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Cueva DF, Zug R, Pozo MJ, Molina S, Cisneros R, Bustamante MR, Torres MDL. Evidence of population genetic structure in Ecuadorian Andean bears. Sci Rep 2024; 14:2834. [PMID: 38310153 PMCID: PMC10838292 DOI: 10.1038/s41598-024-53003-5] [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: 03/31/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024] Open
Abstract
Wildlife conservation in Andean countries is a global priority because of the high levels of biodiversity and endemism. Historically, these countries have had limited resources to monitor wildlife (e.g., through genetic tools) and establish conservation programs. Focusing on the study and emblematic use of a few charismatic species has been a strategic approach to direct efforts for conservation and development planning. Consequently, the Andean bear is a flagship and umbrella species for highly biodiverse Andean countries like Ecuador. The few studies exploring the population genetics of this species have concluded that it has low genetic diversity and few units for conservation as populations appear to be well connected. However, these results might be attributed to ascertainment bias as studies have been performed with heterologous molecular markers. Here, using both mtDNA sequences and species-specific microsatellite markers, we show that Andean bears in Ecuador have population structure. Additionally, we found through the study of three Ecuadorian populations that the species might have a higher genetic diversity than we previously thought. These results could support the revision of research priorities, conservation, and planning strategies to improve connectivity for this species which occurs in crucial biodiversity hotspots.
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Affiliation(s)
- Dario F Cueva
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador
| | - Rebecca Zug
- Laboratorio de Carnívoros, Universidad San Francisco de Quito USFQ, Diego de Robles y Vía Interoceanica s/n, Quito, 170157, Ecuador
| | - María José Pozo
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador
| | - Santiago Molina
- Laboratorio de Carnívoros, Universidad San Francisco de Quito USFQ, Diego de Robles y Vía Interoceanica s/n, Quito, 170157, Ecuador
- Fundación Zoológica del Ecuador, Pircapamaba s/n y Rumichupa, Guayllabamba, Quito, Ecuador
| | - Rodrigo Cisneros
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto, C/París s/n., 1101608, Loja, Ecuador
| | - Martín R Bustamante
- Fundación Zoológica del Ecuador, Pircapamaba s/n y Rumichupa, Guayllabamba, Quito, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador.
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2
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Martin AM, Vonhof MJ, Henshaw M, Dreyer JM, Munster SK, Kirby L, Russell AL. Genetic Structure of the Vulnerable Tricolored Bat (Perimyotis subflavus). ACTA CHIROPTEROLOGICA 2023. [DOI: 10.3161/15081109acc2022.24.2.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Alynn M. Martin
- Caesar Kleberg Wildlife Research Institute, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Maarten J. Vonhof
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Avenue, Kalamazoo, MI 49008, USA
| | - Michael Henshaw
- Department of Biology, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Jessica M. Dreyer
- Department of Ecology and Evolutionary Biology, University of Tennessee, 1502 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Susan K. Munster
- Department of Biology, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Laura Kirby
- Department of Human Genetics, University of Michigan, 500 S. State Street, Ann Arbor, MI 48409, USA
| | - Amy L. Russell
- Department of Biology, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
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3
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Luck C, Jessopp M, Cronin M, Rogan E. Using population viability analysis to examine the potential long-term impact of fisheries bycatch on protected species. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Population genetics informs the management of a controversial Australian waterbird. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01393-8] [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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5
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Luck C, Jessopp M, Tully O, Cosgrove R, Rogan E, Cronin M. Estimating protected species bycatch from limited observer coverage: A case study of seal bycatch in static net fisheries. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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6
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Menchaca A, Arteaga MC, Medellin RA, Jones G. Conservation units and historical matrilineal structure in the tequila bat (Leptonycteris yerbabuenae). Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01164] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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7
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van Deventer R, Rhode C, Marx M, Roodt-Wilding R. The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform. Genomics 2020; 112:3455-3464. [PMID: 32574831 DOI: 10.1016/j.ygeno.2020.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 04/17/2020] [Indexed: 12/30/2022]
Abstract
Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide polymorphism (SNP) markers for blue wildebeest. The DArTseq genotyping platform, commonly used in polyploid plant species, was selected for SNP discovery. A limited number of published articles have described the use of the DArTseq platform in animals and, therefore, this study also provided a unique opportunity to assess the performance of the DArTseq platform in an animal species. A total of 20,563 SNPs, each located within a 69 bp sequence, were generated. The developed SNP markers had a high average scoring reproducibility (>99%) and a low percentage missing data (~9.21%) compared to other reduced representation sequencing approaches that have been used in animal studies. Furthermore, the number of candidate SNPs per nucleotide position decreased towards the 3' end of sequence reads, and the ratio of transitions (Ts) to transversions (Tv) remained similar for each read position. These observations indicate that there was no read position bias, such as the identification of false SNPs due to low sequencing quality, towards the tail-end of sequencing reads. The DArTseq platform was also successful in identifying a large number of informative SNPs with desirable polymorphism parameters such as a high minor allele frequency (MAF). The Bos taurus genome was used for the in silico mapping of the marker sequences and a total of 6020 (29.28%) sequences were successfully mapped against the bovine genome. The marker sequences mapped to all of the bovine chromosomes establishing the genome-wide distribution of the SNPs. Moreover, the high observed Ts:Tv ratio (2.84:1) indicate that the DArTseq platform targeted gene-rich regions of the blue wildebeest genome. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions indicating that these SNP markers can be useful in functional gene studies. The DArTseq platform, therefore, represents a high-throughput, robust and cost-effective genotyping platform, which may find adoption in several other African antelope and animal species.
