The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Yanming Zhang - One of the best experts on this subject based on the ideXlab platform.
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effectiveness of 10 polymorphic microsatellite markers for Parentage and pedigree analysis in plateau pika ochotona curzoniae
BMC Genetics, 2010Co-Authors: Jianing Geng, Yanming ZhangAbstract:The plateau pika (Ochotona curzoniae) is an underground-dwelling mammal, native to the Tibetan plateau of China. A set of 10 polymorphic microsatellite loci has been developed earlier. Its reliability for Parentage assignment has been tested in a plateau pika population. Two family groups with a known pedigree were used to validate the power of this set of markers. The error in Parentage assignment using a combination of these 10 loci was very low as indicated by their power of discrimination (0.803 - 0.932), power of exclusion (0.351 - 0.887), and an effectiveness of the combined probability of exclusion in Parentage assignment of 99.999%. All the offspring of a family could be assigned to their biological mother; and their father or relatives could also be identified. This set of markers therefore provides a powerful and efficient tool for Parentage assignment and other population analyses in the plateau pika.
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isolation and characterization of 13 microsatellite loci in the plateau pika ochotona curzoniae
Conservation Genetics, 2009Co-Authors: Jianing Geng, Jin Yang, Yanming ZhangAbstract:High quality jumping microsatellite libraries of the plateau pika (Ochotona curzoniae) were constructed; 231 out of the 288 clones contained microsatellite repeat motif and 120 pairs of primers were designed accordingly. Polymorphism was assessed for 48 individuals. Only 13 microsatellite loci were polymorphic with high polymorphism information content (PIC) ranging from 0.598 to 0.871, a condition probably resulting from individuals used for assessment being very closely related. This degree of polymorphism, however, is sufficient to conduct Parentage analysis. Expected and observed heterozygosities ranged from 0.219 to 0.935 and 0.659 to 0.890, respectively. One locus was in linkage disequilibrium. This information provides efficient tools to allow future Parentage studies.
Eric C Anderson - One of the best experts on this subject based on the ideXlab platform.
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a validation of Parentage based tagging using hatchery steelhead in the snake river basin
Canadian Journal of Fisheries and Aquatic Sciences, 2013Co-Authors: Craig A Steele, Eric C Anderson, Michael W Ackerman, Maureen A Hess, Nathan R Campbell, Shawn R Narum, Matthew R CampbellAbstract:Parentage-based tagging (PBT) is a promising alternative to traditional coded-wire tag (CWT) methodologies for monitoring and evaluating hatchery stocks. This approach involves the genotyping of hatchery broodstock and uses Parentage assignments to identify the origin and brood year of their progeny. In this study we empirically confirmed that fewer than 100 single nucleotide polymorphisms (SNPs) were needed to accurately conduct PBT, we demonstrated that our selected panel of SNPs was comparable in accuracy to a panel of microsatellites, and we verified that stock assignments made with this panel matched those made using CWTs. We also demonstrated that when sampling of spawners was incomplete, an estimated PBT rate for the offspring could also be predicted with fewer than 100 SNPs. This study in the Snake River basin is one of the first large-scale implementations of PBT in salmonids and lays the foundation for adopting this technology more broadly in the region, thereby allowing the unprecedented ability to mark millions of smolts and an opportunity to address a variety of Parentage-based research and management questions. Resume : Le marquage base sur l'ascendance (PBT) est une solution de rechange interessante aux methodes traditionnelles reposant sur les micromarques magnetisees codees (CWT) pour la surveillance et l'evaluation des stocks issus d'ecloseries. Cette approche comprend le genotypage des geniteurs d'ecloserie et le recours al'assignation parentale pour determiner l'origine et l'annee d'eclosion de la progeniture. Dans la presente etude, nous avons confirme de maniere empirique que moins de 100 polymorphismes mononucleotidiques (SNP) etaient necessaires pour assurer l'exactitude du PBT, demontre que le lot de SNP que nous avons selectionne donnait une exactitude semblable acelle obtenue avec un lot de microsatellites et verifie que les assignations parentales obtenues avec ce lot correspondaient acelles obtenues par la methode des CWT. Nous avons egalement demontre que, dans les cas d'echantillonnage incomplet des geniteurs, un taux de PBT estime pour la progeniture pouvait etre predit avec moins de 100 SNP. Cette etude dans le bassin de la riviere Snake est une des premieres applications agrande echelle du PBT ades salmonides et jette les bases de l'adoption elargie de cette technique dans la region, permettant ainsi, pour la premiere fois, le marquage de millions de saumoneaux et offrant la possibilite d'aborder de multiples questions touchant ala recherche axee sur l'ascendance et ala gestion. (Traduit par la Redaction)
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a validation of Parentage based tagging using hatchery steelhead in the snake river basin
Canadian Journal of Fisheries and Aquatic Sciences, 2013Co-Authors: Craig A Steele, Eric C Anderson, Michael W Ackerman, Maureen A Hess, Nathan R Campbell, Shawn R Narum, Matthew R CampbellAbstract:Parentage-based tagging (PBT) is a promising alternative to traditional coded-wire tag (CWT) methodologies for monitoring and evaluating hatchery stocks. This approach involves the genotyping of ha...
