Genetic variation within and among infrapopulations of the marine digenetic trematode Lecithochirium fusiforme

Parasitology ◽  
2003 ◽  
Vol 126 (5) ◽  
pp. 465-472 ◽  
Author(s):  
R. VILAS ◽  
E. PANIAGUA ◽  
M. L. SANMARTÍN
Keyword(s):  
Genetic Variation ◽  
Digenetic Trematode ◽  
Significant Linkage Disequilibrium ◽  
Polymorphic Loci ◽  
Wahlund Effect ◽  
Hardy Weinberg Equilibrium ◽  
Significant Deficit ◽  
Paratenic Hosts ◽  
Significant Linkage ◽  
Conger Conger

Allozyme markers were used to study genetic variation in Lecithochirium fusiforme within a natural population of Conger conger. Six of 16 enzyme-coding loci studied were found to be polymorphic. These loci were surveyed in 12 infrapopulations of adult flukes. High levels of genetic variation were detected (P=0·375); Ho=0·048; He=0·085). However, the population did not conform to Hardy-Weinberg expectations, as it showed a significant deficit of heterozygotes. L. fusiforme also exhibited low differentiation between infrapopulations (FST=0·064). Despite significant linkage disequilibrium at Pgm-1 and Pgm-2 (P<0·05), mating system does not appear to be the principal reason for the deficit of heterozygotes detected, because some polymorphic loci were in Hardy-Weinberg equilibrium. Association between FIS and FST statistics suggests the existence of the Wahlund effect. However, all infrapopulations showed a strong deficit of heterozygotes for most polymorphic loci (FIS=0·409). Detection of significant genetic differentiation among temporal samples and the existence of paratenic hosts in the life-cycle suggests the Wahlund effect, caused by the mixture of genetically distinct temporal samples in the infrapopulations. Occasional temporal gene flow also might explain the high estimated genetic polymorphism.

Characterization of 17 novel microsatellite loci for the brown spiny lobster Panulirus echinatus Smith, 1869 using MiSeq

Crustaceana ◽  
2018 ◽  
Vol 91 (4) ◽  
pp. 413-424 ◽  
Author(s):  
Juliana Gaeta ◽  
Iván Acevedo ◽  
Annie Machordom
Keyword(s):  
High Throughput Sequencing ◽  
Spiny Lobster ◽  
Null Alleles ◽  
Significant Linkage Disequilibrium ◽  
Sequencing Technology ◽  
Polymorphic Microsatellites ◽  
Hardy Weinberg Equilibrium ◽  
Nucleotide Repeats ◽  
Significant Linkage

Using high-throughput sequencing technology 17 polymorphic microsatellites with perfect tetra-nucleotide repeats were identified for the brown spiny lobsterPanulirus echinatusSmith, 1869. Two to ten alleles were detected per locus across 30 samples analysed from the Canary Archipelago. Observed and expected heterozygosities per locus ranged between 0.100 and 0.867 and 0.095 and 0.799, respectively. No significant linkage disequilibrium was found between pairs of loci, and only one locus (Pe-L43) deviated from Hardy-Weinberg equilibrium, likely due to the presence of null alleles. Despite its economic importance and the threat of overfishing, population genetics studies of this species are lacking. Therefore, these 17 novel microsatellites markers will be a useful genetic resource for future conservation studies ofP. echinatus.

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.

Microsatellite markers for Cattleya walkeriana Gardner, an endangered tropical orchid species

2016 ◽  
Vol 15 (1) ◽  
pp. 93-96 ◽  
Author(s):  
Evandro Vagner Tambarussi ◽  
Lou C. Menezes ◽  
Bruna Ibañes ◽  
Lia Maris Orth Ritter Antiqueira ◽  
Gabriel Dequigiovanni ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Microsatellite Markers ◽  
Significant Linkage Disequilibrium ◽  
Orchid Species ◽  
Polymorphic Loci ◽  
Tropical Orchid ◽  
First Time ◽  
Significant Linkage ◽  
Different Levels

Cattleya walkeriana, one of the most improved Brazilian Cattleyas, is a popular tropical orchid endemic from Brazil and currently endangered. In the present study, for the first time microsatellite markers were developed for C. walkeriana and their transferability was tested for the species C. loddigesii and C. nobilior. The markers were used for genotyping 26 C. walkeriana specimens from different growers and from different levels of improvement. The transferability was successful, with five polymorphic loci transferred to C. loddigesii and six polymorphic loci to C. nobilior. Eight loci were polymorphic, revealing a maximum of two to ten alleles per locus in C. walkeriana and two to four and two to five in C. loddigesii and C. nobilior, respectively. There was no significant linkage disequilibrium in the studied loci. For C. walkeriana, the observed and expected heterozygosities ranged from 0 to 0.963 and from 0.138 to 0.841, respectively. These markers identified polymorphisms and may be used to study the genetic diversity, gene flow or hybridization of these species.

scholarly journals Development and characterisation of 16 novel microsatellite markers for the brown alga Sargassum fusiforme (Harvey) Setchell

