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Liu H, Luo J, Hou W, Pan X, Cai Y, Li J. An Effective Microsatellite Marker Panel for Noninvasive Samples in Tibetan Macaques (Macaca thibetana). INT J PRIMATOL 2022. [DOI: 10.1007/s10764-022-00348-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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2
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Manning JA, Edwards T, Clemons J, Leavitt DJ, Goldberg CS, Culver M. Scat as a source of DNA for population monitoring. Ecol Evol 2022; 12:e9415. [PMID: 36329814 PMCID: PMC9618667 DOI: 10.1002/ece3.9415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 08/22/2022] [Accepted: 09/18/2022] [Indexed: 01/26/2023] Open
Abstract
Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition and increase genotyping success. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii, California, US, and Morafka's desert tortoise, G. morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, was 15% for the study of Agassiz's desert tortoise and for the study of 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study indicates that genotypes can successfully be obtained from swabs of scat from herbivorous reptiles collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for the genetic identification of individuals from non-invasive samples.
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Affiliation(s)
- Jeffrey A. Manning
- School of the EnvironmentWashington State UniversityPullmanWashingtonUSA
| | - Taylor Edwards
- University of Arizona Genetics Core, University of ArizonaTucsonArizonaUSA
| | - John Clemons
- School of Natural Resources and the Environment, Conservation Genetics LaboratoryUniversity of ArizonaTucsonArizonaUSA
| | - Daniel J. Leavitt
- U.S. Fish and Wildlife ServiceArizona Ecological Services Field OfficePhoenixArizonaUSA
| | - Caren S. Goldberg
- School of the EnvironmentWashington State UniversityPullmanWashingtonUSA
| | - Melanie Culver
- School of Natural Resources and the Environment, Conservation Genetics LaboratoryUniversity of ArizonaTucsonArizonaUSA,U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research UnitUniversity of ArizonaTucsonArizonaUSA
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Tourani M. A review of spatial capture-recapture: Ecological insights, limitations, and prospects. Ecol Evol 2022; 12:e8468. [PMID: 35127014 PMCID: PMC8794757 DOI: 10.1002/ece3.8468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/14/2021] [Accepted: 11/29/2021] [Indexed: 11/28/2022] Open
Abstract
First described by Efford (2004), spatial capture-recapture (SCR) has become a popular tool in ecology. Like traditional capture-recapture, SCR methods account for imperfect detection when estimating ecological parameters. In addition, SCR methods use the information inherent in the spatial configuration of individual detections, thereby allowing spatially explicit estimation of population parameters, such as abundance, survival, and recruitment. Paired with advances in noninvasive survey methods, SCR has been applied to a wide range of species across different habitats, allowing for population- and landscape-level inferences with direct consequences for conservation and management. I conduct a literature review of SCR studies published since the first description of the method and provide an overview of their scope in terms of the ecological questions answered with this tool, taxonomic groups targeted, geography, spatio-temporal extent of analyses, and data collection methods. In addition, I review approaches for analytical implementation and provide an overview of parameters targeted by SCR studies and conclude with current limitations and future directions in SCR methods.
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Affiliation(s)
- Mahdieh Tourani
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
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4
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Schultz AJ, Strickland K, Cristescu RH, Hanger J, de Villiers D, Frère CH. Testing the effectiveness of genetic monitoring using genetic non-invasive sampling. Ecol Evol 2022; 12:e8459. [PMID: 35127011 PMCID: PMC8794716 DOI: 10.1002/ece3.8459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/26/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023] Open
Abstract
Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.
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Affiliation(s)
- Anthony James Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Kasha Strickland
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Department of Aquaculture and Fish BiologyHólar UniversityHólarIceland
| | - Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
| | | | | | - Céline H. Frère
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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Bleke CA, Gese EM, French SS. Variations, validations, degradations, and noninvasive determination of pregnancy using fecal steroid metabolites in free-ranging pronghorn. Gen Comp Endocrinol 2021; 312:113841. [PMID: 34217705 DOI: 10.1016/j.ygcen.2021.113841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
Pregnancy status is a key parameter used to assess reproductive performance of a species as it represents a starting point for measuring vital rates. Vital rates allow managers to determine trends in populations such as neonate survival and recruitment; two important factors in ungulate population growth rates. Techniques to determine pregnancy have generally involved capture and restraint of the animal to obtain blood samples for determining serum hormone levels. Non-invasive pregnancy assessment, via feces, eliminates any hazards between handler and animal, as well as removes handling-induced physiological biases. Using noninvasive fecal sampling, we conducted hormone validations, investigated pregnancy rates, and determined hormone degradation rates across five subpopulations of pronghorn (Antilocapra americana) in Idaho. Samples were collected during April-May of 2018 and 2019 from adult pronghorn of known sex and age class. Metabolites of testosterone, cortisol, 17β-estradiol, and progesterone were measured in fecal samples, and concentrations of estradiol and progesterone were examined for pregnancy determination. Average fecal progesterone metabolite (FPM) levels of pregnant females were more than double compared to levels of nonpregnant females. Fecal estrogen metabolite (FEM) levels did not differ during concurrent sampling. The largest difference in FPM levels between pregnant and nonpregnant females began on 28 April. Pregnancy determination sampling showed average FPM levels for all five subpopulations were significantly different than the nonpregnant female validation group. Nonetheless, pregnancy rates for some subpopulations lacked conclusive estimates due to early fecal sampling. Fecal glucocorticoid metabolites (FGM) levels significantly differed between pregnant females and male pronghorn, but did not differ from nonpregnant females. Degradation rates of FPM and FGM differed across days, with values for FPM from Day 1 being significantly different from all subsequent days, and after Day 9 for FGM, demonstrating the requirement of fresh samples to accurately measure hormone concentrations. We concluded that a noninvasive method to diagnosis pregnancy is possible in pronghorn via progesterone metabolites if fresh samples are collected during late gestation.
