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Allele Size (allele + size)
Selected AbstractsMicrosatellite polymorphism and genetic distances between the dog, red fox and arctic foxJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2003J. Klukowska Summary This study compared polymorphism of nine canine-derived microsatellites (MS) (CPH1, CPH3, CPH6, CPH11, 2004, 2010, 2140, 2168 and 2319) in three species of the family Canidae. The DNA samples of 151 dogs, 53 arctic foxes and 91 red foxes were examined. The canine-derived primers did not amplify two MS (CPH1 and CPH11) in genome samples of the arctic fox. The most polymorphic MS in the studied species was the one named 2319. For majority of the loci mean allele size was higher in the dog than in two fox species. The genetic distances between the species were estimated using three formulas: DS, Da and (,,)2. The estimated distances between both fox species were the smallest, while those between the dog and the arctic fox were the largest. Zusammenfassung Genetische Distanz zwischen Hund, Rotfuchs und arktischen Fuchs auf der Basis von Mikrosatelliten Diese Arbeit vergleicht genetische Polymorphismen an neun vom Hund abgeleiteten Mikrosatelliten (CPH1, CPH3, CPH6, CPH11, 2004, 2010, 2140, 2168 und 2319) in drei Arten der Familie der Canidae. Es wurden DNA-Proben von 151 Hunden, 53 arktischer Füchse und 91 Rotfüchse untersucht. Zwei der vom Hund übertragenen Primer (CPH1 und CPH11) führten zu keiner Amplifikation beim arktischen Fuchs. Die meisten Allele innerhalb der untersuchten Arten zeigte der Mikrosatellit 2319. An den meisten Genorten wurde beim Hund eine größere mittlere Allelgröße beobachtet als bei den beiden Fuchsarten. Die genetische Distanz zwischen den Arten wurde mit den drei Maßen Ds, Da und (,µ)2 geschätzt. Zwischen arktischem Fuchs und Rotfuchs wurde die geringste, zwischen Hund und arktischen Fuchs die größte genetische Distanz, geschätzt. [source] Genetic divergence between sympatric Arctic charr Salvelinus alpinus morphs in Gander Lake, Newfoundland: roles of migration, mutation and unequal effective population sizesJOURNAL OF FISH BIOLOGY, Issue 8 2008D. Gomez-Uchida A suite of 10 microsatellite loci was used to examine genetic divergence between two sympatric morphs of Arctic charr Salvelinus alpinus (,dark' and ,pale') inhabiting Gander Lake, Newfoundland. Results can be summarized as follows: (1) the morphs are strongly reproductively isolated , gene flow,migration estimates were consistently low in long and short-term evolutionary timescales of analysis; (2) intermorph divergence based on allele size (RST) was significantly larger than those based on allele state (,) implying a cumulative effect of stepwise-like mutations; (3) historical (coalescent) and current (linkage disequilibrium) point estimates of effective population size (Ne) were consistently higher for dark than for pale S. alpinus. The first and second findings lend support to the hypothesis that divergence between forms may have preceded the last glacial period (ending c. 12 000 years bp). The third finding argues for significant differences in habitat quantity and quality between morphs, which were emphasized in a previous study. Overall, these analyses underscore the importance of genetic assessment and monitoring in the conservation of fish diversity, with emphasis on ,rare' or under-represented forms among temperate species pairs. [source] Cosegregation of a Factor VIII Microsatellite Marker with Mild Hemophilia A in Golden Retriever DogsJOURNAL OF VETERINARY INTERNAL MEDICINE, Issue 2 2005Marjory B. Brooks Mild hemophilia A (factor VIII deficiency) was diagnosed in Golden Retrievers and pedigree studies were undertaken to test the cosegregation of an intragenic factor VIII marker with the disease phenotype. The study population consisted of 30 client-owned dogs (22 males and 8 females). Hemophilic males (n = 12) typically demonstrated prolonged bleeding after trauma or surgery rather than spontaneous hemorrhagic events. The affected males had a proportionate reduction in factor VIII coagulant activity (mean FVIII:C = 4%) and factor VIII protein concentration (mean FVIII:Ag = 3%). Twenty-five dogs (10 affected males, 8 clear males, 2 obligate carrier dams, and 5 suspect carrier daughters) were genotyped for a factor VIII microsatellite marker, with allele size assigned by an automated capillary electrophoresis system. Five distinct marker alleles were present in the study pedigree and a 300-base pair allele was found to segregate with the hemophilia A phenotype. The inheritance of the hemophilia-associated allele defined carrier status for 5 suspect daughters of obligate carrier dams. The limitations inherent to linkage analyses (ie, lack of access to key family members and homozygosity at the marker locus) did not preclude carrier detection in this pedigree. We conclude that genotype analysis for the intragenic factor VIII marker can aid in control of canine hemophilia