Isolation and characterisation of 16 polymorphic microsatellite loci for bight redfish, Centroberyx gerrardi (Actinopterygii : Berycidae), and cross-amplification in two other Centroberyx species

2015 ◽  
Vol 63 (4) ◽  
pp. 275
Author(s):  
Andrea Bertram ◽  
P. Joana Dias ◽  
Sherralee Lukehurst ◽  
W. Jason Kennington ◽  
David Fairclough ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Spatial Scales ◽  
Weinberg Equilibrium ◽  
Cross Amplification ◽  
Stock Assessments ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Population Genetic Analyses ◽  
Upper Slope

Bight redfish, Centroberyx gerrardi, is a demersal teleost endemic to continental shelf and upper slope waters of southern Australia. Throughout most of its range, C. gerrardi is targeted by a number of separately managed commercial and recreational fisheries across several jurisdictions. However, it is currently unknown whether stock assessments and management for this shared resource are being conducted at appropriate spatial scales, thereby requiring knowledge of population structure and connectivity. To investigate population structure and connectivity, we developed 16 new polymorphic microsatellite markers using 454 shotgun sequencing. Two to 15 alleles per locus were detected. There was no evidence of linkage disequilibrium between pairs of loci and all loci except one were in Hardy–Weinberg equilibrium. Cross-amplification trials in the congeneric C. australis and C. lineatus revealed that 11 and 16 loci are potentially useful, respectively. However, deviations from Hardy–Weinberg equilibrium and linkage disequilibrium between pairs of loci were detected at several of the 16 markers for C. australis, and therefore the number of markers useful for population genetic analyses with C. lineatus is likely considerably lower than 11.

scholarly journals Development of 11 Polymorphic Microsatellite Loci from Primula amthystina Franchet. (Primulaceae)

HortScience ◽  
2010 ◽  
Vol 45 (1) ◽  
pp. 148-149
Author(s):  
Yuan Huang ◽  
Xue-qin Wang ◽  
Chun-yan Yang ◽  
Chun-lin Long
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Southwest China ◽  
Herbaceous Plant ◽  
Genetic Population ◽  
Weinberg Equilibrium ◽  
Perennial Herbaceous Plant ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite

Primula amethystina Franchet. is a beautiful perennial herbaceous plant locally endemic to the alpine area in southwest China. We isolated and characterized 11 polymorphic microsatellite primer pairs from this species. The number of alleles ranged from two to five. The observed and expected heterozygosities (HO and HE) were 0.25 to 0.875 and 0.223 to 0.691, respectively. Six loci were significantly deviated from Hardy-Weinberg equilibrium as a result of the heterozygote deficiency. These markers will have great potential to reveal the genetic population structure and genetic diversity of P. amethystina.

scholarly journals Robust, flexible, and scalable tests for Hardy–Weinberg equilibrium across diverse ancestries

Genetics ◽  
2021 ◽  
Author(s):  
Alan M Kwong ◽  
Thomas W Blackwell ◽  
Jonathon LeFaive ◽  
Mariza de Andrade ◽  
John Barnard ◽  
...  
Keyword(s):  
Population Structure ◽  
Statistical Power ◽  
Sequence Data ◽  
Population Heterogeneity ◽  
Alternative Methods ◽  
Data Sets ◽  
Real Sequence ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
The Impact

Abstract Traditional Hardy–Weinberg equilibrium (HWE) tests (the χ2 test and the exact test) have long been used as a metric for evaluating genotype quality, as technical artifacts leading to incorrect genotype calls often can be identified as deviations from HWE. However, in data sets composed of individuals from diverse ancestries, HWE can be violated even without genotyping error, complicating the use of HWE testing to assess genotype data quality. In this manuscript, we present the Robust Unified Test for HWE (RUTH) to test for HWE while accounting for population structure and genotype uncertainty, and to evaluate the impact of population heterogeneity and genotype uncertainty on the standard HWE tests and alternative methods using simulated and real sequence data sets. Our results demonstrate that ignoring population structure or genotype uncertainty in HWE tests can inflate false-positive rates by many orders of magnitude. Our evaluations demonstrate different tradeoffs between false positives and statistical power across the methods, with RUTH consistently among the best across all evaluations. RUTH is implemented as a practical and scalable software tool to rapidly perform HWE tests across millions of markers and hundreds of thousands of individuals while supporting standard VCF/BCF formats. RUTH is publicly available at https://www.github.com/statgen/ruth.

scholarly journals Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data

2021 ◽  
Author(s):  
William S Pearman ◽  
Lara Urban ◽  
Alana Alexander
Keyword(s):  
Population Structure ◽  
Population Genetic ◽  
Best Practice ◽  
Careful Consideration ◽  
Model Organisms ◽  
Reduced Representation ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
Population Genetic Inference ◽  
Filtering Approach