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Affiliation(s)
- Cole A Bleke
- Department of Wildland Resources, Utah State University, Logan, UT 84322, USA.
| | - Eric M Gese
- U.S. Department of Agriculture-Wildlife Services-National Wildlife Research Center, Department of Wildland Resources, Utah State University, Logan, UT 84322, USA.
| | - Susannah S French
- Department of Biology and the Ecology Center, Utah State University, Logan, UT 84322, USA.
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Delgado PM, Argüelles CF, DeMatteo KE. Using noninvasive techniques to monitor game species targeted by poaching in Misiones, Argentina. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.1897354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Pryscilha M. Delgado
- Grupo de Investigación en Genética Aplicada (GIGA), Instituto de Biología Subtropical (IBS) - Nodo Posadas, Universidad Nacional de Misiones (UNaM) – CONICET, Posadas, Misiones, Argentina
- Departamento de Genética, Facultad de Ciencias Exactas, Químicas y Naturales, UNaM, Posadas, Misiones, Argentina
| | - Carina F. Argüelles
- Grupo de Investigación en Genética Aplicada (GIGA), Instituto de Biología Subtropical (IBS) - Nodo Posadas, Universidad Nacional de Misiones (UNaM) – CONICET, Posadas, Misiones, Argentina
- Departamento de Genética, Facultad de Ciencias Exactas, Químicas y Naturales, UNaM, Posadas, Misiones, Argentina
| | - Karen E. DeMatteo
- Department of Biology & Environmental Studies, Washington University in St. Louis, St. Louis, United States
- WildCare Institute at the Saint Louis Zoo, St. Louis, United States
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Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01444-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractThe use of non-invasively collected DNA source material for genetic and genomic applications is usually characterized by low target DNA concentration and quality, genotyping errors and cost-intensive lab procedures. However, for otters (Lutrinae) as elusive species of conservation concern, genetic non-invasive sampling has become an important tool to study their ecology and demography. To increase cost-efficiency of monitoring programmes and to promote the expansion of genomic approaches to non-invasive samples, we aimed to refine sample collection and preparation. Therefore, we examined the effects of intrinsic sample characteristics (including diet), environmental conditions in the field and sample treatment in the molecular laboratory on the success of genotyping and allelic dropout (ADO) rates using microsatellite markers in 1970 fresh Eurasian otter (Lutra lutra) scats. Using fresh samples only, we probably eliminated one of the most important impediments of genotyping DNA from otter faecal samples beforehand. But, we observed higher genotyping success and lower ADO rates for anal glad secretions and faecal samples containing high proportions of mucus. Moist conditions during sample collection may promote DNA degradation and PCR inhibition, leading to decreased genotyping success rates. ADO was further affected by the type of extraction kit. However, a high proportion of variance remaining unexplained by our models implied that additional parameters were acting (amount of PCR inhibitors, non-uniform distribution of intestinal cells, efficiency of PCRs, specific microclimate at marking sites). We summarized influential factors maximizing genotyping quality of otter scats and give recommendations for sample collection, storage and DNA extraction based on our results and current literature.
