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Highly Polymorphic Microsatellite Markers (highly + polymorphic_microsatellite_marker)
Selected AbstractsCharacterization of microsatellite loci in a seed chalcid, Megastigmus spermotrophus (Hymenoptera: Torymidae)MOLECULAR ECOLOGY RESOURCES, Issue 3 2003S. Boivin Abstract Highly polymorphic microsatellite markers can supply demographic information on founder events and range expansion following initial introduction of invasive insect species. Six microsatellite loci were isolated from a partial DNA library in order to study the invasion patterns of a seed chalcid, Megastigmus spermotrophus, introduced to Europe and New Zealand. Allelic diversity at all described loci was high, ranging from 17 to 30 alleles per locus. All six loci were successfully amplified in 15 congeneric species. [source] Biases associated with population estimation using molecular taggingANIMAL CONSERVATION, Issue 3 2000Juliann L. Waits Although capture,recapture techniques are often used to estimate population size, these approaches are difficult to implement for a wide variety of species. Highly polymorphic microsatellite markers are useful in individual identification, and these ,molecular tags' can be collected without having to capture or trap the individual. However, several sources of error associated with molecular identification techniques, including failure to identify individuals with the same genotype for these markers as being different, and incorrect assignment of individual genotypes, could bias population estimates. Simulations of populations sampled for the purpose of estimating population size were used to assess the extent of these potential biases. Population estimates tended to be biased downward as the likelihood of individuals sharing the same genotype increased (as measured by the probability of identity (PI) of the multi-locus genotype); this bias increased with population size. Populations of 1000 individuals were underestimated by ,5% when the PI was as small as 1.4 × 10,7. A similar-sized bias did not occur for populations of 50 individuals until the PI had increased to approximately 2.5 × 10,5. Errors in genotype assignment resulted in overestimates of population size; this problem increased with the number of samples and loci that were genotyped. Population estimates were often >200% the size of the simulated populations when the probability of making a genotyping error was 0.05/locus and 7,10 loci were used to identify individuals. This bias was substantially reduced by decreasing genotyping error rate to 0.005. If possible, only highly polymorphic loci that are critical for the identification of the individual should be used in molecular tagging, and considerable efforts should be made to minimize errors in genotype determination. [source] Mutation analysis in nephronophthisis using a combined approach of homozygosity mapping, CEL I endonuclease cleavage, and direct sequencing,HUMAN MUTATION, Issue 3 2008Edgar A. Otto Abstract Nephronophthisis (NPHP), an autosomal recessive kidney disease, is the most frequent genetic cause of chronic renal failure in the first three decades of life. Mutations in eight genes (NPHP1,8) have been identified. We here describe a combined approach for mutation screening of NPHP1, NPHP2, NPHP3, NPHP4, and NPHP5 in a worldwide cohort of 470 unrelated patients with NPHP. First, homozygous NPHP1 deletions were detected in 97 patients (21%) by multiplex PCR. Second, 25 patients with infantile NPHP were screened for mutations in inversin (NPHP2/INVS). We detected a novel compound heterozygous frameshift mutation (p.[Q485fs]+[R687fs]), and a homozygous nonsense mutation (p.R899X). Third, 37 patients presenting with NPHP and retinitis pigmentosa (Senior-Løken syndrome [SLS]) were screened for NPHP5/IQCB1 mutations by direct sequencing. We discovered five different (three novel) homozygous premature termination codon (PTC) mutations (p.F142fsX; p.R461X; p.R489X; p.W444X; and c.488,1G>A). The remaining 366 patients were further investigated for mutations in NPHP1, NPHP3, and NPHP4. We applied a "homozygosity only" strategy and typed three highly polymorphic microsatellite markers at the respective loci. A total of 32, eight, and 14 patients showed homozygosity, and were screened by heteroduplex crude celery extract (CEL I) endonuclease digests. The sensitivity of CEL I was established as 92%, as it detected 73 out of 79 different known mutations simply on agarose gels. A total of 10 novel PTC mutations were found in NPHP1 (p.P186fs, p.R347X, p.V492fs, p.Y509X, and c.1884+1G>A), in NPHP3 (c.3812+2T>C and p.R1259X), and in NPHP4 (p.R59X, p.T1004fs, and p.V1091fs). The combined homozygosity mapping and CEL I endonuclease mutation analysis approach allowed us to identify rare mutations in a large cohort of patients at low cost. Hum Mutat 29(3), 418,426, 2008. © 2007 Wiley-Liss, Inc. [source] Evolutionary divergence and possible incipient speciation in post-glacial populations of a cosmopolitan aquatic plantJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2005G. Nies Abstract Habitat configuration is expected to have a major influence on genetic exchange and evolutionary divergence among populations. Aquatic organisms occur in two fundamentally different habitat types, the sea and freshwater lakes, making them excellent models to study the contrasting effects of continuity vs. isolation on genetic divergence. We compared the divergence in post-glacial populations of a cosmopolitan aquatic plant, the pondweed Potamogeton pectinatus that simultaneously occurs in freshwater lakes and coastal marine sites. Relative levels of gene flow were inferred in 12 lake and 14 Baltic Sea populations in northern Germany using nine highly polymorphic microsatellite markers developed for P. pectinatus. We found highly significant isolation-by-distance in both habitat types (P < 0.001). Genetic differentiation increased approximately 2.5-times faster among freshwater populations compared with those from the Baltic Sea. As different levels of genetic drift or population history cannot explain these differences, higher population connectivity in the sea relative to freshwater populations is the most likely source of contrasting evolutionary divergence. These findings are consistent with the notion that freshwater angiosperms are more conducive to allopatric speciation than their life-history counterparts in the sea, the relative species poor seagrasses. Surprisingly, population pairs from different habitat types revealed almost maximal genetic divergence expected for complete