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Affiliation(s)
- Riana van Deventer
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa; Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
| | - Munro Marx
- Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
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Monroy-Vilchis O, Heredia-Bobadilla RL, Zarco-González MM, Ávila-Akerberg V, Sunny A. Genetic diversity and structure of two endangered mole salamander species of the Trans-Mexican Volcanic Belt. HERPETOZOA 2019. [DOI: 10.3897/herpetozoa.32.e38023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The most important factor leading to amphibian population declines and extinctions is habitat degradation and destruction. To help prevent further extinctions, studies are needed to make appropriate conservation decisions in small and fragmented populations. The goal of this study was to provide data from the population genetics of two micro-endemic mole salamanders from the Trans-Mexican Volcanic Belt. Nine microsatellite markers were used to study the population genetics of 152 individuals from twoAmbystomaspecies. We sampled 38 individuals in two localities forA. altamiraniandA. rivualre. We found medium to high levels of genetic diversity expressed as heterozygosity in the populations. However, all the populations presented few alleles per locus and genotypes. We found strong genetic structure between populations for each species. Effective population size was small but similar to that of the studies from other mole salamanders with restricted distributions or with recently fragmented habitats. Despite the medium to high levels of genetic diversity expressed as heterozygosity, we found few alleles, evidence of a genetic bottleneck and that the effective population size is small in all populations. Therefore, this study is important to propose better management plans and conservation efforts for these species.
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Kerk M, Onorato DP, Hostetler JA, Bolker BM, Oli MK. Dynamics, Persistence, and Genetic Management of the Endangered Florida Panther Population. WILDLIFE MONOGRAPHS 2019. [DOI: 10.1002/wmon.1041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Madelon Kerk
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
| | - David P. Onorato
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 298 Sabal Palm Road Naples FL 34114 USA
| | - Jeffrey A. Hostetler
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 100 8th Avenue SE St. Petersburg FL 33701 USA
| | - Benjamin M. Bolker
- Departments of Mathematics and Statistics and Biology McMaster University 314 Hamilton Hall Hamilton ON L8S 4K1 Canada
| | - Madan K. Oli
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
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Sunny A, Duarte-deJesus L, Aguilera-Hernández A, Ramírez-Corona F, Suárez-Atilano M, Percino-Daniel R, Manjarrez J, Monroy-Vilchis O, González-Fernández A. Genetic diversity and demography of the critically endangered Roberts' false brook salamander (Pseudoeurycea robertsi) in Central Mexico. Genetica 2019; 147:149-164. [PMID: 30879155 DOI: 10.1007/s10709-019-00058-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/11/2019] [Indexed: 11/28/2022]
Abstract
Land use changes are threatening the maintenance of biodiversity. Genetic diversity is one of the main indicators of biological diversity and is highly important as it shapes the capability of populations to respond to environmental changes. We studied eleven populations of Pseudoeurycea robertsi, a micro-endemic and critically endangered species from the Nevado de Toluca Volcano, a mountain that is part of the Trans-Mexican Volcanic Belt, Mexico. We sequenced the mitochondrial cytochrome b gene from 71 individuals and genotyped 9 microsatellites from 150 individuals. Our results based on the cytochrome b showed two divergent lineages, with moderate levels of genetic diversity and a recently historical demographic expansion. Microsatellite-based results indicated low levels of heterozygosity for all populations and few alleles per locus, as compared with other mole salamander species. We identified two genetically differentiated subpopulations with a significant level of genetic structure. These results provide fundamental data for the development of management plans and conservation efforts for this critically endangered species.
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Affiliation(s)
- Armando Sunny
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico.
| | - Luis Duarte-deJesus
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Arlene Aguilera-Hernández
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Fabiola Ramírez-Corona
- Taller de Sistemática y Biogeografía, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Marco Suárez-Atilano
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Ruth Percino-Daniel
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Javier Manjarrez
- Laboratorio de Biología Evolutiva, Facultad de Ciencias, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Octavio Monroy-Vilchis
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Andrea González-Fernández
- Laboratorio de Biología Evolutiva, Facultad de Ciencias, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
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11
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Skrbinšek T, Luštrik R, Majić-Skrbinšek A, Potočnik H, Kljun F, Jelenčič M, Kos I, Trontelj P. From science to practice: genetic estimate of brown bear population size in Slovenia and how it influenced bear management. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1265-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Bohling J, Small M, Von Bargen J, Louden A, DeHaan P. Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout. CONSERV GENET 2019. [DOI: 10.1007/s10592-018-1134-z] [Citation(s) in RCA: 8] [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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13
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Kalbfleisch TS, Murdoch BM, Smith TPL, Murdoch JD, Heaton MP, McKay SD. A SNP resource for studying North American moose. F1000Res 2018; 7:40. [PMID: 29479424 PMCID: PMC5801567 DOI: 10.12688/f1000research.13501.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Moose ( Alces alces) colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US). Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect), and/or subsequent population bottlenecks in North America. Genetic tests based on informative single nucleotide polymorphism (SNP) markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack of a reference genome assembly and whole genome sequence (WGS) data. Methods: WGS data were generated for four individual moose from the US states of Alaska, Idaho, Wyoming, and Vermont with minimum and average genome coverage depths of 14- and 19-fold, respectively. Cattle and sheep reference genomes were used for aligning sequence reads and identifying moose SNPs. Results: Approximately 11% and 9% of moose WGS reads aligned to cattle and sheep genomes, respectively. The reads clustered at genomic segments, where sequence identity between these species was greater than 95%. In these segments, average mapped read depth was approximately 19-fold. Sets of 46,005 and 36,934 high-confidence SNPs were identified from cattle and sheep comparisons, respectively, with 773 and 552 of those having minor allele frequency of 0.5 and conserved flanking sequences in all three species. Among the four moose, heterozygosity and allele sharing of SNP genotypes were consistent with decreasing levels of moose genetic diversity from west to east. A minimum set of 317 SNPs, informative across all four moose, was selected as a resource for future SNP assay design. Conclusions: All SNPs and associated information are available, without restriction, to support development of SNP-based tests for animal identification, parentage determination, and estimating relatedness in North American moose.
