Level Of Interpopulation Differentiation Research Articles

Morphological Variation and Genetic Diversity of Gymnadenia conopsea (L.) R. Br. (Orchidaceae) Populations in the Northeast of European Russia (Komi Republic)

Using ISSR-PCR approach, the genetic structure of G. conopsea populations have been studied in the Komi Republic (Russia) at the northern boundary of its range, where the populations have a high level of phenotypic variation. It was established that the reaction of G. conopsea specimens to the lack of heat was expressed as a decrease in the most plastic phenotypic traits (shoot height, inflorescence length, number of flowers, leaf size) and determined a clear morphological differentiation in karst landscapes of the Timan Ridge with different temperature conditions. Two ISSR primers made it possible to reveal 839 loci, 37.79% of which were polymorphic. UPGMA analysis divided the pool of G. conopsea populations into two clusters: populations from the limestones of Timan (180 plants) and population from the Mezen-Vychegda Plain (20 plants). The assessment of genetic variability revealed the decreased parameters in the G. conopsea population from the Mezen-Vychegda Plain (P = 26.94%, He = 0.050, Is = 0.084). At limestones of South Timan, the species had both highly variable populations (P = 55.5–60.6%, He = 0.084–0.089) and populations with decreased parameters of genetic variability (P = 29.3–29.6%, He = 0.053–0.059). Despite the high diversity of karst landscapes and territorial fragmentation of the populations, we found a low level of interpopulation differentiation (F = 0.017–0.036) and strong genetic flows between the populations (D = 0.007–0.020, I = 0.980–0.993). A Mantel test did not show a correlation between the genetic and geographic distances among populations (r = –0.047; p = 0.04). A majority of the revealed genetic variability was realized inside the populations. The share of interpopulation variability was only 14%. An analysis of genetic relationships based on the Structure v2.3 software program allowed us to divide the samples according to two geographical areas and to suggest that in South Timan there are at least four separate groups differing in ISSR markers. No clear dependence between the type of karst landscape and genetic variability of the populations was detected.

Microsatellite Genotyping of Plasmodium vivax Isolates from Pregnant Women in Four Malaria Endemic Countries.

Plasmodium vivax is the most widely distributed human parasite and the main cause of human malaria outside the African continent. However, the knowledge about the genetic variability of P. vivax is limited when compared to the information available for P. falciparum. We present the results of a study aimed at characterizing the genetic structure of P. vivax populations obtained from pregnant women from different malaria endemic settings. Between June 2008 and October 2011 nearly 2000 pregnant women were recruited during routine antenatal care at each site and followed up until delivery. A capillary blood sample from the study participants was collected for genotyping at different time points. Seven P. vivax microsatellite markers were used for genotypic characterization on a total of 229 P. vivax isolates obtained from Brazil, Colombia, India and Papua New Guinea. In each population, the number of alleles per locus, the expected heterozygosity and the levels of multilocus linkage disequilibrium were assessed. The extent of genetic differentiation among populations was also estimated. Six microsatellite loci on 137 P. falciparum isolates from three countries were screened for comparison. The mean value of expected heterozygosity per country ranged from 0.839 to 0.874 for P. vivax and from 0.578 to 0.758 for P. falciparum. P. vivax populations were more diverse than those of P. falciparum. In some of the studied countries, the diversity of P. vivax population was very high compared to the respective level of endemicity. The level of inter-population differentiation was moderate to high in all P. vivax and P. falciparum populations studied.

Genetic differentiation of sockeye salmon Oncorhynchus nerka (Walbaum, 1792) populations of eastern Kamchatka

The interpopulation differentiation of the sockeye salmon Oncorhynchus nerka (Walbaum) from the Olyutorskiy and Karaginskiy districts and from the Kamchatka River basin was examined based on the allelic variation at eight microsatellite loci (Ots107, Oki1a, Oki1b, One104, One109, OtsG68, OtsG85, and Oki6). The genetic diversity of samples from the northern rivers was lower, compared to samples from the Kamchatka River basin. Significant heterogeneity was found in the allele-frequency distribution at microsatellite loci of sockeye salmon from the investigated localities. The degree of genetic similarity of populations corresponded to their geographic closeness. The differences between population groups greatly exceeded the level of interpopulation differentiation. The analyzed samples formed four relatively separate groups: Lake Azabachye, Kamchatka River basin, Karaginskiy area (including the Navyrinvayam River in the south of the Olyutorskiy district), and northern Olyutorskiy area. The identification likelihood estimates of eastern Kamchatkan sockeye salmon in mixed aggregations at the level of population groups were fairly high (67.2–81.8%), greatly exceeding the accuracy of identification of individual populations.

Chloroplast phylogeography of threatened aquatic Oxalis (Oxalidaceae): significant inter-population structure, divergent haplotypes and conservation implications

The aquatic lineage consisting of the sister taxa Oxalis dines and O. disticha is confined to a few small vernal pools in the semi-arid Greater Cape Floristic Region of South Africa. All known populations are at risk of extinction due to anthropogenically induced disturbance. To identify priority sites for focused conservation management, the chloroplast intergenic spacer regions psbA-trnH and trnS-trnG were used to determine population structure and genetic diversity in this lineage across its distribution range. Population viability was assessed using flower morph ratios as surrogate for sexual health. Fourteen and four haplotypes were identified from O. disticha and O. dines populations, respectively. Analyses of Molecular Variance indicated an extremely high level of interpopulation differentiation across the entire aquatic lineage as well as within O. disticha and O. dines. Fifty percent of the eighteen haplotypes were confined to single pools, and 84% of populations contained only a single haplotype, even though pool interspacing distance for O. disticha was often less than 5 km. Almost half of O. disticha haplotype diversity was restricted to very small populations. Two O. dines haplotypes were restricted to small populations, with one of these presenting a divergent haplotype sister to the remainder of the aquatic lineage. Flower morph frequency ratio analyses suggested that most populations were reproductively healthy. Low haplotypic diversity within local populations and differentiation between populations are consistent with very low seed-level gene flow and sporadic founder effects. Conservation efforts should be focussed on preserving as many pools as possible with small, genetically distinct populations representing a main concern.

