK
| | - Ammie K Kalan
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mohamed Kambi
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Comoé Chimpanzee Conservation Project, Kakpin, Comoé National Park, Ivory Coast, Côte d'Ivoire
| | - Giovanna Maretti
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alex Piel
- Department of Anthropology, University College London, London, UK
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fiona Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK.,Department of Anthropology, University College London, London, UK
| | | | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Hjalmar S Kühl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Esther Lizano
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Stable Isotopes Reveal Variation in Consumption of Pacific Salmon by Brown Bears, Despite Ready Access in Small Streams. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2020. [DOI: 10.3996/jfwm-20-034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Brown bears Ursus arctos consume a wide range of organisms, including ungulates and plants, but Pacific salmon Oncorhynchus spp. are especially important to their diet where their ranges overlap. Although some brown bears minimize antagonistic encounters with other brown bears or infanticide by avoiding streams where salmon spawn, studies generally assume that brown bears with ready access to salmon feed heavily on them. To test this assumption, and the hypothesis that male brown bears would feed more heavily on salmon than females (owing to their sexual size dimorphism), we collected hair samples from brown bears by using barbed wire placed on six small tributaries of Lake Aleknagik, Alaska, USA, where adult Sockeye Salmon Oncorhynchus nerka are readily accessible and frequently consumed by brown bears. Analysis of DNA distinguished among the different brown bears leaving the hair samples, some of which were sampled multiple times within and among years. We assessed the contribution of salmon to the diet of individual brown bears by using carbon and nitrogen stable isotope signatures. The 77 samples analyzed from 31 different bears over 4 y showed isotopic ratios consistent with reliance on salmon, but the wide range of isotopic signatures included values suggesting variable, and in one case considerable, use of terrestrial resources. Stable isotope signatures did not differ between male and female brown bears, nor did they differ between two sides of the lake, despite marked differences in Sockeye Salmon density. We collected the hair samples when salmon were present, so there was some uncertainty regarding whether they reflected feeding during the current or previous season. Notwithstanding this caveat, the results are consistent with the hypothesis that salmon were sufficiently available to provide food for the brown bears and that the considerable isotopic variation among brown bears with access to salmon reflected their age, status, and behavior.
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12
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Buglione M, Troisi SR, Petrelli S, van Vugt M, Notomista T, Troiano C, Bellomo A, Maselli V, Gregorio R, Fulgione D. The First Report on the Ecology and Distribution of the Wolf Population in Cilento, Vallo di Diano and Alburni National Park. BIOL BULL+ 2020. [DOI: 10.1134/s1062359021010040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Phoebus I, Boulanger J, Eiken HG, Fløystad I, Graham K, Hagen SB, Sorensen A, Stenhouse G. Comparison of grizzly bear hair-snag and scat sampling along roads to inform wildlife population monitoring. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Isobel Phoebus
- I. Phoebus (https://orcid.org/0000-0001-5333-0298) ✉ , K. Graham, A. Sorensen and G. Stenhouse (https://orcid.org/0000-0003-4551-4585), fRI Research Grizzly Bear Program, Hinton, AB, Canada
| | - John Boulanger
- J. Boulanger (https://orcid.org/0000-0001-8222-1445), Integrated Ecological Research, Nelson, BC, Canada
| | - Hans Geir Eiken
- H. G. Eiken (https://orcid.org/0000-0002-5368-3648), I. Fløystad (https://orcid.org/0000-0002-0484-4265) and S. B. Hagen (https://orcid.org/0000-0001-8289-7752), Norwegian Inst. of Bioeconomy Research, Ås, Akershus, Norway
| | - Ida Fløystad
- H. G. Eiken (https://orcid.org/0000-0002-5368-3648), I. Fløystad (https://orcid.org/0000-0002-0484-4265) and S. B. Hagen (https://orcid.org/0000-0001-8289-7752), Norwegian Inst. of Bioeconomy Research, Ås, Akershus, Norway
| | - Karen Graham
- I. Phoebus (https://orcid.org/0000-0001-5333-0298) ✉ , K. Graham, A. Sorensen and G. Stenhouse (https://orcid.org/0000-0003-4551-4585), fRI Research Grizzly Bear Program, Hinton, AB, Canada
| | - Snorre B. Hagen
- H. G. Eiken (https://orcid.org/0000-0002-5368-3648), I. Fløystad (https://orcid.org/0000-0002-0484-4265) and S. B. Hagen (https://orcid.org/0000-0001-8289-7752), Norwegian Inst. of Bioeconomy Research, Ås, Akershus, Norway
| | - Anja Sorensen
- I. Phoebus (https://orcid.org/0000-0001-5333-0298) ✉ , K. Graham, A. Sorensen and G. Stenhouse (https://orcid.org/0000-0003-4551-4585), fRI Research Grizzly Bear Program, Hinton, AB, Canada
| | - Gordon Stenhouse
- I. Phoebus (https://orcid.org/0000-0001-5333-0298) ✉ , K. Graham, A. Sorensen and G. Stenhouse (https://orcid.org/0000-0003-4551-4585), fRI Research Grizzly Bear Program, Hinton, AB, Canada
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14
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Wirsing AJ, Quinn TP, Adams JR, Waits LP. Optimizing Selection of Brown Bear Hair for Noninvasive Genetic Analysis. WILDLIFE SOC B 2020. [DOI: 10.1002/wsb.1057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aaron J. Wirsing
- School of Environmental and Forest SciencesUniversity of Washington Box 352100 Seattle WA 98195 USA
| | - Thomas P. Quinn
- School of Aquatic and Fishery SciencesUniversity of Washington Box 355020 Seattle WA 98195 USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS 1136 Moscow ID 83844‐1136 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS 1136 Moscow ID 83844‐1136 USA
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15
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Schmidt DA, Campbell NR, Govindarajulu P, Larsen KW, Russello MA. Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally invasive DNA samples to support studies in molecular ecology. Mol Ecol Resour 2019; 20:114-124. [PMID: 31483931 DOI: 10.1111/1755-0998.13090] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/02/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Minimally invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping-by-sequencing approaches, which have been traditionally developed for high-quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex amplicon sequencing approach, to effectively genotype minimally invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT-seq from a de novo restriction site-associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT-seq for the same individuals found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT-seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT-seq and RADseq data sets, as were inferred patterns of population structure. Overall, GT-seq can be effectively applied to low-quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.
