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Díaz-Ruiz F, Descalzo E, Martínez-Jauregui M, Soliño M, Márquez AL, Farfán MÁ, Real R, Ferreras P, Delibes-Mateos M. Combining ranger records and biogeographical models to identify the current and potential distribution of an expanding mesocarnivore in southern Europe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174216. [PMID: 38914319 DOI: 10.1016/j.scitotenv.2024.174216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Human-wildlife conflicts (HWC) are increasing and are potentially harmful to both people and wildlife. Understanding the current and potential distribution of wildlife species involved in HWC, such as carnivores, is essential for implementing management and conservation measures for such species. In this study, we assessed both the current distribution and potential distribution (forecast) of the Egyptian mongoose (Herpestes ichneumon) in the central part of the Iberian Peninsula. We acquired data concerning mongoose occurrences through an online questionnaire sent to environmental rangers. We used the municipality level as the sampling unit because all municipalities within the study area were covered at least by one ranger. Using the information provided by rangers (i.e. occurrences in their municipalities), we constructed environmental favourability distribution models to assess current and potential mongoose distribution through current distribution models (CDM) and ecological models (EM), respectively. >300 rangers participated in the survey and mongooses were reported in a total of 181 of 921 municipalities studied. The CDM model showed a current distribution mainly concentrated on the western part of the study area, where intermediate-high favourability values predominated. The EM model revealed a wider potential distribution, including the south-east part of the study area, which was also characterised by intermediate-high favourability values. Our predictions were verified using independent data, including confirmation of mongoose reproduction by rangers, reports by other experts, and field sampling in some areas. Our innovative approach based on an online survey to rangers coupled with environmental favourability models is shown to be a useful methodology for assessing the current distribution of cryptic but expanding wildlife species, while also enabling estimations of future steps in their expansion. The approach proposed may help policy decision-makers seeking to ensure the conservation of expanding wildlife species, for example, by designing awareness campaigns in areas where the target species is expected to arrive.
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Affiliation(s)
- Francisco Díaz-Ruiz
- Conservation Biology Research Group, Departamento de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, 06006 Badajoz, Spain; Biogeography, Diversity, and Conservation Research Team, Dept. Biología Animal, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Esther Descalzo
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071 Ciudad Real, Spain
| | - María Martínez-Jauregui
- Instituto de Ciencias Forestales (ICIFOR), INIA-CSIC, Ctra. de La Coruña km 7.5, 28040 Madrid, Spain
| | - Mario Soliño
- Institute of Marine Research-CSIC, Department of Ecology and Marine Resources, C/Eduardo Cabello 6, Vigo, 36208, Pontevedra, Spain
| | - Ana Luz Márquez
- Biogeography, Diversity, and Conservation Research Team, Dept. Biología Animal, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Miguel Ángel Farfán
- Biogeography, Diversity, and Conservation Research Team, Dept. Biología Animal, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Raimundo Real
- Biogeography, Diversity, and Conservation Research Team, Dept. Biología Animal, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071 Ciudad Real, Spain
| | - Miguel Delibes-Mateos
- Instituto de Estudios Sociales Avanzados (IESA-CSIC), Campo Santo de los Mártires 7, 14004 Córdoba, Spain.
