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DNA Microsatellite Markers (dna + microsatellite_marker)
Selected AbstractsGenetic diversity and phylogeographic analysis of Pinus leiophylla: a post-glacial range expansionJOURNAL OF BIOGEOGRAPHY, Issue 9 2009Abril Rodríguez-Banderas Abstract Aim, Mexico is a centre of diversity for species of the genus Pinus, most of which have restricted geographical distributions. An exception is Pinus leiophylla Schiede and Deppe, which is widely distributed throughout most of Mexico's mountainous regions. We attempt to reconstruct the phylogeographic history of this species, in order to determine if its current broad distribution is associated with major events of environmental change that occurred during the Quaternary. Location, Coniferous forests in Sierra Madre Occidental, Eje Volcánico Transversal and Sierra Montañosa del Norte de Oaxaca, Mexico. Methods, A total of 323 individuals of both P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana sampled from 22 populations were screened for variation at six paternally inherited chloroplast DNA microsatellite markers (cpSSR). In addition to haplotypic diversity estimates and neutrality tests, the following clustering methods were employed: principal components analysis (PCA), analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), haplotype network and a technique similar to Croizat's panbiogeographical method of individual and generalized tracks. Results, The combination of mutations at the six microsatellites yielded a total of 92 different haplotypes. The percentage of shared haplotypes between varieties (P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana) was only 2.2%. The average haplotypic diversity for the species was H = 0.760. PCA and SAMOVA indicate the presence of four main genetic clusters. The estimated divergence time between the two most frequent haplotypes was between 75,000 and 110,000 years. Significantly large negative Fs values suggest that most of the sampled populations are currently expanding. Individual and generalized tracks identified three potential zones that may have harboured ancestral populations of P. leiophylla and from which the expansion of this species started, as well as two secondary contact zones between the two varieties. Main conclusions, The results indicate that one of the three potential areas hypothesized to have harboured ancestral populations of P. leiophylla may be related to the origin of P. leiophylla var. chihuahuana, while the other two may be related to the origin of P. leiophylla var. leiophylla. The current broad distribution of P. leiophylla is probably associated with its strong colonization ability. [source] Variation in pollen dispersal between years with different pollination conditions in a tropical emergent treeMOLECULAR ECOLOGY, Issue 11 2004T. KENTA Abstract We examined differences in pollen dispersal efficiency between 2 years in terms of both spatial dispersal range and genetic relatedness of pollen in a tropical emergent tree, Dipterocarpus tempehes. The species was pollinated by the giant honeybee (Apis dorsata) in a year of intensive community-level mass-flowering or general flowering (1996), but by several species of moths in a year of less-intensive general flowering (1998). We carried out paternity analysis based on six DNA microsatellite markers on a total of 277 mature trees forming four spatially distinct subpopulations in a 70 ha area, and 147 and 188 2-year-old seedlings originating from seeds produced in 1996 and 1998 (cohorts 96 and 98, respectively). Outcrossing rates (0.93 and 0.96 for cohorts 96 and 98, respectively) did not differ between years. Mean dispersal distances (222 and 192 m) were not significantly different between the 2 years but marginally more biased to long distance in 1996. The mean relatedness among cross-pollinated seedlings sharing the same mothers in cohort 96 was lower than that in cohort 98. This can be attributed to the two facts that the proportion of intersubpopulations pollen flow among cross-pollination events was marginally higher in cohort 96 (44%) than in cohort 98 (33%), and that mature trees within the same subpopulations are genetically more related to each other than those between different subpopulations. We conclude that D. tempehes maintained effective pollen dispersal in terms of outcrossing rate and pollen dispersal distance in spite of the large difference in foraging characteristics between two types of pollinators. In terms of pollen relatedness, however, a slight difference was suggested between years in the level of biparental inbreeding. [source] Characteristics of sex-biased dispersal and gene flow in coastal river otters: implications for natural recolonization of extirpated populationsMOLECULAR ECOLOGY, Issue 3 2002G. M. Blundell Abstract River otters (Lontra canadensis) were extirpated from much of their historic distribution because of exposure to pollution and urbanization, resulting