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Affiliation(s)
- Danielle A Schmidt
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
| | | | - Purnima Govindarajulu
- British Columbia Ministry of Environment and Climate Change Strategy, Victoria, BC, Canada
| | - Karl W Larsen
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
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16
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Grauer JA, Gilbert JH, Woodford JE, Eklund D, Anderson S, Pauli JN. Modest immigration can rescue a reintroduced carnivore population. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jennifer A. Grauer
- Department of Forest and Wildlife EcologyUniversity of Wisconsin‐Madison1630 Linden DriveMadisonWI53706USA
| | - Jonathan H. Gilbert
- Biological ServicesGreat Lakes Indian Fish and Wildlife CommissionP.O. Box 9 − 72682 Maple StreetOdanahWI54861USA
| | - James E. Woodford
- Bureau of Natural Heritage ConservationWisconsin Department of Natural Resources107 Sutliff AvenueRhinelanderWI54501USA
| | - Daniel Eklund
- U.S. Forest ServiceChequamegon Nicolet National Forest1170 4th Avenue SPark FallsWI54552USA
| | - Scott Anderson
- U.S. Forest ServiceChequamegon Nicolet National Forest1247 E Wall StreetEagle RiverWI54521USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife EcologyUniversity of Wisconsin‐Madison1630 Linden DriveMadisonWI53706USA
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17
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Rennstam Rubbmark O, Sint D, Horngacher N, Traugott M. A broadly applicable COI primer pair and an efficient single-tube amplicon library preparation protocol for metabarcoding. Ecol Evol 2018; 8:12335-12350. [PMID: 30619549 PMCID: PMC6308894 DOI: 10.1002/ece3.4520] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/06/2018] [Accepted: 06/10/2018] [Indexed: 12/25/2022] Open
Abstract
The nucleotide variation in the cytochrome c oxidase subunit I (COI) gene makes it ideal for assigning sequences to species. However, this variability also makes it difficult to design truly universal primers. Here, we present the forward primer "Sauron-S878," specifically designed to facilitate library preparation for metabarcoding. This primer is modified to improve the coverage of terrestrial species compared to the primer mCOIintF, optimized for aquatic systems, which raised the in silico coverage from 74.4% to 98.3% of available NCBI sequences (perfect match in 3' region, up to three mismatches in remaining primer). When paired with the reverse primer "jgHCO2198" (fragment length ~313 bp), these primers amplified 98.4% of 255 tested DNA extracts from various taxa, which are better than many other common COI barcoding primers. Furthermore, a single-tube protocol was developed, wherein these primers amplify the target gene, and attach MIDs and Illumina sequencing adapters in one reaction. This eliminates the need for re-amplification or enzymatic ligation during library preparation while keeping the flexibility to modularly combine primers and MIDs. Using the single-tube approach, three replicates of three mock samples were sequenced on a MiSeq platform with no adverse effects compared to commercial Nextera indexing kits. From this run, 75% of all included taxa could be recovered, with no considerable bias among taxonomic groups. Despite the fact that 98.4% of the extracts were confirmed to amplify in vitro, this number was lower than expected. A reason for this discrepancy was a clear link between the relative concentration of a specific DNA type in the template and the number of returned reads for this DNA. We would argue that such a bias may be especially problematic in metabarcoding where samples usually contain trace DNA in unknown amounts. However, how this affects the completeness of metabarcoding results has yet been poorly investigated.