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2
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Descalzo E, Jiménez J, Delibes‐Mateos M, Díaz‐Ruiz F, Ferreras P. Assessment of methods for detecting an opportunistic and expanding mesocarnivore in southwestern Europe. J Zool (1987) 2021. [DOI: 10.1111/jzo.12912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Descalzo
- Instituto de Investigación en Recursos Cinegéticos (IREC) CSIC‐UCLM‐JCCM Ciudad Real Spain
| | - J. Jiménez
- Instituto de Investigación en Recursos Cinegéticos (IREC) CSIC‐UCLM‐JCCM Ciudad Real Spain
| | | | - F. Díaz‐Ruiz
- Grupo de Biogeografía Diversidad y Conservación Departamento de Biología Animal Facultad de Ciencias Universidad de Málaga Málaga Spain
- Instituto IBYDA. Centro de Experimentación Grice‐Hutchinson Málaga Spain
| | - P. Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC) CSIC‐UCLM‐JCCM Ciudad Real Spain
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3
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Nittu G, Bhavana PM, Shameer TT, Ramakrishnan B, Archana R, Kaushal KK, Khedkar GD, Mohan G, Jyothi M, Sanil R. Simple Nested Allele-Specific approach with penultimate mismatch for precise species and sex identification of tiger and leopard. Mol Biol Rep 2021; 48:1667-1676. [PMID: 33479828 DOI: 10.1007/s11033-021-06139-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
Accurate species and sex identification of non-invasive and forensic samples of the tiger and leopard is still confusing when using the allele-specific methods. We designed allele-specific methods with penultimate nucleotide mismatch in a nested manner for the exact identification and double-checking of forensic samples. The mismatch design is a novel concept in species and sex identification, making the allele-specific targeting precise. We developed three sets of markers, a 365 bp outer and a 98 bp inner marker for nested tiger species identification assay, 136 bp leopard specific marker, and carnivore sex identification markers. We validated the method with tissue/blood forensic samples of various felids and herbivorous available in our lab and on known fecal samples from Vandalur Zoo. We also collected 37 scat samples at diverse stages of deterioration from the Mudumalai Tiger Reserve, Tamil Nadu, India. The 365 bp targeted markers resulted in 70.2% (n = 22; 22/37) amplification success, while the 98 bp FAM-labelled marker amplified 89% (n = 33; 33/37) scat samples independently. The 136 bp leopard markers answered four scat samples (11%) unrequited by the tiger specific markers. We evaluated species and the sex identification with these markers in another 190 non-invasive samples provided by the Mudumalai Tiger Reserve authorities. Among which 56.3% (n = 107) of samples were recognized as tiger (64 male and 43 female) and 38.9% (n = 74) as leopard (41 male and 33 female). The method supersedes any other previous methods in this regard by its high accuracy and simplicity.
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Affiliation(s)
- George Nittu
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Pudupet Madhavan Bhavana
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Thekke Thumbath Shameer
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Balasundaram Ramakrishnan
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India.,Mudumalai Tiger Conservation Foundation, Mudumalai Tiger Reserve, The Nilgiris, Tamil Nadu, India
| | - Rajan Archana
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Krishan Kumar Kaushal
- Mudumalai Tiger Conservation Foundation, Mudumalai Tiger Reserve, The Nilgiris, Tamil Nadu, India.,Office of the Field Director and Assistant Principal Chief Conservator of Forest, Mudumalai Tiger Reserve & Mukkurthi National Park, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Gulab Dattarao Khedkar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, 431 004, India
| | - Govindarajan Mohan
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Manikkiri Jyothi
- Department of Zoology, Providence College for Women, Coonoor, Tamil Nadu, 643104, India
| | - Raveendranathanpillai Sanil
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India.