2018 ◽  
Vol 65 ◽  
Author(s):  
Qiaochu You ◽  
Yurong Zhang ◽  
Wangdong Fu ◽  
Changfeng Chi ◽  
Tiejun Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Bonferroni Correction ◽  
Ecological Studies ◽  
Significant Linkage Disequilibrium ◽  
Related Research ◽  
Sargassum Fusiforme ◽  
Hardy Weinberg Equilibrium ◽  
Significant Linkage

<p><em>Sargassum fusiforme</em> (Harvey) Setchell (Sargassaceae, Phaeophyta) is an ecologically and economically important kelp species in East Asia. Restoration and responsible utilisation of <em>S. fusiforme</em> would be facilitated by the availability of an appropriate set of molecular markers. In the present study, we developed 16 microsatellite markers for <em>S. fusiforme</em>. A total of 99 different alleles were observed at the 16 microsatellite loci across 50 individual samples. The number of alleles per locus ranged from 4 to 10, with an average of 6.2 per locus. The observed and  xpected heterozygosities ranged from 0.483 to 0.833 and from 0.513 to 0.840, respectively. Only three of the loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni correction. No significant linkage disequilibrium was detected among the microsatellite loci. The obtained microsatellite markers will facilitate related research on <em>S. fusiforme</em>, such as ecological studies and genetic diversity assessments.</p>

scholarly journals Allozyme Based Genetic Variation between Hatchery and Natural Populations of Sahar (Tor putitora)

2015 ◽  
Vol 26 ◽  
pp. 212-223
Author(s):  
Suresh K Wagle ◽  
Neeta Pradhan ◽  
Tek B Gurung ◽  
Jay D Bista
Keyword(s):  
Genetic Variation ◽  
First Generation ◽  
Biological Diversity ◽  
Anthropogenic Activities ◽  
Natural Populations ◽  
Effective Population ◽  
Polymorphic Loci ◽  
Tor Putitora ◽  
Two Generations ◽  
Hardy Weinberg Equilibrium

Sahar (Tor putitora) formed a substantial natural fishery in the major riverine and lacustrine ecosystem of Nepal. Biological diversity of this species is being threatened by various anthropogenic activities. In view of the conservational value and the aquaculture potential of T. putitora, significant development in artificial propagation of this species has been achieved. The successful hatchery production of T. putitora brought to the forefront problematic questions regarding genetic variation of the hatchery stocks. A study was, therefore, conducted to determine the genetic variability within and between hatchery stocks and their wild counterparts of T. putitora using allozyme markers.Analyses of seven enzyme systems resuled in 11 loci being resolved from lake population and two consecutive generations of hatchery populations of T. putitora. Based on five polymorphic loci, all populations had percentage polymorphic loci 45.45. Significant reduction (P<0.01) in number of alleles per locus was evident in hatchery populations (1.45 ±0.181) compared to lake population (1.72 ±0.90). Loss of rear alleles, EST-2*74, IDH*70 and GDH*33 occurred in both of the hatchery populations which were present in wild counterparts- the lake population. All populations under study conform to the Hardy-Weinberg equilibrium at the 1% level. Although not significant (P>0.05), observed heterozygosity increased in first generation of hatchery population (Ho= 0.181 ±0.233) compared to natural population (Ho=0.179±0.221). The Ho of second generation of hatchery population was lowest (0.119 ±0.143) among the populations studied. Loss of rare alleles from the two generations of hatchery population, while these alleles were present in corresponding natural populations suggested the founders (20-30 individuals) of the hatchery populations probably represented bottlenecks to very small effective population size (Ne).J. Nat. Hist. Mus. Vol. 26, 2012: 212-223  

Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 673-687
Author(s):  
Stephen W Schaeffer ◽  
C Scott Walthour ◽  
Donna M Toleno ◽  
Anna T Olek ◽  
Ellen L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Drosophila Pseudoobscura ◽  
Linkage Disequilibrium Mapping ◽  
Nucleotide Polymorphisms ◽  
Neutral Model ◽  
Significant Linkage Disequilibrium ◽  
Single Nucleotide ◽  
Synonymous Sites ◽  
Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura.

Genetics ◽  
1993 ◽  
Vol 135 (2) ◽  
pp. 541-552 ◽  
Author(s):  
S W Schaeffer ◽  
E L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Alcohol Dehydrogenase ◽  
Distance Effect ◽  
Theoretical Distribution ◽  
Drosophila Pseudoobscura ◽  
Significant Linkage Disequilibrium ◽  
Effective Population ◽  
Nucleotide Distance ◽  
Significant Linkage ◽  
Recombination Parameter