Reduced representation sequencing (RRS) is a widely used method to assay the diversity of genetic loci across the genome of an organism. The dominant class of RRS approaches assay loci associated with restriction sites within the genome (restriction site associated DNA sequencing, or RADseq). RADseq is frequently applied to non-model organisms since it enables population genetic studies without relying on well-characterized reference genomes. However, RADseq requires the use of many bioinformatic filters to ensure the quality of genotyping calls. These filters can have direct impacts on population genetic inference, and therefore require careful consideration. One widely used filtering approach is the removal of loci which do not conform to expectations of Hardy-Weinberg equilibrium (HWE). Despite being widely used, we show that this filtering approach is rarely described in sufficient detail to enable replication. Furthermore, through analyses of in silico and empirical datasets we show that some of the most widely used HWE filtering approaches dramatically impact inference of population structure. In particular, the removal of loci exhibiting departures from HWE after pooling across samples significantly reduces the degree of inferred population structure within a dataset (despite this approach being widely used). Based on these results, we provide recommendations for best practice regarding the implementation of HWE filtering for RADseq datasets.

scholarly journals Isolation and Characterization of 17 Polymorphic Microsatellite Loci for Musella lasiocarpa (Musaceae)

HortScience ◽  
2009 ◽  
Vol 44 (7) ◽  
pp. 2041-2042 ◽  
Author(s):  
Chun-yan Yang ◽  
Yuan Huang ◽  
Chunlin Long
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Southwest China ◽  
Microsatellite Primers ◽  
Genetic Population ◽  
Allele Number ◽  
Isolation And Characterization ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite

Seventeen microsatellite markers were isolated from 24 wild individuals collected from three populations of Musella lasiocarpa (Franch.) C. Y. Wu ex H. W. Li, a plant endemic to southwest China. The average allele number of these markers was 3.6 per locus, ranging from two to seven. The expected (He) and observed (Ho) heterozygosities varied from 0.4672 to 0.8183 and from 0.0417 to 1, respectively. Eleven loci were significantly deviated from Hardy-Weinberg equilibrium as a result of the heterozygote deficiency. These microsatellite primers will be used for studying genetic population structure and genetic diversity of M. lasiocarpa.

scholarly journals Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries

2020 ◽  
Author(s):  
Alan M. Kwong ◽  
Thomas W. Blackwell ◽  
Jonathon LeFaive ◽  
Mariza de Andrade ◽  
John Barnard ◽  
...  
Keyword(s):  
Population Structure ◽  
Statistical Power ◽  
Software Tool ◽  
Population Heterogeneity ◽  
Alternative Methods ◽  
Real Sequence ◽  
Exact Test ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
The Impact

ABSTRACTTraditional Hardy-Weinberg equilibrium (HWE) tests (the χ2 test and the exact test) have long been used as a metric for evaluating genotype quality, as technical artifacts leading to incorrect genotype calls often can be identified as deviations from HWE. However, in datasets comprised of individuals from diverse ancestries, HWE can be violated even without genotyping error, complicating the use of HWE testing to assess genotype data quality. In this manuscript, we present the Robust Unified Test for HWE (RUTH) to test for HWE while accounting for population structure and genotype uncertainty, and evaluate the impact of population heterogeneity and genotype uncertainty on the standard HWE tests and alternative methods using simulated and real sequence datasets. Our results demonstrate that ignoring population structure or genotype uncertainty in HWE tests can inflate false positive rates by many orders of magnitude. Our evaluations demonstrate different tradeoffs between false positives and statistical power across the methods, with RUTH consistently amongst the best across all evaluations. RUTH is implemented as a practical and scalable software tool to rapidly perform HWE tests across millions of markers and hundreds of thousands of individuals while supporting standard VCF/BCF formats. RUTH is publicly available at https://www.github.com/statgen/ruth.

scholarly journals Development and characterisation of polymorphic microsatellite markers in the pearl oyster Pteria penguin (Roding, 1798)

2016 ◽  
Vol 63 (4) ◽  
Author(s):  
Nan Zhang ◽  
Zhenhua Ma ◽  
Dianchang Zhang ◽  
Huayang Guo ◽  
Lin Lin ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Microsatellite Markers ◽  
Pearl Oyster ◽  
Significant Linkage Disequilibrium ◽  
Genetic Studies ◽  
Pteria Penguin ◽  
Conservation Genetic ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Significant Linkage

We developed and characterised 12 polymorphic microsatellite loci for Pteria penguin (Roding, 1798), an important pearl oyster species for pearl production in China. The number of observed alleles per locus ranged from 5 to 26 within 46 individuals. The observed and expected heterozygosities per locus ranged from 0.2 to 0.925 and 0.707 to 0.945, respectively. The polymorphism information content values per locus ranged from 0.656 to 0.929. Ten loci were in accordance with Hardy-Weinberg equilibrium and no significant linkage disequilibrium was detected between loci. These new microsatellite markers will be useful for population and conservation genetic studies of P. penguin.

