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Wilson RE, Boyd WS, Sonsthagen SA, Ward DH, Clausen P, Dickson KM, Ebbinge BS, Gudmundsson GA, Sage GK, Rearick JR, Derksen DV, Talbot SL. Where east meets west: Phylogeography of the high Arctic North American brant goose. Ecol Evol 2024; 14:e11245. [PMID: 38601857 PMCID: PMC11004662 DOI: 10.1002/ece3.11245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/07/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Genetic variation in Arctic species is often influenced by vicariance during the Pleistocene, as ice sheets fragmented the landscape and displaced populations to low- and high-latitude refugia. The formation of secondary contact or suture zones during periods of ice sheet retraction has important consequences on genetic diversity by facilitating genetic connectivity between formerly isolated populations. Brant geese (Branta bernicla) are a maritime migratory waterfowl (Anseriformes) species that almost exclusively uses coastal habitats. Within North America, brant geese are characterized by two phenotypically distinct subspecies that utilize disjunct breeding and wintering areas in the northern Pacific and Atlantic. In the Western High Arctic of Canada, brant geese consist of individuals with an intermediate phenotype that are rarely observed nesting outside this region. We examined the genetic structure of brant geese populations from each subspecies and areas consisting of intermediate phenotypes using mitochondrial DNA (mtDNA) control region sequence data and microsatellite loci. We found a strong east-west partition in both marker types consistent with refugial populations. Within subspecies, structure was also observed at mtDNA while microsatellite data suggested the presence of only two distinct genetic clusters. The Western High Arctic (WHA) appears to be a secondary contact zone for both Atlantic and Pacific lineages as mtDNA and nuclear genotypes were assigned to both subspecies, and admixed individuals were observed in this region. The mtDNA sequence data outside WHA suggests no or very restricted intermixing between Atlantic and Pacific wintering populations which is consistent with published banding and telemetry data. Our study indicates that, although brant geese in the WHA are not a genetically distinct lineage, this region may act as a reservoir of genetic diversity and may be an area of high conservation value given the potential of low reproductive output in this species.
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Affiliation(s)
- Robert E. Wilson
- School of Natural ResourcesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Nebraska State MuseumUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - W. Sean Boyd
- Environment and Climate Change CanadaScience and Technology BranchDeltaBritish ColumbiaCanada
| | - Sarah A. Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, School of Natural ResourcesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - David H. Ward
- U.S. Geological SurveyAlaska Science CenterAnchorageAlaskaUSA
| | | | - Kathryn M. Dickson
- Canadian Wildlife ServiceEnvironment and Climate Change CanadaOttawaOntarioCanada
| | | | | | - George K. Sage
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
| | | | - Dirk V. Derksen
- U.S. Geological SurveyAlaska Science CenterAnchorageAlaskaUSA
| | - Sandra L. Talbot
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
- Alaska Center for Conservation ScienceUniversity of AlaskaAnchorageAlaskaUSA
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Cheng Q, Liu QQ, Lu CA. A state-of-the-science review of using mitochondrial DNA copy number as a biomarker for environmental exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123642. [PMID: 38402934 DOI: 10.1016/j.envpol.2024.123642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/06/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Mitochondria are bioenergetic, biosynthetic, and signaling organelles in eukaryotes, and contain their own genomes, mitochondrial DNA (mtDNA), to supply energy to cells by generating ATP via oxidative phosphorylation. Therefore, the threat to mitochondria' integrity and health resulting from environmental exposure could induce adverse health effects in organisms. In this review, we summarized the association between mtDNA copy number (mtDNAcn), and environmental exposures as reported in the literature. We conducted a literature search in the Web of Science using [Mitochondrial DNA copy number] and [Exposure] as two keywords and employed three selection criteria for the final inclusion of 97 papers for review. The consensus of data was that mtDNAcn could be used as a plausible biomarker for cumulative exposures to environmental chemical and physical agents. In order to furtherly expand the application of mtDNAcn in ecological and environmental health research, we suggested a series of algorithms aiming to standardize the calculation of mtDNAcn based on the PCR results in this review. We also discussed the pitfalls of using whole blood/plasma samples for mtDNAcn measurements and regard buccal cells a plausible and practical alternative. Finally, we recognized the importance of better understanding the mechanistic analysis and regulatory mechanism of mtDNAcn, in particular the signals release and regulation pathways. We believe that the development of using mtDNAcn as an exposure biomarker will revolutionize the evaluation of chronic sub-lethal toxicity of chemicals to organisms in ecological and environmental health research that has not yet been implemented.
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Affiliation(s)
- Qing Cheng
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Qing Qing Liu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chensheng Alex Lu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China; School of Public Health, University of Washington, Seattle, WA, 98195, USA.
