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Rainey TA, Tryc EE, Nicholson KE. Comparing skin swabs, buccal swabs, and toe clips for amphibian genetic sampling, a case study with a small anuran ( Acris blanchardi). Biol Methods Protoc 2024; 9:bpae030. [PMID: 38818027 PMCID: PMC11139508 DOI: 10.1093/biomethods/bpae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
Multiple methods for collecting genetic samples from amphibians exist, each with their own implications for study design, animal welfare, and costs. Toe clipping is one common method, but there is ongoing debate regarding its potential detriment. Less invasive methods should be implemented, if efficacious, as amphibians are a particularly vulnerable vertebrate group. Skin and buccal swabbing are less invasive methods for genetic sampling, but the potential for contamination and a lower yield of DNA may exist. To compare these methods, we gathered skin swabs, buccal swabs, and toe clips from the same individuals of a relatively small anuran species, Blanchard's Cricket Frog (Acris blanchardi). We then compared DNA yield, DNA purity, amplification success rate, and genotypic data quality among sample types. We found toe clips and buccal swabs generated similar DNA yield and purity, with skin swabs yielding significantly less DNA of significantly lower purity than the other sample types. Amplification success rate was significantly higher using toe clips compared to the other sample types, though buccal swab samples amplified more readily than skin swabs. Genotypic data from toe clips and buccal swabs did not differ significantly in quality, but skin swab data quality was significantly lowest among sample types. Thus, skin swabbing could produce erroneous data in some situations, but buccal swabbing is likely an effective substitute to toe clipping, even for small species. Our results can help future researchers select which genetic sampling method might best suit their research needs.
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Affiliation(s)
- Travis A Rainey
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Emily E Tryc
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Kirsten E Nicholson
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
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2
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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3
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Rodrigues NT, Saranholi BH, Inforzato AR, Silveira L, Desbiez ALJ, Galetti PM. Reduced gene flow and bottleneck in the threatened giant armadillo (Priodontes maximus): implications for its conservation. Genet Mol Biol 2024; 47:e20230252. [PMID: 38446984 PMCID: PMC10917080 DOI: 10.1590/1678-4685-gmb-2023-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/30/2023] [Indexed: 03/08/2024] Open
Abstract
The progressive fragmentation and loss of habitats represent the main threats for endangered species, causing genetic consequences that may have potential implications for a population's long-term persistence. Large mammals are the most affected species among vertebrates. The giant armadillo Priodontes maximus is a large South American mammal threatened species, showing nocturnal, solitary and fossorial behavior, occurring at low population densities, and its population dynamics are still poorly known. In this study, we carried out the first assessment of genetic variability and population genetic structure of the species, using a panel of 15 polymorphic microsatellites developed by high-throughput genome sequencing. The spatial Bayesian clustering, Fst and Dest results indicated the presence of two genetic clusters (K = 2) in the study area. These results suggest a reduction in gene flow between individuals inhabiting the Brazilian savanna (Cerrado) and the Pantanal wetlands, with the increased human-driven habitat modifications possibly contributing for this scenario. A bottleneck signal was detected in both populations, and a subpopulation structuring in the Cerrado may also be reflecting consequences of the extensive habitat modifications. Findings from this study provide important and useful information for the future maintenance of genetic diversity and long-term conservation of this flagship species.
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Affiliation(s)
- Nayra T. Rodrigues
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Bruno H. Saranholi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
- Imperial College London, Department of Life Sciences, Ascot, United Kingdom
| | - Alexandre R. Inforzato
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | | | - Arnaud Leonard Jean Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Mato Grosso do Sul, Brazil
- Royal Zoological Society of Scotland (RZSS), Murrayfield, Edinburgh, United Kingdom
- Instituto de Pesquisas Ecológicas (IPE), Nazaré Paulista, São Paulo, Brazil
| | - Pedro M. Galetti
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
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4
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Hrabina P, Pernerová L, Suchomel J, Robovský J. Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina). Zookeys 2023; 1181:81-110. [PMID: 38313159 PMCID: PMC10838175 DOI: 10.3897/zookeys.1181.108019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 02/06/2024] Open
Abstract
Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.
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Affiliation(s)
- Petr Hrabina
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Ludmila Pernerová
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
| | - Josef Suchomel
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
- Liberec Zoo, Lidové sady 425/1, Liberec, 46001, Czech Republic Liberec Zoo Liberec Czech Republic
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5
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Akrim F, Mahmood T, Belant JL, Nadeem MS, Qasim S, Dhendup T, Fatima H, Bukhari SA, Aslam A, Younis H, Rafique A, Subhani ZA, Hashmi SA, Munawar N. Niche partitioning by sympatric civets in the Himalayan foothills of Pakistan. PeerJ 2023; 11:e14741. [PMID: 36846462 PMCID: PMC9951805 DOI: 10.7717/peerj.14741] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/22/2022] [Indexed: 02/23/2023] Open
Abstract
Niche overlap between sympatric species can indicate the extent of interspecific competition. Sympatric competing species can exhibit spatial, temporal, and dietary adjustments to reduce competition. We investigated spatial, temporal, and dietary niche overlap of sympatric Asian palm civet (Paradoxurus hermaphroditus) and small Indian civet ( Viverricula indica), in and around Pir Lasura National Park, Pakistan. We used remote cameras to determine the frequency and timing of detections to estimate spatial and temporal overlap, and prey remains from scats to estimate dietary overlap. We collected scat samples of Asian palm civet (n = 108) and small Indian civet (n = 44) for dietary analysis. We found low spatial (Oij = 0.32) and temporal (Δ = 0.39) overlap, but high dietary niche overlap (0.9) between these two civet species. Both civet species were detected at only 11 camera sites and small Indian civets were detected most frequently during 2:00-5:00 h and 8:00-10:00 h, whereas Asian palm civets detections were greatest during 20:00-2:00 h. The overall niche breadth of Asian palm civet was slightly narrower (L = 9.69, Lst = 0.31) than that of the small Indian civet (L = 10, Lst = 0.52). We identified 27 dietary items (15 plant, 12 animal) from scats of Asian palm civet including Himalayan pear (Pyrus pashia; 27%), Indian gerbil (Tatera indica; 10%), Rhesus monkey (Macaca mulatta; 4%), and insects (5%). Scat analysis of small Indian civets revealed 17 prey items (eight plant, nine animal) including Himalayan pear (24%), domestic poultry (15%), Indian gerbil (11%), and house mouse (Mus musculus; 5%). Both civet species consumed fruits of cultivated orchard species. Spatial and temporal partitioning of landscapes containing diverse foods appears to facilitate coexistence between Asian palm civets and small Indian civets.