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4
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Skorupski J. Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals? Genes (Basel) 2020; 11:E1332. [PMID: 33187363 PMCID: PMC7696698 DOI: 10.3390/genes11111332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
The purpose of this review is to present the current state of knowledge about the genetics of European mink Mustela lutreola L., 1761, which is one of the most endangered mammalian species in the world. This article provides a comprehensive description of the studies undertaken over the last 50 years in terms of cytogenetics, molecular genetics, genomics (including mitogenomics), population genetics of wild populations and captive stocks, phylogenetics, phylogeography, and applied genetics (including identification by genetic methods, molecular ecology, and conservation genetics). An extensive and up-to-date review and critical analysis of the available specialist literature on the topic is provided, with special reference to conservation genetics. Unresolved issues are also described, such as the standard karyotype, systematic position, and whole-genome sequencing, and hotly debated issues are addressed, like the origin of the Southwestern population of the European mink and management approaches of the most distinct populations of the species. Finally, the most urgent directions of future research, based on the research questions arising from completed studies and the implementation of conservation measures to save and restore M. lutreola populations, are outlined. The importance of the popularization of research topics related to European mink genetics among scientists is highlighted.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-914-441-685
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
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5
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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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6
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Monterroso P, Díaz-Ruiz F, Lukacs PM, Alves PC, Ferreras P. Ecological traits and the spatial structure of competitive coexistence among carnivores. Ecology 2020; 101:e03059. [PMID: 32333382 DOI: 10.1002/ecy.3059] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 02/06/2020] [Accepted: 02/25/2020] [Indexed: 11/06/2022]
Abstract
Competition is a widespread interaction among carnivores, ultimately manifested through one or more dimensions of the species' ecological niche. One of the most explicit manifestations of competitive interactions regards spatial displacement. Its interpretation under a theoretical context provides an important tool to deepen our understanding of biological systems and communities, but also for wildlife management and conservation. We used Bayesian multispecies occupancy models on camera-trapping data from multiple sites in Southwestern Europe (SWE) to investigate competitive interactions within a carnivore guild, and to evaluate how species' ecological traits are shaping coexistence patterns. Seventeen out of 26 pairwise interactions departed from a hypothesis of independent occurrence, with spatial association being twice as frequent as avoidance. Association behaviors were only detected among mesocarnivores, while avoidance mainly involved mesocarnivores avoiding the apex predator (n = 4) and mesocarnivore-only interactions (n = 2). Body mass ratios, defined as the dominant over the subordinate species body mass, revealed an important negative effect ( β ^ = - 0.38 ; C I 95 = - 0.81 t o - 0.06 ) on co-occurrence probability, and support that spatially explicit competitive interactions are mostly expressed by larger species able to dominate over smaller ones, with a threshold in body mass ratios of ~4, above which local-scale intraguild coexistence is unlikely. We found a weak relationship between pairwise trophic niche overlap and the probability of coexistence ( β ^ = - 0.19 ; C I 95 = - 0.58 t o 0.21 ), suggesting that competition for feeding resources may not be a key driver of competition, at least at the scale of our analysis. Despite local-scale avoidance, regional-scale coexistence appears to be maintained by the spatial structuring of the competitive environment. We provide evidence that SWE ecosystems consist of spatially structured competitive environments, and propose that coexistence among near-sized species is likely achieved through the interplay of "facultative" and "behavioral" character displacements. Factors influencing carnivore coexistence likely include context-dependent density and trait-mediated effects, which should be carefully considered for a sound understanding of the mechanisms regulating these communities.
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Affiliation(s)
- Pedro Monterroso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quinta 7, Vairão, 3385-661, Portugal
| | - Francisco Díaz-Ruiz
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo 12, Ciudad Real, 12071, Spain.,Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga, Avda. Cervantes 2, Málaga, 29071, Spain
| | - Paul M Lukacs
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA
| | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quinta 7, Vairão, 3385-661, Portugal.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Edificio FC4, Porto, 4169-007, Portugal
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo 12, Ciudad Real, 12071, Spain
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7
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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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8
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Monterroso P, Godinho R, Oliveira T, Ferreras P, Kelly MJ, Morin DJ, Waits LP, Alves PC, Mills LS. Feeding ecological knowledge: the underutilised power of faecal