Report of 14 novel microsatellites from the swimming crab Portunus trituberculatus (Miers, 1876) (Decapoda, Brachyura)

Crustaceana ◽  
2014 ◽  
Vol 87 (1) ◽  
pp. 35-40 ◽  
Author(s):  
Zhiguo Dong ◽  
Xugan Wu ◽  
Xiaoying Li ◽  
Qingqi Zhang ◽  
Jiale Li ◽  
...  
Keyword(s):  
Genome Mapping ◽  
Population Level ◽  
Portunus Trituberculatus ◽  
Swimming Crab ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Future Population ◽  
Biotinylated Probes ◽  
Population Genetic Analyses

The swimming crab, Portunus trituberculatus (Miers, 1876) is one of the most common edible marine crabs in East Asia. In this study, a multiple mixed probes hybridization method was used to isolate microsatellites to improve experimental efficiency and streamline the procedure. The mix of biotinylated probes included microsatellite GA, CA and CAT motifs. Fourteen novel polymorphic microsatellite loci were isolated and characterized from a wild population of P. trituberculatus. The number of alleles varied between three and nine, and the observed and expected heterozygosity at population level ranged from 0.542 to 1.000 and 0.616 to 0.851, respectively. Two loci, Ptr1 and Ptr3, significantly deviated from the Hardy-Weinberg equilibrium (). These informative microsatellite markers could be useful for future population genetic analyses and genome mapping studies in this species.

Characterisation of microsatellite markers for fig-pollinating wasps in the Pleistodontes imperialis species complex

2015 ◽  
Vol 63 (2) ◽  
pp. 122 ◽  
Author(s):  
Timothy L. Sutton ◽  
Caroline Reuter ◽  
Markus Riegler ◽  
James M. Cook
Keyword(s):  
Clustering Analysis ◽  
Species Complex ◽  
Natural Populations ◽  
Fig Wasps ◽  
Weinberg Equilibrium ◽  
Eastern Australia ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Port Jackson ◽  
Sydney Australia

We characterised a set of nine polymorphic microsatellite loci for Pleistodontes imperialis sp. 1, the pollinator wasp of Port Jackson fig (Ficus rubiginosa) in south-eastern Australia. Characterisation was performed on 30 female individuals collected from a population in Sydney, Australia. The average number of alleles per locus was 7.33, and eight loci were not in Hardy–Weinberg equilibrium. This was expected as fig wasps are known to be highly inbred. A test of genetic differentiation between two natural populations of P. imperialis sp. 1 (Sydney and Newcastle, Australia – some 120 km apart) yielded a very low FST value of 0.012, suggesting considerable gene flow. Bayesian clustering analysis using TESS 2.3.1, which does not assume Hardy–Weinberg equilibrium, however, indicated potential spatial substructuring between the Sydney and Newcastle populations, as well as within the Sydney population. The described loci were also characterised for two other species in the P. imperialis complex: P. imperialis sp. 2 (Townsville, Australia) and P. imperialis sp. 4 (Brisbane, Australia). Seven and six of the nine loci were polymorphic for P. imperialis sp. 2 and P. imperialis sp. 4, respectively.

Isolation and Characterisation of Novel Polymorphic Microsatellite Markers for the Wedge-Billed Woodcreeper Glyphorynchus Spirurus

2017 ◽  
Vol 10 (1) ◽  
pp. 24-26 ◽  
Author(s):  
Jasmin Unrein ◽  
Juliana Menger ◽  
Anne Weigert ◽  
Klaus Henle ◽  
Martin Schlegel
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Microsatellite Markers ◽  
Population Genetic ◽  
Ecological Studies ◽  
Central Amazonia ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Future Population

In order to study the population genetic structure of the Amazonian understorey bird Glyphorynchus spirurus, we have isolated eight polymorphic microsatellite loci using next-generation sequencing. All loci were screened using 40 samples from central Amazonia. The number of alleles varied from five to 22. The observed heterozygosities ranged from 0.475 to 0.875. No linkage disequilibrium was found among the loci. None of the loci showed significant deviation from Hardy–Weinberg equilibrium. These novel microsatellite markers will be a useful tool for future population genetics and ecological studies of the Wedge-billed Woodcreeper.

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