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Affiliation(s)
- Faraz Akrim
- Department of Zoology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | - Tariq Mahmood
- Department of Wildlife Management, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan,Department of Zoology Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Jerrold L. Belant
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Muhammad Sajid Nadeem
- Department of Zoology Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Siddiqa Qasim
- Department of Wildlife Management, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Tashi Dhendup
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - Hira Fatima
- Department of Wildlife & Ecology, University of Okara, Okara, Punjab, Pakistan
| | - Syed Afaq Bukhari
- Department of Zoology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | - Asad Aslam
- Department of Zoology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | - Humera Younis
- Department of Zoology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | - Aamish Rafique
- Department of Zoology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | - Zahid Ahmed Subhani
- Department of Zoology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | | | - Nadeem Munawar
- Department of Wildlife Management, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
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6
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Dupont PPA, Bischof R, Milleret C, Peters W, Edelhoff H, Ebert C, Klamm A, Hohmann U. An evaluation of spatial capture‐recapture models applied to ungulate non‐invasive genetic sampling data. J Wildl Manage 2023. [DOI: 10.1002/jwmg.22373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Pierre P. A. Dupont
- Faculty of Environmental Sciences and Natural Resource Management PB 5003, NO‐1432 Ås Norway
| | - Richard Bischof
- Faculty of Environmental Sciences and Natural Resource Management PB 5003, NO‐1432 Ås Norway
| | - Cyril Milleret
- Faculty of Environmental Sciences and Natural Resource Management PB 5003, NO‐1432 Ås Norway
| | - Wibke Peters
- Bavarian State Institute for Forestry Hans‐Carl‐von‐Carlowitzplatz 1 D‐85354 Freising Germany
| | - Hendrik Edelhoff
- Bavarian State Institute for Forestry Hans‐Carl‐von‐Carlowitzplatz 1 D‐85354 Freising Germany
| | - Cornelia Ebert
- Seq‐IT GmbH & Co. KG, Department of Wildlife Genetics Pfaffplatz 10 D‐67655 Kaiserslautern Germany
| | - Alisa Klamm
- Hainich National Park Bei der Marktkirche 9 D‐99947 Bad Langensalza Germany
| | - Ulf Hohmann
- Research Institute for Forest Ecology and Forestry Hauptstrasse 16 D‐67705 Trippstadt Germany
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7
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From species detection to population size indexing: the use of sign surveys for monitoring a rare and otherwise elusive small mammal. EUR J WILDLIFE RES 2023. [DOI: 10.1007/s10344-022-01634-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AbstractMonitoring the occupancy and abundance of wildlife populations is key to evaluate their conservation status and trends. However, estimating these parameters often involves time and resource-intensive techniques, which are logistically challenging or even unfeasible for rare and elusive species that occur patchily and in small numbers. Hence, surveys based on field identification of signs (e.g. faeces, footprints) have long been considered a cost-effective alternative in wildlife monitoring, provided they produce reliable detectability and meaningful indices of population abundance. We tested the use of sign surveys for monitoring rare and otherwise elusive small mammals, focusing on the Cabrera vole (Microtus cabrerae) in Portugal. We asked how sampling intensity affects true positive detection of the species, and whether sign abundance is related to population size. We surveyed Cabrera voles’ latrines in 20 habitat patches known to be occupied, and estimated ‘true’ population size at each patch using DNA-based capture-recapture techniques. We found that a searching rate of ca. 3 min/250m2 of habitat based on adaptive guided transects was sufficient to provide true positive detection probabilities > 0.85. Sign-based abundance indices were at best moderately correlated with estimates of ‘true’ population size, and even so only for searching rates > 12 min/250m2. Our study suggests that surveys based on field identification of signs should provide a reliable option to estimate occupancy of Cabrera voles, and possibly for other rare or elusive small mammals, but cautions should be exercised when using this approach to infer population size. In case of practical constraints to the use of more accurate methods, a considerable sampling intensity is needed to reliably index Cabrera voles’ abundance from sign surveys.