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Affiliation(s)
- Theodore S Kalbfleisch
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, Kentucky, USA
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Escudero PC, Tucker DB, Avila LJ, Sites JW, Morando M. Distribution of Genetic Diversity within a Population ofLiolaemus xanthoviridisand an Assessment of its Mating System, as Inferred with Microsatellite Markers. J HERPETOL 2017. [DOI: 10.2994/sajh-d-16-00037.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Paula C. Escudero
- Grupo de Herpetología Patagónica. Instituto Patagónico para el Estudio de los Ecosistemas Continentales. Centro Nacional Patagónico- Consejo Nacional de Investigaciones Científicas. Puerto Madryn, Argentina
| | - Derek B. Tucker
- Department of Biology 4102 LSB, Brigham Young University, Provo, USA
| | - Luciano J. Avila
- Grupo de Herpetología Patagónica. Instituto Patagónico para el Estudio de los Ecosistemas Continentales. Centro Nacional Patagónico- Consejo Nacional de Investigaciones Científicas. Puerto Madryn, Argentina
| | - Jack W. Sites
- Department of Biology 4102 LSB, Brigham Young University, Provo, USA
| | - Mariana Morando
- Grupo de Herpetología Patagónica. Instituto Patagónico para el Estudio de los Ecosistemas Continentales. Centro Nacional Patagónico- Consejo Nacional de Investigaciones Científicas. Puerto Madryn, Argentina
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15
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Trapp SE, Flaherty EA. Noninvasive and cost‐effective trapping method for monitoring sensitive mammal populations. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Stephanie E. Trapp
- Department of Forestry and Natural ResourcesPurdue University195 Marstellar StreetWest LafayetteIN47907USA
| | - Elizabeth A. Flaherty
- Department of Forestry and Natural ResourcesPurdue University195 Marstellar StreetWest LafayetteIN47907USA
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16
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Koczur LM, Williford D, DeYoung RW, Ballard BM. Bringing back the dead: Genetic data from avian carcasses. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lianne M. Koczur
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Bart M. Ballard
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
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Popescu VD, Iosif R, Pop MI, Chiriac S, Bouroș G, Furnas BJ. Integrating sign surveys and telemetry data for estimating brown bear ( Ursus arctos) density in the Romanian Carpathians. Ecol Evol 2017; 7:7134-7144. [PMID: 28944005 PMCID: PMC5606905 DOI: 10.1002/ece3.3177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 05/07/2017] [Accepted: 05/25/2017] [Indexed: 11/06/2022] Open
Abstract
Accurate population size estimates are important information for sustainable wildlife management. The Romanian Carpathians harbor the largest brown bear (Ursus arctos) population in Europe, yet current management relies on estimates of density that lack statistical oversight and ignore uncertainty deriving from track surveys. In this study, we investigate an alternative approach to estimate brown bear density using sign surveys along transects within a novel integration of occupancy models and home range methods. We performed repeated surveys along 2-km segments of forest roads during three distinct seasons: spring 2011, fall-winter 2011, and spring 2012, within three game management units and a Natura 2000 site. We estimated bears abundances along transects using the number of unique tracks observed per survey occasion via N-mixture hierarchical models, which account for imperfect detection. To obtain brown bear densities, we combined these abundances with the effective sampling area of the transects, that is, estimated as a function of the median (± bootstrapped SE) of the core home range (5.58 ± 1.08 km2) based on telemetry data from 17 bears tracked for 1-month periods overlapping our surveys windows. Our analyses yielded average brown bear densities (and 95% confidence intervals) for the three seasons of: 11.5 (7.8-15.3), 11.3 (7.4-15.2), and 12.4 (8.6-16.3) individuals/100 km2. Across game management units, mean densities ranged between 7.5 and 14.8 individuals/100 km2. Our method incorporates multiple sources of uncertainty (e.g., effective sampling area, imperfect detection) to estimate brown bear density, but the inference fundamentally relies on unmarked individuals only. While useful as a temporary approach to monitor brown bears, we urge implementing DNA capture-recapture methods regionally to inform brown bear management and recommend increasing resources for GPS collars to improve estimates of effective sampling area.
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Affiliation(s)
- Viorel D Popescu
- Department of Biological Sciences Ohio University Athens OH USA.,Centre for Environmental Research (CCMESI) University of Bucharest Bucharest Romania
| | - Ruben Iosif
- Centre for Environmental Research (CCMESI) University of Bucharest Bucharest Romania
| | - Mihai I Pop
- Centre for Environmental Research (CCMESI) University of Bucharest Bucharest Romania.,Asociatia pentru Conservarea Diversitatii Biologice (ACDB) Focsani Romania
| | | | - George Bouroș
- Asociatia pentru Conservarea Diversitatii Biologice (ACDB) Focsani Romania
| | - Brett J Furnas
- California Department of Fish and Wildlife Wildlife Investigations Laboratory Rancho Cordova CA USA.,Department of Environmental Science, Policy and Management University of California Berkeley CA USA
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18
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Rando HM, Stutchman JT, Bastounes ER, Johnson JL, Driscoll CA, Barr CS, Trut LN, Sacks BN, Kukekova AV. Y-Chromosome Markers for the Red Fox. J Hered 2017; 108:678-685. [PMID: 28821189 DOI: 10.1093/jhered/esx066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/11/2017] [Indexed: 01/17/2023] Open
Abstract
The de novo assembly of the red fox (Vulpes vulpes) genome has facilitated the development of genomic tools for the species. Efforts to identify the population history of red foxes in North America have previously been limited by a lack of information about the red fox Y-chromosome sequence. However, a megabase of red fox Y-chromosome sequence was recently identified over 2 scaffolds in the reference genome. Here, these scaffolds were scanned for repeated motifs, revealing 194 likely microsatellites. Twenty-three of these loci were selected for primer development and, after testing, produced a panel of 11 novel markers that were analyzed alongside 2 markers previously developed for the red fox from dog Y-chromosome sequence. The markers were genotyped in 76 male red foxes from 4 populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland (eastern United States), and 9 from the island of Great Britain, as well as 48 foxes of known North American origin maintained on an experimental farm in Novosibirsk, Russia. The full marker panel revealed 22 haplotypes among these red foxes, whereas the 2 previously known markers alone would have identified only 10 haplotypes. The haplotypes from the 4 populations clustered primarily by continent, but unidirectional gene flow from Great Britain and farm populations may influence haplotype diversity in the Maryland population. The development of new markers has increased the resolution at which red fox Y-chromosome diversity can be analyzed and provides insight into the contribution of males to red fox population diversity and patterns of phylogeography.