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the power of single nucleotide polymorphisms for large scale Parentage inference
Genetics, 2006Co-Authors: Eric C Anderson, John Carlos GarzaAbstract:Likelihood-based Parentage inference depends on the distribution of a likelihood-ratio statistic, which, in most cases of interest, cannot be exactly determined, but only approximated by Monte Carlo simulation. We provide importance-sampling algorithms for efficiently approximating very small tail probabilities in the distribution of the likelihood-ratio statistic. These importance-sampling methods allow the estimation of small false-positive rates and hence permit likelihood-based inference of Parentage in large studies involving a great number of potential parents and many potential offspring. We investigate the performance of these importance-sampling algorithms in the context of Parentage inference using single-nucleotide polymorphism (SNP) data and find that they may accelerate the computation of tail probabilities >1 millionfold. We subsequently use the importance-sampling algorithms to calculate the power available with SNPs for large-scale Parentage studies, paying particular attention to the effect of genotyping errors and the occurrence of related individuals among the members of the putative mother–father–offspring trios. These simulations show that 60–100 SNPs may allow accurate pedigree reconstruction, even in situations involving thousands of potential mothers, fathers, and offspring. In addition, we compare the power of exclusion-based Parentage inference to that of the likelihood-based method. Likelihood-based inference is much more powerful under many conditions; exclusion-based inference would require 40% more SNP loci to achieve the same accuracy as the likelihood-based approach in one common scenario. Our results demonstrate that SNPs are a powerful tool for Parentage inference in large managed and/or natural populations.
Matthew R Campbell - One of the best experts on this subject based on the ideXlab platform.
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a validation of Parentage based tagging using hatchery steelhead in the snake river basin
Canadian Journal of Fisheries and Aquatic Sciences, 2013Co-Authors: Craig A Steele, Eric C Anderson, Michael W Ackerman, Maureen A Hess, Nathan R Campbell, Shawn R Narum, Matthew R CampbellAbstract:Parentage-based tagging (PBT) is a promising alternative to traditional coded-wire tag (CWT) methodologies for monitoring and evaluating hatchery stocks. This approach involves the genotyping of hatchery broodstock and uses Parentage assignments to identify the origin and brood year of their progeny. In this study we empirically confirmed that fewer than 100 single nucleotide polymorphisms (SNPs) were needed to accurately conduct PBT, we demonstrated that our selected panel of SNPs was comparable in accuracy to a panel of microsatellites, and we verified that stock assignments made with this panel matched those made using CWTs. We also demonstrated that when sampling of spawners was incomplete, an estimated PBT rate for the offspring could also be predicted with fewer than 100 SNPs. This study in the Snake River basin is one of the first large-scale implementations of PBT in salmonids and lays the foundation for adopting this technology more broadly in the region, thereby allowing the unprecedented ability to mark millions of smolts and an opportunity to address a variety of Parentage-based research and management questions. Resume : Le marquage base sur l'ascendance (PBT) est une solution de rechange interessante aux methodes traditionnelles reposant sur les micromarques magnetisees codees (CWT) pour la surveillance et l'evaluation des stocks issus d'ecloseries. Cette approche comprend le genotypage des geniteurs d'ecloserie et le recours al'assignation parentale pour determiner l'origine et l'annee d'eclosion de la progeniture. Dans la presente etude, nous avons confirme de maniere empirique que moins de 100 polymorphismes mononucleotidiques (SNP) etaient necessaires pour assurer l'exactitude du PBT, demontre que le lot de SNP que nous avons selectionne donnait une exactitude semblable acelle obtenue avec un lot de microsatellites et verifie que les assignations parentales obtenues avec ce lot correspondaient acelles obtenues par la methode des CWT. Nous avons egalement demontre que, dans les cas d'echantillonnage incomplet des geniteurs, un taux de PBT estime pour la progeniture pouvait etre predit avec moins de 100 SNP. Cette etude dans le bassin de la riviere Snake est une des premieres applications agrande echelle du PBT ades salmonides et jette les bases de l'adoption elargie de cette technique dans la region, permettant ainsi, pour la premiere fois, le marquage de millions de saumoneaux et offrant la possibilite d'aborder de multiples questions touchant ala recherche axee sur l'ascendance et ala gestion. (Traduit par la Redaction)
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a validation of Parentage based tagging using hatchery steelhead in the snake river basin
Canadian Journal of Fisheries and Aquatic Sciences, 2013Co-Authors: Craig A Steele, Eric C Anderson, Michael W Ackerman, Maureen A Hess, Nathan R Campbell, Shawn R Narum, Matthew R CampbellAbstract:Parentage-based tagging (PBT) is a promising alternative to traditional coded-wire tag (CWT) methodologies for monitoring and evaluating hatchery stocks. This approach involves the genotyping of ha...
Jianing Geng - One of the best experts on this subject based on the ideXlab platform.