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8
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Methodological improvements for detecting and identifying scats of an expanding mesocarnivore in south-western Europe. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00062-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Buglione M, Petrelli S, Troiano C, Notomista T, Rivieccio E, Fulgione D. The diet of otters ( Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach. PeerJ 2020; 8:e9606. [PMID: 32821542 PMCID: PMC7395603 DOI: 10.7717/peerj.9606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/05/2020] [Indexed: 01/14/2023] Open
Abstract
Background The Eurasian otter (Lutra lutra) underwent a strong decline in large areas of the Central-Western part of its distribution range, during the second half of the twentieth century. In Italy, only residual fragmented nuclei survive in the Central-Southern part of the peninsula. Nowadays, the otter is one of the most endangered mammals in Italy, and increasing the knowledge about the ecology of this species is a key step in defining fitting management strategies. Here we provide information about the diet of otter on the Agri river system, one of the most important presence sites in Italy, to understand both the species’ food requirements and the impact on fish communities. Methods DNA metabarcoding and High Throughput Sequencing were used on DNA extracted from spraints. We amplified DNA with a primer set for vertebrates, focusing efforts on the bulk of the otter’s diet (fishes and amphibians). Results Our findings showed that the diet of the otter was dominated by cyprinids (97.77%, and 99.14% of fishes), while amphibians represented 0.85% of the sequences analyzed. Results are in general accordance with previous studies based on morphological characterization; however, molecular analyses allow the resolving of some morphological uncertainties. Although the study area offers a very wide range of available prey, the diet of the otters shows marked selectivity. We highlighted a variation in prey consumed, in accordance with the typology of water system (i.e., river, lake, tributary). Some of the preys found in the diet were alien species introduced by man for sport fishing. Our findings could help define strategies useful for the conservation of the otter population in Southern Italy, suggesting management actions directed at avoiding fish community alterations through illegal stockings without severe controls on their taxonomic status. These introductions could result in a general reduction in the diversity of the otter’s preys, affecting its predatory behavior.
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Affiliation(s)
- Maria Buglione
- Department of Biology, University of Naples Federico II, Naples, Italy, Italy
| | - Simona Petrelli
- Department of Biology, University of Naples Federico II, Naples, Italy, Italy
| | - Claudia Troiano
- Department of Humanities, University of Naples Federico II, Naples, Italy, Italy
| | - Tommaso Notomista
- Department of Biology, University of Naples Federico II, Naples, Italy, Italy
| | - Eleonora Rivieccio
- Department of Biology, University of Naples Federico II, Naples, Italy, Italy
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Naples, Italy, Italy
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10
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Who is who? High Resolution Melting analysis to discern between hare species using non-invasive sampling. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01153-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Tighe AJ, Overby S, Thurman K, Gandola R, Fulanda B, Byrne J, Carlsson J. Investigating a simplified method for noninvasive genetic sampling in East African mammals using silica dried scat swabs. Ecol Evol 2020; 10:3330-3337. [PMID: 32273990 PMCID: PMC7141023 DOI: 10.1002/ece3.6115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 11/06/2022] Open
Abstract
Swabbing scat has proved to be an effective noninvasive method to collect DNA from mammals in the field. Previously, this method has relied on preservative liquids or freezing to preserve the DNA collected on swabs. In this study, we determine the effectiveness of using silica to simply dry the swab in field as an alternative way to prevent DNA degredation. Four species were included in the study; reticulated giraffe, impala, fringe-eared oryx, and lion. Swabs were taken at multiple time points for giraffe and impala scat samples, with the lion and oryx sampled opportunistically. Mitochondrial DNA was successfully amplified and sequenced from scat swabs from all species; however, effectiveness varied between species, with 81.8% amplification success rate from swabs taken from impala scat compared to 25% amplification success rate in giraffe. This variation in success rate was overcome by taking multiple swabs, thus increasing the probability of a successful amplification. The true merit of this method is in its simplicity and cheapness; no preservative liquids were required to be brought into the field, at no stage in the 2 weeks of field sampling were samples frozen, and no commercial kits were used for DNA extraction.
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Affiliation(s)
- Andrew J Tighe
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
- Fish Health Unit Marine Institute Oranmore Ireland
| | - Sarah Overby
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED) University of Valencia Valencia Spain
| | - Kiera Thurman
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
| | - Robert Gandola
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
| | - Bernerd Fulanda
- Department of Biological Sciences Pwani University Kilifi Kenya
| | - John Byrne
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
| | - Jens Carlsson
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
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12
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Development of a mitochondrial DNA marker that distinguishes domestic dogs from Washington state gray wolves. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01130-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Walker FM, Tobin A, Simmons NB, Sobek CJ, Sanchez DE, Chambers CL, Fofanov VY. A fecal sequel: Testing the limits of a genetic assay for bat species identification. PLoS One 2019; 14:e0224969. [PMID: 31725795 PMCID: PMC6855431 DOI: 10.1371/journal.pone.0224969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/26/2019] [Indexed: 11/23/2022] Open
Abstract
DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon’s fecal DNA. Here, we defined the constraints of an assay called ‘Species from Feces’ used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays.