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8
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Sugita A, Shigeta M, Tamura N, Okazaki H, Kutsukake N, Terai Y. Development of Genetic Markers for Sex and Individual Identification of the Japanese Giant Flying Squirrel ( Petaurista leucogenys) by an Efficient Method Using High-Throughput DNA Sequencing. Zoolog Sci 2023; 40:24-31. [PMID: 36744707 DOI: 10.2108/zs220045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022]
Abstract
DNA markers that detect differences in the number of microsatellite repeats can be highly effective for genotyping individuals that lack differences in external morphology. However, isolation of sequences with different microsatellite repeat numbers between individuals has been a time-consuming process in the development of DNA markers. Individual identification of Japanese giant flying squirrels (Petaurista leucogenys) has been challenging because this species is arboreal and nocturnal and exhibits little to no morphological variation between individuals. In this study, we developed DNA markers for sex and individual identification of this species by an efficient method using high-throughput DNA sequence data. Paired-end 5 Gb (2 × 250 bp) and 15 Gb (2 × 150 bp) genome sequences were determined from a female and a male Japanese giant flying squirrel, respectively. We searched SRY and XIST genes located on Y and X chromosomes, respectively, from high-throughput sequence data and designed primers to amplify these genes. Using these primer sets, we succeeded to identify the sex of individuals. In addition, we selected 12 loci containing microsatellites with different numbers of repeats between two individuals from the same data set, and designed primers to amplify these sequences. Twenty individuals from nine different locations were discriminated using these primer sets. Furthermore, both sex and microsatellite markers were amplified from DNA extracted non-invasively from single fecal pellet samples. Based on our results for flying squirrels, we expect our efficient method for developing non-invasive high-resolution individual- and sex-specific genotyping to be applicable to a diversity of mammalian species.
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Affiliation(s)
- Aki Sugita
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Hayama, Kanagawa 240-0193, Japan,
| | - Mayumi Shigeta
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, Hachioji City, Tokyo 193-0843, Japan
| | - Noriko Tamura
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, Hachioji City, Tokyo 193-0843, Japan
| | - Hiroyuki Okazaki
- Chuo University Junior and Senior High School, Koganei City, Tokyo 184-8575, Japan
| | - Nobuyuki Kutsukake
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Hayama, Kanagawa 240-0193, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Hayama, Kanagawa 240-0193, Japan
| | - Yohey Terai
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Hayama, Kanagawa 240-0193, Japan, .,SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Hayama, Kanagawa 240-0193, Japan
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9
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Shea MM, Kuppermann J, Rogers MP, Smith DS, Edwards P, Boehm AB. Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility. PeerJ 2023; 11:e14993. [PMID: 36992947 PMCID: PMC10042160 DOI: 10.7717/peerj.14993] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/12/2023] [Indexed: 03/31/2023] Open
Abstract
The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR-findable, accessible, interoperable, and reusable-despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.
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Affiliation(s)
- Meghan M. Shea
- Emmett Interdisciplinary Program in Environment & Resources (E-IPER), Stanford University, Stanford, CA, United States of America
| | - Jacob Kuppermann
- Earth Systems Program, Stanford University, Stanford, CA, United States of America
| | - Megan P. Rogers
- Program in Human Biology, Stanford University, Stanford, CA, United States of America
| | - Dustin Summer Smith
- Earth Systems Program, Stanford University, Stanford, CA, United States of America
| | - Paul Edwards
- Program in Science, Technology and Society, Stanford University, Stanford, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
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10
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Lee Y, Jung M, Wee J, Kim Y, Lee D, Lee D, Kim T, Cho K, Sim C. Species‐specific environmental DNA analysis of the index species in soil ecosystem, Allonychiurus kimi (Collembola: Onychiuridae). Ecol Evol 2022; 12:e9598. [PMCID: PMC9745010 DOI: 10.1002/ece3.9598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Collembola are abundant and have significant roles in the soil ecosystem. Therefore, the phenotypic endpoints of Collembola population or community have been used as an effective bioindicator for assessing soil quality. Since the identification and counting the collembolans in the soil is a laborious and costly procedure, environmental DNA (eDNA)‐based biomonitoring was proposed as an analysis tool of collembolan species found in the soil. In this study, standard primer sets for the species‐specific eDNA analysis using Allonychiurus kimi, a soil bioindicator species was selected. Then, the primers were tested for specificity and sensitivity from the soil samples. Two different eDNA samples were tested: (1) eDNA samples were extracted from the soil with A. kimi individuals (intra‐organismal eDNA). (2) The samples from the soil without A. kimi individuals (extra‐organismal eDNA). The two primers were confirmed in their sensitivity and specificity to the two types of eDNA samples selected. Ct‐values from both intra‐ and extra‐organismal eDNA showed the significant correlations to the number of inoculated A. kimi (adj. R2 = 0.7453–0.9489). These results suggest that in excretion, egg, and other exuviae had a significant effect on eDNA analysis from soil samples taken. Furthermore, our results suggest that environmental factors should be considered when analyzing eDNA collected from soil.