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Affiliation(s)
- Oskar Rennstam Rubbmark
- Mountain Agriculture Research UnitInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Daniela Sint
- Mountain Agriculture Research UnitInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Nina Horngacher
- Mountain Agriculture Research UnitInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Michael Traugott
- Mountain Agriculture Research UnitInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
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18
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How to spot a black-footed cat? Successful application of cross-species markers to identify captive-bred individuals from non-invasive genetic sampling. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0407-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Wirsing AJ, Quinn TP, Cunningham CJ, Adams JR, Craig AD, Waits LP. Alaskan brown bears ( Ursus arctos) aggregate and display fidelity to foraging neighborhoods while preying on Pacific salmon along small streams. Ecol Evol 2018; 8:9048-9061. [PMID: 30271565 PMCID: PMC6157690 DOI: 10.1002/ece3.4431] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/30/2018] [Accepted: 07/06/2018] [Indexed: 11/11/2022] Open
Abstract
The interaction between brown bears (Ursus arctos) and Pacific salmon (Oncorhynchus spp.) is important to the population dynamics of both species and a celebrated example of consumer-mediated nutrient transport. Yet, much of the site-specific information we have about the bears in this relationship comes from observations at a few highly visible but unrepresentative locations and a small number of radio-telemetry studies. Consequently, our understanding of brown bear abundance and behavior at more cryptic locations where they commonly feed on salmon, including small spawning streams, remains limited. We employed a noninvasive genetic approach (barbed wire hair snares) over four summers (2012-2015) to document patterns of brown bear abundance and movement among six spawning streams for sockeye salmon, O. nerka, in southwestern Alaska. The streams were grouped into two trios on opposite sides of Lake Aleknagik. Thus, we predicted that most bears would forage within only one trio during the spawning season because of the energetic costs associated with swimming between them or traveling around the lake and show fidelity to particular trios across years because of the benefits of familiarity with local salmon dynamics and stream characteristics. Huggins closed-capture models based on encounter histories from genotyped hair samples revealed that as many as 41 individuals visited single streams during the annual 6-week sampling season. Bears also moved freely among trios of streams but rarely moved between these putative foraging neighborhoods, either during or between years. By implication, even small salmon spawning streams can serve as important resources for brown bears, and consistent use of stream neighborhoods by certain bears may play an important role in spatially structuring coastal bear populations. Our findings also underscore the efficacy of noninvasive hair snagging and genetic analysis for examining bear abundance and movements at relatively fine spatial and temporal scales.
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Affiliation(s)
- Aaron J. Wirsing
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashington
| | - Thomas P. Quinn
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashington
| | - Curry J. Cunningham
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashington
| | - Jennifer R. Adams
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdaho
| | - Apryle D. Craig
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashington
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdaho
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20
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Comparing performance of multiple non-invasive genetic capture–recapture methods for abundance estimation: a case study with the Sonoran pronghorn Antilocapra americana sonoriensis. ORYX 2018. [DOI: 10.1017/s003060531800011x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractDemographic monitoring is required in threatened species management, yet effective and efficient monitoring is challenging for species that are difficult to capture or susceptible to capture stress. One possible monitoring approach for such species is non-invasive genetic sampling with capture–recapture methods (genetic capture–recapture). We evaluated the performance of genetic capture–recapture in a challenging model system, monitoring the threatened Sonoran pronghorn Antilocapra americana sonoriensis. In an effort to determine the best (i.e. efficient, accurate, precise, cost-effective) method for abundance estimation, we used simulations to examine the optimal genetic capture–recapture faecal sampling design for this population. We simulated encounter histories for 100–300 individuals, with 0.33–3.33 samples/individual/session, in 1–3 sampling sessions. We explored trade-offs between sample size, number of sessions and multi-session (MARK) versus single-session (capwire) closed capture–recapture abundance estimators, and an accurate and precise estimate. We also compared the cost between the genetic capture–recapture approaches and current aerial monitoring methods. Abundance was biased positively in capwire and negatively in MARK. Bias increased and precision decreased with fewer samples/individual/session. Annual genetic capture–recapture monitoring cost was nearly twice the cost of aerial surveys, although genetic capture–recapture methods provided much higher precision. However at the current estimated abundance (c. 200), the same level of precision achieved with aerial methods can be obtained by collecting 0.75 samples/individual in a single session, for an annual cost saving of > USD 4,000. This approach of comparing estimator performance and cost can easily be applied to other systems and is a useful evaluation for managers to implement prior to designing capture–recapture studies.
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21
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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22
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le Roex N, Paxton M, Adendorff J, Ferreira S, O'Riain MJ. Starting small: long‐term consequences in a managed large‐mammal population. J Zool (1987) 2018. [DOI: 10.1111/jzo.12572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- N. le Roex
- Institute for Communities and Wildlife in Africa (iCWild) Department of Biological Sciences University of Cape Town Cape Town South Africa
- School of Biology and Environmental Sciences University of Mpumalanga Mbombela South Africa
| | - M. Paxton
- Conservation Management South African National Parks Addo Elephant National Park Port Elizabeth South Africa
| | - J. Adendorff
- Conservation Management South African National Parks Addo Elephant National Park Port Elizabeth South Africa
| | - S. Ferreira
- Scientific Services South African National Parks Skukuza South Africa
| | - M. J. O'Riain
- Institute for Communities and Wildlife in Africa (iCWild) Department of Biological Sciences University of Cape Town Cape Town South Africa
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23
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Nilsen EB, Strand O. Integrating data from multiple sources for insights into demographic processes: Simulation studies and proof of concept for hierarchical change-in-ratio models. PLoS One 2018; 13:e0194566. [PMID: 29596430 PMCID: PMC5875752 DOI: 10.1371/journal.pone.0194566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 03/06/2018] [Indexed: 12/02/2022] Open
Abstract
We developed a model for estimating demographic rates and population abundance based on multiple data sets revealing information about population age- and sex structure. Such models have previously been described in the literature as change-in-ratio models, but we extend the applicability of the models by i) using time series data allowing the full temporal dynamics to be modelled, by ii) casting the model in an explicit hierarchical modelling framework, and by iii) estimating parameters based on Bayesian inference. Based on sensitivity analyses we conclude that the approach developed here is able to obtain estimates of demographic rate with high precision whenever unbiased data of population structure are available. Our simulations revealed that this was true also when data on population abundance are not available or not included in the modelling framework. Nevertheless, when data on population structure are biased due to different observability of different age- and sex categories this will affect estimates of all demographic rates. Estimates of population size is particularly sensitive to such biases, whereas demographic rates can be relatively precisely estimated even with biased observation data as long as the bias is not severe. We then use the models to estimate demographic rates and population abundance for two Norwegian reindeer (Rangifer tarandus) populations where age-sex data were available for all harvested animals, and where population structure surveys were carried out in early summer (after calving) and late fall (after hunting season), and population size is counted in winter. We found that demographic rates were similar regardless whether we include population count data in the modelling, but that the estimated population size is affected by this decision. This suggest that monitoring programs that focus on population age- and sex structure will benefit from collecting additional data that allow estimation of observability for different age- and sex classes. In addition, our sensitivity analysis suggests that focusing monitoring towards changes in demographic rates might be more feasible than monitoring abundance in many situations where data on population age- and sex structure can be collected.