DNA
approaches for carnivore diet analysis. Mamm Rev 2018. [DOI: 10.1111/mam.12144] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pedro Monterroso
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
| | - Raquel Godinho
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Teresa Oliveira
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM) Ronda de Toledo 12 Ciudad Real 13071 Spain
| | - Marcella J. Kelly
- Department of Fish and Wildlife ConservationVirginia Tech 146 Cheatham Hall Blacksburg VA 24061‐0321 USA
| | - Dana J. Morin
- Cooperative Wildlife Research LaboratorySouthern Illinois University 251 Lincoln Drive Carbondale IL 62901 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS 1136 Moscow ID 83844‐1136 USA
| | - Paulo C. Alves
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
| | - L. Scott Mills
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
- Office of Research and Creative ScholarshipUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
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9
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How to spot a black-footed cat? Successful application of cross-species markers to identify captive-bred individuals from non-invasive genetic sampling. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0407-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Non-invasive genetic identification of two sympatric sister-species: ocelot (Leopardus pardalis) and margay (L. wiedii) in different biomes. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-0992-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Park CS, Cho GJ. Individual identification of Eurasian otters (Lutra lutra) in South Korea (Sincheon River, Daegu) by microsatellite markers. J Vet Med Sci 2017; 79:1064-1067. [PMID: 28428484 PMCID: PMC5487784 DOI: 10.1292/jvms.16-0563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The objective of this study was to determine the number of Eurasian otters (Lutra
lutra) that occupied the Sincheon River in Daegu, South Korea. Twenty-seven
spraints collected from February to May 2016 at four sites (Jangam Bridge approximately
6.1 km from the Gachang Dam, Docheong Bridge approximately 13.5 km, Chimsan Bridge
approximately 15.1 km and Nogoek Bridge approximately 18 km) along the Sincheon River
(approximately 27.06 km) were analyzed using 12 microsatellite markers. The analyses
resulted in the identification of 16 (59.3%) individual Eurasian otters in the Sincheon
River based on the 27 spraints. Of the 16 individual Eurasian otters, seven were male, and
nine were female. Groups were centered at the Jangam Bridge (3 males and 2 females),
Chimsan Bridge (2 males and 3 females) and Docheong Bridge (2 males and 4 females). Thus,
the 16 Eurasian otters formed three genetically related groups in each sampling area. The
number of alleles per locus varied from three to seven, with a mean value of 5.08
alleles.
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Affiliation(s)
- Chul-Song Park
- College of Veterinary Medicine and Institute of Equine Medicine, Kyungpook National University, Daegu 41566, South Korea
| | - Gil-Jae Cho
- College of Veterinary Medicine and Institute of Equine Medicine, Kyungpook National University, Daegu 41566, South Korea
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12
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Monterroso P, Rebelo P, Alves PC, Ferreras P. Niche partitioning at the edge of the range: a multidimensional analysis with sympatric martens. J Mammal 2016. [DOI: 10.1093/jmammal/gyw016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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13
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Lobo D, Godinho R, Álvares F, López-Bao JV, Rodríguez A. A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research. PLoS One 2015; 10:e0139765. [PMID: 26496352 PMCID: PMC4619700 DOI: 10.1371/journal.pone.0139765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/17/2015] [Indexed: 11/25/2022] Open
Abstract
Noninvasive samples for genetic analyses have become essential to address ecological questions. Popular noninvasive samples such as faeces contain degraded DNA which may compromise genotyping success. Saliva is an excellent alternative DNA source but scarcity of suitable collection methods makes its use anecdotal in field ecological studies. We develop a noninvasive method of collection that combines baits and porous materials able to capture saliva. We report its potential in optimal conditions, using confined dogs and collecting saliva early after deposition. DNA concentration in saliva extracts was generally high (mean 14 ng μl-1). We correctly identified individuals in 78% of samples conservatively using ten microsatellite loci, and 90% of samples using only eight loci. Consensus genotypes closely matched reference genotypes obtained from hair DNA (99% of identification successes and 91% of failures). Mean genotyping effort needed for identification using ten loci was 2.2 replicates. Genotyping errors occurred at a very low frequency (allelic dropout: 2.3%; false alleles: 1.5%). Individual identification success increased with duration of substrate handling inside dog’s mouth and the volume of saliva collected. Low identification success was associated with baits rich in DNA-oxidant polyphenols and DNA concentrations <1 ng μl-1. The procedure performed at least as well as other noninvasive methods, and could advantageously allow detection of socially low-ranked individuals underrepresented in sources of DNA that are involved in marking behaviour (faeces or urine). Once adapted and refined, there is promise for this technique to allow potentially high rates of individual identification in ecological field studies requiring noninvasive sampling of wild vertebrates.