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Turcu MC, Paștiu AI, Bel LV, Pusta DL. Minimally Invasive Sampling Methods for Molecular Sexing of Wild and Companion Birds. Animals (Basel) 2023; 13:3417. [PMID: 37958172 PMCID: PMC10648277 DOI: 10.3390/ani13213417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Birds are highly social and must be paired in order to increase their welfare. Most bird species are monomorphic; therefore, molecular sexing helps provide appropriate welfare for birds. Moreover, early sex determination can be of great value for bird owners. The aim of this study was to demonstrate that sex identification in birds achieved using molecular methods and samples collected via minimally invasive methods is fast, efficient, and accurate. A total of 100 samples (29 paired samples of feathers and oral swabs and 14 tripled samples of feathers, oral swabs, and blood) from 43 birds were included in this study, as follows: wild birds (Falconiformes, Accipitriformes, landfowl-Galliformes, waterfowl-Anseriformes) and companion birds (Passeriformes, Psittaciformes-large-, medium-, and small-sized parrots). Amplification of CHD1-Z and CHD1-W genes was performed via conventional PCR. The results obtained from feathers were compared to those obtained from oral swabs and to those obtained from blood samples, where applicable. The obtained results show that all types of samples can be used for molecular sexing of all studied bird species. To the best of our knowledge, the present study reports, for the first time, molecular sex identification in Red Siskin (Carduelis cucullata) and Goldfinch (Carduelis carduelis major). For higher accuracy, our recommendation is to use minimally invasive samples (oral swabs and feathers) and to test both types of samples for each bird instead of blood samples.
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Affiliation(s)
- Maria-Carmen Turcu
- Department of Genetics and Hereditary Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (M.-C.T.); (D.L.P.)
- New Companion Animals Veterinary Clinic, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania;
| | - Anamaria Ioana Paștiu
- Department of Genetics and Hereditary Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (M.-C.T.); (D.L.P.)
| | - Lucia-Victoria Bel
- New Companion Animals Veterinary Clinic, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania;
| | - Dana Liana Pusta
- Department of Genetics and Hereditary Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (M.-C.T.); (D.L.P.)
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4
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Sorum MS, Cameron MD, Crupi A, Sage GK, Talbot SL, Hilderbrand GV, Joly K. Pronounced brown bear aggregation along anadromous streams in interior Alaska. WILDLIFE BIOLOGY 2023. [DOI: 10.1002/wlb3.01057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Affiliation(s)
- Mathew S. Sorum
- Gates of the Arctic National Park and Preserve, National Park Service Fairbanks Alaska USA
| | - Matthew D. Cameron
- Gates of the Arctic National Park and Preserve, National Park Service Fairbanks Alaska USA
| | | | - George K. Sage
- Far Northwestern Inst. of Art and Science, Alaska Office Alaska USA
| | - Sandra L. Talbot
- Far Northwestern Inst. of Art and Science, Alaska Office Alaska USA
| | | | - Kyle Joly
- Gates of the Arctic National Park and Preserve, National Park Service Fairbanks Alaska USA
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A Comparison of Feathers and Oral Swab Samples as DNA Sources for Molecular Sexing in Companion Birds. Animals (Basel) 2023; 13:ani13030525. [PMID: 36766417 PMCID: PMC9913368 DOI: 10.3390/ani13030525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The early age determinism of the sex in case of monomorphic birds is very important, because most companion birds have no distinct sexual dimorphic traits. Molecular genetic sexing was proved to be one of the most accurate sex determinations in monomorphic birds. The aim of this study was to compare the results obtained by PCR performed on isolate genomic DNA from paired samples of feathers and oral swabs collected from the same individuals. Samples of oral swabs (n = 101) and feathers (n = 74) were collected from 101 companion birds from four different species (Columba livia domestica, Psittacula krameri, Neophema splendida and Agapornis spp.). The PCR was performed for the amplification of the CHD1W and CHD1Z genes in females and the CHD1Z gene in males. The overall PCR success rate of sex determination was significantly higher from oral swabs than from feathers. The PCR success rate from oral swabs was higher in juveniles and from feathers was significantly higher in adults. The similarity between the oral swab and feathers was obtained in 78.38% of the birds. Oral swabs proved to be a more reliable sample for genetic sex determination in the species tested in this study.
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Gousy-Leblanc M, Yannic G, Therrien JF, Lecomte N. Mapping our knowledge on birds of prey population genetics. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01368-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Gill LF, van Schaik J, von Bayern AMP, Gahr ML. Genetic monogamy despite frequent extrapair copulations in "strictly monogamous" wild jackdaws. Behav Ecol 2020; 31:247-260. [PMID: 32372855 PMCID: PMC7191249 DOI: 10.1093/beheco/arz185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 09/29/2019] [Accepted: 10/05/2019] [Indexed: 11/23/2022] Open
Abstract
"Monogamy" refers to different components of pair exclusiveness: the social pair, sexual partners, and the genetic outcome of sexual encounters. Avian monogamy is usually defined socially or genetically, whereas quantifications of sexual behavior remain scarce. Jackdaws (Corvus monedula) are considered a rare example of strict monogamy in songbirds, with lifelong pair bonds and little genetic evidence for extrapair (EP) offspring. Yet jackdaw copulations, although accompanied by loud copulation calls, are rarely observed because they occur visually concealed inside nest cavities. Using full-day nest-box video surveillance and on-bird acoustic bio-logging, we directly observed jackdaw sexual behavior and compared it to the corresponding genetic outcome obtained via molecular parentage analysis. In the video-observed nests, we found genetic monogamy but frequently detected forced EP sexual behavior, accompanied by characteristic male copulation calls. We, thus, challenge the long-held notion of strict jackdaw monogamy at the sexual level. Our data suggest that male mate guarding and frequent intrapair copulations during the female fertile phase, as well as the forced nature of the copulations, could explain the absence of EP offspring. Because EP copulation behavior appeared to be costly for both sexes, we suggest that immediate fitness benefits are an unlikely explanation for its prevalence. Instead, sexual conflict and dominance effects could interact to shape the spatiotemporal pattern of EP sexual behavior in this species. Our results call for larger-scale investigations of jackdaw sexual behavior and parentage and highlight the importance of combining social, sexual, and genetic data sets for a more complete understanding of mating systems.