Allozyme diversity in pheasants (Phasianus spp.) from breeding stations in Serbia

The pheasant breeds are widely used for restocking of natural populations depleted by hunting. The pheasant population number decline was detected during the 1970s in many hunting areas of Europe. One of its possible reasons might be the loss of adaptability in populations originating from breeding stations, which was caused by inbreeding depression. The aim of this paper was the analysis of genetic variability in pheasant populations from three breeding stations in Vojvodina province (Serbia) by means of allozyme diversity detection. The allozyme variability analysis of pheasants from all three breeding stations revealed polymorphisms at nine loci: Ldh-1, Mor-1, Mor-2, Es-1, Mod-2, Pgd, Gpi-2, Odh, and Sod. The analysis of individuals from three different breeding stations showed mean values of observed heterozygosity of Ho=0.137, polymorphism P95%=30%, and H/P ratio H/P=0.430, which indicate a normal level of genetic variability for bird populations. Comparative analysis of three pheasant populations showed a high level of interpopulation differentiation.

Levels of interpopulation differentiation among different functional classes of immunologically important genes

It has been postulated that gene function may influence the degree to which allele frequencies differ among populations. In order to evaluate this effect, genotypic data from resequencing studies of genes classified as cytokines, cytokine receptors, cell adhesion molecules, Toll-like receptors and coagulation proteins were analysed for genetic differentiation (FST) between population samples of European and African descent. FST values did not differ statistically among functional groups when all polymorphic sites were included in the analyses. However, analysis based on nonsynonymous SNPs alone suggested weak heterogeneity among functional classes (P=0.0424). Particularly high levels of differentiation were shown by individual nonsynonymous SNPs at some genes, most notably ICAM1 and some Toll-like receptors. These genes interact directly with pathogens, and may therefore have been subject to geographically localised natural selection. Such loci warrant particular attention in studies of genetic disease risk and local adaptation to environmental conditions.

Sampling Issues Affecting Accuracy of Likelihood-based Classification Using Genetical Data

We demonstrate the effectiveness of a genetic algorithm for discovering multi-locus combinations that provide accurate individual assignment decisions and estimates of mixture composition based on likelihood classification. Using simulated data representing different levels of inter-population differentiation (Fst ∼ 0.01 and 0.10), genetic diversities (four or eight alleles per locus), and population sizes (20, 40, 100 individuals in baseline populations), we show that subsets of loci can be identified that provide comparable levels of accuracy in classification decisions relative to entire multi-locus data sets, where 5, 10, or 20 loci were considered. Microsatellite data sets from hatchery strains of lake trout, Salvelinus namaycush, representing a comparable range of inter-population levels of differentiation in allele frequencies confirmed simulation results. For both simulated and empirical data sets, assignment accuracy was achieved using fewer loci (e.g., three or four loci out of eight for empirical lake trout studies). Simulation results were used to investigate properties of the ‘leave-one-out’ (L1O) method for estimating assignment error rates. Accuracy of population assignments based on L1O methods should be viewed with caution under certain conditions, particularly when baseline population sample sizes are low (<50).

Allozyme Diversity and Genetic Relationships among North American Members of the Short-Beaked Taxa of Carex sect. Vesicariae (Cyperaceae)

Morphological studies of the short-beaked members of Carex sect. Vesicariae have indicated that three species can be recognized: C. saxatilis (incl. C. miliaris and C. physocarpa), C. membranacea, and C. rotundata. To assess genetic relationships among species and gene diversity within species, 44 populations from throughout North America were surveyed electrophoretically for 12 enzymes encoded by 17 putative loci. Populations of the same species exhibited high genetic identities, with average values exceeding 0.950. Interspecific genetic identities ranged from 0.636 (between C. saxatilis and C. rotundata) to 0.880 (C. membranacea and C. rotundata). Alleles for the isozymes AAT-1, AAT-2, 6-PGD, PGI-2, PGM-2, and SKDH were useful in distinguishing C. saxatilis from C. membranacea and C. rotundata. Carex membranacea and C. rotundata were best distinguished by alleles of 6-PGD. There was little allozyme differentiation within the C. saxatilis complex; however, a weak east/west cline was evident. Within populations, observed heterozygosity closely matched expected levels of heterozygosity: F values averaged 0.039, indicating outcrossing is prevalent. Genetic variation was found to be largely apportioned within populations as Nei's gene diversity statistic (GST) was close to 0.19 in each species. Past electrophoretic studies of Carex have disclosed low levels of intrapopulation genetic variation and high levels of interpopulation differentiation indicating high levels of inbreeding. Large population sizes, dichogamy, a rhizomatous habit, and self-incompatibility are discussed as possible mechanisms for maintaining genetic diversity within populations of the short-beaked species.