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Affiliation(s)
- Halie M Rando
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Jeremy T Stutchman
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Estelle R Bastounes
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Jennifer L Johnson
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Carlos A Driscoll
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Christina S Barr
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Lyudmila N Trut
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Benjamin N Sacks
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Anna V Kukekova
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
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A simple and cost-effective method for obtaining DNA from a wide range of animal wildlife samples. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0735-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Evidence of Subdivisions on Evolutionary Timescales in a Large, Declining Marsupial Distributed across a Phylogeographic Barrier. PLoS One 2016; 11:e0162789. [PMID: 27732594 PMCID: PMC5061365 DOI: 10.1371/journal.pone.0162789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 08/29/2016] [Indexed: 01/25/2023] Open
Abstract
Major prehistoric forces, such as the climatic shifts of the Pleistocene, can remain visible in a species’ population genetics. Inference of refuges via genetic tools is useful for conservation management as it can identify populations whose preservation may help retain a species’ adaptive potential. Such investigation is needed for Australia’s southern hairy-nosed wombat (Lasiorhinus latifrons), whose conservation status has recently deteriorated, and whose phylogeographic history during the Pleistocene may be atypical compared to other species. Its contemporary range spans approximately 2000 km of diverse habitat on either side of the Spencer Gulf, which was a land bridge during periods of Pleistocene aridity that may have allowed for migration circumventing the arid Eyrean barrier. We sampled from animals in nearly all known sites within the species’ current distribution, mainly using non-invasive methods, and employed nuclear and mitochondrial DNA analyses to assess alternative scenarios for Pleistocene impacts on population structure. We found evidence for mildly differentiated populations at the range extremes on either side of Spencer Gulf, with secondary contact between locations neighbouring each side of the barrier. These extreme western and eastern regions, and four other regions in between, were genetically distinct in genotypic clustering analyses. Estimates indicate modest, but complex gene flow patterns among some of these regions, in some cases possibly restricted for several thousand years. Prior to this study there was little information to aid risk assessment and prioritization of conservation interventions facilitating gene flow among populations of this species. The contributions of this study to that issue are outlined.
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21
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Harrison RL. Noninvasive Identification of Individual American Badgers by Features of Their Dorsal Head Stripes. WEST N AM NATURALIST 2016. [DOI: 10.3398/064.076.0208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Assessing temporal genetic variation in a cougar population: influence of harvest and neighboring populations. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0790-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Damm DL, Armstrong JB, Arjo WM, Piaggio AJ. Assessment of Population Structure of Coyotes in East-Central Alabama using Microsatellite DNA. SOUTHEAST NAT 2015. [DOI: 10.1656/058.014.0118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Spencer PB, Hampton JO, Pacioni C, Kennedy MS, Saalfeld K, Rose K, Woolnough AP. Genetic relationships within social groups influence the application of the Judas technique: A case study with wild dromedary camels. J Wildl Manage 2014. [DOI: 10.1002/jwmg.807] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Peter B.S. Spencer
- School of Veterinary and Life Sciences; Murdoch University; Western Australia 6150 Australia
| | - Jordan O. Hampton
- Ecotone Wildlife Veterinary Services; P.O. Box 1126; Canberra ACT 2601 Australia
| | - Carlo Pacioni
- School of Veterinary and Life Sciences; Murdoch University; Western Australia 6150 Australia
| | - Malcolm S. Kennedy
- Invasive Species Science; Department of Agriculture and Food; Forrestfield Western Australia 6058 Australia
| | - Keith Saalfeld
- Wildlife Use; Department of Natural Resources; Environment; the Arts and Sport; Northern Territory Government; Alice Springs Northern Territory Australia
| | - Ken Rose
- Invasive Species Science; Department of Agriculture and Food; Forrestfield Western Australia 6058 Australia
| | - Andrew P. Woolnough
- Vertebrate Pest Research Section; Department of Agriculture and Food; Forrestfield Western Australia 6058 Australia
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25
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Cosse M, Del Moral Sachetti JF, Mannise N, Acosta M. Genetic evidence confirms presence of Andean bears in Argentina. URSUS 2014. [DOI: 10.2192/ursus-d-14-00020.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Mariana Cosse
- Genética de la Conservación-Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318 C. P. 11600, Montevideo, Uruguay
| | | | - Natalia Mannise
- Genética de la Conservación-Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318 C. P. 11600, Montevideo, Uruguay
| | - Miguel Acosta
- Proyecto Juco, Eduardo Wilde N° 450, V Soledad, Dpto. A, C. P. 4400, Salta, Argentina
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26
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Aryal A, Brunton D, Ji W, Karmacharya D, McCarthy T, Bencini R, Raubenheimer D. Multipronged strategy including genetic analysis for assessing conservation options for the snow leopard in the central Himalaya. J Mammal 2014. [DOI: 10.1644/13-mamm-a-243] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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27
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Yamashiro A, Yamashiro T, Mori K, Kamada M. Indirect estimation of Recent Sika Deer (Cervus nippon) Migration in Tsurugi Quasi-National Park, Shikoku, Japan. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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28
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Sovic MG, Kubatko LS, Fuerst PA. The effects of locus number, genetic divergence, and genotyping error on the utility of dominant markers for hybrid identification. Ecol Evol 2014; 4:462-73. [PMID: 24634730 PMCID: PMC3936392 DOI: 10.1002/ece3.833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/03/2013] [Accepted: 09/06/2013] [Indexed: 11/27/2022] Open
Abstract
In surveys of hybrid zones, dominant genetic markers are often used to identify individuals of hybrid origin and assign these individuals to one of several potential hybrid classes. Quantitative analyses that address the statistical power of dominant markers in such inference are scarce. In this study, dominant genotype data were simulated to evaluate the effects of, first, the number of loci analyzed, second, the magnitude of differentiation between the markers scored in the groups that are hybridizing, and third, the level of genotyping error associated with the data when assigning individuals to various parental and hybrid categories. The overall performance of the assignment methods was relatively modest at the lowest level of divergence examined (Fst ˜ 0.4), but improved substantially at higher levels of differentiation (Fst ˜ 0.67 or 0.8). The effect of genotyping error was dependent on the level of divergence between parental taxa, with larger divergences tempering the effects of genotyping error. These results highlight the importance of considering the effects of each of the variables when assigning individuals to various parental and hybrid categories, and can help guide decisions regarding the number of loci employed in future hybridization studies to achieve the power and level of resolution desired.