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Affiliation(s)
- Lisa F Gill
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, Seewiesen, Germany
| | - Jaap van Schaik
- Department of Applied Zoology and Nature Conservation, University of Greifswald, Greifswald, Germany
| | - Auguste M P von Bayern
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, Seewiesen, Germany
- Department of Biology II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Manfred L Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, Seewiesen, Germany
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Development and characterization of polymorphic microsatellite markers in northern fulmar, Fulmarus glacialis (Procellariiformes), and cross-species amplification in eight other seabirds. Genes Genomics 2019; 41:1015-1026. [PMID: 31134591 DOI: 10.1007/s13258-019-00819-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 04/11/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND In the North Pacific, northern fulmar (Fulmarus glacialis) forms extensive colonies in few locales, which may lead to limited gene flow and locale-specific population threats. In the Atlantic, there are thousands of colonies of varying sizes and in Europe the species is considered threatened. Prior screens and classical microsatellite development in fulmar failed to provide a suite of markers adequate for population genetics studies. OBJECTIVES The objective of this study was to isolate a suite of polymorphic microsatellite loci with sufficient variability to quantify levels of gene flow, population affinity, and identify familial relationships in fulmar. We also performed a cross-species screening of these markers in eight other species. METHODS We used shotgun sequencing to isolate 26 novel microsatellite markers in fulmar to screen for variability using individuals from two distinct regions: the Pacific (Chagulak Island, Alaska) and the Atlantic (Hafnarey Island, Iceland). RESULTS Polymorphism was present in 24 loci in Chagulak and 23 in Hafnarey, while one locus failed to amplify in either colony. Polymorphic loci exhibited moderate levels of genetic diversity and this suite of loci uncovered genetic structuring between the regions. Among the other species screened, polymorphism was present in one to seven loci. CONCLUSION The loci yielded sufficient variability for use in population studies and estimation of familial relationships; as few as five loci provide resolution to determine individual identity. These markers will allow further insight into the global population dynamics and phylogeography of fulmars. We also demonstrated some markers are transferable to other species.
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Monge O, Dumas D, Baus I. Environmental DNA from avian residual saliva in fruits and its potential uses in population genetics. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1074-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Thalinger B, Oehm J, Zeisler C, Vorhauser J, Traugott M. Sex-specific prey partitioning in breeding piscivorous birds examined via a novel, noninvasive approach. Ecol Evol 2018; 8:8985-8998. [PMID: 30271560 PMCID: PMC6157673 DOI: 10.1002/ece3.4421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 01/02/2023] Open
Abstract
Piscivorous birds frequently display sex-specific differences in their hunting and feeding behavior, which lead to diverging impacts on prey populations. Cormorants (Phalacrocoracidae), for example, were previously studied to examine dietary differences between the sexes and males were found to consume larger fish in coastal areas during autumn and winter. However, information on prey partitioning during breeding and generally on sex-specific foraging in inland waters is missing. Here, we assess sex-specific prey choice of Great Cormorants (Phalacrocorax carbo) during two subsequent breeding seasons in the Central European Alpine foreland, an area characterized by numerous stagnant and flowing waters in close proximity to each other. We developed a unique, noninvasive approach and applied it to regurgitated pellets: molecular cormorant sexing combined with molecular fish identification and fish-length regression analysis performed on prey hard parts. Altogether, 364 pellets delivered information on both, bird sex, and consumed prey. The sexes differed significantly in their overall prey composition, even though Perca fluviatilis, Rutilus rutilus, and Coregonus spp. represented the main food source for both. Albeit prey composition did not indicate the use of different water bodies by the sexes, male diet was characterized by higher prey diversity within a pellet and the consumption of larger fish. The current findings show that female and male cormorants to some extent target the available prey spectrum at different levels. Finally, the comprehensive and noninvasive approach has great potential for application in studies of other piscivorous bird species.
