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Average Heterozygosity (average + heterozygosity)
Selected AbstractsPopulation genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of CaliforniaJOURNAL OF FISH BIOLOGY, Issue 2 2010S. M. Plank The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small FST values (,0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep-water channel from the coastal sites, however, was significantly divergent (large FST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size. [source] Fine-scale population structure and dispersal in Biomphalaria glabrata, the intermediate snail host of Schistosoma mansoni, in VenezuelaMOLECULAR ECOLOGY, Issue 5 2002J. Mavárez Abstract Biomphalaria glabrata is the main intermediate host of Schistosoma mansoni in America and one of the most intensely studied species of freshwater snails, yet very little is known about its population biology. Here, we used seven highly polymorphic microsatellite loci to analyse genetic diversity in the Valencia lake basin, which represents the core of the endemic area for schistosomiasis in Venezuela. Populations were sampled at short spatial scale (a few kilometres), both inside the lake and in ponds or rivers near the lake. Our results indicate that B. glabrata essentially cross-fertilizes, with little variation in selfing rates among populations. Our markers detected considerable genetic variation, with an average heterozygosity of 0.60. More diversity per population was found within than outside the lake, suggesting an influence of connectivity among populations on the levels of genetic diversity. A marked population structure was detected and lake populations were less structured than other populations. Most individuals were assigned to their population of origin using an assignment test. No strong demographic signal (e.g. bottleneck) was detected, though lake populations are likely to experience bottlenecks more frequently than the other populations analysed. Differences in gene flow therefore seem to play an important role in population differentiation and in the restoring of genetic diversity in demographically unstable populations. [source] Development and characterization of polymorphic markers for the sap-stain fungus Ophiostoma quercusMOLECULAR ECOLOGY RESOURCES, Issue 1 2009J. W. GROBBELAAR Abstract Eight polymorphic markers were developed from South African isolates of Ophiostoma quercus. The genome was screened for repeat regions using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol and 20 de novo primer pairs flanking putative microsatellite regions were designed. Eight loci were optimized and their polymorphisms evaluated by sequencing. The repeat and flanking regions were highly polymorphic containing both indels and base-pair substitutions revealing a total of 46 alleles in 14 isolates and an average heterozygosity of 0.68. Substantial sequence variability makes these markers useful for genotyping populations in order to calculate diversity and monitor global movement of O. quercus. [source] Development of 25 gene-associated microsatellite markers of Atlantic cod (Gadus morhua L.)MOLECULAR ECOLOGY RESOURCES, Issue 4 2006JŘRGEN STENVIK Abstract Microsatellites were identified by screening 2294 GenBank entries available for Atlantic cod (Gadus morhua L.), mainly representing expressed sequence tags and cDNA sequences. Ninety-two novel microsatellite loci (tetra-, tri- and dinucleotides) were characterized on 96 individuals. This strategy yielded 25 gene-associated polymorphic microsatellite markers (11 tri- and 14 dinucleotides) with two to 20 alleles and an average heterozygosity of 0.48 in the population studied (range 0.02,0.89). One marker exhibited significant homozygote excess, and one of the primer pairs amplified two linked markers. The gene identity was determined at nine of the loci, confirming the associated microsatellites as type I markers. [source] Isolation of dinucleotide microsatellite loci from red-backed salamander (Plethodon cinereus)MOLECULAR ECOLOGY RESOURCES, Issue 1 2003Lisa M. Connors Abstract We isolated 13 variable dinucleotide microsatellites from red-backed salamanders (Plethodon cinereus). After generating fragments using degenerate oligonucleotide primer-polymerase chain reaction (DOP-PCR), AC repeats were captured using biotinylated probes and streptavidin-coated magnetic particles. Captured fragments were cloned into plasmids, screened for microsatellites with a simple PCR reaction, and select plasmids then sequenced. PCR primers were designed and optimized for robust amplification, and nine primers have been further optimized for multiplex reactions with fluorescent primers. These nine loci are variable with an average of 6.11 alleles per locus and an average heterozygosity of 0.61. [source] Dinucleotide microsatellite loci isolated from flowering dogwood (Cornus florida L.)MOLECULAR ECOLOGY RESOURCES, Issue 2 2002Paul R. Cabe Abstract We report eight variable dinucleotide microsatellite loci cloned from flowering dogwood (Cornus florida L.) using a biotin enrichment protocol. Degenerate oligonucleotide primer-polymerase chain reaction (DOP-PCR) was used to generate a population of DNA fragments, from which adenine-cytosine