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Affiliation(s)
- Michael G Sovic
- Department of Evolution, Ecology, and Organismal Biology, 314 Aronoff Laboratory, The Ohio State University 318 W. 12th Ave, Columbus, Ohio, 43210
| | - Laura S Kubatko
- Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University 404 Cockins Hall, 1958 Neil Ave., Columbus, Ohio, 43210
| | - Paul A Fuerst
- Department of Evolution, Ecology, and Organismal Biology, 386 Aronoff Laboratory, The Ohio State University 318 W. 12th Ave, Columbus, Ohio, 43210
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29
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Mating systems, reproductive success, and sexual selection in secretive species: a case study of the western diamond-backed rattlesnake, Crotalus atrox. PLoS One 2014; 9:e90616. [PMID: 24598810 PMCID: PMC3944027 DOI: 10.1371/journal.pone.0090616] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/31/2014] [Indexed: 11/19/2022] Open
Abstract
Long-term studies of individual animals in nature contribute disproportionately to our understanding of the principles of ecology and evolution. Such field studies can benefit greatly from integrating the methods of molecular genetics with traditional approaches. Even though molecular genetic tools are particularly valuable for species that are difficult to observe directly, they have not been widely adopted. Here, we used molecular genetic techniques in a 10-year radio-telemetric investigation of the western diamond-backed rattlesnake (Crotalus atrox) for an analysis of its mating system and to measure sexual selection. Specifically, we used microsatellite markers to genotype 299 individuals, including neonates from litters of focal females to ascertain parentage using full-pedigree likelihood methods. We detected high levels of multiple paternity within litters, yet found little concordance between paternity and observations of courtship and mating behavior. Larger males did not father significantly more offspring, but we found evidence for size-specific male-mating strategies, with larger males guarding females for longer periods in the mating seasons. Moreover, the spatial proximity of males to mothers was significantly associated with reproductive success. Overall, our field observations alone would have been insufficient to quantitatively measure the mating system of this population of C. atrox, and we thus urge more widespread adoption of molecular tools by field researchers studying the mating systems and sexual selection of snakes and other secretive taxa.
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30
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Hernández-Mendoza PM, Parra-Bracamonte GM, de la Rosa-Reyna XF, Chassin-Noria O, Sifuentes-Rincón AM. Genetic shifts in the transition from wild to farmed white-tailed deer (Odocoileus virginianus) population. INTERNATIONAL JOURNAL OF BIODIVERSITY SCIENCE, ECOSYSTEM SERVICES & MANAGEMENT 2013. [DOI: 10.1080/21513732.2013.857364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Perla M. Hernández-Mendoza
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro SN. Esq. Elías Piña, Col. Narciso Mendoza, CP. 88710 Reynosa, Tamaulipas, México
| | - Gaspar M. Parra-Bracamonte
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro SN. Esq. Elías Piña, Col. Narciso Mendoza, CP. 88710 Reynosa, Tamaulipas, México
| | - Xochitl F. de la Rosa-Reyna
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro SN. Esq. Elías Piña, Col. Narciso Mendoza, CP. 88710 Reynosa, Tamaulipas, México
| | - Omar Chassin-Noria
- Centro Multidisciplinario de Estudios en Biotecnología, Universidad Michoacana de San Nicolás de Hidalgo, Facultad de Medicina Veterinaria y Zootecnia, Km. 9.5 Carretera Morelia-Zinapécuaro. C.P., 58893 Morelia, Michoacán, México
| | - Ana M. Sifuentes-Rincón
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro SN. Esq. Elías Piña, Col. Narciso Mendoza, CP. 88710 Reynosa, Tamaulipas, México
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31
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Norén K, Angerbjörn A. Genetic perspectives on northern population cycles: bridging the gap between theory and empirical studies. Biol Rev Camb Philos Soc 2013; 89:493-510. [PMID: 24779519 DOI: 10.1111/brv.12070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 01/13/2023]
Abstract
Many key species in northern ecosystems are characterised by high-amplitude cyclic population demography. In 1924, Charles Elton described the ecology and evolution of cyclic populations in a classic paper and, since then, a major focus has been the underlying causes of population cycles. Elton hypothesised that fluctuations reduced population genetic variation and influenced the direction of selection pressures. In concordance with Elton, present theories concern the direct consequences of population cycles for genetic structure due to the processes of genetic drift and selection, but also include feedback models of genetic composition on population dynamics. Most of these theories gained mathematical support during the 1970s and onwards, but due to methodological drawbacks, difficulties in long-term sampling and a complex interplay between microevolutionary processes, clear empirical data allowing the testing of these predictions are still scarce. Current genetic tools allow for estimates of genetic variation and identification of adaptive genomic regions, making this an ideal time to revisit this subject. Herein, we attempt to contribute towards a consensus regarding the enigma described by Elton almost 90 years ago. We present nine predictions covering the direct and genetic feedback consequences of population cycles on genetic variation and population structure, and review the empirical evidence. Generally, empirical support for the predictions was low and scattered, with obvious gaps in the understanding of basic population processes. We conclude that genetic variation in northern cyclic populations generally is high and that the geographic distribution and amount of diversity are usually suggested to be determined by various forms of context- and density-dependent dispersal exceeding the impact of genetic drift. Furthermore, we found few clear signatures of selection determining genetic composition in cyclic populations. Dispersal is assumed to have a strong impact on genetic structuring and we suggest that the signatures of other microevolutionary processes such as genetic drift and selection are weaker and have been over-shadowed by density-dependent dispersal. We emphasise that basic biological and demographical questions still need to be answered and stress the importance of extensive sampling, appropriate choice of tools and the value of standardised protocols.
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Affiliation(s)
- Karin Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
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32
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Noble DW, Choquette JD, Placyk JS, Brooks RJ. Population genetic structure of the endangered Butler’s Gartersnake (Thamnophis butleri): does the Short-headed Gartersnake (Thamnophis brachystoma) exist in Canada? CAN J ZOOL 2013. [DOI: 10.1139/cjz-2013-0068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Understanding population genetic structure is fundamental to conservation of endangered species. It is particularly important when working with species that are morphologically conserved because strong genetic divisions could represent cryptic species. Butler’s Gartersnake (Thamnophis butleri (Cope, 1889)) is an endangered species in Canada, having a fragmented distribution and being restricted to southwestern Ontario. Furthermore, it is difficult to distinguish morphologically from a closely related species, the Short-headed Gartersnake (Thamnophis brachystoma (Cope, 1892)). We use mitochondrial DNA (mtDNA) and seven microsatellite DNA loci to evaluate the genetic structure of Canadian T. butleri populations and to test for the presence of T. brachystoma in one of these populations. All individuals had the same mtDNA haplotype, and there was no evidence of multiple, syntopic genetic clusters, thereby rejecting the hypothesis that T. butleri and T. brachystoma co-exist in Canada. Two different model-based assignment tests using microsatellite DNA data suggest that there are four to five genetically distinct clusters of T. butleri (FST from 0.12 to 0.20). We provide the first population genetic study of T. butleri in Canada and refute the presence of T. brachystoma. Our results may provide guidance on recovery strategies for this species and identify areas to target fine-scale genetic analyses.