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Affiliation(s)
- Diana Lobo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail: (AR); (RG)
| | - Francisco Álvares
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - José V. López-Bao
- Research Unit of Biodiversity (UO/CSIC/PA), Oviedo University, Mieres, Spain
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU), Riddarhyttan, Sweden
| | - Alejandro Rodríguez
- Department of Conservation Biology, Estación Biológica de Doñana, CSIC, Sevilla, Spain
- * E-mail: (AR); (RG)
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14
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Piñeiro A, Barja I, Otero GP, Silván G, Illera JC. No Effects of Habitat, Prey Abundance and Competitor Carnivore Abundance on Fecal Cortisol Metabolite Levels in Wildcats (Felis silvestris). ANN ZOOL FENN 2015. [DOI: 10.5735/086.052.0208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Ermakov OA, Simonov E, Surin VL, Titov SV, Brandler OV, Ivanova NV, Borisenko AV. Implications of hybridization, NUMTs, and overlooked diversity for DNA Barcoding of Eurasian ground squirrels. PLoS One 2015; 10:e0117201. [PMID: 25617768 PMCID: PMC4305304 DOI: 10.1371/journal.pone.0117201] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/19/2014] [Indexed: 11/30/2022] Open
Abstract
The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5-4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic 'mini-barcodes'.
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Affiliation(s)
- Oleg A. Ermakov
- Department of Zoology and Ecology, Penza State University, Penza, Russia
| | - Evgeniy Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Tomsk State University, Tomsk, Russia
| | - Vadim L. Surin
- Hematological Research Center, Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergey V. Titov
- Department of Zoology and Ecology, Penza State University, Penza, Russia
| | - Oleg V. Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alex V. Borisenko
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
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Wadley JJ, Austin JJ, Fordham DA. Genetic inference as a method for modelling occurrence: A viable alternative to visual surveys. AUSTRAL ECOL 2014. [DOI: 10.1111/aec.12160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jessica J. Wadley
- Australian Centre for Ancient DNA; University of Adelaide; North Terrace Adelaide SA 5005 Australia
- Environment Institute and School of Earth and Environmental Sciences; University of Adelaide; Adelaide South Australia Australia
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA; University of Adelaide; North Terrace Adelaide SA 5005 Australia
- Environment Institute and School of Earth and Environmental Sciences; University of Adelaide; Adelaide South Australia Australia
- Sciences Department; Museum Victoria; Melbourne Victoria Australia
| | - Damien A. Fordham
- Environment Institute and School of Earth and Environmental Sciences; University of Adelaide; Adelaide South Australia Australia
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17
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Silva TL, Godinho R, Castro D, Abáigar T, Brito JC, Alves PC. Genetic identification of endangered North African ungulates using noninvasive sampling. Mol Ecol Resour 2014; 15:652-61. [PMID: 25256349 DOI: 10.1111/1755-0998.12335] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/28/2022]
Abstract
North African ungulates include several threatened and emblematic species, yet are poorly studied mainly due to their remoteness and elusiveness. Noninvasive sampling provides a useful approach to obtain ecological and genetic information essential to guide conservation actions. The very first and most important step in conservation planning is to accurately identify species, and molecular genetics has been proved to be a useful tool. Several molecular genetics protocols are available for species identification, even for samples with poor quality DNA, such as faeces, hairs or bones. Most of these protocols use mitochondrial DNA for barcoding despite this marker being especially prone to problems, including mtDNA introgression, nuclear insert copies, high intraspecific diversity or heteroplasmy. In this work, we developed a molecular method based on polymorphisms in small fragments of the mitochondrial cytochrome b (cytb, mtDNA) and the nuclear kappa casein genes (KCAS, nDNA) for identifying endangered North African ungulates. These fragments revealed polymorphisms, including species-specific variation, which allowed species identification of nine ungulate species that co-occur in North Africa. The method was validated across more than 400 samples, including different types of noninvasive samples collected in the field. The simplicity, high reliability and relative low cost of the described method make it a promising tool to improve ecological studies of the North African ungulates and consequently, the implementation of more efficient management and conservation plans for these endangered ungulates.