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Affiliation(s)
- Faith M. Walker
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
| | - Abby Tobin
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Colin J. Sobek
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Daniel E. Sanchez
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Carol L. Chambers
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Viacheslav Y. Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
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Moolman L, Morney MAD, Ferreira SM, Ganswindt A, Poole JH, Kerley GI. And Then There was One: A Camera Trap Survey of the Declining Population of African Elephants in Knysna, South Africa. AFRICAN JOURNAL OF WILDLIFE RESEARCH 2019. [DOI: 10.3957/056.049.0016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Lizette Moolman
- Scientific Services, South African National Parks, P.O. Box 3542, Knysna, 6570 South Africa
| | - Melanie A. de Morney
- Scientific Services, South African National Parks, P.O. Box 3542, Knysna, 6570 South Africa
| | - Sam M. Ferreira
- Scientific Services, South African National Parks, Private Bag X402, Skukuza, 1350 South Africa
| | - André Ganswindt
- Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028 South Africa
| | | | - Graham I.H. Kerley
- Centre for African Conservation Ecology, Nelson Mandela University, P.O. Box 77000, Port Elizabeth, 6031 South Africa
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15
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Crossey B, Ganswindt A, Chimimba C. Faecal glucocorticoid metabolite concentrations and their alteration post-defaecation in African wild dogs Lycaon pictus from South Africa. WILDLIFE BIOLOGY 2018. [DOI: 10.2981/wlb.00469] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Bruce Crossey
- B. Crossey , A. Ganswindt and C. Chimimba, Mammal Research Inst. (MR
| | - Andre Ganswindt
- BC and AG also at: Endocrine Research Laboratory, Dept of Anatomy and Physiology, Univ. of Pretoria,
| | - Christian Chimimba
- CC also at: DST-NRF Centre of Excellence for Invasion Biology (CIB), Dept of Zoology and Entomology,
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How Behavior of Nontarget Species Affects Perceived Accuracy of Scat Detection Dog Surveys. Sci Rep 2018; 8:13830. [PMID: 30218000 PMCID: PMC6138736 DOI: 10.1038/s41598-018-32244-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/03/2018] [Indexed: 01/18/2023] Open
Abstract
Detection dogs, specially trained domestic dogs (Canis familiaris), have become a valuable, noninvasive, conservation tool because they remove the dependence of attracting species to a particular location. Further, detection dogs locate samples independent of appearance, composition, or visibility allowing researchers to collect large sets of unbiased samples that can be used in complex ecological queries. One question not fully addressed is why samples from nontarget species are inadvertently collected during detection dog surveys. While a common explanation has been incomplete handler or dog training, our study aimed to explore alternative explanations. Our trials demonstrate that a scat’s genetic profile can be altered by interactions of nontarget species with target scat via urine-marking, coprophagy, and moving scats with their mouths, all pathways to contamination by nontarget species’ DNA. Because detection dogs are trained to locate odor independent of masking, the collection of samples with a mixed olfactory profile (target and nontarget) is possible. These scats will likely have characteristics of target species’ scats and are therefore only discovered faulty once genetic results indicate a nontarget species. While the collection of nontarget scats will not impact research conclusions so long as samples are DNA tested, we suggest ways to minimize their collection and associated costs.
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17
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Behringer V, Deimel C, Hohmann G, Negrey J, Schaebs FS, Deschner T. Applications for non-invasive thyroid hormone measurements in mammalian ecology, growth, and maintenance. Horm Behav 2018; 105:66-85. [PMID: 30063897 DOI: 10.1016/j.yhbeh.2018.07.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/22/2022]
Abstract
Thyroid hormones (THs) play a pivotal role in the regulation of metabolic activity throughout all life stages. Cross-talk with other hormone systems permits THs to coordinate metabolic changes as well as modifications in growth and maintenance in response to changing environmental conditions. The scope of this review is to explain the relevant basics of TH endocrinology, highlight pertinent topics that have been investigated so far, and offer guidance on measuring THs in non-invasively collected matrices. The first part of the review provides an overview of TH biochemistry, which is necessary to understand and interpret the findings of existing studies and to apply non-invasive TH monitoring. The second part focuses on the role of THs in mammalian ecology, and the third part highlights the role of THs in growth and maintenance. The fourth part deals with the advantages and difficulties of measuring THs in non-invasively collected samples. This review concludes with a summary that considers future directions in the study of THs.
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Affiliation(s)
- V Behringer
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - C Deimel
- Department of Anthropology, Indiana University Bloomington, 701 E Kirkwood Ave, Bloomington, IN 47405, USA
| | - G Hohmann
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - J Negrey
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA 02215, USA
| | - F S Schaebs
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - T Deschner
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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A pilot study on the application of DNA metabarcoding for non-invasive diet analysis in the Italian hare. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2017.10.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Maia TA, Vilaça ST, Silva LRD, Santos FR, Dantas GPDM. DNA sampling from eggshells and microsatellite genotyping in rare tropical birds: Case study on Brazilian Merganser. Genet Mol Biol 2017; 40:808-812. [PMID: 28981560 PMCID: PMC5738623 DOI: 10.1590/1678-4685-gmb-2016-0297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 08/04/2017] [Indexed: 11/29/2022] Open
Abstract
This study shows that sampling maternal DNA from hatched and abandoned eggshells
is a viable noninvasive strategy for studying the genetics of rare or endangered
tropical birds, as exemplified here by the Brazilian Merganser (Mergus
octosetaceus). Eighteen microsatellites were isolated from enriched
libraries and nine heterologous loci from related species were tested. Seven
loci were amplified successfully, with five of them being polymorphic. These
loci exhibited amplicons ranging from 110 to 254 bp for 132 samples, with 60
from eggshells and 72 from blood or muscle samples. The number of alleles for
M. octosetaceus ranged from one to six (mean = 3.71), which
is low compared to M. merganser (1-15 alleles), a ‘least
concern’ species. Genetic diversity did not differ significantly between
noninvasive and invasive samples (Z(u) = 0.31, p = 0.37). Thus,
noninvasive sampling, as demonstrated here with eggshells, provides an efficient
means to assess genetic diversity in tropical birds without the need to capture
and handle them.