Abstract The alcohol dehydrogenase (Adh) region of Drosophila pseudoobscura, which includes the two genes Adh and Adh-Dup, was used to examine the pattern and organization of linkage disequilibrium among pairs of segregating nucleotide sites. A collection of 99 strains from the geographic range of D. pseudoobscura were nucleotide-sequenced with polymerase chain reaction-mediated techniques. All pairs of the 359 polymorphic sites in the 3.5-kb Adh region were tested for significant linkage disequilibrium with Fisher's exact test. Of the 74,278 pairwise comparisons of segregating sites, 127 were in significant linkage disequilibrium at the 5% level. The distribution of five linkage disequilibrium estimators D(ij), D2, r(ij), r2 and D(ij) were compared to theoretical distributions. The observed distributions of D(ij), D2, r(ij) and r2 were consistent with the theoretical distribution given an infinite sites model. The observed distribution of D(ij) differed from the theoretical distribution because of an excess of values at -1 and 1. No spatial pattern was observed in the linkage disequilibrium pattern in the Adh region except for two clusters of sites nonrandomly associated in the adult intron and intron 2 of Adh. The magnitude of linkage disequilibrium decreases significantly as nucleotide distance increases, or a distance effect. Adh-Dup had a larger estimate of the recombination parameter, 4Nc, than Adh, where N is the effective population size and c is the recombination rate. A comparison of the mutation and recombination parameters shows that 7-17 recombination events occur for each mutation event. The heterogeneous estimates of the recombination parameter and the inverse relationship between linkage disequilibrium and nucleotide distance are no longer significant when the two clusters of Adh intron sites are excluded from analyses. The most likely explanation for the two clusters of linkage disequilibria is epistatic selection between sites in the cluster to maintain pre-mRNA secondary structure.

scholarly journals POPULATION GENETIC CONSEQUENCES OF FEEDING HABITS IN SOME FOREST LEPIDOPTERA

Genetics ◽  
1979 ◽  
Vol 92 (3) ◽  
pp. 1005-1021
Author(s):  
Charles Mitter ◽  
Douglas J Futuyma
Keyword(s):  
Genetic Variation ◽  
Environmental Heterogeneity ◽  
Feeding Habits ◽  
Functional Relation ◽  
Allozyme Variation ◽  
Unexpected Result ◽  
Polymorphic Loci ◽  
Allozyme Loci ◽  
Race Formation ◽  
Relationship Of

ABSTRACT By surveying variation at allozyme loci in several phytophagous lepidopteran species (Geometridae), we have tested two hypotheses about the relationship of genetic variation to environmental heterogeneity: (1) that allozyme polymorphisms may exist because of associations between genotypes and "niches" (different host plants, in this instance), and (2) that the overall genetic variation of a species is correlated with environmental heterogeneity (or breadth of the species' overall ecological niche) .—Genetic differentiation among samples of oligophagous or polyphagous species taken from different host species was observed in one of three species, at only one of seven polymorphic loci. The data thus provide no evidence for pronounced genetic sub-structuring, or "host race" formation in these sexually reproducing species, although host plant-genotype associations in a parthenogenetic moth give evidence of the potential for diversifying selection.—In a comparison of allozyme variation in polyphagous ("generalized") and oligophagous ("specialized") species, heterozygosity appeared to be higher in specialized species, at all polymorphic loci but one. I t is possible that this unexpected result arises from a functional relation between breadth of diet and genetic variation.

scholarly journals Linkage disequilibrium in growing and stable populations.

Genetics ◽  
1994 ◽  
Vol 137 (1) ◽  
pp. 331-336 ◽  
Author(s):  
M Slatkin
Keyword(s):  
Linkage Disequilibrium ◽  
Sequence Data ◽  
Significant Linkage Disequilibrium ◽  
Rapid Population Growth ◽  
Exact Test ◽  
Dna Sequence Data ◽  
Constant Size ◽  
Significant Linkage ◽  
Stable Populations ◽  
Growing Population

Abstract Nonrandom associations between alleles at different loci can be tested for using Fisher's exact test. Extensive simulations show that there is a substantial probability of obtaining significant nonrandom associations between closely or completely linked polymorphic neutral loci in a population of constant size at equilibrium under mutation and genetic drift. In a rapidly growing population, however, there will be little chance of finding significant nonrandom associations even between completely linked loci if the growth has been sufficiently rapid. This result is illustrated by the analysis of mitochondrial DNA sequence data from humans. In comparing all pairs of informative sites, fewer than 5% of the pairs show significant disequilibrium in Sardinians, which have apparently undergone rapid population growth, while 20% to 30% in !Kung and Pygmies, which apparently have not undergone rapid growth, show significance. The extent of linkage disequilibrium in a population is closely related to the gene genealogies of the loci examined, with "star-like" genealogies making significant linkage disequilibrium unlikely.

scholarly journals Genetic analysis of silver-fir populations in the Beskids

2011 ◽  
Vol 72 (2) ◽  
pp. 115-119 ◽  
Author(s):  
Leon Mejnartowicz
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Abies Alba ◽  
Genetic Distances ◽  
Silver Fir ◽  
Geographical Distance ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (<em>Abies alba</em>): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (<em>I</em> = <em>0.42</em>), percentage of polymorphic loci <em>(%PoL </em>= <em>64.29</em>) and number of rare alleles (<em>NoRa </em>= <em>5</em>). Besides, the BM population has the highest observed heterozygosity (<em>Ho </em>= <em>0.291</em>), which exceeds the expected heterozygosity (<em>He </em>= <em>0.254</em>), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of <em>He </em>= <em>0.262 </em>and <em>Ho </em>= <em>0.264</em>.

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