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Affiliation(s)
- Daniel W.A. Noble
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Jonathan D. Choquette
- School of Environmental Design and Rural Development, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John S. Placyk
- Department of Biology, University of Texas at Tyler, 3900 University Boulevard, Tyler, TX 75799, USA
| | - Ronald J. Brooks
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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33
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Mumma MA, Soulliere CE, Mahoney SP, Waits LP. Enhanced understanding of predator-prey relationships using molecular methods to identify predator species, individual and sex. Mol Ecol Resour 2013; 14:100-8. [PMID: 23957886 DOI: 10.1111/1755-0998.12153] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 10/26/2022]
Abstract
Predator species identification is an important step in understanding predator-prey interactions, but predator identifications using kill site observations are often unreliable. We used molecular tools to analyse predator saliva, scat and hair from caribou calf kills in Newfoundland, Canada to identify the predator species, individual and sex. We sampled DNA from 32 carcasses using cotton swabs to collect predator saliva. We used fragment length analysis and sequencing of mitochondrial DNA to distinguish between coyote, black bear, Canada lynx and red fox and used nuclear DNA microsatellite analysis to identify individuals. We compared predator species detected using molecular tools to those assigned via field observations at each kill. We identified a predator species at 94% of carcasses using molecular methods, while observational methods assigned a predator species to 62.5% of kills. Molecular methods attributed 66.7% of kills to coyote and 33.3% to black bear, while observations assigned 40%, 45%, 10% and 5% to coyote, bear, lynx and fox, respectively. Individual identification was successful at 70% of kills where a predator species was identified. Only one individual was identified at each kill, but some individuals were found at multiple kills. Predator sex was predominantly male. We demonstrate the first large-scale evaluation of predator species, individual and sex identification using molecular techniques to extract DNA from swabs of wild prey carcasses. Our results indicate that kill site swabs (i) can be highly successful in identifying the predator species and individual responsible; and (ii) serve to inform and complement traditional methods.
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Affiliation(s)
- Matthew A Mumma
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID, 83844, USA
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34
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Fietz K, Graves JA, Olsen MT. Control control control: a reassessment and comparison of GenBank and chromatogram mtDNA sequence variation in Baltic grey seals (Halichoerus grypus). PLoS One 2013; 8:e72853. [PMID: 23977362 PMCID: PMC3745392 DOI: 10.1371/journal.pone.0072853] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 07/06/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic data can provide a powerful tool for those interested in the biology, management and conservation of wildlife, but also lead to erroneous conclusions if appropriate controls are not taken at all steps of the analytical process. This particularly applies to data deposited in public repositories such as GenBank, whose utility relies heavily on the assumption of high data quality. Here we report on an in-depth reassessment and comparison of GenBank and chromatogram mtDNA sequence data generated in a previous study of Baltic grey seals. By re-editing the original chromatogram data we found that approximately 40% of the grey seal mtDNA haplotype sequences posted in GenBank contained errors. The re-analysis of the edited chromatogram data yielded overall similar results and conclusions as the original study. However, a significantly different outcome was observed when using the uncorrected dataset based on the GenBank haplotypes. We therefore suggest disregarding the existing GenBank data and instead using the correct haplotypes reported here. Our study serves as an illustrative example reiterating the importance of quality control through every step of a research project, from data generation to interpretation and submission to an online repository. Errors conducted in any step may lead to biased results and conclusions, and could impact management decisions.
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Affiliation(s)
- Katharina Fietz
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- * E-mail: (FK); (MTO)
| | - Jeff A. Graves
- School of Biology, University of St Andrews, St Andrews, Scotland, United Kingdom
| | - Morten Tange Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Department of Bioscience, Aarhus University, Roskilde, Denmark
- * E-mail: (FK); (MTO)
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35
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Seidel SA, Comer CE, Conway WC, Deyoung RW, Hardin JB, Calkins GE. Influence of translocations on eastern wild turkey population genetics in Texas. J Wildl Manage 2013. [DOI: 10.1002/jwmg.575] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sabrina A. Seidel
- Arthur Temple College of Forestry and Agriculture; Stephen F. Austin State University; Box 6109 SFA Station Nacogdoches TX 75962 USA
| | - Christopher E. Comer
- Arthur Temple College of Forestry and Agriculture; Stephen F. Austin State University; Box 6109 SFA Station Nacogdoches TX 75962 USA
| | - Warren C. Conway
- Arthur Temple College of Forestry and Agriculture; Stephen F. Austin State University; Box 6109 SFA Station Nacogdoches TX 75962 USA
| | - Randy W. Deyoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
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Isolation and characterization of nine microsatellite loci in a Malagasy endemic rodent, Eliurus carletoni (Rodentia: Nesomyinae). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-012-9768-5] [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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37
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Reding DM, Carter CE, Hiller TL, Clark WR. Using population genetics for management of bobcats in oregon. WILDLIFE SOC B 2013. [DOI: 10.1002/wsb.243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dawn M. Reding
- Department of Ecology, Evolution, and Organismal Biology; Iowa State University; 251 Bessey Hall; Ames; IA 50011; USA
| | | | - Tim L. Hiller
- Oregon Department of Fish and Wildlife; Wildlife Division; 3406 Cherry Avenue NE; Salem; OR 97303; USA
| | - William R. Clark
- Department of Ecology, Evolution, and Organismal Biology; Iowa State University; 251 Bessey Hall; Ames; IA 50011; USA
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38
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Pennell MW, Stansbury CR, Waits LP, Miller CR. Capwire: a
R
package for estimating population census size from non‐invasive genetic sampling. Mol Ecol Resour 2012; 13:154-7. [DOI: 10.1111/1755-0998.12019] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew W. Pennell
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho 441B Life Science South Moscow ID 83844USA
- Department of Biological Sciences University of Idaho 252 Life Sciences South Moscow ID 83844 USA
| | - Carisa R. Stansbury
- Department of Fish and Wildlife Sciences University of Idaho 975 West 6th Street Moscow ID 83844 USA
| | - Lisette P. Waits
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho 441B Life Science South Moscow ID 83844USA
- Department of Fish and Wildlife Sciences University of Idaho 975 West 6th Street Moscow ID 83844 USA
| | - Craig R. Miller
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho 441B Life Science South Moscow ID 83844USA
- Department of Biological Sciences University of Idaho 252 Life Sciences South Moscow ID 83844 USA
