Description of microsatellite markers and genotyping performances using feathers and buccal swabs for the Ivory gull (<i>Pagophila eburnea</i>)

Yannic, Glenn; Sermier, Roberto; Aebischer, Adrian; Gavrilo, Maria; Gilg, Olivier; Miljeteig, Cecilie; Sabard, Brigitte; Strøm, Hallvard; Pouivé, Emmanuelle; Broquet, Thomas

doi:10.1111/j.1755-0998.2011.03015.x

Cited by 20 publications

(17 citation statements)

References 49 publications

(90 reference statements)

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“…In comparison with a previous non-invasive study using ivory gull (Pagophila eburnea) feather samples (Yannic et al 2011), our newly developed marker set showed a higher amplification success rate (96.2% on average vs 93% in Yannic et al 2011; P < 0.05, Wilcoxon rank sum test) and similar ADO (6.43 vs 7.60; P = 0.32, Wilcoxon rank sum test) for molted feathers. For the plucked feathers, our marker set showed significantly lower ADO (0.28 vs 0.95; P < 0.01, Wilcoxon rank sum test) and a comparable amplification success rate (98.4% vs 99.57%).…”

Section: Discussionmentioning

confidence: 51%

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Hou

Lin

et al. 2018

Integrative Zoology

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Accurate individual identification is required to estimate survival rates in avian populations. For endangered species, non-invasive methods of obtaining individual identification, such as using molted feathers as a source of DNA for microsatellite markers, are preferred because of less disturbance, easy sample preparation and high efficiency. With the availability of many avian genomes, a few pipelines isolating genome-wide microsatellites have been published, but it is still a challenge to isolate microsatellites from the reference genome efficiently. Here, we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome. We have identified over 95 000 microsatellite loci and established a system comprising 10 highly polymorphic markers (PIC value: 0.49-0.93, mean: 0.79) for an endangered species, saker falcon (Falco cherrug). These markers (except 1) were successfully amplified in 126 molted feathers, exhibiting high amplification success rates (83.9-99.7%), high quality index (0.90-0.97) and low allelic dropout rates (1-9.5%). To further assess the efficiency of this marker system in a population study, we identified individual sakers using these molted feathers (adult) and 146 plucked feathers (offspring). The use of parent and offspring samples enabled us to infer the genotype of missing samples (N = 28), and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers. Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.

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Section: Discussionmentioning

confidence: 51%

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Hou

Lin

et al. 2018

Integrative Zoology

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“…Buccal swabs are now regularly used for population genetics in a number of species: amphibians (Pidancier et al 2003;Broquet et al 2007a;Gallardo et al 2012), fish (Reid et al 2012) and mammals (Corthals et al 2015). Buccal swabs have lately been used in bird studies (e.g., Bush et al 2005;Handel et al 2006;Brubaker et al 2011;Yannic et al 2011), and a few studies have demonstrated the reliability of this sampling method for bird sex identification (Arima and Ohnishi 2006;Handel et al 2006;Wellbrock et al 2012;Dawson et al 2015). Finally, a strictly noninvasive approach would be to sex birds using DNA extracted from shed feathers.…”

Section: Introductionmentioning

confidence: 99%

“…Finally, a strictly noninvasive approach would be to sex birds using DNA extracted from shed feathers. Shed feathers yield DNA that is both less concentrated and more degraded (e.g., Yannic et al 2011), and its applicability for sexing has yet to be assessed (but see Hogan et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Genetic and morphological sex identification methods reveal a male-biased sex ratio in the Ivory Gull Pagophila eburnea

et al. 2016

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International audienceSex identification of birds is relevant to studies of evolutionary biology and ecology and is often a central issue for the management and conservation of populations. The Ivory Gull Pagophila eburnea (Phipps, 1774) is a rare high-Arctic species whose main habitat is sea ice throughout the year. This species is currently listed Near Threatened by the IUCN, because populations have drastically declined in part of the species distribution in the recent past. Here we tested molecular sexing methods with different types of samples. Molecular sexing appeared to be very efficient with DNA extracted from muscle, blood, and buccal swabs, both for adults and young chicks. We also performed morphological analyses to characterize sexual size dimorphism in Ivory Gulls sampled in three distinct regions: Greenland, Svalbard, and Russia. Males were larger than females for all morphometric measurements, with little overlap between sexes. Discriminant analysis based on six morphometric variables correctly classified ~95 % of the individuals, even when using two variables only, i.e., gonys height and skull length. Therefore, both molecular and biometric methods are useful for sexing Ivory Gulls. Interestingly, our results indicate a male-biased sex ratio across all Ivory Gull populations studied, including two samples of offspring (67.8 % males)

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“…; Yannic et al . ) and amphibians (Prunier et al . ), swabbing for DNA proved to be an extremely useful technique in worm pipefish.…”

Section: Discussionmentioning

confidence: 99%

Validating the use of colouration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers

Monteiro

Silva

Cunha³

et al. 2013

Molecular Ecology Resources

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In studies of behaviour, ecology and evolution, identification of individual organisms can be an invaluable tool, capable of unravelling otherwise cryptic information regarding group structure, movement patterns, population size and mating strategies. The use of natural markings is arguably the least invasive method for identification. However, to be truly useful natural markings must be sufficiently variable to allow for unique identification, while being stable enough to permit long-term studies. Non-invasive marking techniques are especially important in fishes of the Family Syngnathidae (pipefishes, seahorses and seadragons), as many of these taxa are of conservation concern or used extensively in studies of sexual selection. Here, we assessed the reliability of natural markings as a character for individual identification in a wild population of Nerophis lumbriciformis by comparing results from natural markings to individual genetic assignments based on eight novel microsatellite loci. We also established a minimally invasive method based on epithelial cell swabbing to sample DNA. All pipefish used in the validation of natural markings, independently of sex or time between recaptures, were individually recognized through facial colouration patterns. Their identities were verified by the observation of the same multilocus genotype at every sampling event for each individual that was identified on the basis of natural markings. Successful recaptures of previously swabbed pipefish indicated that this process probably did not induce an elevated rate of mortality. Also, the recapture of newly pregnant males showed that swabbing did not affect reproductive behaviour.

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Description of microsatellite markers and genotyping performances using feathers and buccal swabs for the Ivory gull (Pagophila eburnea)

Cited by 20 publications

References 49 publications

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Genetic and morphological sex identification methods reveal a male-biased sex ratio in the Ivory Gull Pagophila eburnea

Validating the use of colouration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers

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