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Affiliation(s)
| | - Johannes Oehm
- Institute of EcologyUniversity of InnsbruckInnsbruckAustria
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Gravley MC, Sage GK, Talbot SL, Carlson ML. Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, Honckenya peploides. JOURNAL OF PLANT RESEARCH 2018; 131:879-885. [PMID: 29687245 DOI: 10.1007/s10265-018-1036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Codominant marker systems are better suited to analyze population structure and assess the source of an individual in admixture analyses. Currently, there is no codominant marker system using microsatellites developed for the sea sandwort, Honckenya peploides (L.) Ehrh., an early colonizer in island systems. We developed and characterized novel microsatellite loci from H. peploides, using reads collected from whole genome shotgun sequencing on a 454 platform. The combined output from two shotgun runs yielded a total of 62,669 reads, from which 58 loci were screened. We identified 12 polymorphic loci that amplified reliably and exhibited disomic inheritance. Microsatellite data were collected and characterized for the 12 polymorphic loci in two Alaskan populations of H. peploides: Fossil Beach, Kodiak Island (n = 32) and Egg Bay, Atka Island (n = 29). The Atka population exhibited a slightly higher average number of alleles (3.9) and observed heterozygosity (0.483) than the Kodiak population (3.3 and 0.347, respectively). The overall probability of identity values for both populations was PID = 2.892e-6 and PIDsib = 3.361e-3. We also screened the 12 polymorphic loci in Wilhelmsia physodes (Fisch. ex Ser.) McNeill, the most closely related species to H. peploides, and only one locus was polymorphic. These microsatellite markers will allow future investigations into population genetic and colonization patterns of the beach dune ruderal H. peploides on new and recently disturbed islands.
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Affiliation(s)
- Meg C Gravley
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA.
- Biological Sciences Department, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK, 99508, USA.
| | - George K Sage
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Sandra L Talbot
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Matthew L Carlson
- Biological Sciences Department, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK, 99508, USA
- University of Alaska Anchorage, Alaska Center for Conservation Science, 3211 Providence Drive, Anchorage, AK, 99508, USA
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Pande A, Rawat N, Sivakumar K, Sathyakumar S, Mathur VB, Mondol S. Cross-species screening of microsatellite markers for individual identification of snow petrel Pagodroma nivea and Wilson's storm petrel Oceanites oceanicus in Antarctica. PeerJ 2018; 6:e5243. [PMID: 30042893 PMCID: PMC6055593 DOI: 10.7717/peerj.5243] [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] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/26/2018] [Indexed: 11/20/2022] Open
Abstract
Seabirds are important indicators of marine ecosystem health. Species within the order Procellariiformes are the most abundant seabird species group distributed from warm tropical to cold temperate regions including Antarctica. There is a paucity of information on basic biology of the pelagic seabird species nesting on the Antarctic continents, and long-term studies are required to gather data on their population demography, genetics and other ecological parameters. Under the 'Biology and Environmental Sciences' component of the Indian Antarctic programme, long-term monitoring of Antarctic biodiversity is being conducted. In this paper, we describe results of cross-species screening of a panel of 12 and 10 microsatellite markers in two relatively little studied seabird species in Antarctica, the snow petrel Pagodroma nivea and the Wilson's storm petrel Oceanites oceanicus, respectively. These loci showed high amplification success and moderate levels of polymorphism in snow petrel (mean no. of alleles 7.08 ± 3.01 and mean observed heterozygosity 0.35 ± 0.23), but low polymorphism in Wilson's storm petrel (mean no. of alleles 3.9 ± 1.3 and mean observed heterozygosity 0.28 ± 0.18). The results demonstrate that these panels can unambiguously identify individuals of both species (cumulative PIDsibs for snow petrel is 3.7 × 10-03 and Wilson's storm petrel is 1.9 × 10-02) from field-collected samples. This work forms a baseline for undertaking long-term genetic research of these Antarctic seabird species and provides critical insights into their population genetics.
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Affiliation(s)
- Anant Pande
- Endangered Species Management, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Nidhi Rawat
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Kuppusamy Sivakumar
- Endangered Species Management, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Sambandam Sathyakumar
- Endangered Species Management, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | | | - Samrat Mondol
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India
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Ruiz CA, Chaney ME, Tosi AJ. Medical-grade buccal swabs versus drugstore cotton swabs: No difference in DNA yield. MethodsX 2018; 5:39-42. [PMID: 30622908 PMCID: PMC6318096 DOI: 10.1016/j.mex.2018.01.006] [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] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 01/12/2018] [Indexed: 12/01/2022] Open
Abstract
We tested three types of medical-grade buccal swabs against standard cotton swabs for differences in DNA yield. A panel of swab types – one drugstore (Q-tips®) and three medical-grade – was used for buccal cell collection from three different individuals. DNA was extracted from all swabs using a QIAcube robot; quantitation values were measured by an Alu-based qPCR assay; and differences were compared through a 2-way ANOVA. Our results demonstrate that cotton swabs recover as much DNA as medical-grade swabs, but at a tremendously lower cost. Cotton swabs also display the greatest consistency of DNA yield, as indicated by the lowest coefficient of variation among the four tested swab types. These findings suggest that the use of standard cotton swabs for buccal cell collection offers not only a significant cost savings, but a more consistent method compared to the use of medical-grade swabs.
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Affiliation(s)
- Cody A Ruiz
- Department of Anthropology, Kent State University, Kent, OH 44242, United States
| | - Morgan E Chaney
- Department of Anthropology, Kent State University, Kent, OH 44242, United States
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, Kent, OH 44242, United States
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Abstract
Skin swabbing, a minimally invasive DNA sampling method recently proposed for adult amphibians, was tested on the dendrobatid frog Allobates femoralis. I compared DNA yield from skin swabs and toe clips by evaluating obtained DNA concentrations and purity of extracts, as well as amplification success using eleven polymorphic microsatellite loci. I also tested whether storing skin swabs for two months at −20°C affected the properties of the extract or microsatellite analysis. Results show that skin swabs of adult A. femoralis suffered from high contamination and yielded significantly lower DNA quality and quantity, resulting in insufficient genotyping success, than DNA obtained from toe clips. The relatively dry skin in dendrobatid frogs may have impeded the collection of sufficient viable cells, and the presence of skin alkaloids and microbiota in the frog mucus may lead to high contamination load of skin swabs.