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Affiliation(s)
- Yun‐Sik Lee
- Department of BiologyBaylor UniversityWacoTexasUSA,Ojeong Eco‐Resilience InstituteKorea UniversitySeoulSouth Korea
| | - Minhyung Jung
- Department of Life ScienceGachon UniversitySeongnamSouth Korea
| | - June Wee
- BK21 FOUR R&E Center for Environmental Science and Ecological EngineeringKorea UniversitySeoulSouth Korea
| | - Yongeun Kim
- Ojeong Eco‐Resilience InstituteKorea UniversitySeoulSouth Korea
| | - Doo‐Hyung Lee
- Department of Life ScienceGachon UniversitySeongnamSouth Korea
| | - Dong‐Sung Lee
- Department of Life ScienceUniversity of SeoulSeoulSouth Korea
| | - Taewoo Kim
- Division of Environmental Science and Ecological EngineeringKorea UniversitySeoulSouth Korea
| | - Kijong Cho
- Division of Environmental Science and Ecological EngineeringKorea UniversitySeoulSouth Korea
| | - Cheolho Sim
- Department of BiologyBaylor UniversityWacoTexasUSA
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11
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Davidović S, Marinković S, Hribšek I, Patenković A, Stamenković-Radak M, Tanasković M. Sex ratio and relatedness in the Griffon vulture ( Gyps fulvus) population of Serbia. PeerJ 2022; 10:e14477. [PMID: 36523455 PMCID: PMC9745909 DOI: 10.7717/peerj.14477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Background Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region's reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well. Methods During the annual monitoring that was performed in the period from 2013-2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers. Results The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn't demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds should be used instead.
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Affiliation(s)
- Slobodan Davidović
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia,Birds of Prey Protection Foundation, Belgrade, Serbia
| | - Saša Marinković
- Birds of Prey Protection Foundation, Belgrade, Serbia,Department of Ecology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Irena Hribšek
- Birds of Prey Protection Foundation, Belgrade, Serbia,Natural History Museum Belgrade, Belgrade, Serbia
| | - Aleksandra Patenković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marina Stamenković-Radak
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia,Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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12
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New strategies for characterizing genetic structure in wide-ranging, continuously distributed species: A Greater Sage-grouse case study. PLoS One 2022; 17:e0274189. [PMID: 36099302 PMCID: PMC9469985 DOI: 10.1371/journal.pone.0274189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Wide-ranging species residing in continuously distributed habitat pose substantial challenges for the characterization of genetic structure as many analytical methods used are less effective when isolation by distance is an underlying biological pattern. Here, we illustrate strategies for overcoming these challenges using a species of significant conservation concern, the Greater Sage-grouse (Centrocercus urophasianus), providing a new method to identify centers of genetic differentiation and combining multiple methods to help inform management and conservation strategies for this and other such species. Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. Gene flow was greater, and differentiation reduced in areas of contiguous habitat (eastern Montana, most of Wyoming, much of Oregon, Nevada, and parts of Idaho). As expected, areas of fragmented habitat such as in Utah (with 6 subpopulation centers) exhibited the greatest genetic differentiation and lowest effective migration. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species.
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13
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Shall the Wild Boar Pass? A Genetically Assessed Ecological Corridor in the Geneva Region. SUSTAINABILITY 2022. [DOI: 10.3390/su14127463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Landscape fragmentation caused by road infrastructures represents a major threat to the genetic diversity of a region. The resulting genetic isolation between subpopulations may lead to consanguinity, and consequently to population collapse and extinction. However, the construction of wildlife crossings can help maintain connectivity. In the present paper, we evaluated the genetic spatial structuring of populations of wild boars (Sus scrofa) in three areas of the Geneva region connected by an ecological corridor. Those areas are cut off either by a highway that is crossed by a wildlife overpass or by an anthropized sector. Genetic profiling with 9 nuclear microsatellite markers yielded 61 single profiles, which allowed for clustering, parentage, and linkage disequilibrium analyses, uncovering the populations’ genetic structure. We also evaluated whether the genetic structure was affected by the sex of individuals. In our analyses, all individuals clustered into a single genetic group, suggesting that no structure limited significantly the gene flow in the region. However, a recent admixture indicated a potential increase in the gene flow between two of the subpopulations due to the wildlife overpass, while the other part of the ecological corridor was not or was only partially functional. Genetic distances between males were significantly higher than between females, although the role of sex remains unclear as to its influence on population genetics. Finally, in order to avoid a subregion becoming fully isolated, urbanization planning should consider this genetic evaluation and proceed with further monitoring, especially by focusing on species more sensitive to landscape fragmentation.
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Saccò M, Guzik MT, van der Heyde M, Nevill P, Cooper SJB, Austin AD, Coates PJ, Allentoft ME, White NE. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153223. [PMID: 35063529 DOI: 10.1016/j.scitotenv.2022.153223] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.
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Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia.
| | - Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide 5000, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Peterson J Coates
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, 1006, Dartmouth, Nova Scotia B2Y 4A2, Canada
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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15
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Saranholi BH, Sanches A, Moreira-Ramírez JF, Carvalho CDS, Galetti M, Galetti Jr PM. Long-term persistence of the large mammal lowland tapir is at risk in the largest Atlantic forest corridor. Perspect Ecol Conserv 2022. [DOI: 10.1016/j.pecon.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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16
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Neveceralova P, Carroll EL, Steel D, Vermeulen E, Elwen S, Zidek J, Stafford JK, Chivell W, Hulva P. Population Changes in a Whale Breeding Ground Revealed by Citizen Science Noninvasive Genetics. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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17
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Landscape Characteristics Affecting Small Mammal Occurrence in Heterogeneous Olive Grove Agro-Ecosystems. CONSERVATION 2022. [DOI: 10.3390/conservation2010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Understanding how small mammals (SM) are associated with environmental characteristics in olive groves is important to identify potential threats to agriculture and assess the overall conservation value and functioning of agro-ecosystems. Here, we provide first insights on this topic applied to traditional olive groves in northeast (NE) Portugal by assessing the landscape attributes that determine SM occurrence, focusing on one species of conservation concern (Microtus cabrerae Thomas 1906) and one species often perceived as a potential pest of olives (Microtus lusitanicus Gerbe 1879). Based on SM genetic non-invasive sampling in 51 olive groves and surrounding habitats, we identified seven rodent species and one insectivore. Occupancy modelling indicated that SM were generally less detected within olive groves than in surrounding habitats. The vulnerable M. cabrerae reached a mean occupancy (95% CI) of 0.77 (0.61–0.87), while M. lusitanicus stood at 0.37 (0.24–0.52). M. cabrerae was more likely to occur in land mosaics with high density of agricultural field edges, while M. lusitanicus was more associated with high density of pastureland patches. Overall, our study suggests that the complex structure and spatial heterogeneity of traditionally managed olive grove agro-ecosystems may favor the occurrence of species-rich SM communities, possibly including well-established populations of species of conservation importance, while keeping potential pest species at relatively low occupancy rates.
