Microsatellite genotype datafile for Maugean skate (Zearaja maugeana)

UQ eSpace ◽  
2018 ◽  
Author(s):  
Kay Weltz ◽  
Jeremy Lyle ◽  
Jayson Semmens ◽  
Jennifer Ovenden
Keyword(s):  
Microsatellite Genotype

scholarly journals Linkage Disequilibrium in Domestic Sheep

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1113-1122
Author(s):  
A F McRae ◽  
J C McEwan ◽  
K G Dodds ◽  
T Wilson ◽  
A M Crawford ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Type I Error ◽  
Statistical Significance ◽  
Domestic Sheep ◽  
Type I ◽  
Single Nucleotide ◽  
Microsatellite Genotype ◽  
Marker Distance ◽  
The Relationship ◽  
Two Populations

Abstract The last decade has seen a dramatic increase in the number of livestock QTL mapping studies. The next challenge awaiting livestock geneticists is to determine the actual genes responsible for variation of economically important traits. With the advent of high density single nucleotide polymorphism (SNP) maps, it may be possible to fine map genes by exploiting linkage disequilibrium between genes of interest and adjacent markers. However, the extent of linkage disequilibrium (LD) is generally unknown for livestock populations. In this article microsatellite genotype data are used to assess the extent of LD in two populations of domestic sheep. High levels of LD were found to extend for tens of centimorgans and declined as a function of marker distance. However, LD was also frequently observed between unlinked markers. The prospects for LD mapping in livestock appear encouraging provided that type I error can be minimized. Properties of the multiallelic LD coefficient D′ were also explored. D′ was found to be significantly related to marker heterozygosity, although the relationship did not appear to unduly influence the overall conclusions. Of potentially greater concern was the observation that D′ may be skewed when rare alleles are present. It is recommended that the statistical significance of LD is used in conjunction with coefficients such as D′ to determine the true extent of LD.

Conditional Genotypic Probabilities for Microsatellite Loci

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1973-1980
Author(s):  
Jinko Graham ◽  
James Curran ◽  
B S Weir
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Dirichlet Distribution ◽  
Forensic Dna ◽  
Match Probability ◽  
Microsatellite Genotype ◽  
Allelic State ◽  
Forensic Assessments ◽  
Dna Profiles ◽  
Short Tandem

Abstract Modern forensic DNA profiles are constructed using microsatellites, short tandem repeats of 2–5 bases. In the absence of genetic data on a crime-specific subpopulation, one tool for evaluating profile evidence is the match probability. The match probability is the conditional probability that a random person would have the profile of interest given that the suspect has it and that these people are different members of the same subpopulation. One issue in evaluating the match probability is population differentiation, which can induce coancestry among subpopulation members. Forensic assessments that ignore coancestry typically overstate the strength of evidence against the suspect. Theory has been developed to account for coancestry; assumptions include a steady-state population and a mutation model in which the allelic state after a mutation event is independent of the prior state. Under these assumptions, the joint allelic probabilities within a subpopulation may be approximated by the moments of a Dirichlet distribution. We investigate the adequacy of this approximation for profiled loci that mutate according to a generalized stepwise model. Simulations suggest that the Dirichlet theory can still overstate the evidence against a suspect with a common microsatellite genotype. However, Dirichlet-based estimators were less biased than the product-rule estimator, which ignores coancestry.

scholarly journals Use of GRA6-Derived Synthetic Polymorphic Peptides in an Immunoenzymatic Assay To Serotype Toxoplasma gondii in Human Serum Samples Collected from Three Continents

2008 ◽  
Vol 15 (9) ◽  
pp. 1380-1386 ◽  
Author(s):  
Susana Sousa ◽  
Daniel Ajzenberg ◽  
Manuel Vilanova ◽  
José Costa ◽  
Marie-Laure Dardé
Keyword(s):  
Toxoplasma Gondii ◽  
Latin American ◽  
Enzyme Linked Immunosorbent Assay ◽  
Clear Correlation ◽  
Type I ◽  
Serum Samples ◽  
Typing Method ◽  
Microsatellite Genotype ◽  
Human Infections ◽  
Immunoenzymatic Assay

ABSTRACT Serotyping is a simple typing method that consists of an immunoenzymatic assay (enzyme-linked immunosorbent assay [ELISA]) using synthetic polymorphic peptides derived from Toxoplasma gondii antigens. We developed a new ELISA based on GRA6 C-terminal polymorphic peptides. Serum samples from 41 human infections due to 23 archetypal (type I, II, or III) and 18 nonarchetypal strains were selected in order to validate this approach. For 20 out of the 23 archetypal infections, there was a clear correlation between microsatellite genotype and GRA6 serotyping. All infections due to nonarchetypal strains were misclassified as archetypal strain infections. The GRA6 C-terminal peptides from these strains were analyzed to explain this misclassification. A second group of 455 patients with acute and chronic toxoplasmosis due to unknown genotypes from different European, African, and Latin American countries were included in this study, and the strain type predicted by this method. The results suggest that serotyping is a promising method for typing strains, although limitations exist for African and South American strains as a consequence of higher peptide polymorphism. Other peptides from different markers must be studied in order to discriminate archetypal from nonarchetypal strains.

scholarly journals Genetic Diversity and In Vitro Antifungal Susceptibility of 200 Clinical and Environmental Aspergillus flavus Isolates

