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PubMed2005

Genetic structure and migration from mainland to island populations in Abies procera Rehd.

Noble fir (Abies procera Rehd) is a narrowly distributed conifer with a typical mainland-island structure of natural distribution. Here, we examined the genetic structure of populations native to the Pacific coast from Oregon to Washington (5 island and 16 mainland populations) with 14 polymorphic allozyme loci. A general method for estimating the number of unidirectional migrants from the mainland to island populations is presented in terms of the relation of average heterozygosity between the mainland and island populations. The results indicated that there were substantial island-mainland population differentiations (Fst = 0.107+/-0.029~0.154+/-0.039) but small differentiation within the mainland/submainland populations (0.037+/-0.008 approximately 0.054+/-0.010). Significant isolation by distance existed among the island-mainland populations and among the populations in Washington submainland. Four islands investigated received different numbers of migrants from the mainland/submainland. The southern island populations received a smaller number of migrants from the mainland but had greater genetic diversity, implying that there could be introgression with A. magnifica and (or) they represented possible glacial refuges and had expanded northwards after the last glaciations. The island populations close to the Pacific coast were more likely mainland-dependent.

Abies↗
PubMed2004

Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain.

The genetic structure of the population of Watermelon mosaic virus (WMV) in Spain was analysed by the biological and molecular characterisation of isolates sampled from its main host plant, melon. The population was a highly homogeneous one, built of a single pathotype, and comprising isolates closely related genetically. There was indication of temporal replacement of genotypes, but not of spatial structure of the population. Analyses of nucleotide sequences in three genomic regions, that is, in the cistrons for the P1, cylindrical inclusion (CI) and capsid (CP) proteins, showed lower similar values of nucleotide diversity for the P1 than for the CI or CP cistrons. The CI protein and the CP were under tighter evolutionary constraints than the P1 protein. Also, for the CI and CP cistrons, but not for the P1 cistron, two groups of sequences, defining two genetic strains, were apparent. Thus, different genomic regions of WMV show different evolutionary dynamics. Interestingly, for the CI and CP cistrons, sequences were clustered into two regions of the sequence space, defining the two strains above, and no intermediary sequences were identified. Recombinant isolates were found, accounting for at least 7% of the population. These recombinants presented two interesting features: (i) crossover points were detected between the analysed regions in the CI and CP cistrons, but not between those in the P1 and CI cistrons, (ii) crossover points were not observed within the analysed coding regions for the P1, CI or CP proteins. This indicates strong selection against isolates with recombinant proteins, even when originated from closely related strains. Hence, data indicate that genotypes of WMV, generated by mutation or recombination, outside of acceptable, discrete, regions in the evolutionary space, are eliminated from the virus population by negative selection.

Citrullus↗
PubMed2005

Genetic structure and colonization processes in European populations of the common vole, Microtus arvalis.

The level of genetic differentiation within and between evolutionary lineages of the common vole (Microtus arvalis) in Europe was examined by analyzing mitochondrial sequences from the control region (mtDNA) and 12 nuclear microsatellite loci (nucDNA) for 338 voles from 18 populations. The distribution of evolutionary lineages and the affinity of populations to lineages were determined with additional sequence data from the mitochondrial cytochrome b gene. Our analyses demonstrated very high levels of differentiation between populations (overall FST: mtDNA 70%; nucDNA 17%). The affinity of populations to evolutionary lineages was strongly reflected in mtDNA but not in nucDNA variation. Patterns of genetic structure for both markers visualized in synthetic genetic maps suggest a postglacial range expansion of the species into the Alps, as well as a potentially more ancient colonization from the northeast to the southwest of Europe. This expansion is supported by estimates for the divergence times between evolutionary lineages and within the western European lineage, which predate the last glacial maximum (LGM). Furthermore, all measures of genetic diversity within populations increased significantly with longitude and showed a trend toward increase with latitude. We conclude that the detected patterns are difficult to explain only by range expansions from separate LGM refugia close to the Mediterranean. This suggests that some M. arvalis populations persisted during the LGM in suitable habitat further north and that the gradients in genetic diversity may represent traces of a more ancient colonization of Europe by the species.

Animals↗
PubMed1984

Genetic structure of natural populations of the red-spotted newt, Notophthalmus viridescens.