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18
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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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19
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Whole genome sequences from non-invasively collected caribou faecal samples. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01235-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractConservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics.
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20
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The Application of NIRS to Determine Animal Physiological Traits for Wildlife Management and Conservation. REMOTE SENSING 2021. [DOI: 10.3390/rs13183699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ability to measure and monitor wildlife populations is important for species management and conservation. The use of near-infrared spectroscopy (NIRS) to rapidly detect physiological traits from wildlife scat and other body materials could play an important role in the conservation of species. Previous research has demonstrated the potential for NIRS to detect diseases such as the novel COVID-19 from saliva, parasites from feces, and numerous other traits from animal skin, hair, and scat, such as cortisol metabolites, diet quality, sex, and reproductive status, that may be useful for population monitoring. Models developed from NIRS data use light reflected from a sample to relate the variation in the sample’s spectra to variation in a trait, which can then be used to predict that trait in unknown samples based on their spectra. The modelling process involves calibration, validation, and evaluation. Data sampling, pre-treatments, and the selection of training and testing datasets can impact model performance. We review the use of NIRS for measuring physiological traits in animals that may be useful for wildlife management and conservation and suggest future research to advance the application of NIRS for this purpose.
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21
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Schoenecker KA, King SRB, Ekernas LS, Oyler‐McCance SJ. Using Fecal DNA and Closed‐Capture Models to Estimate Feral Horse Population Size. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Sarah R. B. King
- Natural Resource Ecology Laboratory Colorado State University Fort Collins CO 80523 USA
| | - L. Stefan Ekernas
- U.S. Geological Survey, Fort Collins Science Center Fort Collins CO 80526 USA
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22
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Recent population expansion in wild gaur (Bos gaurus gaurus) as revealed by microsatellite markers. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00145-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Considerations for Initiating a Wildlife Genomics Research Project in South and South-East Asia. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00243-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Kessler C, Brambilla A, Waldvogel D, Camenisch G, Biebach I, Leigh DM, Grossen C, Croll D. A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics. Mol Ecol Resour 2021; 22:66-85. [PMID: 34152681 PMCID: PMC9292246 DOI: 10.1111/1755-0998.13452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Polymorphism for immune functions can explain significant variation in health and reproductive success within species. Drastic loss in genetic diversity at such loci constitutes an extinction risk and should be monitored in species of conservation concern. However, effective implementations of genome‐wide immune polymorphism sets into high‐throughput genotyping assays are scarce. Here, we report the design and validation of a microfluidics‐based amplicon sequencing assay to comprehensively capture genetic variation in Alpine ibex (Capra ibex). This species represents one of the most successful large mammal restorations recovering from a severely depressed census size and a massive loss in diversity at the major histocompatibility complex (MHC). We analysed 65 whole‐genome sequencing sets of the Alpine ibex and related species to select the most representative markers and to prevent primer binding failures. In total, we designed ~1,000 amplicons densely covering the MHC, further immunity‐related genes as well as randomly selected genome‐wide markers for the assessment of neutral population structure. Our analysis of 158 individuals shows that the genome‐wide markers perform equally well at resolving population structure as RAD‐sequencing or low‐coverage genome sequencing data sets. Immunity‐related loci show unexpectedly high degrees of genetic differentiation within the species. Such information can now be used to define highly targeted individual translocations. Our design strategy can be realistically implemented into genetic surveys of a large range of species. In conclusion, leveraging whole‐genome sequencing data sets to design targeted amplicon assays allows the simultaneous monitoring of multiple genetic risk factors and can be translated into species conservation recommendations.
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Affiliation(s)
- Camille Kessler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Alice Brambilla
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Alpine Wildlife Research Center, Gran Paradiso National Park, Italy
| | - Dominique Waldvogel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Iris Biebach
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Deborah M Leigh
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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25
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Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01208-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractFor conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide polymorphisms (SNPs) has become available, expanding the use of genomic methods to include non-model species of conservation concern. We have developed a 96-marker SNP array for use in applied conservation monitoring of the Scandinavian wolverine (Gulo gulo) population. By genotyping more than a thousand non-invasively collected samples, we were able to obtain precise estimates of different types of genotyping errors and sample dropout rates. The SNP panel significantly outperforms the SSR markers (and DBY intron markers for sexing) both in terms of precision in genotyping, sex assignment and individual identification, as well as in the proportion of samples successfully genotyped. Furthermore, SNP genotyping offers a simplified laboratory and analysis pipeline with fewer samples needed to be repeatedly genotyped in order to obtain reliable consensus data. In addition, we utilised a unique opportunity to successfully demonstrate the application of SNP genotype data for reconstructing pedigrees in wild populations, by validating the method with samples from wild individuals with known relatedness. By offering a simplified workflow with improved performance, we anticipate this methodology will facilitate the use of non-invasive samples to improve genetic management of many different types of populations that have previously been challenging to survey.