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Affiliation(s)
- Erlend B. Nilsen
- Norwegian Institute for Nature Research, Torgarden, Trondheim, Norway
- * E-mail:
| | - Olav Strand
- Norwegian Institute for Nature Research, Torgarden, Trondheim, Norway
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24
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King SRB, Schoenecker KA, Fike JA, Oyler‐McCance SJ. Long-term persistence of horse fecal DNA in the environment makes equids particularly good candidates for noninvasive sampling. Ecol Evol 2018; 8:4053-4064. [PMID: 29721279 PMCID: PMC5916305 DOI: 10.1002/ece3.3956] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/30/2018] [Accepted: 02/05/2018] [Indexed: 11/10/2022] Open
Abstract
Fecal DNA collected noninvasively can provide valuable information about genetic and ecological characteristics. This approach has rarely been used for equids, despite the need for conservation of endangered species and management of abundant feral populations. We examined factors affecting the efficacy of using equid fecal samples for conservation genetics. First, we evaluated two fecal collection methods (paper bag vs. ethanol). Then, we investigated how time since deposition and month of collection impacted microsatellite amplification success and genotyping errors. Between May and November 2014, we collected feral horse fecal samples of known age each month in a feral horse Herd Management Area in western Colorado and documented deterioration in the field with photographs. Samples collected and dried in paper bags had significantly higher amplification rates than those collected and stored in ethanol. There was little difference in the number of loci that amplified per sample between fresh fecal piles and those that had been exposed to the environment for up to 2 months (in samples collected in paper bags). After 2 months of exposure, amplification success declined. When comparing fresh (0–2 months) and old (3–6 months) fecal piles, samples from fresh piles had more matching genotypes across samples, better amplification success and less allelic dropout. Samples defecated during the summer and collected within 2 months of deposition had highest number of genotypes matching among samples, and lowest rates of amplification failure and allelic dropout. Due to the digestive system and amount of fecal material produced by equids, as well as their occurrence in arid ecosystems, we suggest that they are particularly good candidates for noninvasive sampling using fecal DNA.
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Affiliation(s)
- Sarah R. B. King
- Natural Resource Ecology LaboratoryDepartment of Ecosystem Science and SustainabilityColorado State UniversityFort CollinsCOUSA
| | | | - Jennifer A. Fike
- United States Geological SurveyFort Collins Science CenterFort CollinsCOUSA
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25
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Davoli F, Cozzo M, Angeli F, Groff C, Randi E. Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. NATURE CONSERVATION 2018. [DOI: 10.3897/natureconservation.25.23776] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sexually Selected Infanticide (SSI) is thought of as a male reproductive strategy in social mammalian species, because females who lose cubs may quickly re-enter oestrus. SSI has rarely been documented in non-social mammals and, in brown bears, SSI has been studied mainly in an eco-ethological perspective. The authors examined the first genetically documented infanticide case which occurred in May 2015 in brown bears in Italy (Trentino, Central-Eastern Alps). The infanticide killed two cubs and their mother. Hair samples were collected from the corpses as well as saliva, through swabs on mother’s wounds, with the aim of identifying the genotype of the perpetrator. The samples were genotyped by PCR amplification of 15 autosomal microsatellite loci, following the protocol routinely used for individual bear identifications within the Interregional Action Plan for Brown Bear Conservation in the Central-Eastern Alps (PACOBACE). Reliable genotypes were obtained from the mother, cubs and putative perpetrator. The genotypes were matched with those populating the PACOBACE database and genealogies were reconstructed. Both mother and perpetrator genotypes were already present in the database. Kinship analyses confirmed mother-cubs relationships and identified the father of the cubs. In this study, for the first time, the authors used the open-source LRmix STUDIO software, designed to analyse human forensic genetic profiles, to solve a case in wildlife. Through LRmix STUDIO, those alleles that do not belong to the victims were isolated and, finally, the perpetrator was identified. This study presents a method that allows, through the application of different models, the genetic identification of the conspecific perpetrator with the highest probability. The identification of the infanticidal male is relevant for the better management and conservation of wild populations with small effective population size (Ne) and low population growth rate, especially in the case of recently established populations in human-dominated landscapes. This procedure will have predictably wide applications, supplying important data in the monitoring of small and isolated populations.