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Affiliation(s)
- Teresa Luísa Silva
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Porto, 4169-007, Portugal; Estación Experimental de Zonas Áridas (EEZA), CSIC, Carretera de Sacramento s/n, Almería, Spain
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18
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19
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A SNP chip to detect introgression in wildcats allows accurate genotyping of single hairs. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0806-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Monterroso P, Rich LN, Serronha A, Ferreras P, Alves PC. Efficiency of hair snares and camera traps to survey mesocarnivore populations. EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0780-1] [Citation(s) in RCA: 16] [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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21
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O'Neill D, Turner PD, O'Meara DB, Chadwick EA, Coffey L, O'Reilly C. Development of novel real‐time
T
aq
M
an
®
PCR
assays for the species and sex identification of otter (
L
utra lutra
) and their application to noninvasive genetic monitoring. Mol Ecol Resour 2013; 13:877-83. [DOI: 10.1111/1755-0998.12141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/29/2013] [Accepted: 06/14/2013] [Indexed: 11/30/2022]
Affiliation(s)
- David O'Neill
- Mammals In a Sustainable Environment Project Eco‐Innovation Research Centre, Department of Chemical and Life Sciences Waterford Institute of Technology Cork Road Waterford Ireland
| | - Peter D. Turner
- Mammals In a Sustainable Environment Project Eco‐Innovation Research Centre, Department of Chemical and Life Sciences Waterford Institute of Technology Cork Road Waterford Ireland
| | - Denise B. O'Meara
- Mammals In a Sustainable Environment Project Eco‐Innovation Research Centre, Department of Chemical and Life Sciences Waterford Institute of Technology Cork Road Waterford Ireland
| | - Elizabeth A. Chadwick
- Cardiff School of Biosciences Biological Sciences Building Museum Avenue Cardiff CF10 3AT UK
| | - Lee Coffey
- Mammals In a Sustainable Environment Project Eco‐Innovation Research Centre, Department of Chemical and Life Sciences Waterford Institute of Technology Cork Road Waterford Ireland
| | - Catherine O'Reilly
- Mammals In a Sustainable Environment Project Eco‐Innovation Research Centre, Department of Chemical and Life Sciences Waterford Institute of Technology Cork Road Waterford Ireland
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22
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Wadley JJ, Austin JJ, Fordham DA. Rapid species identification of eight sympatric northern Australian macropods from faecal-pellet DNA. WILDLIFE RESEARCH 2013. [DOI: 10.1071/wr13005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context Conservation of vulnerable and endangered species requires a comprehensive understanding of their distribution and habitat requirements, so as to implement effective management strategies. Visual scat surveys are a common non-invasive method for monitoring populations. However, morphological similarity of scats among sympatric species presents a problem for accurate identification. Visual misidentifications of scats can have major impacts on the accuracy of abundance and distribution surveys of target species, wasting resources and misdirecting management and conservation actions. DNA identification of scats can overcome this issue, while simultaneously providing a rich source of genetic information for population and dietary studies. Aims We developed a simple and reliable method to identify morphologically similar macropod scats from eight sympatric species in north-eastern Australia, using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of a portion of the mtDNA ND2 gene. Methods We identified a short (275-bp) polymorphic region of ND2, which is easily amplifiable from degraded DNA, developed a primer set, and identified a set of three restriction endonucleases (AluI, BstNI and HphI) which, in combination, can discriminate among the eight target species. So as to test the effectiveness of this protocol, we collected 914 macropod scats from 53 sites in the north-eastern Australia. Key results In total, 406 of these scats were extracted, with 398 (98%) containing amplifiable macropod DNA. All 398 scats were subsequently identified to species by using our RFLP protocol. Sequencing of a subset of these samples confirmed the accuracy of the test. Species identification of scats by using DNA identified eight species of macropods, five of which were outside their documented distributions, one of which was ~400 km. Conclusions Our PCR–RFLP method is a simple and efficient means to identify macropod scats to species, eliminating the need for sequencing, which is costly, time-consuming and requires additional laboratory equipment. Implications The method allows for rapid and non-invasive assessment of macropod species and is particularly useful for surveying populations across multiple sites.