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26
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Bourgeois S, Ouitavon K, Kongmee P, Veeramaethaphan T, Kaden J, McEwing R. A simple sexing test for elephant species and its application to faecal DNA. J Appl Genet 2021; 62:507-509. [PMID: 33759056 DOI: 10.1007/s13353-021-00627-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/11/2020] [Accepted: 03/04/2021] [Indexed: 11/30/2022]
Abstract
We developed a novel real-time PCR assay for rapid sexing in all three elephant species, which amplifies small fragments of the orthologous sexual chromosome zinc finger protein genes ZFX/ZFY (65 bp). This assay is a simple, inexpensive and reliable tool that is suitable for non-invasive DNA samples and can be incorporated into larger SNP panels for individual identification and population genetic studies.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs Nationaux, B.P. 20379, Libreville, Gabon. .,WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, EH12 6TS, UK. .,Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - K Ouitavon
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, Thailand
| | - P Kongmee
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, Thailand
| | - T Veeramaethaphan
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, Thailand
| | - J Kaden
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, EH12 6TS, UK
| | - R McEwing
- TRACE Wildlife Forensics Network, PO Box 17477, Edinburgh, EH12 1NY, UK
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27
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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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28
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Jerde CL. Can we manage fisheries with the inherent uncertainty from eDNA? JOURNAL OF FISH BIOLOGY 2021; 98:341-353. [PMID: 31769024 DOI: 10.1111/jfb.14218] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Environmental (e)DNA, as a general approach in aquatic systems, seeks to connect the presence of species' genetic material in the water and hence to infer the species' physical presence. However, fisheries managers face making decisions with risk and uncertainty when eDNA indicates a fish is present but traditional methods fail to capture the fish. In comparison with traditional methods such as nets, electrofishing and piscicides, eDNA approaches have more sources of underlying error that could give rise to false positives. This has resulted in some managers to question whether eDNA can be used to make management decisions because there is no fish in hand. As a relatively new approach, the methods and techniques have quickly evolved to improve confidence in eDNA. By evaluating an eDNA based research programmes through the pattern of the eDNA signal, assay design, experimental design, quality assurance and quality control checks, data analyses and concurrent search for fish using traditional gears, the evidence for fish presence can be evaluated to build confidence in the eDNA approach. The benefits for fisheries management from adopting an eDNA approach are numerous but include cost effectiveness, broader geographic coverage of habitat occupancy, early detection of invasive species, non-lethal stock assessments, exploration of previously inaccessible aquatic environments and discovery of new species hidden beneath the water's surface. At a time when global freshwater and marine fisheries are facing growing threats from over-harvest, pollution and climate change, we anticipate that growing confidence in eDNA will overcome the inherent uncertainty of not having a fish in hand and will empower the informed management actions necessary to protect and restore our fisheries.
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Affiliation(s)
- Christopher L Jerde
- Marine Science Institute, University of California, Santa Barbara, California, USA
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29
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Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC. Urine as a high-quality source of host genomic DNA from wild populations. Mol Ecol Resour 2021; 21:170-182. [PMID: 32985084 PMCID: PMC7746602 DOI: 10.1111/1755-0998.13260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022]
Abstract
The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, urine, dentin and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbours significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as faeces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.
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Affiliation(s)
- Andrew T. Ozga
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University
- Center for Evolution and Medicine, Arizona State University
| | - Timothy H. Webster
- Department of Anthropology, University of Utah
- School of Life Sciences, Arizona State University
| | - Ian C. Gilby
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
| | - Melissa A. Wilson
- Center for Evolution and Medicine, Arizona State University
- School of Life Sciences, Arizona State University
| | | | - Michael L. Wilson
- Department of Anthropology, University of Minnesota
- Department of Ecology, Evolution and Behavior, University of Minnesota
| | | | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Anne C. Stone
- Center for Evolution and Medicine, Arizona State University
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
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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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Ethical publication of research on genetics and genomics of biological material: guidelines and recommendations. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2020. [DOI: 10.1016/j.fsir.2020.100091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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De Kort H, Baguette M, Lenoir J, Stevens VM. Toward reliable habitat suitability and accessibility models in an era of multiple environmental stressors. Ecol Evol 2020; 10:10937-10952. [PMID: 33144939 PMCID: PMC7593202 DOI: 10.1002/ece3.6753] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 12/24/2022] Open
Abstract
Global biodiversity declines, largely driven by climate and land-use changes, urge the development of transparent guidelines for effective conservation strategies. Species distribution modeling (SDM) is a widely used approach for predicting potential shifts in species distributions, which can in turn support ecological conservation where environmental change is expected to impact population and community dynamics. Improvements in SDM accuracy through incorporating intra- and interspecific processes have boosted the SDM field forward, but simultaneously urge harmonizing the vast array of SDM approaches into an overarching, widely adoptable, and scientifically justified SDM framework. In this review, we first discuss how climate warming and land-use change interact to govern population dynamics and species' distributions, depending on species' dispersal and evolutionary abilities. We particularly emphasize that both land-use and climate change can reduce the accessibility to suitable habitat for many species, rendering the ability of species to colonize new habitat and to exchange genetic variation a crucial yet poorly implemented component of SDM. We then unite existing methodological SDM practices that aim to increase model accuracy through accounting for multiple global change stressors, dispersal, or evolution, while shifting our focus to model feasibility. We finally propose a roadmap harmonizing model accuracy and feasibility, applicable to both common and rare species, particularly those with poor dispersal abilities. This roadmap (a) paves the way for an overarching SDM framework allowing comparison and synthesis of different SDM studies and (b) could advance SDM to a level that allows systematic integration of SDM outcomes into effective conservation plans.