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effectiveness of 10 polymorphic microsatellite markers for Parentage and pedigree analysis in plateau pika ochotona curzoniae
BMC Genetics, 2010Co-Authors: Jianing Geng, Yanming ZhangAbstract:The plateau pika (Ochotona curzoniae) is an underground-dwelling mammal, native to the Tibetan plateau of China. A set of 10 polymorphic microsatellite loci has been developed earlier. Its reliability for Parentage assignment has been tested in a plateau pika population. Two family groups with a known pedigree were used to validate the power of this set of markers. The error in Parentage assignment using a combination of these 10 loci was very low as indicated by their power of discrimination (0.803 - 0.932), power of exclusion (0.351 - 0.887), and an effectiveness of the combined probability of exclusion in Parentage assignment of 99.999%. All the offspring of a family could be assigned to their biological mother; and their father or relatives could also be identified. This set of markers therefore provides a powerful and efficient tool for Parentage assignment and other population analyses in the plateau pika.
-
isolation and characterization of 13 microsatellite loci in the plateau pika ochotona curzoniae
Conservation Genetics, 2009Co-Authors: Jianing Geng, Jin Yang, Yanming ZhangAbstract:High quality jumping microsatellite libraries of the plateau pika (Ochotona curzoniae) were constructed; 231 out of the 288 clones contained microsatellite repeat motif and 120 pairs of primers were designed accordingly. Polymorphism was assessed for 48 individuals. Only 13 microsatellite loci were polymorphic with high polymorphism information content (PIC) ranging from 0.598 to 0.871, a condition probably resulting from individuals used for assessment being very closely related. This degree of polymorphism, however, is sufficient to conduct Parentage analysis. Expected and observed heterozygosities ranged from 0.219 to 0.935 and 0.659 to 0.890, respectively. One locus was in linkage disequilibrium. This information provides efficient tools to allow future Parentage studies.
Adam Jones - One of the best experts on this subject based on the ideXlab platform.
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the future of Parentage analysis from microsatellites to snps and beyond
Molecular Ecology, 2019Co-Authors: Sarah P Flanagan, Adam JonesAbstract:Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of Parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next-generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of Parentage analysis and see how it stands to be affected by the emergence of next-generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next-generation sequencing marker, remain underutilized in Parentage analysis but are gaining momentum, with 58 SNP-based Parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a Parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100-500 SNPs are sufficient to resolve Parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next-generation Parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next-generation sequencing data for Parentage analysis and conclude that the future is bright for this important realm of molecular ecology.
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a practical guide to methods of Parentage analysis
Molecular Ecology Resources, 2010Co-Authors: Adam Jones, Clayton M Small, Kimberly A Paczolt, Nicholas L RattermanAbstract:The use of molecular techniques for Parentage analysis has been a booming science for over a decade. The most important technological breakthrough was the introduction of microsatellite markers to molecular ecology, an advance that was accompanied by a proliferation and refinement of statistical techniques for the analysis of Parentage data. Over the last several years, we have seen steady progress in a number of areas related to Parentage analysis, and the prospects for successful studies continue to improve. Here, we provide an updated guide for scientists interested in embarking on Parentage analysis in natural or artificial populations of organisms, with a particular focus on computer software packages that implement various methods of analysis. Our survey of the literature shows that there are a few established methods that perform extremely well in the analysis of most types of Parentage studies. However, particular experimental designs or study systems can benefit from some of the less well-known computer packages available. Overall, we find that Parentage analysis is feasible and satisfying in most systems, and we try to provide a simple roadmap to help other scientists navigate the confusing topography of statistical techniques.
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methods of Parentage analysis in natural populations
Molecular Ecology, 2003Co-Authors: Adam Jones, William R ArdrenAbstract:The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of Parentage in natural and experimental populations. Consequently, the potential for meaningful studies of paternity and maternity is at an all-time high. However, the details and implementation of the multifarious techniques often differ in subtle ways that can influence the results of Parentage analyses. Now is a good time to reflect on the available techniques and to consider their strengths and weaknesses. Here, we review the leading techniques in Parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages. Our survey leads to some important insights with respect to the utility of the different approaches. This review should serve as a useful guide to anyone who wishes to embark on the study of Parentage.
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microsatellite evidence for monogamy and sex biased recombination in the western australian seahorse hippocampus angustus
Molecular Ecology, 1998Co-Authors: Adam Jones, Charlotta Kvarnemo, Glenn I Moore, Leigh W Simmons, John C AviseAbstract:Four polymorphic microsatellite loci were used to assess biological Parentage of 453 offspring from 15 pregnant males from a natural population of the Western Australian seahorse Hippocampus angustus. Microsatellite genotypes in the progeny arrays were consistent with a monogamous mating system in which both females and males had a single mate during a male brooding period. Multilocus genotypes implicated four females in the adult population sample as contributors of eggs to the broods of collected males, but there was no evidence for multiple mating by females. Based on genotypic data from the progeny arrays, two loci were linked tightly and the recombination rate appeared to be ∪ 10-fold higher in females than in males. The utility of linked loci for Parentage analyses is discussed.