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Affiliation(s)
- Eva Ringler
- Department of Integrative Biology and Physiology, University of California Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA.,Department of Integrative Zoology, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.,Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna, University of Vienna, Veterinaerplatz 1, A-1210 Vienna, Austria
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15
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Talbot SL, Sage GK, Sonsthagen SA, Gravley MC, Swem T, Williams JC, Longmire JL, Ambrose S, Flamme MJ, Lewis SB, Phillips L, Anderson C, White CM. Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes. PLoS One 2017; 12:e0188185. [PMID: 29149202 PMCID: PMC5693296 DOI: 10.1371/journal.pone.0188185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/02/2017] [Indexed: 11/22/2022] Open
Abstract
Subspecies relationships within the peregrine falcon (Falco peregrinus) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons–F. p. tundrius, anatum, and pealei–for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping (pealei) and a boreal/Arctic grouping (currently anatum and tundrius)–each comprised of discrete populations that are variously intra-regionally connected.
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Affiliation(s)
- Sandra L. Talbot
- U.S. Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
- * E-mail:
| | - George K. Sage
- U.S. Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
| | - Sarah A. Sonsthagen
- U.S. Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
| | - Meg C. Gravley
- U.S. Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
| | - Ted Swem
- Fairbanks Fish and Wildlife Field Office, U. S. Fish and Wildlife Service, Fairbanks, Alaska, United States of America
| | - Jeffrey C. Williams
- Alaska Maritime National Wildlife Refuge, U. S. Fish and Wildlife Service, Homer, Alaska, United States of America
| | - Jonathan L. Longmire
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Skip Ambrose
- Fairbanks Fish and Wildlife Field Office, U. S. Fish and Wildlife Service, Fairbanks, Alaska, United States of America
| | - Melanie J. Flamme
- Yukon-Charley River National Preserve and Gates of the Arctic National Park and Preserve, National Park Service, Fairbanks, Alaska, United States of America
| | - Stephen B. Lewis
- Migratory Bird Management, U. S. Fish and Wildlife Service, Juneau, Alaska, United States of America
| | - Laura Phillips
- Alaska Regional Office, National Park Service, Anchorage, Alaska, United States of America
| | | | - Clayton M. White
- Department of Plant and Wildlife Sciences and Monte L. Bean Life Science Museum, Brigham Young University, Provo, Utah, United States of America
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16
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Li Q, Li W, Li X, Liu L, Zhang Y, Guo Y, Chen X, Xu G, Zheng J. The Distribution Characteristics and Applications for Maternal Cells on Chicken Egg Vitelline Membrane. Sci Rep 2017; 7:6626. [PMID: 28747770 PMCID: PMC5529465 DOI: 10.1038/s41598-017-06996-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/21/2017] [Indexed: 11/09/2022] Open
Abstract
The major components of vitelline membrane (VM) are ovomucin, VM outer (VMO) I and VMO II. At present, the distribution pattern of maternal cells on the VM has not been described in detail. In this study, the existence and distribution characteristics of maternal cells on VM were observed. There were more than 3.2 × 105 somatic cells on VM, which were uneven distributed. The calcein AM/PI staining of the maternal cells on the VM showed that the cells' viability changed with the freshness of the eggs, and that the maternal cells gradually underwent apoptosis and became degraded. The results of morphology of different tissues indicated that the most of maternal cells on the VM were granulosa cells. Moreover, the karyotype of the cultured granulosa cells, which is the main source of cells on VM, were identified as the normal diploid karyotype of chicken. Furthermore, the VM DNA extracted from chickens and quails, which represent the eggs of different size, was adequate for further genetic analysis. The VM DNA was easily accessible and relatively constant, without cross-contamination. Therefore, the VM DNA could potentially be applied for the molecular traceability between eggs and chickens, and be beneficial in avian ecology research studies.