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26
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Lee TS, Toft JD, Cordell JR, Dethier MN, Adams JW, Kelly RP. Quantifying the effectiveness of shoreline armoring removal on coastal biota of Puget Sound. PeerJ 2018; 6:e4275. [PMID: 29492331 PMCID: PMC5825941 DOI: 10.7717/peerj.4275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/29/2017] [Indexed: 11/20/2022] Open
Abstract
Shoreline armoring is prevalent around the world with unprecedented human population growth and urbanization along coastal habitats. Armoring structures, such as riprap and bulkheads, that are built to prevent beach erosion and protect coastal infrastructure from storms and flooding can cause deterioration of habitats for migratory fish species, disrupt aquatic–terrestrial connectivity, and reduce overall coastal ecosystem health. Relative to armored shorelines, natural shorelines retain valuable habitats for macroinvertebrates and other coastal biota. One question is whether the impacts of armoring are reversible, allowing restoration via armoring removal and related actions of sediment nourishment and replanting of native riparian vegetation. Armoring removal is targeted as a viable option for restoring some habitat functions, but few assessments of coastal biota response exist. Here, we use opportunistic sampling of pre- and post-restoration data for five biotic measures (wrack % cover, saltmarsh % cover, number of logs, and macroinvertebrate abundance and richness) from a set of six restored sites in Puget Sound, WA, USA. This broad suite of ecosystem metrics responded strongly and positively to armor removal, and these results were evident after less than one year. Restoration responses remained positive and statistically significant across different shoreline elevations and temporal trajectories. This analysis shows that removing shoreline armoring is effective for restoration projects aimed at improving the health and productivity of coastal ecosystems, and these results may be widely applicable.
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Affiliation(s)
- Timothy S Lee
- Department of Biology, East Carolina University, Greenville, NC, USA.,School of Marine and Environmental Affairs, University of Washington, Seattle, WA, USA
| | - Jason D Toft
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Jeffery R Cordell
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Megan N Dethier
- Department of Biology, Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, USA
| | - Jeffrey W Adams
- Washington Sea Grant, College of the Environment, University of Washington, Seattle, WA, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, USA
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27
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Berezowska-Cnota T, Luque-Márquez I, Elguero-Claramunt I, Bojarska K, Okarma H, Selva N. Effectiveness of different types of hair traps for brown bear research and monitoring. PLoS One 2017; 12:e0186605. [PMID: 29073161 PMCID: PMC5657975 DOI: 10.1371/journal.pone.0186605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/04/2017] [Indexed: 11/19/2022] Open
Abstract
Non-invasive sampling by hair-trapping is increasingly used worldwide in wildlife research. Despite this rise and the potential of hair samples for ecology and conservation studies, the relative performance of hair collection devices has been rarely tested. Here, we compare the effectiveness of five types of hair traps for brown bears Ursus arctos in the Carpathian Mountains (SE Poland) and test the effects of trap type, season, number of days elapsed since trap installation and trap features on the trapping success in order to provide recommendations for optimal sampling in future studies. The trap types were corral, path-trap, "smola"(beechwood tar) tree-trap, turpentine tree-trap and natural rub. In 2010, we collected 858 hair samples during 2330 inspections of 175 hair traps and found that the most effective traps were smola tree-traps (mean percentage of successful inspections ± SD: 30.2% ± 26.0) and natural rubs (50.8% ± 16.7). Based on this finding, over the following 2 years we focused on 24 smola tree-traps and eight natural rubs. During this long-term survey (2010-2012, 969 inspections, 1322 samples collected) the trapping success increased with time and smola tree-traps achieved similar effectiveness to natural rubs (45.5% ± 29.7 and 45.9 ± 23.4, respectively). We show that when baiting smola tree-traps ten weeks prior to research or monitoring, sampling effectiveness can reach up to 30%. Taking into account the logistical and methodological constraints associated with detecting and using natural rubs for a proper survey design, we recommend using smola tree-traps baited in advance for hair sampling in wildlife studies.
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Affiliation(s)
- Teresa Berezowska-Cnota
- Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
- * E-mail: (TBC); (NS)
| | | | | | - Katarzyna Bojarska
- Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
| | - Henryk Okarma
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - Nuria Selva
- Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
- * E-mail: (TBC); (NS)
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28
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Tenan S, Pedrini P, Bragalanti N, Groff C, Sutherland C. Data integration for inference about spatial processes: A model-based approach to test and account for data inconsistency. PLoS One 2017; 12:e0185588. [PMID: 28973034 PMCID: PMC5626469 DOI: 10.1371/journal.pone.0185588] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/17/2017] [Indexed: 11/18/2022] Open
Abstract
Recently-developed methods that integrate multiple data sources arising from the same ecological processes have typically utilized structured data from well-defined sampling protocols (e.g., capture-recapture and telemetry). Despite this new methodological focus, the value of opportunistic data for improving inference about spatial ecological processes is unclear and, perhaps more importantly, no procedures are available to formally test whether parameter estimates are consistent across data sources and whether they are suitable for integration. Using data collected on the reintroduced brown bear population in the Italian Alps, a population of conservation importance, we combined data from three sources: traditional spatial capture-recapture data, telemetry data, and opportunistic data. We developed a fully integrated spatial capture-recapture (SCR) model that included a model-based test for data consistency to first compare model estimates using different combinations of data, and then, by acknowledging data-type differences, evaluate parameter consistency. We demonstrate that opportunistic data lend itself naturally to integration within the SCR framework and highlight the value of opportunistic data for improving inference about space use and population size. This is particularly relevant in studies of rare or elusive species, where the number of spatial encounters is usually small and where additional observations are of high value. In addition, our results highlight the importance of testing and accounting for inconsistencies in spatial information from structured and unstructured data so as to avoid the risk of spurious or averaged estimates of space use and consequently, of population size. Our work supports the use of a single modeling framework to combine spatially-referenced data while also accounting for parameter consistency.