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Affiliation(s)
- Thais Augusta Maia
- Laboratório de Ecologia e Evolução de Aves, Programa de Pós-Graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sibelle Torres Vilaça
- Department Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, and Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Luciana Resende da Silva
- Laboratório de Biodiversidade e Evolução Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fabricio Rodrigues Santos
- Laboratório de Biodiversidade e Evolução Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gisele Pires de Mendonça Dantas
- Laboratório de Ecologia e Evolução de Aves, Programa de Pós-Graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, MG, Brazil
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Nakamura M, Godinho R, Rio-Maior H, Roque S, Kaliontzopoulou A, Bernardo J, Castro D, Lopes S, Petrucci-Fonseca F, Álvares F. Evaluating the predictive power of field variables for species and individual molecular identification on wolf noninvasive samples. EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1112-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Carpenter FM, Dziminski MA. Breaking down scats: degradation of DNA from greater bilby (Macrotis lagotis) faecal pellets. AUSTRALIAN MAMMALOGY 2017. [DOI: 10.1071/am16030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Isolating DNA from scats (faeces) of threatened species is a valuable, non-invasive method for identifying individuals. To establish whether genotyping of greater bilby (Macrotis lagotis) individuals from faecal pellets collected in the field can be useful for population monitoring, an understanding of the DNA degradation rates is necessary. To determine the relationship between time and degradation of bilby faecal DNA, and assess whether a two-step elution process during extraction results in better-quality DNA, faecal pellets were collected from captive individuals, maintained under seminatural conditions, then harvested at known periods. DNA was amplified from faecal pellets with a 99% success rate and error rates of less than 5% up to 14 days after deposition. The amplification rate decreases, and the rate of allelic dropout increases with time, but DNA can still be amplified at rates above 60% and error rates below 15% at 90–180 days. We found that a second elution step was unnecessary, with more DNA amplified over a longer period using the first eluate. Viable DNA exists on bilby faecal pellets for a long period after deposition, which is useful for obtaining genetic samples for population monitoring programs and studies on population genetics.
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22
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McInnes JC, Alderman R, Deagle BE, Lea M, Raymond B, Jarman SN. Optimised scat collection protocols for dietary
DNA
metabarcoding in vertebrates. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12677] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julie C. McInnes
- Institute for Marine and Antarctic Studies University of Tasmania Private Bag 129 Hobart TAS 7001 Australia
- Australian Antarctic Division 203 Channel Highway Kingston TAS 7050 Australia
| | - Rachael Alderman
- Department of Primary Industries, Parks, Water and Environment 134 Macquarie Street Hobart TAS 7000 Australia
| | - Bruce E. Deagle
- Australian Antarctic Division 203 Channel Highway Kingston TAS 7050 Australia
| | - Mary‐Anne Lea
- Institute for Marine and Antarctic Studies University of Tasmania Private Bag 129 Hobart TAS 7001 Australia
| | - Ben Raymond
- Institute for Marine and Antarctic Studies University of Tasmania Private Bag 129 Hobart TAS 7001 Australia
- Australian Antarctic Division 203 Channel Highway Kingston TAS 7050 Australia
| | - Simon N. Jarman
- Australian Antarctic Division 203 Channel Highway Kingston TAS 7050 Australia
- CIBIO‐InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão 4485‐661 Portugal
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23
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Lee PS, Gan HM, Clements GR, Wilson JJ. Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests. Genome 2016; 59:1008-1022. [DOI: 10.1139/gen-2015-0193] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.
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Affiliation(s)
- Ping-Shin Lee
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia
- Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia
| | - Gopalasamy Reuben Clements
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia
- Centre for Tropical Environmental and Sustainability Science, and College of Marine and Environmental Sciences, James Cook University, 4870 Cairns, Queensland, Australia
- Kenyir Research Institute, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Malaysia
- Rimba, 4 Jalan 1/9D, 43650 Bandar Baru Bangi, Selangor, Malaysia
| | - John-James Wilson
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Keiter DA, Cunningham FL, Rhodes OE, Irwin BJ, Beasley JC. Optimization of Scat Detection Methods for a Social Ungulate, the Wild Pig, and Experimental Evaluation of Factors Affecting Detection of Scat. PLoS One 2016; 11:e0155615. [PMID: 27224453 PMCID: PMC4880348 DOI: 10.1371/journal.pone.0155615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/02/2016] [Indexed: 11/29/2022] Open
Abstract
Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.