- Department of Mathematics University of Idaho 300 Brink Hall Moscow ID 83844 USA
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Holbrook JD, DeYoung RW, Janecka JE, Tewes ME, Honeycutt RL, Young JH. Genetic diversity, population structure, and movements of mountain lions (Puma concolor) in Texas. J Mammal 2012. [DOI: 10.1644/11-mamm-a-326.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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40
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Identification and management of a single large population of wild dromedary camels. J Wildl Manage 2012. [DOI: 10.1002/jwmg.381] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Andreou D, Vacquie-Garcia J, Cucherousset J, Blanchet S, Gozlan RE, Loot G. Individual genetic tagging for teleosts: an empirical validation and a guideline for ecologists. JOURNAL OF FISH BIOLOGY 2012; 80:181-194. [PMID: 22220897 DOI: 10.1111/j.1095-8649.2011.03165.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The efficiency of individual genetic tagging was determined by using passive integrated transponders (PIT) as a comparative conventional tagging method. Fifty-five common dace Leuciscus leuciscus were captured in the wild, PIT tagged and fin clipped (for DNA analysis). Thirty fish were recaptured on three occasions and tissue samples were collected. Using 18 microsatellite loci, 79-94% of the recaptures were correctly assigned. Experience with scoring L. leuciscus microsatellites led to more individuals correctly assigned. Allowing matches that differed by one or two alleles resulted in 100% of all recaptures successfully assigned irrespective of the observer. Reducing the set of loci to five to six loci appropriately selected did not affect the assignment rate, demonstrating that costs can be subsequently reduced. Despite their potential benefits, the application of genetic tags for teleosts has been limited. Here, it was demonstrated that genetic tagging could be applied, and a clear guideline (flowchart) is provided on how this method can be developed for teleosts and other organisms, with subsequent practical applications to ecology, evolutionary biology and conservation management.
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Affiliation(s)
- D Andreou
- Centre for Conservation Ecology and Environmental Sciences, School of Applied Sciences, Bournemouth University, Poole, Dorset BH12 5BB, UK
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42
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Genetic Monitoring for Managers: A New Online Resource. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2011. [DOI: 10.3996/082011-jfwm-048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Karmacharya DB, Thapa K, Shrestha R, Dhakal M, Janecka JE. Noninvasive genetic population survey of snow leopards (Panthera uncia) in Kangchenjunga conservation area, Shey Phoksundo National Park and surrounding buffer zones of Nepal. BMC Res Notes 2011; 4:516. [PMID: 22117538 PMCID: PMC3247909 DOI: 10.1186/1756-0500-4-516] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 11/28/2011] [Indexed: 11/15/2022] Open
Abstract
Background The endangered snow leopard is found throughout major mountain ranges of Central Asia, including the remote Himalayas. However, because of their elusive behavior, sparse distribution, and poor access to their habitat, there is a lack of reliable information on their population status and demography, particularly in Nepal. Therefore, we utilized noninvasive genetic techniques to conduct a preliminary snow leopard survey in two protected areas of Nepal. Results A total of 71 putative snow leopard scats were collected and analyzed from two different areas; Shey Phoksundo National Park (SPNP) in the west and Kangchanjunga Conservation Area (KCA) in the east. Nineteen (27%) scats were genetically identified as snow leopards, and 10 (53%) of these were successfully genotyped at 6 microsatellite loci. Two samples showed identical genotype profiles indicating a total of 9 individual snow leopards. Four individual snow leopards were identified in SPNP (1 male and 3 females) and five (2 males and 3 females) in KCA. Conclusions We were able to confirm the occurrence of snow leopards in both study areas and determine the minimum number present. This information can be used to design more in-depth population surveys that will enable estimation of snow leopard population abundance at these sites.
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Affiliation(s)
- Dibesh B Karmacharya
- Center for Molecular Dynamics Nepal, Swaraj Sadan 5th Floor, Thapathali-11, Kathmandu, Nepal.
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Influence of habitat fragmentation on the genetic structure of large mammals: evidence for increased structuring of African buffalo (Syncerus caffer) within the Serengeti ecosystem. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0291-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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45
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Thulin CG, Englund L, Ericsson G, Spong G. The impact of founder events and introductions on genetic variation in the muskox Ovibos moschatus in Sweden. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13364-011-0035-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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46
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Song N, Nwafili SA, Gao TX. Genetic diversity and population structure of Chrysichthys nigrodigitatus from Niger Delta based on AFLP analysis. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Schubert G, Stoneking CJ, Arandjelovic M, Boesch C, Eckhardt N, Hohmann G, Langergraber K, Lukas D, Vigilant L. Male-mediated gene flow in patrilocal primates. PLoS One 2011; 6:e21514. [PMID: 21747938 PMCID: PMC3128582 DOI: 10.1371/journal.pone.0021514] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 06/02/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Many group-living species display strong sex biases in dispersal tendencies. However, gene flow mediated by apparently philopatric sex may still occur and potentially alters population structure. In our closest living evolutionary relatives, dispersal of adult males seems to be precluded by high levels of territoriality between males of different groups in chimpanzees, and has only been observed once in bonobos. Still, male-mediated gene flow might occur through rare events such as extra-group matings leading to extra-group paternity (EGP) and female secondary dispersal with offspring, but the extent of this gene flow has not yet been assessed. METHODOLOGY/PRINCIPAL FINDINGS Using autosomal microsatellite genotyping of samples from multiple groups of wild western chimpanzees (Pan troglodytes verus) and bonobos (Pan paniscus), we found low genetic differentiation among groups for both males and females. Characterization of Y-chromosome microsatellites revealed levels of genetic differentiation between groups in bonobos almost as high as those reported previously in eastern chimpanzees, but lower levels of differentiation in western chimpanzees. By using simulations to evaluate the patterns of Y-chromosomal variation expected under realistic assumptions of group size, mutation rate and reproductive skew, we demonstrate that the observed presence of multiple and highly divergent Y-haplotypes within western chimpanzee and bonobo groups is best explained by successful male-mediated gene flow. CONCLUSIONS/SIGNIFICANCE The similarity of inferred rates of male-mediated gene flow and published rates of EGP in western chimpanzees suggests this is the most likely mechanism of male-mediated gene flow in this subspecies. In bonobos more data are needed to refine the estimated rate of gene flow. Our findings suggest that dispersal patterns in these closely related species, and particularly for the chimpanzee subspecies, are more variable than previously appreciated. This is consistent with growing recognition of extensive behavioral variation in chimpanzees and bonobos.