in expansive reintroduction programmes that continue today for this and other species of otters worldwide. Bioaccumulation of toxins negatively affects fecundity among mustelids, but high vagility and different dispersal distances between genders may permit otter populations to recover from extirpation caused by localized environmental pollution. Without understanding the influence of factors such as social structure and sex-biased dispersal on genetic variation and gene flow among populations, effects of local extirpation and the potential for natural recolonization (i.e. the need for translocations) cannot be assessed. We studied gene flow among seven study areas for river otters (n = 110 otters) inhabiting marine environments in Prince William Sound, Alaska, USA. Using nine DNA microsatellite markers and assignment tests, we calculated immigration rates and dispersal distances and tested for isolation by distance. In addition, we radiotracked 55 individuals in three areas to determine characteristics of dispersal. Gender differences in sociality and spatial relationships resulted in different dispersal distances. Male river otters had greater gene flow among close populations (within 16,30 km) mostly via breeding dispersal, but both genders exhibited an equal, low probability of natal dispersal; and some females dispersed 60,90 km. These data, obtained in a coastal environment without anthropogenic barriers to dispersal (e.g. habitat fragmentation or urbanization), may serve as baseline data for predicting dispersal under optimal conditions. Our data may indicate that natural recolonization of coastal river otters following local extirpation could be a slow process because of low dispersal among females, and recolonization may be substantially delayed unless viable populations occurred nearby. Because of significant isolation by distance for male otters and low gene flow for females, translocations should be undertaken with caution to help preserve genetic diversity in this species. [source] Development and characterization of nine polymorphic microsatellite markers in the sand goby Pomatoschistus minutus (Gobiidae)MOLECULAR ECOLOGY RESOURCES, Issue 1 2007M. H. D. LARMUSEAU Abstract A microsatellite-enriched genomic library was constructed for the sand goby, Pomatoschistus minutus (Pallas 1770), and nine polymorphic DNA microsatellite markers of high quality were successfully optimized. Characterization of 96 individuals from the Vaccarès lagoon (France) showed moderate to high levels of polymorphism (two to 54 alleles). All the markers conformed to Hardy,Weinberg equilibrium and showed no evidence of null alleles, large allele dropout, stuttering and linkage disequilibrium between pairs of loci. These markers successfully amplify in three closely related species and can be employed to investigate population genetic structure and to clarify paternity in Pomatoschistus species. [source] Development of DNA microsatellite markers in tropical yam (Dioscorea sp.)MOLECULAR ECOLOGY RESOURCES, Issue 1 2006S. TOSTAIN Abstract We developed new simple sequence repeat (SSR) markers in different species of yam (Dioscorea sp.). A microsatellite-enriched bank was created from Dioscorea alata, Dioscorea abyssinica and Dioscorea praehensilis. Sixteen polymorphic loci were characterized. Several of these markers are transferable to species of other Dioscorea sections. [source] Characterization of nuclear DNA microsatellite markers in the ant Cataglyphis cursorMOLECULAR ECOLOGY RESOURCES, Issue 4 2004M. PEARCY Abstract The ant Cataglyphis cursor is exceptional in that unmated workers are potentially able to lay both male and female eggs. We characterized eight pairs of primers for microsatellite loci, developed from genomic DNA for this species. Variability was tested with DNA from 19 workers and all eight loci were highly polymorphic, displaying 5,10 alleles and a high level of heterozygosity. Cross-species amplifications indicate that these microsatellites might be useful in genetic studies of other species belonging to the genus Cataglyphis. [source] Development of DNA microsatellite markers in the Andean root crop arracacha: Arracacia xanthorrhiza Banc. (Apiaceae)MOLECULAR ECOLOGY RESOURCES, Issue 4 2004E. MORILLO Abstract A microsatellite-enriched library was constructed in the Andean root crop arracacha (Arracacia xanthorriza B). Of 18 loci tested, 14 were found to be polymorphic after screening for diversity in different cultivars and related wild forms. Allelic diversity in the crop was low but the transferability of the primers to closely related wild forms was good. The loci reported here are the first genetic markers to be published for this species and will be useful for future germplasm characterization and studies of genetic diversity. [source] Familial fibronectin glomerulopathy: analysis of chromosome 1q32 and uteroglobin gene loci in a large New Zealand familyNEPHROLOGY, Issue 5 2001Robert Walker SUMMARY: Recently, a