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Affiliation(s)
- David A. Keiter
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
- D. B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Fred L. Cunningham
- National Wildlife Research Center, United States Department of Agriculture Animal and Plant Health Inspection Service, Starkville, Mississippi, United States of America
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
| | - Brian J. Irwin
- U. S. Geological Survey, Georgia Cooperative Fish and Wildlife Research Unit, D. B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - James C. Beasley
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
- D. B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
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25
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Chetri M, Jhala YV, Jnawali SR, Subedi N, Dhakal M, Yumnam B. Ancient Himalayan wolf (Canis lupus chanco) lineage in Upper Mustang of the Annapurna Conservation Area, Nepal. Zookeys 2016:143-56. [PMID: 27199590 PMCID: PMC4857050 DOI: 10.3897/zookeys.582.5966] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 03/16/2016] [Indexed: 11/12/2022] Open
Abstract
The taxonomic status of the wolf (Canis lupus) in Nepal's Trans-Himalaya is poorly understood. Recent genetic studies have revealed the existence of three lineages of wolves in the Indian sub-continent. Of these, the Himalayan wolf, Canis lupus chanco, has been reported to be the most ancient lineage historically distributed within the Nepal Himalaya. These wolves residing in the Trans-Himalayan region have been suggested to be smaller and very different from the European wolf. During October 2011, six fecal samples suspected to have originated from wolves were collected from Upper Mustang in the Annapurna Conservation Area of Nepal. DNA extraction and amplification of the mitochondrial (mt) control region (CR) locus yielded sequences from five out of six samples. One sample matched domestic dog sequences in GenBank, while the remaining four samples were aligned within the monophyletic and ancient Himalayan wolf clade. These four sequences which matched each other, were new and represented a novel Himalayan wolf haplotype. This result confirms that the endangered ancient Himalayan wolf is extant in Nepal. Detailed genomic study covering Nepal's entire Himalayan landscape is recommended in order to understand their distribution, taxonomy and, genetic relatedness with other wolves potentially sharing the same landscape.
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Affiliation(s)
| | | | | | - Naresh Subedi
- National Trust for Nature Conservation, Khumaltar, Lalitpur, Kathmandu, Nepal
| | - Maheshwar Dhakal
- Department of National Parks and Wildlife Conservation, Babarmahal, Kathmandu, Nepal
| | - Bibek Yumnam
- Wildlife Institute of India, Chandrabani, Dehradun 248001, India
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26
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Miles KA, Holtz MN, Lounsberry ZT, Sacks BN. A paired comparison of scat-collecting versus scat-swabbing methods for noninvasive recovery of mesocarnivore DNA from an arid environment. WILDLIFE SOC B 2015. [DOI: 10.1002/wsb.600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kathleen A. Miles
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Michelle N. Holtz
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Zachary T. Lounsberry
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Benjamin N. Sacks
- Department of Population Health and Reproduction and Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
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27
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DeMatteo KE, Rinas MA, Argüelles CF, Holman BE, Di Bitetti MS, Davenport B, Parker PG, Eggert LS. Using detection dogs and genetic analyses of scat to expand knowledge and assist felid conservation in Misiones, Argentina. Integr Zool 2015; 9:623-39. [PMID: 25236691 DOI: 10.1111/1749-4877.12113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many carnivores require large ranges to meet their ecological and energetic needs; however, anthropogenic changes threaten species and their habitats. Camera traps have been used to effectively collect data on carnivores in a variety of habitat types; however, a single survey effort is typically limited to species that have similar body size, habitat use and movement patterns, and individual identification of animals is not always possible. We evaluated whether scat detection dogs could effectively survey for 4 wide-ranging felids that vary in these characteristics: jaguars (Panthera onca), pumas (Puma concolor), ocelots (Leopardus pardalis) and oncillas (Leopardus tigrinus). From June to October 2009 and May to August 2011, a detection dog-handler team detected 588 scats, from which 176 unique genotypes were detected. We assigned sex to 84.7% of the genotyped scats and identified 55 individuals multiple times. The effectiveness of these noninvasive techniques (detection dogs and genetic analyses of scat) not only opens the door for additional studies in areas that were previously difficult or impossible with standard survey techniques, but also provides conservationists with a set of tools that overcome some of the limitations associated with the use of camera traps alone.