reproductive isolation, regardless of their respective geographical distance. Hence, the barrier to gene flow between lake and sea habitat types cannot be due to dispersal limitation. We may thus have identified a case of rapid incipient speciation in post-glacial populations of a widespread aquatic plant. [source] Genetic signatures in an invasive parasite of Anguilla anguilla correlate with differential stock managementJOURNAL OF FISH BIOLOGY, Issue 1 2010S. Wielgoss In this article, it is shown that available genetic tools for the omnipresent parasite Anguillicoloides crassus in European eels Anguilla anguilla are sensitive to different immigration rates into local A. anguilla stocks for two separated river systems. Relying on four highly polymorphic microsatellite markers, it was inferred that under natural recruitment, nematode samples meet Hardy,Weinberg expectations for a single panmictic population, while genetic signals show signs for a strong Wahlund effect most likely due to very recent population mixing under frequent restocking of young A. anguilla. This was indicated by a low but significant FST value among within-host populations (infrapopulations) along with high inbreeding indices FIS consistent over all loci. The latter signal is shown to stem from high levels of admixture and the presence of first-generation migrants, and alternative explanations such as marker- and sex-specific biases in the nematode populations could be dismissed. Moreover, the slightly increased degree of relatedness within infrapopulations in the stocked river system cannot explain the excessive inbreeding values found and are most likely a direct consequence of recent influx of already infected fish harbouring parasites with different genetic signatures. Applying a simulation approach using known variables from the nematode's invasion history, only the artificial introduction of a Wahlund effect leads to a close match between simulated and real data, which is a strong argument for using the parasite as a biological tag for detecting and characterizing fish translocation. [source] Polyandry and fitness in the western harvester ant, Pogonomyrmex occidentalisMOLECULAR ECOLOGY, Issue 6 2004Diane C. Wiernasz Abstract Using four highly polymorphic microsatellite markers (12,28 alleles), we gentoyped workers from 63 colonies of Pogonomyrmex occidentalis. Colonies have a single, multiply mated queen, and an average number of 6.3 patrilines per colony. Colony growth was measured over an 8-year period in the study population. Intracolonial relatedness and colony growth are correlated negatively, indicating a substantial fitness benefit to multiple mating. [source] A suite of highly polymorphic microsatellite markers in turbot (Scophthalmus maximus L.) with potential for use across several flatfish speciesMOLECULAR ECOLOGY, Issue 3 2000A. Iyengar [source] Rapid prenatal diagnosis of aneuploidies and zygosity in multiple pregnancies by amniocentesis with single insertion of the needle and quantitative fluorescent PCRPRENATAL DIAGNOSIS, Issue 8 2003Vincenzo Cirigliano Abstract Objective To investigate amniotic fluid (AF) samples retrieved in multiple pregnancies by single insertion of the needle, for rapid assessment of chromosome copy number, zygosity, and cross-contamination between fetuses, using Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) amplification of highly polymorphic microsatellite markers. Methods Fifty-two multiple pregnancies were selected (47 twins, 5 triplets) and 108 samples of amniotic fluid were sampled between 12 to 20 weeks of gestation (mean 15.5) using the single-needle technique. Aneuploidy screening by QF-PCR amplification of short tandem repeats (STRs) on chromosomes X, Y, 21, 13, and 18 was carried out within 24 h of collection. Owing to the sampling procedure, the eventual presence of contamination between fetuses was also evaluated in every case. Results Normal and aneuploid fetuses were readily identified by QF-PCR. Fetal reduction was made available, for trisomic fetuses, without further waiting for completion of fetal karyotyping. In twin gestations, the ultrasound examination of chorionicity was always in agreement with the molecular assessment of zygosity. Contamination between fetuses due to the sampling procedure with a single puncture was never observed. Conclusion Rapid prenatal diagnosis of aneuploidies by QF-PCR is a sensitive, efficient, and reliable assay. When applied in multiple pregnancies, it has the added value of allowing the assessment of zygosity in all cases, independently of chorionicity and fetal sex. Copyright © 2003 John Wiley & Sons, Ltd. [source] Influence of parental origin of the X chromosome on physical phenotypes and GH responsiveness of patients with Turner syndromeCLINICAL ENDOCRINOLOGY, Issue 1 2010Jung Min Ko Summary Objective, Previous studies have reported the effects of parental origin of the X chromosome on specific phenotypic and cognitive profiles in Turner syndrome (TS). Here, we investigate the possible parent-of-origin effects on physical phenotypes and responsiveness to GH in Korean patients with TS. Design and patients, Thirty-three patients with TS with nonmosaic karyotype and their parents participated in this study. The parental origin of the normal X chromosome was determined by comparing parental DNA polymorphisms using nine highly polymorphic microsatellite markers on the X chromosome. For the evaluation of parent-of-origin effects, typical phenotypic traits, including congenital malformations, auxological and endocrinological profiles, were compared. Results, The retained X chromosome was of maternal (Xm) origin in 60·6% patients and paternal (Xp) origin in 39·4% patients. No significant parent-of-origin effects on stature, body mass index, cardiac, renal, skeletal, lymphatic, hearing or ocular systems were evident. We observed no differences in height gain after GH treatment. In patients with the 45,X karyotype, patient height was positively correlated with maternal height in the Xm group (r = 0·60, P = 0·04). Moreover, patient height was more significantly correlated with maternal than paternal height, irrespective of the parental origin of the retained X chromosome. Conclusion, While we observed no significant impact of parental origin of the X chromosome on several phenotypic traits in patients with TS, a maternal imprinting effect on stature was suggested at least in patients with 45,X. Further studies on a larger number of patients with TS are essential to define the potential imprinting effects of undetermined genes on the X chromosome. [source] | ||||||||||