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23
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Ruiz-González A, Madeira MJ, Randi E, Urra F, Gómez-Moliner BJ. Non-invasive genetic sampling of sympatric marten species (Martes martes and Martes foina): assessing species and individual identification success rates on faecal DNA genotyping. EUR J WILDLIFE RES 2012. [DOI: 10.1007/s10344-012-0683-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Monterroso P, Castro D, Silva TL, Ferreras P, Godinho R, Alves PC. Factors affecting the (in)accuracy of mammalian mesocarnivore scat identification in South-western Europe. J Zool (1987) 2012. [DOI: 10.1111/jzo.12000] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Monterroso
- CIBIO/InBio; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Porto Portugal
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM); Ciudad Real Spain
| | - D. Castro
- CIBIO/InBio; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - T. L. Silva
- CIBIO/InBio; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Porto Portugal
| | - P. Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM); Ciudad Real Spain
| | - R. Godinho
- CIBIO/InBio; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - P. C. Alves
- CIBIO/InBio; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Porto Portugal
- Wildlife Biology Program; College of Forestry and Conservation; University of Montana; Missoula MT USA
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25
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Applications and techniques for non-invasive faecal genetics research in felid conservation. EUR J WILDLIFE RES 2012. [DOI: 10.1007/s10344-012-0675-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Barbosa S, Pauperio J, Searle JB, Alves PC. Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to noninvasive sampling. Mol Ecol Resour 2012; 13:43-56. [PMID: 23095787 DOI: 10.1111/1755-0998.12024] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/10/2012] [Accepted: 08/16/2012] [Indexed: 11/29/2022]
Abstract
Species identification through noninvasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Noninvasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining, while several others are poorly studied. Here, we develop a genetic tool for identifying all rodent species in Iberia by noninvasive genetic sampling. To achieve this purpose, we selected one mitochondrial gene [cytochrome b (cyt-b)] and one nuclear gene [interphotoreceptor retinoid-binding protein (IRBP)], which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and Microtus duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to noninvasive samples, we selected a short highly diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from noninvasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation.
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Affiliation(s)
- S Barbosa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
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27
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The plant physical features selected by wildcats as signal posts: an economic approach to fecal marking. Naturwissenschaften 2012; 99:801-9. [DOI: 10.1007/s00114-012-0962-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 08/09/2012] [Accepted: 08/14/2012] [Indexed: 10/28/2022]
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28
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Vanhaecke D, Garcia de Leaniz C, Gajardo G, Young K, Sanzana J, Orellana G, Fowler D, Howes P, Monzon-Arguello C, Consuegra S. DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes. PLoS One 2012; 7:e32939. [PMID: 22412956 PMCID: PMC3295793 DOI: 10.1371/journal.pone.0032939] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 02/02/2012] [Indexed: 11/19/2022] Open
Abstract
The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.
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Affiliation(s)
- Delphine Vanhaecke
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | | | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Kyle Young
- Laboratorio de Genética, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Jose Sanzana
- Laboratorio de Genética, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Gabriel Orellana
- Laboratorio de Genética, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Daniel Fowler
- Falkland Islands Fisheries Department, Stanley, Falkland Islands
| | - Paul Howes
- Department of BioSciences, College of Science, Swansea University, Swansea, United Kingdom
| | - Catalina Monzon-Arguello
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- Department of BioSciences, College of Science, Swansea University, Swansea, United Kingdom
| | - Sofia Consuegra
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail:
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Ferreira EC, Gontijo CM, Cruz I, Melo MN, Silva AM. Alternative PCR protocol using a single primer set for assessing DNA quality in several tissues from a large variety of mammalian species living in areas endemic for leishmaniasis. Mem Inst Oswaldo Cruz 2011; 105:895-8. [PMID: 21120359 DOI: 10.1590/s0074-02762010000700009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 08/12/2010] [Indexed: 11/22/2022] Open
Abstract
The aim of this work was to establish a modified pre-diagnostic polymerase chain reaction (PCR) protocol using a single primer set that enables successful amplification of a highly conserved mammalian sequence in order to determine overall sample DNA quality for multiple mammalian species that inhabit areas endemic for leishmaniasis. The gene encoding interphotoreceptor retinoid-binding protein (IRBP), but not other conserved genes, was efficiently amplified in DNA samples from tail skin, ear skin, bone marrow, liver and spleen from all of the species tested. In tissue samples that were PCR-positive for Leishmania, we found that DNA from 100%, 55% and 22% of the samples tested resulted in a positive PCR reaction for the IRBP, beta-actin and beta-globin genes, respectively. Nucleotide sequencing of an IRBP amplicon resolved any questions regarding the taxonomical classification of a rodent, which was previously based simply on the morphological features of the animal. Therefore, PCR amplification and analysis of the IRBP amplicon are suitable for pre-diagnostically assessing DNA quality and identifying mammalian species living in areas endemic to leishmaniasis and other diseases.