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Affiliation(s)
- Simone Tenan
- Vertebrate Zoology Section, MUSE - Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122 Trento, Italy
- * E-mail:
| | - Paolo Pedrini
- Vertebrate Zoology Section, MUSE - Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122 Trento, Italy
| | - Natalia Bragalanti
- Vertebrate Zoology Section, MUSE - Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122 Trento, Italy
- Provincia Autonoma di Trento, Servizio Foreste e Fauna, Via Trener 3, 38100 Trento, Italy
| | - Claudio Groff
- Provincia Autonoma di Trento, Servizio Foreste e Fauna, Via Trener 3, 38100 Trento, Italy
| | - Chris Sutherland
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, 01003, United States of America
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Gervasi V, Boitani L, Paetkau D, Posillico M, Randi E, Ciucci P. Estimating survival in the Apennine brown bear accounting for uncertainty in age classification. POPUL ECOL 2017. [DOI: 10.1007/s10144-017-0587-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Tenan S, Iemma A, Bragalanti N, Pedrini P, De Barba M, Randi E, Groff C, Genovart M. Evaluating mortality rates with a novel integrated framework for nonmonogamous species. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:1307-1319. [PMID: 27112366 DOI: 10.1111/cobi.12736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 03/18/2016] [Accepted: 04/01/2016] [Indexed: 06/05/2023]
Abstract
The conservation of wildlife requires management based on quantitative evidence, and especially for large carnivores, unraveling cause-specific mortalities and understanding their impact on population dynamics is crucial. Acquiring this knowledge is challenging because it is difficult to obtain robust long-term data sets on endangered populations and, usually, data are collected through diverse sampling strategies. Integrated population models (IPMs) offer a way to integrate data generated through different processes. However, IPMs are female-based models that cannot account for mate availability, and this feature limits their applicability to monogamous species only. We extended classical IPMs to a two-sex framework that allows investigation of population dynamics and quantification of cause-specific mortality rates in nonmonogamous species. We illustrated our approach by simultaneously modeling different types of data from a reintroduced, unhunted brown bear (Ursus arctos) population living in an area with a dense human population. In a population mainly driven by adult survival, we estimated that on average 11% of cubs and 61% of adults died from human-related causes. Although the population is currently not at risk, adult survival and thus population dynamics are driven by anthropogenic mortality. Given the recent increase of human-bear conflicts in the area, removal of individuals for management purposes and through poaching may increase, reversing the positive population growth rate. Our approach can be generalized to other species affected by cause-specific mortality and will be useful to inform conservation decisions for other nonmonogamous species, such as most large carnivores, for which data are scarce and diverse and thus data integration is highly desirable.
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Affiliation(s)
- Simone Tenan
- Vertebrate Zoology Section, MUSE - Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122, Trento, Italy.
| | - Aaron Iemma
- Vertebrate Zoology Section, MUSE - Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122, Trento, Italy
| | - Natalia Bragalanti
- Vertebrate Zoology Section, MUSE - Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122, Trento, Italy
- Servizio Foreste e Fauna, Provincia Autonoma di Trento, Via Trener 3, 38100, Trento, Italy
| | - Paolo Pedrini
- Vertebrate Zoology Section, MUSE - Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122, Trento, Italy
| | - Marta De Barba
- Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), F-38000, Grenoble, France
- Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Ca' Fornacetta 9, 40064, Ozzano Emilia (BO), Italy
- Department 18/Section of Environmental Engineering, Aalborg University, Sohngårdsholmsvej 57, 9000, Aalborg, Denmark
| | - Claudio Groff
- Servizio Foreste e Fauna, Provincia Autonoma di Trento, Via Trener 3, 38100, Trento, Italy
| | - Meritxell Genovart
- Vertebrate Zoology Section, MUSE - Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122, Trento, Italy
- Population Ecology Group, IMEDEA (CSIC-UIB), Miquel Marquès 21, 07190, Esporles (Mallorca), Spain
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Wheat RE, Allen JM, Miller SDL, Wilmers CC, Levi T. Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (Ursus arctos). PLoS One 2016; 11:e0165259. [PMID: 27828988 PMCID: PMC5102439 DOI: 10.1371/journal.pone.0165259] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/07/2016] [Indexed: 11/21/2022] Open
Abstract
Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (Oncorhynchus spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (Ursus arctos). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (O. nerka) and a late season run of stream-spawning chum (O. keta) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species.
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Affiliation(s)
- Rachel E. Wheat
- Department of Environmental Studies, Center for Integrated Spatial Research, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Sophie D. L. Miller
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Christopher C. Wilmers
- Department of Environmental Studies, Center for Integrated Spatial Research, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
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Non-invasive genetic population density estimation of mountain hares (Lepus timidus) in the Alps: systematic or opportunistic sampling? EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-1053-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Woodruff SP, Lukacs PM, Christianson D, Waits LP. Estimating Sonoran pronghorn abundance and survival with fecal DNA and capture-recapture methods. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:1102-1111. [PMID: 26918820 DOI: 10.1111/cobi.12710] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/15/2015] [Accepted: 02/13/2016] [Indexed: 06/05/2023]
Abstract
Population abundance estimates are important for management but can be challenging to determine in low-density, wide-ranging, and endangered species, such as Sonoran pronghorn (Antilocapra americana sonoriensis). The Sonoran pronghorn population has been increasing; however, population estimates are currently derived from a biennial aerial count that does not provide survival or recruitment estimates. We identified individuals through noninvasively collected fecal DNA and used robust-design capture-recapture to estimate abundance and survival for Sonoran pronghorn in the United States from 2013 to 2014. In 2014 we generated separate population estimates for pronghorn gathered near 13 different artificial water holes and for pronghorn not near water holes. The population using artificial water holes had 116 (95% CI 102-131) and 121 individuals (95% CI 112-132) in 2013 and 2014, respectively. For all locations, we estimated there were 144 individuals (95% CI 132-157). Adults had higher annual survival probabilities (0.83, 95% CI 0.69-0.92) than fawns (0.41, 95% CI 0.21-0.65). Our use of targeted noninvasive genetic sampling and capture-recapture with Sonoran pronghorn fecal DNA was an effective method for monitoring a large proportion of the population. Our results provided the first survival estimates for this population in over 2 decades and precise estimates of the population using artificial water holes. Our method could be used for targeted sampling of broadly distributed species in other systems, such as in African savanna ecosystems, where many species congregate at watering sites.