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Affiliation(s)
- Quanlin Li
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wenbo Li
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xingzheng Li
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lulu Liu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Zhang
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yuying Guo
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xia Chen
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Guiyun Xu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jiangxia Zheng
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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17
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Arnold AE, Andersen EM, Taylor MJ, Steidl RJ. Using cytochrome b to identify nests and museum specimens of cryptic songbirds. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-016-0680-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Espinosa‐de Aquino W, Olvera‐Ramírez A, Arellano‐Carbajal F, Lanz‐Mendoza H, Villagrán‐Herrera E, Acevedo‐Whitehouse K. Protein and
RNA
extraction from mucosal swabs: a minimally invasive source of ecological data for studies of natural populations. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wendy Espinosa‐de Aquino
- Unit for Basic and Applied Microbiology School of Natural Sciences Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
| | - Andrea Olvera‐Ramírez
- Department of Veterinary Medicine School of Natural Sciences Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
| | - Fausto Arellano‐Carbajal
- Unit for Basic and Applied Microbiology School of Natural Sciences Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
| | - Humberto Lanz‐Mendoza
- Center for Infectious Diseases National Institute of Public Health Cuernavaca Morelos 62100 Mexico
| | - Elena Villagrán‐Herrera
- School of Medicine Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
| | - Karina Acevedo‐Whitehouse
- Unit for Basic and Applied Microbiology School of Natural Sciences Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
- The Marine Mammal Center 2000 Bunker Road Sausalito CA 94965 USA
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Blood Serum Chemistry of Wild Alaskan Black-capped Chickadees (Poecile atricapillus) with Avian Keratin Disorder. J Wildl Dis 2016; 52:927-930. [DOI: 10.7589/2016-02-034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Grendelmeier A, Arlettaz R, Olano-Marin J, Pasinelli G. Experimentally provided conspecific cues boost bird territory density but not breeding performance. Behav Ecol 2016. [DOI: 10.1093/beheco/arw144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Wilkinson LC, Handel CM, Van Hemert C, Loiseau C, Sehgal RN. Avian malaria in a boreal resident species: long-term temporal variability, and increased prevalence in birds with avian keratin disorder. Int J Parasitol 2016; 46:281-90. [DOI: 10.1016/j.ijpara.2015.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 01/16/2023]
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22
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Cascade Screening for Fragile X Syndrome/CGG Repeat Expansions in Children Attending Special Education in Sri Lanka. PLoS One 2015; 10:e0145537. [PMID: 26694146 PMCID: PMC4687912 DOI: 10.1371/journal.pone.0145537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/04/2015] [Indexed: 01/08/2023] Open
Abstract
Fragile X syndrome (FXS) is the commonest cause of inherited mental retardation and clinically presents with learning, emotional and behaviour problems. FXS is caused by expansion of cytosine-guanine-guanine (CGG) repeats present in the 5’ untranslated region of the FMR1 gene. The aim of this study was to screen children attending special education institutions in Sri Lanka to estimate the prevalence of CGG repeat expansions. The study population comprised a representative national sample of 850 children (540 males, 310 females) with 5 to 18 years of age from moderate to severe mental retardation of wide ranging aetiology. Screening for CGG repeat expansion was carried out on DNA extracted from buccal cells using 3’ direct triplet primed PCR followed by melting curve analysis. To identify the expanded status of screened positive samples, capillary electrophoresis, methylation specific PCR and Southern hybridization were carried out using venous blood samples. Prevalence of CGG repeat expansions was 2.2%. Further classification of the positive samples into FXS full mutation, pre-mutation and grey zone gave prevalence of 1.3%, 0.8% and 0.1% respectively. All positive cases were male. No females with FXS were detected in our study may have been due to the small sample size.
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Henry L, Biquand V, Craig AJFK, Hausberger M. Sexing Adult Pale-Winged Starlings Using Morphometric and Discriminant Function Analysis. PLoS One 2015; 10:e0135628. [PMID: 26367269 PMCID: PMC4569554 DOI: 10.1371/journal.pone.0135628] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/24/2015] [Indexed: 11/29/2022] Open
Abstract
Accurate sexing of birds is vital for behavioral studies but can be a real problem in the field, especially for monomorphic species. Our goal here was to characterize the morphology of male and female monomorphic pale-winged starlings (Onychognathus nabouroup), a South African sturnid whose plumage is sexually monomorphic. Morphological measurements of genetically sexed animals indicated that males were statistically larger than females for five measurements: Mass, tail length, tarsus length and wing length. By using a Discriminant Function Analysis based on the measurements taken by one ringer, we were able to predict correctly the sex of 81.10% of the birds of data collected in the field and 77.9% of museum skins independently of year of capture and ringer. The model developed here should be useful for further field studies of this species.
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Affiliation(s)
- Laurence Henry
- Université de Rennes 1, UMR CNRS 6552 Ethologie Animale et Humaine, Rennes, France
- * E-mail:
| | - Véronique Biquand
- Université de Rennes 1, UMR CNRS 6552 Ethologie Animale et Humaine, Rennes, France
| | | | - Martine Hausberger
- CNRS, Université de Rennes 1, UMR 6552 Ethologie Animale et Humaine, Rennes, France
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24
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Handel CM, Van Hemert C. Environmental contaminants and chromosomal damage associated with beak deformities in a resident North American passerine. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:314-327. [PMID: 25376148 DOI: 10.1002/etc.2799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 10/30/2014] [Accepted: 11/04/2014] [Indexed: 06/04/2023]
Abstract
A large cluster of beak abnormalities among black-capped chickadees (Poecile atricapillus) in Alaska raised concern about underlying environmental factors in this region. Metals and trace elements, organochlorine pesticides, polychlorinated biphenyls (PCBs), and polychlorinated dibenzo-dioxins and polychlorinated dibenzofurans (PCDD-Fs) were analyzed in adults, nestlings, and eggs of the affected population; local bird seed was also tested for organochlorine pesticides. The results offered no support for the hypothesis that selenium or any other inorganic element was responsible for beak deformities among chickadees, but some evidence that organochlorine compounds may be contributing factors. Adults with beak deformities had an elevated level of chromosomal damage, which was correlated with lipid level and concentrations of several organochlorine compounds. Multivariate analyses of pesticides and PCBs did not distinguish abnormal from normal adults, but subsequent univariate analysis demonstrated higher concentrations of heptachlor epoxide and PCB-123 in abnormal adults. Concentrations of all organochlorine compounds were low, and none is known to cause beak or keratin abnormalities. Patterns of PCB congener concentrations differed between nestlings with normal and abnormal parents. Eggs from clutches with low hatchability had higher concentrations of hexachlorobenzene and PCDD-Fs than those with high hatching success, and hexachlorobenzene was found in seeds. Additional testing for PCDD-Fs, polycyclic aromatic hydrocarbons, and other emerging contaminants, including brominated compounds, is needed to rule out environmental contaminants as a cause of beak deformities in chickadees in Alaska.