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Affiliation(s)
- Hanne De Kort
- Plant Conservation and Population BiologyBiology DepartmentUniversity of LeuvenLeuvenBelgium
| | - Michel Baguette
- Station d'Ecologie Théorique et Expérimentale (UMR 5321 SETE)National Center for Scientific Research (CNRS)Université Toulouse III – Paul SabatierMoulisFrance
- Institut de Systématique, Evolution, Biodiversité (UMR 7205)Muséum National d’Histoire NaturelleParisFrance
| | - Jonathan Lenoir
- UR “Ecologie et Dynamique des Systèmes Anthropisés” (EDYSANUMR 7058 CNRS‐UPJV)Université de Picardie Jules VerneAmiens Cedex 1France
| | - Virginie M. Stevens
- Station d'Ecologie Théorique et Expérimentale (UMR 5321 SETE)National Center for Scientific Research (CNRS)Université Toulouse III – Paul SabatierMoulisFrance
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Guibinga Mickala A, Ntie S, Nicolas V. Distinguishing Central African rodents and shrews using their hair morphology. Afr J Ecol 2020. [DOI: 10.1111/aje.12788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Amour Guibinga Mickala
- Laboratoire de Biologie Moléculaire et Cellulaire (LABMC) Département de Biologie Université des Sciences et Techniques de Masuku (USTM) Franceville Gabon
| | - Stephan Ntie
- Laboratoire de Biologie Moléculaire et Cellulaire (LABMC) Département de Biologie Université des Sciences et Techniques de Masuku (USTM) Franceville Gabon
| | - Violaine Nicolas
- Institut de Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelleCNRSSorbonne UniversitéEPHE Paris France
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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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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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Ethical publication of research on genetics and genomics of biological material: guidelines and recommendations. Forensic Sci Int Genet 2020; 48:102299. [DOI: 10.1016/j.fsigen.2020.102299] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
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Schenker L, Bollmann K, Rehnus M, Brodbeck S, Gugerli F. Hare's affairs: Lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals. Ecol Evol 2020; 10:10150-10166. [PMID: 33005371 PMCID: PMC7520196 DOI: 10.1002/ece3.6676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 01/31/2023] Open
Abstract
Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the 5-year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex ratio changes and sex-specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2,300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and, thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.
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Affiliation(s)
- Laura Schenker
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Kurt Bollmann
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Maik Rehnus
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Sabine Brodbeck
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Felix Gugerli
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
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Gil-Sánchez JM, Antorán-Pilar E. Camera-trapping for abundance estimation of otters in seasonal rivers: a field evaluation. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01409-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Zemanova MA. Towards more compassionate wildlife research through the 3Rs principles: moving from invasive to non-invasive methods. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00607] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Miriam A. Zemanova
- M. A. Zemanova (https://orcid.org/0000-0002-5002-3388) ✉ , Dept of Philosophy, Univ. of Basel, Steinengraben 5, CH-4051 Basel, Switzerland
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40
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Marking behaviour and census of Eurasian otters (Lutra lutra) in riverine habitats: what can scat abundances and non-invasive genetic sampling tell us about otter numbers? MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00486-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractGrowing human-wildlife conflicts and legal conservation obligations increased the need for precise information on Eurasian otter (Lutra lutra) population parameters for species status assessment and wildlife management measures. Scat surveys have become the method of choice to monitor species distribution range, abundance and habitat use. Although methodological concerns exist, scat abundance is often used as main indicator for otter population estimates and trends. To evaluate whether scat counts serve as good proxy for otter densities in linear stream habitats, we modelled the relationship between old/fresh scat abundance and otter numbers on two spatial scales, including also seasonal effects. Actual otter densities and marking behaviour were ascertained by genotyping of otter faeces collected at 218 marking sites along 132.6 km of four salmonid streams. Otter densities in our study areas ranged from 0.16 to 0.28 otters per stream kilometre. The age of scats and the level of spatial scale were determining factors when evaluating the suitability of scat abundance as index for otter densities. Covering large parts of an otter’s territory, fresh scat abundance increased with otter density, irrespectively of season. On the spatial scale of single marking sites, the relationship was not well supported, and no relationship could be found when using old scats in the models. Otter marking behaviour and differences in marking site use intensity, as well as seasonal differences in traceability and accumulation of old scats were discussed to bias the relationship between scat abundance and otter numbers.
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41
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de Oliveira ML, de Faria Peres PH, Gatti A, Morales-Donoso JA, Mangini PR, Duarte JMB. Faecal DNA and camera traps detect an evolutionarily significant unit of the Amazonian brocket deer in the Brazilian Atlantic Forest. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-1367-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Silva BFSD, Oliveira MLD, Duarte JMB. Assessing the morphological identification of guard hairs from Brazilian deer. IHERINGIA. SERIE ZOOLOGIA 2020. [DOI: 10.1590/1678-4766e2020029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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Zhang M, Wei M, Dong Z, Duan H, Mao S, Feng S, Li W, Sun Z, Li J, Yan K, Liu H, Meng X, Ge H. Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment. BMC Biotechnol 2019; 19:99. [PMID: 31856784 PMCID: PMC6923993 DOI: 10.1186/s12896-019-0595-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Background To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA. Results The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor. Conclusions The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.