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Mojtaba Taghizadeh-Armaki ◽  
Mohammad Taghi Hedayati ◽  
Saham Ansari ◽  
Saeed Mahdavi Omran ◽  
Sasan Saber ◽  
...  
Keyword(s):  
Amphotericin B ◽  
Aspergillus Flavus ◽  
Susceptibility Testing ◽  
Antifungal Susceptibility ◽  
Content Type ◽  
Microdilution Method ◽  
Microsatellite Genotype ◽  
Broth Microdilution Method ◽  
In Vitro Antifungal Susceptibility

ABSTRACT Aspergillus flavus has been frequently reported as the leading cause of invasive aspergillosis in certain tropical and subtropical countries. Two hundred A. flavus strains originating from clinical and environmental sources and collected between 2008 and 2015 were phylogenetically identified at the species level by analyzing partial β-tubulin and calmodulin genes. In vitro antifungal susceptibility testing was performed against antifungals using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) broth microdilution method. In addition, genotyping was performed using a short-tandem-repeat (STR) assay of a panel of six microsatellite markers (A. flavus 2A, 2B, 2C, 3A, 3B, and 3C), in order to determine the genetic variation and the potential relationship between clinical and environmental isolates. The geometric means of the minimum inhibitory concentrations/minimum effective concentrations (MICs/MECs) of the antifungals across all isolates were (in increasing order): posaconazole, 0.13 mg/liter; anidulafungin, 0.16 mg/liter; itraconazole, 0.29 mg/liter; caspofungin, 0.42 mg/liter; voriconazole, 0.64 mg/liter; isavuconazole, 1.10 mg/liter; amphotericin B, 3.35 mg/liter; and flucytosine, 62.97 mg/liter. All of the clinical isolates were genetically different. However, an identical microsatellite genotype was found between a clinical isolate and two environmental strains. In conclusion, posaconazole and anidulafungin showed the greatest in vitro activity among systemic azoles and echinocandins, respectively. However, the majority of the A. flavus isolates showed reduced susceptibility to amphotericin B. Antifungal susceptibility of A. flavus was not linked with the clinical or environmental source of isolation. Microsatellite genotyping may suggest an association between clinical and environmental strains, although this requires further investigation.

scholarly journals Trailing or paradoxical growth of Aspergillus flavus exposed to caspofungin is independent of genotype

2014 ◽  
Vol 63 (12) ◽  
pp. 1584-1589 ◽  
Author(s):  
Inès Hadrich ◽  
Sourour Neji ◽  
Fattouma Makni ◽  
Ali Ayadi ◽  
Moez Elloumi ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Invasive Aspergillosis ◽  
Aspergillus Flavus ◽  
Susceptibility Testing ◽  
Clinical Isolates ◽  
Limited Data ◽  
Microsatellite Genotype ◽  
Paradoxical Growth

There are limited data on in vitro susceptibility testing of echinocandins against Aspergillus species. The objective of this study was to describe the phenotypes of Aspergillus flavus observed on exposure to caspofungin in vitro and to test whether these phenotypes were associated with A. flavus genotypes. The caspofungin MICs of 37 A. flavus clinical isolates collected from 14 patients with invasive aspergillosis were determined using Etest assays. Caspofungin MICs ranged from 0.012 to 0.064 mg l−1; the modal MIC was 0.023 mg l−1 and the MIC50 and MIC90 were 0.032 and 0.064 mg l−1, respectively. A clear end point was noted in 24 (65 %) isolates, whereas seven (19 %) displayed a trailing effect and six (16 %) showed paradoxical growth when exposed to caspofungin. In these A. flavus isolates, the absence of a significant population structure or genetic differentiation indicated that trailing or paradoxical growth phenotypes were independent of microsatellite genotype.

scholarly journals Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables

2015 ◽  
Author(s):  
Lindsay V. Clark ◽  
Andrea Drauch Schreier
Keyword(s):  
Random Mating ◽  
Simulated Data ◽  
R Package ◽  
White Sturgeon ◽  
Mathematical Property ◽  
Mendelian Segregation ◽  
Infinite Population ◽  
Marker Data ◽  
Microsatellite Genotype ◽  
Single Marker

AbstractA major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite dataset from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.5.

scholarly journals Molecular genetic polymorphism of American mink populations (Neovison vison) in model fur farms and on the adjacent territories in Belarus

2020 ◽  
Vol 64 (6) ◽  
pp. 685-693
Author(s):  
A. A. Valnisty ◽  
K. V. Homel ◽  
E. E. Kheidorova ◽  
A. V. Shpak ◽  
M. E. Nikiforov
Keyword(s):  
Invasive Species ◽  
Genetic Polymorphism ◽  
American Mink ◽  
Molecular Genetic ◽  
Microsatellite Analysis ◽  
Neovison Vison ◽  
Genotype Data ◽  
Wild Populations ◽  
Microsatellite Genotype ◽  
Feral Populations

American mink (Neovison vison) is both a problematic invader and an economically valuable fur breed species in Belarus. The increasing scale of mink breeding for fur and the growing impact of this invasive species on the local ecosystems requires sound, novel strategies for managing both farm and wild populations. Containment of wild American mink populations under the effects of possible migration from the fur farms could be especially problematic. With that issue in mind, we have used microsatellite analysis todetermine the genetic polymorphism in two color breeds of farm-bred American mink in the populations of several Belorussian model fur farms, as well as the same characteristics for the feral populations on the territories adjacent to said fur farms. We confirm the presence of effective influx of mink into the wild from fur farms, determined through the means of analyzing microsatellite genotype data of feral and farm populations.

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