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Affiliation(s)
- Grit Schubert
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Junior Research Group Novel Zoonoses, Robert Koch Institute, Berlin, Germany
| | | | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nadin Eckhardt
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gottfried Hohmann
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kevin Langergraber
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, Boston University, Boston, Massachusetts, United States of America
| | - Dieter Lukas
- Large Animal Research Group, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- * E-mail:
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Guerreiro MPG, Fontdevila A. Osvaldo and Isis retrotransposons as markers of the Drosophila buzzatii colonisation in Australia. BMC Evol Biol 2011; 11:111. [PMID: 21513573 PMCID: PMC3098803 DOI: 10.1186/1471-2148-11-111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 04/24/2011] [Indexed: 11/10/2022] Open
Abstract
Background Transposable elements (TEs) constitute an important source of genetic variability owing to their jumping and regulatory properties, and are considered to drive species evolution. Several factors that are able to induce TE transposition in genomes have been documented (for example environmental stress and inter- and intra-specific crosses) but in many instances the reasons for TE mobilisation have yet to be elucidated. Colonising populations constitute an ideal model for studying TE behaviour and distribution as they are exposed to different environmental and new demographic conditions. In this study, the distribution of two TEs, Osvaldo and Isis, was examined in two colonising populations of D. buzzatii from Australia. Comparing Osvaldo copy numbers between Australian and Old World (reported in previous studies) colonisations provides a valuable tool for elucidating the colonisation process and the effect of new conditions encountered by colonisers on TEs. Results The chromosomal distributions of Osvaldo and Isis retrotransposons in two colonising populations of D. buzzatii from Australia revealed sites of high insertion frequency (>10%) and low frequency sites. Comparisons between Osvaldo insertion profiles in colonising populations from the Old World and Australia demonstrate a tendency towards a higher number of highly occupied sites with higher insertion frequency in the Old World than in Australian populations. Tests concerning selection against deleterious TE insertions indicate that Isis is more controlled by purifying selection than Osvaldo. The distribution of both elements on chromosomal arms follows a Poisson distribution and there are non-significant positive correlations between highly occupied sites and chromosomal inversions. Conclusions The occupancy profile of Osvaldo and Isis retrotransposons is characterised by the existence of high and low insertion frequency sites in the populations. These results demonstrate that Australian D. buzzatii populations were subjected to a founder effect during the colonisation process. Moreover, there are more sites with high insertion frequency in the Old World colonisation than in the Australian colonisation, indicating a probable stronger bottleneck effect in Australia. The results suggest that selection does not seem to play a major role, compared to demography, in the distribution of transposable elements in the Australian populations.
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Affiliation(s)
- María Pilar García Guerreiro
- Grup de Biología Evolutiva, Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Spain.
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Fine-scale population genetic structure and sex-biased dispersal in the smooth snake (Coronella austriaca) in southern England. Heredity (Edinb) 2011; 107:231-8. [PMID: 21343947 DOI: 10.1038/hdy.2011.7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Human-induced alteration of natural habitats has the potential to impact on the genetic structuring of remnant populations at multiple spatial scales. Species from higher trophic levels, such as snakes, are expected to be particularly susceptible to land-use changes. We examined fine-scale population structure and looked for evidence of sex-biased dispersal in smooth snakes (Coronella austriaca), sampled from 10 heathland localities situated within a managed coniferous forest in Dorset, United Kingdom. Despite the limited distances between heathland areas (maximum <6 km), there was a small but significant structuring of populations based on eight microsatellite loci. This followed an isolation-by-distance model using both straight line and 'biological' distances between sampling sites, suggesting C. austriaca's low vagility as the causal factor, rather than closed canopy conifer forest exerting an effect as a barrier to dispersal. Within population comparisons of male and female snakes showed evidence for sex-biased dispersal, with three of four analyses finding significantly higher dispersal in males than in females. We suggest that the fine-scale spatial genetic structuring and sex-biased dispersal have important implications for the conservation of C. austriaca, and highlight the value of heathland areas within commercial conifer plantations with regards to their future management.
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A Demo-Genetic Analysis of a Small Reintroduced Carnivore Population: The Otter (Lutra lutra) in The Netherlands. INTERNATIONAL JOURNAL OF ECOLOGY 2011. [DOI: 10.1155/2011/870853] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Assessing the viability of reintroduced animal populations is a complicated task. Reintroductions are usually carried out with a small number of individuals, thereby, limiting the possibilities for monitoring because of the possible negative effects of intensive monitoring on survival and reproduction. Moreover, reintroduction studies are part of a socioeconomic interplay of forces, thereby, also limiting monitoring possibilities. Also, knowledge of population demography and abundance can be incomplete or unattainable. Here, we illustrate how we combined traditional telemetry and novel non-invasive genetic methodology to construct a detailed life table of a small reintroduced otter population in The Netherlands. Combining an appropriate capture-mark-recapture framework with a matrix modelling approach provides, in general, useful insights for such populations. The data indicated that (i) male survival is lower than female survival, (ii) the reintroduced population is currently growing (estimatedλ=1.26: range [1.06, 1.42]) and seems viable, (iii) increasing adult survival is currently the critical stage at which efforts of field managers should concentrate, and (iv) the modelling framework allowed us to determine the boundary conditions for the vital rates under which the population would go extinct. The applied approach directs at measurements that help field managers to implement the right conservation strategy after reintroductions.
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