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Haplotype Composition (haplotype + composition)
Selected AbstractsH intragenic polymorphisms and haplotype analysis in the ornithine transcarbamylase (OTC) gene and their relevance for tracking the inheritance of OTC deficiency,,HUMAN MUTATION, Issue 5 2002Consuelo Climent Abstract The "private" nature of most mutations causing ornithine transcarbamylase (OTC) deficiency makes mutation identification in the patients difficult. Further, the PCR-amplification technology generally used for the genetic diagnosis of the deficiency misses large deletions in carrier females. Intragenic OTC polymorphisms may allow detection of these deletions and may represent an alternative to mutation detection for prenatal diagnosis and carrier identification in families with a history of inherited OTC deficiency. A new highly informative polymorphism (allele frequencies, 0.66/0.34) in intron 3 of the OTC gene (IVS3-39_40insT) is reported here, and allelic frequencies of 16 additional intragenic OTC polymorphisms are determined in 133-35 (average per polymorphism, 72) unrelated chromosomes. In addition to the novel polymorphism, only three of the studied polymorphisms (Lys46Arg, allelic frequency 0.68/0.32; IVS3-8A>T, 0.34/0.66; Gln270Arg, 0.97/0.03) are confirmed to be informative. These provide, together with another reported polymorphism (IVS4-7A>G; reported allelic frequency 0.71/0.29; Plante and Tuchman, 1998), a set of highly valuable markers of the OTC gene. Nevertheless, the combined informativity of the studied polymorphisms is limited by their distribution in only four haplotypes with one of them predominating (65% of the sampled chromosomes). Although this haplotype composition may be restricted to the Iberian peninsula (the origin of the samples), more informative polymorphisms are required to increase the diagnostic potential and, particularly, to identify large deletions affecting OTC gene exons 5-10, where only one polymorphism of weak diagnostic value is known. © 2002 Wiley-Liss, Inc. [source] Patterns of population subdivision and gene flow in the ant Nothomyrmecia macrops reflected in microsatellite and mitochondrial DNA markersMOLECULAR ECOLOGY, Issue 9 2003M. Sanetra Abstract The Australian endemic ant Nothomyrmecia macrops is renowned for having retained a large proportion of ,primitive' morphological and behavioural characters. Another less studied peculiarity of this species is the production of short-winged (brachypterous) female sexuals, which presumably are poor dispersers. The males, in contrast, bear a full set of normally developed wings and thus may disperse widely. We investigated patterns of genetic differentiation within and among three distantly separated populations in South Australia using nine polymorphic microsatellite loci and four regions of mitochondrial DNA (COI, COII, Cytb, lrRNA). We sampled eight subpopulations, one in the Lake Gilles CP, two near Penong and five around Poochera where distances ranged from 360 km to sites separated by 2,10 km. Only little differentiation was found at the local scale (within the assumed dispersal distance of males) using nuclear markers, whereas the three distant locations were moderately differentiated (FST = 0.06). Mitochondrial DNA genetic structure was much more pronounced on all scales (,ST = 0.98), with regular differences in both haplotype composition and frequency even occurring among closely located sites. This lack of congruence between nuclear and mitochondrial markers strongly suggests limited female dispersal and male-biased gene flow among populations. As to the conservation status of the species there is no evidence for severe population reductions in the recent past, which would have left populations genetically depauperate. [source] Plastid DNA haplotype variation in Dactylorhiza incarnata (Orchidaceae): evidence for multiple independent colonization events into ScandinaviaNORDIC JOURNAL OF BOTANY, Issue 1 2009Mikael Hedrén The early marsh orchid, Dactylorhiza incarnata (L.) Soó s. l., grows in medium-rich to rich fens and marshes over much of Europe and parts of Asia. The species is highly polymorphic and different forms may grow together at the same site. In the present study, I tested the hypothesis that these forms represent different migrant populations that have colonized Scandinavia independently of each other, possibly from different source areas. Accessions from Scandinavia and elsewhere were screened for variation at three size-variable plastid marker loci, one polyA repeat, one polyA-polyTA-polyT repeat and one 9 bp indel. Ten haplotypes were defined on basis on the combined variation pattern. The common occurrence of several haplotypes in southern Scandinavia and adjacent areas to the south and the east of the Baltic Sea suggests that D. incarnata has been dispersed on repeated occasions across the Baltic. Also, there was some correlation between haplotype composition and morphological form on the island of Gotland, in agreement with the independent colonization hypothesis. Material from northernmost Sweden, Finland and northwest Russia was fixed for a single widespread haplotype, indicating that populations in this area are located farther away from the Pleistocene refugia. Dactylorhiza incarnata ssp. lobelii from southwest Norway was characterized by a haplotype that was not encountered elsewhere in Scandinavia. Given its proximity to British populations dominated by the same haplotype, it is suggested that D. incarnata ssp. lobelii was established independently of the other Scandinavian populations, from coastal refugia located in western Europe. [source] Genetic characterization of specific pathogen-free rhesus macaque (Macaca mulatta) populations at the California National Primate Research Center (CNPRC)AMERICAN JOURNAL OF PRIMATOLOGY, Issue 7 2010Sree Kanthaswamy Abstract A study based on 14 STRs was conducted to understand intergenerational genetic changes that have occurred within the California National Primate Research Center's (CNPRC) regular specific pathogen-free (SPF) and super-SPF captive rhesus macaque populations relative to their conventional founders. Intergenerational genetic drift has caused age cohorts of each study population, especially within the conventional population, to become increasingly differentiated from each other and from their founders. Although there is still only minimal stratification between the conventional population and either of the two SPF populations, separate derivation of the regular and super-SPF animals from their conventional founders has caused the two SPF populations to remain marginally different from each other. The regular SPF and, especially, the super-SPF populations have been influenced by the effects of differential ancestry, sampling, and lost rare alleles, causing a substantial degree of genetic divergence between these subpopulations. The country of origin of founders is the principal determinant of the MHC haplotype composition of the SPF stocks at the CNPRC. Selection of SPF colony breeders bearing desired genotypes of Mamu-A*01 or -B*01 has not affected the overall genetic heterogeneity of the conventional and the SPF research stocks. Because misclassifying the ancestry of research stocks can undermine experimental outcomes by excluding animals with regional-specific genotypes or phenotypes of importance, understanding founder/descendent genetic relationships is crucial for investigating candidate genes with distinct geographic origins. Together with demographic management, population genetic assessments of SPF colonies can curtail excessive phenotypic variation among the study stocks and facilitate successful production goals. Am. J. Primatol. 72:587,599, 2010. © 2010 Wiley-Liss, Inc. [source] | ||||||||||