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Affiliation(s)
- Colleen M Handel
- Alaska Science Center, US Geological Survey, Anchorage, Alaska, USA
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25
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Isolation and characterization of microsatellite DNA markers in the Greater Roadrunner (Geococcyx californianus). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-012-9793-4] [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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26
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Morinha F, Travassos P, Seixas F, Santos N, Sargo R, Sousa L, Magalhães P, Cabral JA, Bastos E. High-resolution melting analysis for bird sexing: a successful approach to molecular sex identification using different biological samples. Mol Ecol Resour 2013; 13:473-83. [PMID: 23433263 DOI: 10.1111/1755-0998.12081] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 01/10/2013] [Accepted: 01/10/2013] [Indexed: 12/19/2022]
Abstract
High-resolution melting (HRM) analysis is a very attractive and flexible advanced post-PCR method with high sensitivity/specificity for simple, fast and cost-effective genotyping based on the detection of specific melting profiles of PCR products. Next generation real-time PCR systems, along with improved saturating DNA-binding dyes, enable the direct acquisition of HRM data after quantitative PCR. Melting behaviour is particularly influenced by the length, nucleotide sequence and GC content of the amplicons. This method is expanding rapidly in several research areas such as human genetics, reproductive biology, microbiology and ecology/conservation of wild populations. Here we have developed a successful HRM protocol for avian sex identification based on the amplification of sex-specific CHD1 fragments. The melting curve patterns allowed efficient sexual differentiation of 111 samples analysed (plucked feathers, muscle tissues, blood and oral cavity epithelial cells) of 14 bird species. In addition, we sequenced the amplified regions of the CHD1 gene and demonstrated the usefulness of this strategy for the genotype discrimination of various amplicons (CHD1Z and CHD1W), which have small size differences, ranging from 2 bp to 44 bp. The established methodology clearly revealed the advantages (e.g. closed-tube system, high sensitivity and rapidity) of a simple HRM assay for accurate sex differentiation of the species under study. The requirements, strengths and limitations of the method are addressed to provide a simple guide for its application in the field of molecular sexing of birds. The high sensitivity and resolution relative to previous real-time PCR methods makes HRM analysis an excellent approach for improving advanced molecular methods for bird sexing.
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Affiliation(s)
- Francisco Morinha
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes e Alto Douro (IBB/CGB-UTAD), Quinta de Prados, Vila Real, 5001-801, Portugal.
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27
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Newsome TM, Stephens D, Ballard GA, Dickman CR, Fleming PJS. Genetic profile of dingoes (Canis lupus dingo) and free-roaming domestic dogs (C. l. familiaris) in the Tanami Desert, Australia. WILDLIFE RESEARCH 2013. [DOI: 10.1071/wr12128] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context Many rare and endangered species are threatened by the effects of hybridisation with their domesticated and often numerically dominant relatives. However, factors that influence interactions between hybridising species are poorly understood, thus limiting our ability to develop ameliorative strategies. Aims Here, we identify family groups and investigate patterns of gene flow between dingoes (Canis lupus dingo) and domestic dogs (C. l. familiaris) in the Tanami Desert of central Australia. We aimed to determine whether human-provided resources facilitate hybridisation or alter typical patterns of dingo breeding and social behaviour. We also ask whether remote townships are arenas for dingo–dog hybridisation. Methods Tissue samples and morphological details were collected from dingo-like animals around two mine sites where humans provide abundant supplementary food and water. Using molecular DNA analyses, we assigned animals to population clusters, determined kinship and the numbers of family groups. Rates of hybridisation were assessed around the mines and in two nearby townships. Key results Of 142 samples from mine sites, ‘pure’ dingoes were identified genetically in 89% of cases. This predominance of dingoes was supported by our observations on coat colour and body morphology. Only 2 of 86 domestic dogs sampled at the two townships showed evidence of dingo ancestry. Around the mine sites, there were two distinct population clusters, including a large family group of 55 individuals around a refuse facility. Conclusions Where superabundant and consistent food, and reliable water, was available, dingo packs were much larger and co-existed with others, contrary to expectations derived from previous research. Dingo sociality and pack structures can therefore be altered where human-provided food and water are constantly available, and this could facilitate accelerated rates of hybridisation. Implications The development of appropriate domestic-waste management strategies should be a high priority in remote areas to ensure only normal rates of population increase by dingoes, and other canids more broadly. It will also potentially impede hybridisation rates if typical canid social and behavioural traits remain intact. Additionally, areas surrounding remote human settlements are likely arenas for accentuated dingo–domestic dog interactions and should be a target for future studies.