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Affiliation(s)
- Min Zhang
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Min Wei
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China. .,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China.
| | - Haibao Duan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Shuang Mao
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Senlei Feng
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Wenqian Li
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Zepeng Sun
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Jiawei Li
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Kanglu Yan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Hao Liu
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Xueping Meng
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Hongxing Ge
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
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Mitelberg A, Vandergast AG, Nussear KE, Dutcher K, Esque TC. Development of a Genotyping Protocol for Mojave Desert Tortoise Scat. CHELONIAN CONSERVATION AND BIOLOGY 2019. [DOI: 10.2744/ccb-1394.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anna Mitelberg
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
| | - Amy G. Vandergast
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
| | - Ken E. Nussear
- University of Nevada, Department of Geography, Mackay Science Hall, 1664 North Virginia Street, Reno, Nevada 89557 USA [; ]
| | - Kirsten Dutcher
- University of Nevada, Department of Geography, Mackay Science Hall, 1664 North Virginia Street, Reno, Nevada 89557 USA [; ]
| | - Todd C. Esque
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
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45
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Novel real-time PCR species identification assays for British and Irish bats and their application to a non-invasive survey of bat roosts in Ireland. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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46
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Pourmoghadam MN, Poorbagher H, de Oliveira Fernandes JM, Jafari O. Diazinon negatively affects the integrity of environmental DNA stability: a case study with common carp (Cyprinus carpio). ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:672. [PMID: 31650301 DOI: 10.1007/s10661-019-7816-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Environmental DNA (eDNA) has been used to detect the presence of various species in aquatic ecosystems, but its degradation by several environmental factors can influence the correct identification of aquatic organisms. The present study examined the effects of a pesticide, diazinon, on breakage of Cyprinus carpio eDNA. The specimens were exposed to 0 (control), 0.06, 0.1, and 1 ppm of diazinon for 9 days. Water samples were collected at three time points (3, 6, and 9 days postexposure, dpe), and eDNA was extracted. The cytochrome oxidase I (COI) gene was successfully amplified by PCR, and a fuzzy inference system was used to convert DNA smears and breakage to numerical values. eDNA breakage percentage increased with diazinon concentration at all sampling times. At 3 dpe, the maximum eDNA breakage percentage occurred at 0.06 and 0.1 ppm of diazinon; whereas at 6 and 9 dpe, the maximum breakage was found at 1 ppm of diazinon, while exposure time had no significant effect. To the best of our knowledge, this is the first study to demonstrate that eDNA integrity can be compromised by a diazinon in surface waters. Hence, it is recommended that future eDNA studies take into account pesticide pollution when detecting aquatic species.
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Affiliation(s)
- Maryam Nasrolah Pourmoghadam
- Department of Fisheries, Faculty of Natural Resources, University of Tehran, Box 4314, Karaj, PO, Iran
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Hadi Poorbagher
- Department of Fisheries, Faculty of Natural Resources, University of Tehran, Box 4314, Karaj, PO, Iran.
| | | | - Omid Jafari
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
- Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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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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Using Noninvasive Genetic Sampling to Survey Rare Butterfly Populations. INSECTS 2019; 10:insects10100311. [PMID: 31547512 PMCID: PMC6835262 DOI: 10.3390/insects10100311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 11/17/2022]
Abstract
Advances in nondestructive genetic sampling techniques continue to offer new opportunities for studying organisms, particularly those of conservation concern where more traditional invasive sampling methods are often not available. As part of a proof-of-concept, we investigated the effectiveness of using the chorion from residual butterfly egg debris as a source of viable genetic material for analysis. Laboratory material from a captive breeding population of the federally endangered Miami blue butterfly (Cyclargus thomasi bethunebakeri) was used to test efficacy and refine the methodology. The resulting best practices were subsequently evaluated using field-collected material from extant north Florida populations of the at-risk frosted elfin butterfly (Callophyrs irus). Our results demonstrated that it is possible to extract DNA of sufficiently high quantity and quality for successful gene sequencing. We additionally describe a simple, low-cost, and reliable method of collecting and storing egg debris samples that can be consistently adopted for field or laboratory work as well as deployed with projects that have a larger geographic scope and/or involve citizen scientists. Potential limitations related to field sample collection are discussed as well as needs for future evaluation.
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Peelle LE, Wirsing AJ, Pilgrim KL, Schwartz MK. Identifying predators from saliva at kill sites with limited remains. WILDLIFE SOC B 2019. [DOI: 10.1002/wsb.992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Laurel E. Peelle
- University of WashingtonSchool of Environmental and Forest Sciences Box 352100, 3715 West Stevens Way NE Seattle WA 98195 USA
| | - Aaron J. Wirsing
- University of WashingtonSchool of Environmental and Forest Sciences Box 352100, 3715 West Stevens Way NE Seattle WA 98195 USA
| | - Kristine L. Pilgrim
- U.S. Forest Service, Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Michael K. Schwartz
- U.S. Forest Service, Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
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Salvatori V, Godinho R, Braschi C, Boitani L, Ciucci P. High levels of recent wolf × dog introgressive hybridization in agricultural landscapes of central Italy. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1313-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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