dinucleotide (AC) and adenine-guanine dinucleotide (AG) repeats were captured using biotinylated probes and streptavidin coated magnetic particles. The captured fragments were cloned into plasmids, and the plasmid library was screened for microsatellites using a simple PCR technique. Selected plasmids were sequenced, and PCR primers were designed and optimized using a thermal-gradient thermocycler. The loci reported are highly variable with an average of 9.25 allele per locus and an average heterozygosity of 0.84. [source] Demographic genetics of American beech (Fagus grandifolia Ehrh.) IV.PLANT SPECIES BIOLOGY, Issue 3 2008Development of genetic variability, gene flow during succession in a coastal plain forest in Maryland Abstract Genetic recovery of an American beech (Fagus grandifolia) population in deciduous forests that were once pastures was studied using 16 allozyme loci from 410 individuals in a 600 m × 600 m study plot in Maryland, USA. We also examined the spatio-temporal genetic structure of the American beech population at a regional scale. Overall genetic diversity of mature trees was measured by estimating average heterozygosity (H = 0.156). Rare alleles were observed in five loci, Lap, 6Pdgh3, Pgi, Adh1 and Got3. Mature individuals were divided into three size classes based on d.b.h. The genetic component of each size class was compared and it was revealed that several alleles (Pgm-a, 6Pgdh3-a and Lap-b) were shared only in specific size classes. The spatial distribution of the genotypes demonstrated a conspicuous localization in three loci (Aco, Adh1 and Idh). Spatial autocorrelation analyses were carried out among the mature trees for a 20 m interval, and were positive for 0,120 m and negative for >180 m. Distrograms indicated that a unique genetic localization occurs among mature individuals. Seven hundred and seventy-five seedlings in the 10 m × 120 m transect were analyzed to measure gene flow via seed and/or pollen. We obtained a genetic neighborhood area of 1.17 ha and an effective population size of 32.4. The temporal and spatial modes of genetic recovery of the population are discussed in the context of conservation biology. [source] The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markersANIMAL GENETICS, Issue 1 2005M. Fang Summary A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour-joining tree constructed from Modified Cavalli-Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds. [source] Milk protein polymorphisms in cattle (Bos indicus), mithun (Bos frontalis) and yak (Bos grunniens) breeds and their hybrids indigenous to BhutanANIMAL SCIENCE JOURNAL, Issue 5 2010Tashi DORJI ABSTRACT In the current study, milk protein variation was examined in cattle (Bos indicus), mithun (Bos frontalis), yak (Bos grunniens) and their hybrid populations in Bhutan to estimate genetic variability, conduct genetic characterization and assess the possibility of gene flow between mithun and cattle. Isoelectric focusing of 372 milk samples from 11 populations detected four molecular types of ,- lactoglobulin (A, B, E and M), five molecular types of ,S1 -casein (A, B, C, E and X) and three molecular types of k -casein (A, B and X). Mithun and yak shared alleles but were found to exhibit different allele frequencies for the proteins studied. The degree of genetic variability within populations was measured by average heterozygosity and ranged from 24,40% in cattle, 26% for yak and 33% for mithun. We also resolved the traditional mithun and cattle hybridization system via principal component analysis. Our results suggested secondary introgression of mithun genes to the village Thrabum population, and a close genetic relationship between Bhutanese indigenous cattle and Indian cattle. [source] A genome scan of 18 families with chronic lymphocytic leukaemiaBRITISH JOURNAL OF HAEMATOLOGY, Issue 6 2003Lynn R. Goldin Summary. Chronic lymphocytic leukaemia (CLL) accounts for about 30% of all leukaemias and is most prevalent in older individuals. Significant familial aggregation has been demonstrated but the mode of inheritance is unknown. Recurrent cytogenetic abnormalities are frequently found in CLL tumour cells but no susceptibility genes have been confirmed. We have collected clinical data and biospecimens on families ascertained for having at least two living patients with CLL. The current study included DNA samples from 94 individuals (38 affected patients) in 18 families. We have carried out a genome scan using the ABI 28-panel medium density linkage mapping set (average spacing of 10 cM and average heterozygosity of 80%). Genotypes for 359 markers were scored. Multipoint limit of detection (lod) scores were calculated, assuming both dominant and recessive inheritance and allowing for increased penetrance with age and genetic heterogeneity. Non-parametric linkage scores were also calculated. Lod scores of 1·0 or greater were found on regions of chromosomes 1, 3, 6, 12, 13 and 17, but none of these loci achieved statistical significance. Four of these six regions (6q, 13q, 12 and 17p) coincide with areas where cytogenetic abnormalities are frequently observed in CLL tumour cells and are, therefore, strong candidate regions for containing germ line changes. [source] | ||||||||||