A through enhanced carrier detection. [source] Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiaeMOLECULAR ECOLOGY, Issue 2 2004Joanna Sumner Abstract To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50,80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in FST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (FST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low. [source] Y chromosome microsatellite isolation from BAC clones in the greater white-toothed shrew (Crocidura russula)MOLECULAR ECOLOGY RESOURCES, Issue 1 2006LORI J. LAWSON HANDLEY Abstract We constructed a microsatellite library from four Crocidura russula Y chromosome-specific bacterial artificial chromosome (BAC) clones. Only one of eight microsatellites was male-specific, despite genome walking to obtain more flanking sequence and testing of 93 primer combinations. Potential reasons for this low success are discussed. The male-specific locus, CRY3, was genotyped in 90 males, including C. russula from across the species range and two related species. The large difference in CRY3 allele size between eastern and western lineages supports earlier reports of high divergence between them. Despite polymorphism of CRY3 in Morocco, only one allele was found throughout the whole of Europe, consistent with previous studies that suggest recent colonization of Europe from a small number of Moroccan founders. [source] Preconceptional and prenatal screening for fragile X syndrome: Experience with 40 000 testsPRENATAL DIAGNOSIS, Issue 11 2007Michal Berkenstadt Abstract Objectives To determine the carrier frequency of fragile X syndrome, and the rate of expansion from premutation (PM) carrier to full mutation (FM) fetus. Methods Results were analyzed on women with no family history of fragile X syndrome, or who were PM/FM carriers, who were tested between January 1994 and June 2004. PM was defined 55,199 repeats, FM above 200. Results Out of 40 079 women screened, 5 FM and 255 PM carriers were detected. There was no significant difference in carrier frequency between those with versus those without family history of mental retardation or developmental abnormalities: 1 in 128 (28/3596) versus 1 in 157 (232/36 483). However, the median of repeats differed significantly: 58 and 66 repeats, respectively, (P < 0.0001). Invasive prenatal diagnosis was carried out in 370 pregnancies (7 FM and 363 PM). Thirty FM fetuses were detected. There was a lower expansion rate in cases without a family history: 10% (17/169 PMs) compared to 50% (11/22 PMs) in those with a history, but this could be accounted for by the difference in allele size. Conclusion There is now sufficient information on screening parameters and prenatal diagnosis of fragile X syndrome to offer testing to women of reproductive age. Copyright © 2007 John Wiley & Sons, Ltd. [source] Length variability and interspersion patterns of the HRAS1 minisatellite: a new approach for the reconstruction of human population relationshipsANNALS OF HUMAN GENETICS, Issue 4 2001A. VEGA During recent years the HRAS1 minisatellite has been analysed by several authors because of its putative association with cancer susceptibility. The aim of this report is to test the usefulness of this minisatellite in investigating human population relationships. We have studied 370 chromosomes from two well-differentiated populations: Galicia (North-west Iberia) and South-east Africa, as well as available data on allele length gene frequencies. The fragment analysis results show a strong tendency to differentiate between non-African and African populations. In spite of the usefulness of fragment analysis, the minisatellite variant repeat (MVR) approach of the HRAS1 minisatellite appears to be a more powerful method for use in human population studies, due to the high level of diversity of its interspersion pattern structures. In addition, this approach has allowed us to define some new structural characteristics of this minisatellite. Four different major groups of human HRAS1 minisatellite alleles could be distinguished following a structural criterion based on the MVR code. Furthermore, the characterisation of the HRAS1 minisatellite in chimpanzees revealed clear differences when compared to humans, not only with respect to the allele size but also to the internal structure. [source] Gene flow and melanism in garter snakes revisited: a comparison of molecular markers and island vs. coalescent modelsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2003TONYA D. BITTNER Within populations, the stochastic effect of genetic drift and deterministic effect of natural selection are potentially weakened or altered by gene flow among populations. The influence of gene flow on Lake Erie populations of the common garter snake has been of particular interest because of a discontinuous colour pattern polymorphism (striped vs. melanistic) that is a target of natural selection. We reassessed the relative contributions of gene flow and