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28
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Roffler GH, Adams LG, Talbot SL, Sage GK, Dale BW. Range overlap and individual movements during breeding season influence genetic relationships of caribou herds in south-central Alaska. J Mammal 2012. [DOI: 10.1644/11-mamm-a-275.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Morinha F, Cabral J, Bastos E. Molecular sexing of birds: A comparative review of polymerase chain reaction (PCR)-based methods. Theriogenology 2012; 78:703-14. [DOI: 10.1016/j.theriogenology.2012.04.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/18/2012] [Accepted: 04/26/2012] [Indexed: 02/08/2023]
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30
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Sonsthagen SA, McClaren EL, Doyle FI, Titus K, Sage GK, Wilson RE, Gust JR, Talbot SL. Identification of metapopulation dynamics among Northern Goshawks of the Alexander Archipelago, Alaska, and Coastal British Columbia. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0352-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yannic G, Sermier R, Aebischer A, Gavrilo MV, Gilg O, Miljeteig C, Sabard B, Strøm H, Pouivé E, Broquet T. Description of microsatellite markers and genotyping performances using feathers and buccal swabs for the Ivory gull (Pagophila eburnea). Mol Ecol Resour 2011; 11:877-89. [PMID: 21518427 DOI: 10.1111/j.1755-0998.2011.03015.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report 22 new polymorphic microsatellites for the Ivory gull (Pagophila eburnea), and we describe how they can be efficiently co-amplified using multiplexed polymerase chain reactions. In addition, we report DNA concentration, amplification success, rates of genotyping errors and the number of genotyping repetitions required to obtain reliable data with three types of noninvasive or nondestructive samples: shed feathers collected in colonies, feathers plucked from living individuals and buccal swabs. In two populations from Greenland (n=21) and Russia (Severnaya Zemlya Archipelago, n=21), the number of alleles per locus varied between 2 and 17, and expected heterozygosity per population ranged from 0.18 to 0.92. Twenty of the markers conformed to Hardy-Weinberg and linkage equilibrium expectations. Most markers were easily amplified and highly reliable when analysed from buccal swabs and plucked feathers, showing that buccal swabbing is a very efficient approach allowing good quality DNA retrieval. Although DNA amplification success using single shed feathers was generally high, the genotypes obtained from this type of samples were prone to error and thus need to be amplified several times. The set of microsatellite markers described here together with multiplex amplification conditions and genotyping error rates will be useful for population genetic studies of the Ivory gull.
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Affiliation(s)
- Glenn Yannic
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.
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MARTÍN‐GÁLVEZ DAVID, PERALTA‐SÁNCHEZ JUANM, DAWSON DEBORAHA, MARTÍN‐PLATERO ANTONIOM, MARTÍNEZ‐BUENO MANUEL, BURKE TERRY, SOLER JUANJ. DNA sampling from eggshell swabbing is widely applicable in wild bird populations as demonstrated in 23 species. Mol Ecol Resour 2010; 11:481-93. [DOI: 10.1111/j.1755-0998.2010.02953.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- DAVID MARTÍN‐GÁLVEZ
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), E‐04120, Spain
- Grupo de Coevolución, Unidad Asociada al CSIC, Universidad de Granada, Granada, E‐18071, Spain
| | - JUAN M. PERALTA‐SÁNCHEZ
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), E‐04120, Spain
- Grupo de Coevolución, Unidad Asociada al CSIC, Universidad de Granada, Granada, E‐18071, Spain
| | - DEBORAH A. DAWSON
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - ANTONIO M. MARTÍN‐PLATERO
- Grupo de Coevolución, Unidad Asociada al CSIC, Universidad de Granada, Granada, E‐18071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, E‐18071, Spain
| | - MANUEL MARTÍNEZ‐BUENO
- Grupo de Coevolución, Unidad Asociada al CSIC, Universidad de Granada, Granada, E‐18071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, E‐18071, Spain
| | - TERRY BURKE
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - JUAN J. SOLER
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), E‐04120, Spain
- Grupo de Coevolución, Unidad Asociada al CSIC, Universidad de Granada, Granada, E‐18071, Spain
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BEJA‐PEREIRA ALBANO, OLIVEIRA RITA, ALVES PAULOC, SCHWARTZ MICHAELK, LUIKART GORDON. Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Resour 2009; 9:1279-301. [DOI: 10.1111/j.1755-0998.2009.02699.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- ALBANO BEJA‐PEREIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
| | - RITA OLIVEIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - PAULO C. ALVES
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - MICHAEL K. SCHWARTZ
- USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - GORDON LUIKART
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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Harding A, Kitaysky A, Hamer K, Hall M, Welcker J, Talbot S, Karnovsky N, Gabrielsen G, Grémillet D. Impacts of experimentally increased foraging effort on the family: offspring sex matters. Anim Behav 2009. [DOI: 10.1016/j.anbehav.2009.05.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Harding AM, Kitaysky AS, Hall ME, Welcker J, Karnovsky NJ, Talbot SL, Hamer KC, Grémillet D. Flexibility in the parental effort of an Arctic-breeding seabird. Funct Ecol 2009. [DOI: 10.1111/j.1365-2435.2008.01488.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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