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Coghlan ML, White NE, Parkinson L, Haile J, Spencer PBS, Bunce M. Egg forensics: an appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs. Forensic Sci Int Genet 2011; 6:268-73. [PMID: 21741338 PMCID: PMC7102845 DOI: 10.1016/j.fsigen.2011.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 05/12/2011] [Accepted: 06/13/2011] [Indexed: 10/29/2022]
Abstract
Psittaciformes (parrots and cockatoos) are charismatic birds, their plumage and capacity for learning make them highly sought after pets. The illegal trade in parrots and cockatoos poses a serious threat to the viability of native populations; in addition, species transported to non-endemic areas may potentially vector disease and genetically 'pollute' local native avifauna. To reduce the logistical difficulties associated with trafficking live birds, smugglers often transport eggs. This creates a problem for authorities in elucidating accurate species identification without the laborious task of incubation and hand rearing until a morphological identification can be made. Here, we use 99 avian eggs seized from carriers coming into and within Australia, as a result of suspected illegal trade. We investigate and evaluate the use of mitochondrial DNA (mtDNA) to accurately identify eggs to family, genus or species level. However, Identification of a species based on percentage mtDNA similarities is difficult without good representations of the inter- and intra-levels of species variation. Based on the available reference database, we were able to identify 52% of the eggs to species level. Of those, 10 species from eight genera were detected, all of which belong to the parrot (Psittacidae) and cockatoo (Cacatuidae) families. Of the remaining 48%, a further 36% of eggs were identified to genus level, and 12% identified to family level using our assignment criteria. Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny.
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Affiliation(s)
- Megan L Coghlan
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, South St, Murdoch, WA 6150, Australia
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Biogeographical region and host trophic level determine carnivore endoparasite richness in the Iberian Peninsula. Parasitology 2011; 138:758-65. [DOI: 10.1017/s0031182011000345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARYWe address the question of whether host and/or environmental factors might affect endoparasite richness and distribution, using carnivores as a model. We reviewed studies published in international peer-reviewed journals (34 areas in the Iberian Peninsula), describing parasite prevalence and richness in carnivores, and collected information on site location, host bio-ecology, climate and detected taxa (Helminths, Protozoa andMycobacteriumspp.). Three hypotheses were tested (i) host based, (ii) environmentally based, and (iii) hybrid (combination of environmental and host). Multicollinearity reduced candidate variable number for modelling to 5: host weight, phylogenetic independent contrasts (host weight), mean annual temperature, host trophic level and biogeographical region. General Linear Mixed Modelling was used and the best model was a hybrid model that included biogeographical region and host trophic level. Results revealed that endoparasite richness is higher in Mediterranean areas, especially for the top predators. We suggest that the detected parasites may benefit from mild environmental conditions that occur in southern regions. Top predators have larger home ranges and are likely to be subjected to cascading effects throughout the food web, resulting in more infestation opportunities and potentially higher endoparasite richness. This study suggests that richness may be more affected by historical and regional processes (including climate) than by host ecological processes.
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