genetic drift using genetic data and population size estimates. We compared all combinations of two marker systems and two analytical approaches to the estimation of gene flow rates: allozymes (data previously published), microsatellite DNA (new data), the island model (FST -based approach), and a coalescence-based approach. For the coalescence approach, mutation rates and sampling effects were also investigated. While the two markers produced similar results, gene flow based on FST was considerably higher (Nm > 4) than that from the coalescence-based method (Nm < 1). Estimates of gene flow are likely to be inflated by lack of migration-drift equilibrium and changing population size. Potentially low rates of gene flow (Nm < 1), small population size at some sites, and positive correlations of number of microsatellite DNA alleles and island size and between M, mean ratio of number of alleles to range in allele size, and island size suggest that in addition to selection, random genetic drift may influence colour pattern frequencies. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 79, 389,399. [source] Microsatellite diversity and genetic structure of fragmented populations of the rare, fire-dependent shrub Grevillea macleayanaMOLECULAR ECOLOGY, Issue 6 2002Phillip R. England Abstract Recent habitat loss and fragmentation superimposed upon ancient patterns of population subdivision are likely to have produced low levels of neutral genetic diversity and marked genetic structure in many plant species. The genetic effects of habitat fragmentation may be most pronounced in species that form small populations, are fully self-compatible and have limited seed dispersal. However, long-lived seed banks, mobile pollinators and long adult lifespans may prevent or delay the accumulation of genetic effects. We studied a rare Australian shrub species, Grevillea macleayana (Proteaceae), that occurs in many small populations, is self-compatible and has restricted seed dispersal. However, it has a relatively long adult lifespan (c. 30 years), a long-lived seed bank that germinates after fire and is pollinated by birds that are numerous and highly mobile. These latter characteristics raise the possibility that populations in the past may have been effectively large and genetically homogeneous. Using six microsatellites, we found that G. macleayana may have relatively low within-population diversity (3.2,4.2 alleles/locus; Hexp= 0.420,0.530), significant population differentiation and moderate genetic structure (FST = 0.218) showing isolation by distance, consistent with historically low gene flow. The frequency distribution of allele sizes suggest that this geographical differentiation is being driven by mutation. We found a lack mutation-drift equilibrium in some populations that is indicative of population bottlenecks. Combined with evidence for large spatiotemporal variation of selfing rates, this suggests that fluctuating population sizes characterize the demography in this species, promoting genetic drift. We argue that natural patterns of pollen and seed dispersal, coupled with the patchy, fire-shaped distribution, may have restricted long-distance gene flow in the past. [source] combi.pl: a computer program to combine data sets with inconsistent microsatellite marker allele size informationMOLECULAR ECOLOGY RESOURCES, Issue 3 2008HELGE TÄUBERT Abstract Combining two data sets with allele information from overlapping microsatellite markers is often desirable, particularly in population genetic studies where a substantial body of published data exists. When genotyping is performed in different laboratories, allele size calling may not be presumed to be consistent. Our approach solves this problem by assigning allele sizes across studies using maximum-likelihood theory. Using data overlaps in samples and markers, allele shifts between two studies are calculated for each overlapping marker and a single file containing allele frequencies of consistent alleles is produced. The program (combi.pl) is written in PERL and available at http://data40.uni-tz.gwdg.de/~htaeube. [source] Development of 10 microsatellite loci for Yellow-billed Magpies (Pica nuttalli) and corvid ecology and West Nile virus studiesMOLECULAR ECOLOGY RESOURCES, Issue 1 2008HOLLY B. ERNEST Abstract We developed 10 polymorphic microsatellite loci for Yellow-billed Magpies (Pica nuttalli). The primers were tested across a population of 57 Central California Yellow-billed Magpies and displayed an average of 3.9 alleles per locus. Forty-one American Crows (Corvus brachyrhynchos) from California were polymorphic for seven of the loci with an average of 2.9 alleles per locus. One additional microsatellite-containing locus displayed diagnostic allele sizes and may be useful to distinguish between the two species. These corvid specific microsatellites will aid ecological studies of the population-level effects of diseases, such as West Nile virus. [source] | |||||||||||||