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Affiliation(s)
- Karen E DeMatteo
- Department of Biology, University of Missouri, St. Louis, USA; WildCare Institute at the Saint Louis Zoo, St. Louis, USA
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28
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Rocha RG, Justino J, Leite YLR, Costa LP. DNA from owl pellet bones uncovers hidden biodiversity. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2015.1044048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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Wultsch C, Waits LP, Hallerman EM, Kelly MJ. Optimizing collection methods for noninvasive genetic sampling of neotropical felids. WILDLIFE SOC B 2015. [DOI: 10.1002/wsb.540] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Claudia Wultsch
- Department of Fish and Wildlife Conservation; Virginia Tech; 318 Cheatham Hall, Blacksburg VA 24061 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Resources; University of Idaho; 875 Perimeter Drive, ID 83844 USA
| | - Eric M. Hallerman
- Department of Fish and Wildlife Conservation; Virginia Tech; 100 Cheatham Hall, Blacksburg VA 24061 USA
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation; Virginia Tech; 146 Cheatham Hall, Blacksburg VA 24061 USA
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30
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Leigh KA, Dominick M. An assessment of the effects of habitat structure on the scat finding performance of a wildlife detection dog. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12374] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Kellie A. Leigh
- Science for Wildlife PO Box 286 Cammeray NSW 2062 Australia
- Faculty of Veterinary Science University of Sydney Sydney NSW Australia
| | - Martin Dominick
- Australian Canine Services Pty Ltd PO Box 109 Burpengary Qld4504 Australia
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31
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Cristescu RH, Foley E, Markula A, Jackson G, Jones D, Frère C. Accuracy and efficiency of detection dogs: a powerful new tool for koala conservation and management. Sci Rep 2015; 5:8349. [PMID: 25666691 PMCID: PMC4322364 DOI: 10.1038/srep08349] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 12/18/2014] [Indexed: 11/29/2022] Open
Abstract
Accurate data on presence/absence and spatial distribution for fauna species is key to their conservation. Collecting such data, however, can be time consuming, laborious and costly, in particular for fauna species characterised by low densities, large home ranges, cryptic or elusive behaviour. For such species, including koalas (Phascolarctos cinereus), indicators of species presence can be a useful shortcut: faecal pellets (scats), for instance, are widely used. Scat surveys are not without their difficulties and often contain a high false negative rate. We used experimental and field-based trials to investigate the accuracy and efficiency of the first dog specifically trained for koala scats. The detection dog consistently out-performed human-only teams. Off-leash, the dog detection rate was 100%. The dog was also 19 times more efficient than current scat survey methods and 153% more accurate (the dog found koala scats where the human-only team did not). This clearly demonstrates that the use of detection dogs decreases false negatives and survey time, thus allowing for a significant improvement in the quality and quantity of data collection. Given these unequivocal results, we argue that to improve koala conservation, detection dog surveys for koala scats could in the future replace human-only teams.
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Affiliation(s)
- Romane H. Cristescu
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia 4558
| | - Emily Foley
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia 4111
| | - Anna Markula
- Logan City Council, 150 Wembley Road, Logan Central, Queensland, Australia 4114
| | - Gary Jackson
- Gary Jackson Dog Trainer, 190 McPhail Road, Narangba, Queensland, Australia 4504
| | - Darryl Jones
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia 4111
| | - Céline Frère
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia 4558
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32
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Increased stress in Asiatic black bears relates to food limitation, crop raiding, and foraging beyond nature reserve boundaries in China. Glob Ecol Conserv 2014. [DOI: 10.1016/j.gecco.2014.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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DEMatteo KE, Rinas MA, Argüelles CF, Zurano JP, Selleski N, Bitetti MSD, Eggert LS. Noninvasive techniques provide novel insights for the elusive bush dog (Speothos venaticus). WILDLIFE SOC B 2014. [DOI: 10.1002/wsb.474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Karen E. DEMatteo
- University of Missouri; Division of Biological Sciences; 226 Tucker Hall Columbia MO 65211 USA
- WildCare Institute; Saint Louis Zoo; One Government Drive St. Louis 63110 MO USA
| | - Miguel A. Rinas
- Ministerio de Ecología RNRyT; Leandro N Alem 4907 3300 Posadas Misiones Argentina
| | - Carina F. Argüelles
- Instituto de Biología Subtropical-nodo Posadas; Universidad Nacional de Misiones; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Argentina and Universidad Nacional de Misiones; Facultad de Ciencias Exactas; Químicas y Naturales; Dpto. de Genética; Félix de Azara 1552 CPA 3300LQH Posadas Misiones Argentina
| | - Juan Pablo Zurano
- Universidad Nacional de Misiones; Facultad de Ciencias Exactas; Químicas y Naturales; Dpto. de Genética; Félix de Azara 1552 CPA 3300LQH Posadas Misiones Argentina
| | - Nicole Selleski
- Universidad Nacional de Misiones; Facultad de Ciencias Exactas; Químicas y Naturales; Dpto. de Genética; Félix de Azara 1552 CPA 3300LQH Posadas Misiones Argentina
| | - Mario S. Di Bitetti
- Instituto de Biología Subtropical-nodo Puerto Iguazú; Universidad Nacional de Misiones, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Argentina and Asociación Civil Centro de Investigaciones del Bosque Atlántico (CeIBA); Bertoni 85 (3370) Puerto Iguazú Misiones Argentina