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Affiliation(s)
- Susannah P Woodruff
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844-1136, U.S.A..
| | - Paul M Lukacs
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, 32 Campus Drive, Missoula, MT, 59812, U.S.A
| | - David Christianson
- School of Natural Resources and the Environment, University of Arizona, 1311 East 4th Street, Tucson, AZ 85721, U.S.A
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844-1136, U.S.A
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34
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Woodruff SP, Johnson TR, Waits LP. Examining the use of fecal pellet morphometry to differentiate age classes in Sonoran pronghorn. WILDLIFE BIOLOGY 2016. [DOI: 10.2981/wlb.00209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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35
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Barja I, Navarro-Castilla Á, Pérez L. Effectiveness and Applications of Hair Traps for the Study of Wild mammal populations. POLISH JOURNAL OF ECOLOGY 2016. [DOI: 10.3161/15052249pje2016.64.3.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Draheim HM, Lopez V, Etter D, Winterstein SR, Scribner KT. Effects of sampling scale on American black bear spatial genetic structure. URSUS 2015. [DOI: 10.2192/ursus-d-15-00011.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Hope M. Draheim
- Eagle Fish Genetics Lab, Idaho Department of Fish and Game, 1800 Trout Road, Eagle, ID 83616, USA
| | - Veronica Lopez
- Allegheny National Forest, Marienville Ranger District, 131 Smokey Lane, Marienville, PA 16239, USA
| | - Dwayne Etter
- Michigan Department of Natural Resources, Wildlife Division, 8562 E Stoll Road, East Lansing, MI 48823, USA
| | - Scott R. Winterstein
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Kim T. Scribner
- Eagle Fish Genetics Lab, Idaho Department of Fish and Game, 1800 Trout Road, Eagle, ID 83616, USA
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37
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Wilson TL, Schmidt JH. Scale dependence in occupancy models: implications for estimating bear den distribution and abundance. Ecosphere 2015. [DOI: 10.1890/es15-00250.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Linking GPS Telemetry Surveys and Scat Analyses Helps Explain Variability in Black Bear Foraging Strategies. PLoS One 2015; 10:e0129857. [PMID: 26132204 PMCID: PMC4489386 DOI: 10.1371/journal.pone.0129857] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/13/2015] [Indexed: 11/19/2022] Open
Abstract
Studying diet is fundamental to animal ecology and scat analysis, a widespread approach, is considered a reliable dietary proxy. Nonetheless, this method has weaknesses such as non-random sampling of habitats and individuals, inaccurate evaluation of excretion date, and lack of assessment of inter-individual dietary variability. We coupled GPS telemetry and scat analyses of black bears Ursus americanus Pallas to relate diet to individual characteristics and habitat use patterns while foraging. We captured 20 black bears (6 males and 14 females) and fitted them with GPS/Argos collars. We then surveyed GPS locations shortly after individual bear visits and collected 139 feces in 71 different locations. Fecal content (relative dry matter biomass of ingested items) was subsequently linked to individual characteristics (sex, age, reproductive status) and to habitats visited during foraging bouts using Brownian bridges based on GPS locations prior to feces excretion. At the population level, diet composition was similar to what was previously described in studies on black bears. However, our individual-based method allowed us to highlight different intra-population patterns, showing that sex and female reproductive status had significant influence on individual diet. For example, in the same habitats, females with cubs did not use the same food sources as lone bears. Linking fecal content (i.e., food sources) to habitat previously visited by different individuals, we demonstrated a potential differential use of similar habitats dependent on individual characteristics. Females with cubs-of-the-year tended to use old forest clearcuts (6-20 years old) to feed on bunchberry, whereas females with yearling foraged for blueberry and lone bears for ants. Coupling GPS telemetry and scat analyses allows for efficient detection of inter-individual or inter-group variations in foraging strategies and of linkages between previous habitat use and food consumption, even for cryptic species. This approach could have interesting ecological implications, such as supporting the identification of habitats types abundant in important food sources for endangered species targeted by conservation measures or for management actions for depredating animals.
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Ciucci P, Gervasi V, Boitani L, Boulanger J, Paetkau D, Prive R, Tosoni E. Estimating abundance of the remnant Apennine brown bear population using multiple noninvasive genetic data sources. J Mammal 2015. [DOI: 10.1093/jmammal/gyu029] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Mumma MA, Zieminski C, Fuller TK, Mahoney SP, Waits LP. Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance. Mol Ecol Resour 2015; 15:1133-44. [PMID: 25693632 DOI: 10.1111/1755-0998.12390] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 02/08/2015] [Accepted: 02/13/2015] [Indexed: 11/30/2022]
Abstract
Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23-39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances.
