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Microsatellite Diversity (microsatellite + diversity)
Selected AbstractsMicrosatellite 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] Microsatellite diversity associated with ecological factors in Hordeum spontaneum populations in IsraelMOLECULAR ECOLOGY, Issue 6 2001Timo Turpeinen Abstract Microsatellite diversity at 18 loci was analysed in 94 individual plants of 10 wild barley, Hordeum spontaneum (C. Koch) Thell., populations sampled from Israel across a southward transect of increasing aridity. Allelic distribution in populations was not distributed randomly. Estimates of mean gene diversity were highest in stressful arid-hot environments. Sixty-four per cent of the genetic variation was partitioned within populations and 36% between populations. Associations between ecogeographical variables and gene diversity, He, were established in nine microsatellite loci. By employing principle component analysis we reduced the number of ecogeographical variables to three principal components including water factors, temperature and geography. At three loci, stepwise multiple regression analysis explained significantly the gene diversity by a single principal component (water factors). Based on these observations it is suggested that simple sequence repeats are not necessarily biologically neutral. [source] BALANCING SELECTION, RANDOM GENETIC DRIFT, AND GENETIC VARIATION AT THE MAJOR HISTOCOMPATIBILITY COMPLEX IN TWO WILD POPULATIONS OF GUPPIES (POECILIA RETICULATA)EVOLUTION, Issue 12 2006Cock van Oosterhout Abstract Our understanding of the evolution of genes of the major histocompatibility complex (MHC) is rapidly increasing, but there are still enigmatic questions remaining, particularly regarding the maintenance of high levels of MHC polymorphisms in small, isolated populations. Here, we analyze the genetic variation at eight microsatellite loci and sequence variation at exon 2 of the MHC class IIB (DAB) genes in two wild populations of the Trinidadian guppy, Poecilia reticulata. We compare the genetic variation of a small (Ne, 100) and relatively isolated upland population to that of its much larger (Ne, 2400) downstream counterpart. As predicted, microsatellite diversity in the upland population is significantly lower and highly differentiated from the population further downstream. Surprisingly, however, these guppy populations are not differentiated by MHC genetic variation and show very similar levels of allelic richness. Computer simulations indicate that the observed level of genetic variation can be maintained with overdominant selection acting at three DAB loci. The selection coefficients differ dramatically between the upland (s 0.2) and lowland (s, 0.01) populations. Parasitological analysis on wild-caught fish shows that parasite load is significantly higher on upland than on lowland fish, which suggests that large differences in selection intensity may indeed exist between populations. Based on the infection intensity, a substantial proportion of the upland fish would have suffered direct or indirect fitness consequences as a result of their high parasite loads. Selection by parasites plays a particularly important role in the evolution of guppies in the upland habitat, which has resulted in high levels of MHC diversity being maintained in this population despite considerable genetic drift. [source] Genetic diversity, but not hatching success, is jointly affected by postglacial colonization and isolation in the threatened frog, Rana latasteiMOLECULAR ECOLOGY, Issue 9 2007GENTILE FRANCESCO FICETOLA Abstract Both postglacial colonization and habitat fragmentation can reduce the genetic diversity of populations, which in turn can affect fitness. However, since these processes occur at different spatial and temporal scales, the consequences of either process may differ. To disentangle the relative role of isolation and postglacial colonization in determining genetic diversity and fitness, we studied microsatellite diversity of 295 individuals from 10 populations and measured the hatch rate of 218 clutches from eight populations of a threatened frog, R. latastei. The populations that were affected by fragmentation to a greater extent suffered higher embryo mortality and reduced hatch rate, while no effects of distance from glacial refugium on hatch rate were detected. Altogether, distance from glacial refugium and isolation explained > 90% of variation in genetic diversity. We found that the genetic diversity was lowest in populations both isolated and far from the glacial refugium, and that distance from refugium seems to have the primary role in determining genetic diversity. The relationship between genetic diversity and hatch rate was not significant. However, the proportion of genetic diversity lost through recent isolation had a significant, negative effect on fitness. It is possible that selection at least partially