| | - Lori S. Eggert
- University of Missouri; Division of Biological Sciences; 226 Tucker Hall Columbia MO 65211 USA
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34
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Vynne C, Booth RK, Wasser SK. Physiological implications of landscape use by free-ranging maned wolves (Chrysocyon brachyurus) in Brazil. J Mammal 2014. [DOI: 10.1644/12-mamm-a-247] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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35
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Wultsch C, Waits LP, Kelly MJ. Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and faecal DNA. Mol Ecol Resour 2014; 14:1171-82. [DOI: 10.1111/1755-0998.12266] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Claudia Wultsch
- Department of Fish and Wildlife Conservation; Virginia Tech; 100 Cheatham Hall Blacksburg VA 24061 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; 79th Street at Central Park West New York NY 10024 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Resources; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation; Virginia Tech; 100 Cheatham Hall Blacksburg VA 24061 USA
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36
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Development of genetic structure in a heterogeneous landscape over a short time frame: the reintroduced Asiatic wild ass. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0614-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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37
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Mesa-Cruz JB, Brown JL, Kelly MJ. Effects of natural environmental conditions on faecal glucocorticoid metabolite concentrations in jaguars (Panthera onca) in Belize. CONSERVATION PHYSIOLOGY 2014; 2:cou039. [PMID: 27293660 PMCID: PMC4732494 DOI: 10.1093/conphys/cou039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 05/03/2023]
Abstract
In situ studies that rely on non-invasive faecal hormone monitoring are subject to problems due to potential changes in hormone concentrations in samples exposed to field conditions. In this study, we conducted an environmental validation for measurement of faecal glucocorticoid metabolites (FGMs) in jaguars (Panthera onca). We collected fresh faeces (e.g. no older than 8 h) from jaguars (six males and four females), housed at the Belize Zoo, and exposed them randomly to two environmental conditions: shade and sun. A control (first sub-sample) was immediately frozen, after which sub-samples were frozen daily over a 5 day period in both the dry and wet seasons. We quantified FGMs using a cortisol enzyme immunoassay (EIA) and a corticosterone radioimmunoassay (RIA), both capable of identifying relevant metabolites. Results indicated that FGMs assessed with the cortisol EIA were stable for 5 days during the dry season but for <1 day during the wet season, while FGMs assessed with the corticosterone RIA were stable for 5 days during both the dry and wet seasons. Exposure of jaguar faeces to sun or shade had no effect on FGM concentrations, despite significant differences in weather parameters. Analysis of faecal morphology proved unreliable in identifying faecal age. We conclude that the corticosterone RIA is suitable for assessing FGMs in free-ranging Belizean jaguars by surveying the same transects every 3-4 days in both seasons. The cortisol EIA can be used during the dry season, but there are possible shifts in metabolite immunoactivity in wet conditions. Assessment of adrenal activity in jaguars ranging areas of varying human disturbance is a timely application of this methodology in Belize.
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Affiliation(s)
- J. Bernardo Mesa-Cruz
- Department of Fish and Wildlife Conservation, Virginia Polytechnic and State University, Cheatham Hall, 310 West Campus Drive, Blacksburg, VA 24061, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, 1500 Remount Road, Front Royal, VA 22630, USA
- Corresponding author: Department of Fish and Wildlife Conservation, Virginia Polytechnic and State University, Cheatham Hall, 310 West Campus Drive, Blacksburg, VA 24061, USA. Tel: +1 443 745 9544.
| | - Janine L. Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, 1500 Remount Road, Front Royal, VA 22630, USA
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Polytechnic and State University, Cheatham Hall, 310 West Campus Drive, Blacksburg, VA 24061, USA
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Sollmann R, Betsch J, Furtado MM, Hofer H, Jácomo ATA, Palomares F, Roques S, Tôrres NM, Vynne C, Silveira L. Note on the diet of the jaguar in central Brazil. EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0708-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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RENAN SHARON, SPEYER EDITH, SHAHAR NAAMA, GUETA TOMER, TEMPLETON ALANR, BAR‐DAVID SHIRLI. A factorial design experiment as a pilot study for noninvasive genetic sampling. Mol Ecol Resour 2012; 12:1040-7. [DOI: 10.1111/j.1755-0998.2012.03170.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- SHARON RENAN
- Department of Life Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva 85104, Israel
| | - EDITH SPEYER
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben‐Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben‐Gurion 84990, Israel
| | - NAAMA SHAHAR
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben‐Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben‐Gurion 84990, Israel
| | - TOMER GUETA
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben‐Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben‐Gurion 84990, Israel
| | - ALAN R. TEMPLETON
- Department of Biology, Washington University, St. Louis, MO 63130, USA
- Department of Evolutionary and Environmental Ecology, University of Haifa, Haifa 31905, Israel
| | - SHIRLI BAR‐DAVID
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben‐Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben‐Gurion 84990, Israel
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