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Affiliation(s)
- Matthew A Mumma
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Chris Zieminski
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, 01003, USA
| | - Todd K Fuller
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, 01003, USA
| | - Shane P Mahoney
- Sustainable Development and Strategic Science, Department of Environment and Conservation, Government of Newfoundland and Labrador, Sir Brian Dunfield Bldg., St. John's, A1B 4J6, NL, Canada
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, 83844, USA
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Woodruff SP, Johnson TR, Waits LP. Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn. Mol Ecol Resour 2014; 15:843-54. [DOI: 10.1111/1755-0998.12362] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 11/28/2022]
Affiliation(s)
- S. P. Woodruff
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844-1136 USA
| | - T. R. Johnson
- Department of Statistical Science; University of Idaho; Moscow ID 83844-1104 USA
| | - L. P. Waits
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844-1136 USA
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42
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Karamanlidis AA, Paunović M, Ćirović D, Karapandža B, Skrbinšek T, Zedrosser A. Population genetic parameters of brown bears in western Serbia: implications for research and conservation. URSUS 2014. [DOI: 10.2192/ursus-d-1--00033.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Tsaparis D, Karaiskou N, Mertzanis Y, Triantafyllidis A. Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region – Greece. J NAT HIST 2014. [DOI: 10.1080/00222933.2013.877992] [Citation(s) in RCA: 3] [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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44
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Estimating pumaPuma concolorpopulation size in a human-disturbed landscape in Brazil, using DNA mark–recapture data. ORYX 2014. [DOI: 10.1017/s0030605312000841] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractThe genetics and ecology of pumas are well documented in North America but there is a lack of studies in South America, especially in Brazil. By means of a noninvasive method, faecal DNA analysis, we estimated puma abundance in two protected areas embedded in a human-disturbed landscape in the north-east of São Paulo state, in south-east Brazil. In 8 months of mark–recapture faeces sampling, 15 individual pumas were identified using seven microsatellite loci. The estimated abundance of pumas with the Jolly–Seber open population model was 23.81 ± SE 6.22. This is the first estimate of the abundance of pumas in a human-dominated landscape in São Paulo state, the most populous, developed and industrialized state of Brazil. The absence of high-quality habitats in the north-east of the state, the absence of direct competitors and the high availability of prey in protected areas are probably contributing to the high number of pumas concentrated in a relatively small area (c. 260 km2). Our results will contribute to the long-term monitoring of this puma population and, combined with other ecological, behavioural and genetic data, will help guide conservation action to maintain a viable population of the puma in this region.
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Cullingham CI, Moehrenschlager A. Temporal analysis of genetic structure to assess population dynamics of reintroduced swift foxes. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2013; 27:1389-1398. [PMID: 24033503 DOI: 10.1111/cobi.12122] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 01/04/2013] [Indexed: 06/02/2023]
Abstract
Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Análisis Temporal de la Estructura Genética para Evaluar la Dinámica Poblacional de Zorros (Vulpes velox) Reintroducidos.
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Affiliation(s)
- Catherine I Cullingham
- Department of Biological Sciences, Biological Science Building CW405, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada.
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46
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Kopatz A, Hagen SB, Smith ME, Ollila LE, Aspholm PE, Eiken HG. A Modification of the Hair-Trapping Method for Surveillance of Problematic Bear Activity Close to a Farm — a Case Study from the Pasvik Valley in Norway. ANN ZOOL FENN 2013. [DOI: 10.5735/086.050.0605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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Mumma MA, Soulliere CE, Mahoney SP, Waits LP. Enhanced understanding of predator-prey relationships using molecular methods to identify predator species, individual and sex. Mol Ecol Resour 2013; 14:100-8. [PMID: 23957886 DOI: 10.1111/1755-0998.12153] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 10/26/2022]
Abstract
Predator species identification is an important step in understanding predator-prey interactions, but predator identifications using kill site observations are often unreliable. We used molecular tools to analyse predator saliva, scat and hair from caribou calf kills in Newfoundland, Canada to identify the predator species, individual and sex. We sampled DNA from 32 carcasses using cotton swabs to collect predator saliva. We used fragment length analysis and sequencing of mitochondrial DNA to distinguish between coyote, black bear, Canada lynx and red fox and used nuclear DNA microsatellite analysis to identify individuals. We compared predator species detected using molecular tools to those assigned via field observations at each kill. We identified a predator species at 94% of carcasses using molecular methods, while observational methods assigned a predator species to 62.5% of kills. Molecular methods attributed 66.7% of kills to coyote and 33.3% to black bear, while observations assigned 40%, 45%, 10% and 5% to coyote, bear, lynx and fox, respectively. Individual identification was successful at 70% of kills where a predator species was identified. Only one individual was identified at each kill, but some individuals were found at multiple kills. Predator sex was predominantly male. We demonstrate the first large-scale evaluation of predator species, individual and sex identification using molecular techniques to extract DNA from swabs of wild prey carcasses. Our results indicate that kill site swabs (i) can be highly successful in identifying the predator species and individual responsible; and (ii) serve to inform and complement traditional methods.
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Affiliation(s)
- Matthew A Mumma
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID, 83844, USA
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48
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Latham E, Stetz JB, Seryodkin I, Miquelle D, Gibeau ML. Non-invasive genetic sampling of brown bears and Asiatic black bears in the Russian Far East: A pilot study. URSUS 2012. [DOI: 10.2192/ursus-d-11-00022r2.1] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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COLANGELO PAOLO, LOY ANNA, HUBER DJURO, GOMERČIĆ TOMISLAV, VIGNA TAGLIANTI AUGUSTU, CIUCCI PAOLO. Cranial distinctiveness in the Apennine brown bear: genetic drift effect or ecophenotypic adaptation? Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01926.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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