purged the negative effects of the ancestral loss of genetic diversity. [source] Conservation implications of complex population structure: lessons from the loggerhead turtle (Caretta caretta)MOLECULAR ECOLOGY, Issue 8 2005B. W. BOWEN Abstract Complex population structure can result from either sex-biased gene flow or population overlap during migrations. Loggerhead turtles (Caretta caretta) have both traits, providing an instructive case history for wildlife management. Based on surveys of maternally inherited mtDNA, pelagic post-hatchlings show no population structure across the northern Atlantic (,ST < 0.001, P = 0.919), subadults in coastal habitat show low structure among locations (,ST = 0.01, P < 0.005), and nesting colonies along the southeastern coast of the United States have strong structure (,ST = 0.42, P < 0.001). Thus the level of population structure increases through progressive life history stages. In contrast, a survey of biparentally inherited microsatellite DNA shows no significant population structure: RST < 0.001; FST = 0.002 (P > 0.05) across the same nesting colonies. These results indicate that loggerhead females home faithfully to their natal nesting colony, but males provide an avenue of gene flow between regional nesting colonies, probably via opportunistic mating in migratory corridors. As a result, all breeding populations in the southeastern United States have similar levels of microsatellite diversity (HE = 0.70,0.89), whereas mtDNA haplotype diversity varies dramatically (h = 0.00,0.66). Under a conventional interpretation of the nuclear DNA data, the entire southeastern United States would be regarded as a single management unit, yet the mtDNA data indicate multiple isolated populations. This complex population structure mandates a different management strategy at each life stage. Perturbations to pelagic juveniles will have a diffuse impact on Atlantic nesting colonies, mortality of subadults will have a more focused impact on nearby breeding populations, and disturbances to adults will have pinpoint impact on corresponding breeding populations. These findings demonstrate that surveys of multiple life stages are desirable to resolve management units in migratory marine species. [source] Optimization of novel polymorphic microsatellites in muskox (Ovibos Moschatus) leads to an increased estimate of muskox microsatellite diversityMOLECULAR ECOLOGY RESOURCES, Issue 4 2004PETER J. VAN COEVERDEN Abstract Initial microsatellite studies suggested that muskoxen display the lowest microsatellite polymorphism in a large ungulate. We optimized 17 di-nucleotide microsatellites with longer repeats from a muskox DNA library and surveyed 18 animals from across their natural range. Loci with perfect repeats were more variable than imperfect loci: Hperfect = 0.504 ± 0.045 (± SE) vs. Himperfect = 0.067 ± 0.055. Our Hperfect estimate is higher than previous low estimates of HE = 0.018 and HE = 0.059. [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] Analysis of durum wheat germplasm adapted to different climatic conditionsANNALS OF APPLIED BIOLOGY, Issue 2 2010L. Mondini A study of the extent and patterns of microsatellite diversity in 234 genotypes from Ethiopian durum wheat (Triticum turgidum) landraces was conducted to identify areas of diversity that could be used as a source of new germplasm for developing high yielding and stable varieties. Landraces belonging to nine populations, from three Ethiopian regions [Tigray (T), Gonder (G) and Shewa (S)] with different climates, were analysed by using 28 simple sequence repeat (SSR) markers. The level of polymorphism was high and quite consistent among populations underlining the great diversity existing. The highest level of diversity was found within populations, about 75.9%, while about 5.3% was attributed to differences between regions. The level of expected heterozygosity was on an average, rather high, ranging from 39% to 56%, whereas the observed heterozygosity was, on an average, limited to 14%. An average of about five alleles per locus was detected in each population. Nevertheless, alleles were not equally present in populations as confirmed by the high level of expected heterozygosity. The polymorphism information content (PIC) for the markers assessed showed a wide range of values from 0.14 to 0.92. The likelihood relationships among the nine Ethiopian populations indicated that the material collected in the Gonder region (a wet climate) was genetically more diverse than the materials from Shewa and Tigray (dryer climates). The high number of loci in linkage disequilibrium (LD), up to 23, has demonstrated that the loci were associated irrespective of their physical location. This holds true even if the loci are located on different chromosome arms. Genetic diversity values between populations was very different and was used to produce a dendrogram showing population relationships. [source] | ||||||||||