newly recognized familial glomerulopathy with predominant fibronectin deposits has been reported. This is the first report of a family with this condition in Australasia and spans two generations over a 30-year period, with the histologically confirmed glomerulopathy present in the father and five out of eight siblings. The clinical presentations have ranged from asymptomatic proteinuria, pregnancy-associated proteinuria and the nephrotic syndrome to hypertension and proteinuria with progressive renal failure. The time-course from presentation to renal failure was over a 20 years. Histology demonstrated global and diffuse thickening of capillary loops, but no cellular proliferation. Immunofluorescence demonstrated granular positivity for IgM in the capillary loops only. Electron microscopy demonstrated massive electron-dense subendothelial granular deposits with occasional small fibrils and unremarkable epithelial cell foot processes. Immunohistochemical staining was strongly positive for fibronectin and negative for type I or type IV collagen and transforming growth factor , in all biopsies. Genetic studies of familial fibronectin glomerulopathy have recently highlighted two genetic loci. Firstly, a large five-generation pedigree has been described with linkage of fibronectin glomerulopathy to chromosome 1q32. Secondly, fibronectin glomerulopathy has been reported in uteroglobin gene knockout mice. In our studies, DNA sequence analysis of the uteroglobin gene showed that it was normal in all family members, and a DNA polymorphism in the uteroglobin gene did not co-segregate with the disease. In addition, DNA microsatellite markers at the 1q32 locus did not co-segregate with the disease in our family. We presume that the underlying abnormality involves as yet undefined glomerular extracellular matrix regulation and is inherited as an autosomal dominant condition. These data favour genetic heterogeneity for the aetiology of fibronectin glomerulopathy. [source] Population genetic structure and conservation of Asian elephants (Elephas maximus) across IndiaANIMAL CONSERVATION, Issue 4 2005T. N. C. Vidya This study examines the population genetic structure of Asian elephants (Elephas maximus) across India, which harbours over half the world's population of this endangered species. Mitochondrial DNA control region sequences and allele frequencies at six nuclear DNA microsatellite markers obtained from the dung of free-ranging elephants reveal low mtDNA and typical microsatellite diversity. Both known divergent clades of mtDNA haplotypes in the Asian elephant are present in India, with southern and central India exhibiting exclusively the , clade of Fernando et al. (2000), northern India exhibiting exclusively the , clade and northeastern India exhibiting both, but predominantly the , clade. A nested clade analysis revealed isolation by distance as the principal mechanism responsible for the observed haplotype distributions within the , and , clades. Analyses of molecular variance and pairwise population FST tests based on both mitochondrial and microsatellite DNA suggest that northern-northeastern India, central India, Nilgiris (in southern India) and Anamalai-Periyar (in southern India) are four demographically autonomous population units and should be managed separately. In addition, evidence for female philopatry, male-mediated gene flow and two possible historical biogeographical barriers is described. [source] QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labraxANIMAL GENETICS, Issue 4 2010C. Massault Summary Natural mating and mass spawning in the European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) complicate genetic studies and the implementation of selective breeding schemes. We utilized a two-step experimental design for detecting QTL in mass-spawning species: 2122 offspring from natural mating between 57 parents (22 males, 34 females and one missing) phenotyped for body weight, eight morphometric traits and cortisol levels, had been previously assigned to parents based on genotypes of 31 DNA microsatellite markers. Five large full-sib families (five sires and two dams) were selected from the offspring (570 animals), which were genotyped with 67 additional markers. A new genetic map was compiled, specific to our population, but based on the previously published map. QTL mapping was performed with two methods: half-sib regression analysis (paternal and maternal) and variance component analysis accounting for all family relationships. Two significant QTL were found for body weight on linkage group 4 and 6, six significant QTL for morphometric traits on linkage groups 1B, 4, 6, 7, 15 and 23 and three suggestive QTL for stress response on linkage groups 3, 14 and 23. The QTL explained between 8% and 38% of phenotypic variance. The results are the first step towards identifying genes involved in economically important traits like body weight and stress response in European sea bass. [source] | ||||||||||