Genetic variation is described at 15 loci in 2 neotenic and 12 nonneotenic populations of red-spotted newts. Though high levels of genetic similarity (I = 0.990) were found among all populations, allele frequencies at six of the eight most polymorphic loci show significant heterogeneity across populations. Change in allele frequencies at two of these loci (Pep-2 and Ldh-1) is significantly correlated with latitude. Interspecific homologies are established for newt peptidases based on substrate specificities and lactate dehydrogenases based on tissue distribution, thermal stability, and kinetic properties. Nonneotenic populations are highly variable (H = 0.157) and neotenic populations are only slightly, but significantly, less variable (H = 0.120). The high levels of heterozygosity detected in nonneotenic populations may result from large effective population size and/or environmental heterogeneity. The unexpectedly high heterozygosity values obtained for the neotenic populations may indicate adult dispersal or the presence of some previously undetected red efts at these localities. In any case, a major change in life history has apparently had little effect on the genetic structure of these populations.

Alleles↗
PubMed2005

Pollution and genetic structure of North American populations of the common dandelion (Taraxacum officinale).

Assessing the genetic structure of natural populations differentially impacted by anthropogenic contaminants can be a useful tool for evaluating the population genetic consequences of exposure to pollution. In this study, measures of genetic diversity at variable-number-tandem-repeat loci in six dandelion populations (3 urban and 3 rural) showed patterns that may have been influenced by exposure to environmental contaminants. Mean genetic similarity among individuals within a population was significantly and positively correlated with increasing levels of airborne particulate matter (< or = 10 microm, PM10) and soil concentrations of four metals (Cd, Fe, Ni and Pb). In addition, mean genetic similarity was always significantly higher at the urban sites compared to rural sites. There was a significant negative correlation between the number of genotypes at a site and increasing amounts of PM10, concentrations of five soil metals (Cd, Cu, Fe, Ni and Pb), leaf tissue levels of Fe and a significant positive correlation between the extent of clonality at a site and levels of PM10 and soil concentrations of five metals (Cd, Cu, Fe, Ni and Pb). Although, this study does not directly establish a causal link between the specific contaminants detected at the study sites and differences in genetic diversity, our data are consistent with the hypothesis that pollution-induced selection has contributed in some fashion to the lower genetic diversity found at the urban sites.

DNA, Plant↗
PubMedDate not supplied

[Comparative analysis of the genetic structure of Red Polish cattle in Poland and the Ukraine].

Comparative analysis of genetic structure of two groups of Red Polish cattle, which reproduce in Poland and Ukraine, was made. Six molecular-genetic markers (kappa-casein, beta-lactoglobulin, leptin, myostatin, growth hormone, and pituitary-specific transcription factor Pit-I) were tested by PCR-RFLP. No significant differences between the considered intrabreed groups were found. High frequency of some alleles (Csn kappa B, Blg B, and Gh L) related to the important productivity traits were observed. The rare alleles in some genes were revealed. The obtained results are evidence of the unique characteristics of the investigated breed.

Animals↗
PubMed1998

Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera.

We developed genetic markers for three microsatellite loci in the tropical tree Symphonia globulifera and used them to examine the demographic genetic consequences of forest fragmentation. High levels of genetic variation were revealed in samples of adults, saplings, and seedlings. The more-variable loci exhibited less stability in allelic composition across sites and stages. The number of alleles per hectare (ha) of forest was similar when continuous forest plots were compared to plots from fragmented forest for all three stages. This pattern also held for the number of unique multilocus adult and sapling genotypes, but the number of unique seedling genotypes per ha of fragmented forest greatly exceeded expectations based on continuous forest data, probably due to the concentration of seeds into remnant forest patches by foraging bats. Significant inbreeding and genetic differentiation were most often associated with the fragmented forest and the seedlings. Finally, principal component analysis reaffirmed that a bottleneck, acting in concert with pre-existing genetic structure in the adults, had led to enhanced and rapid divergence in the seedlings following deforestation, a result that is of central interest for landscape management.

Age Factors↗
PubMed2004

New insights from fine-scale spatial genetic structure analyses in plant populations.

Many empirical studies have assessed fine-scale spatial genetic structure (SGS), i.e. the nonrandom spatial distribution of genotypes, within plant populations using genetic markers and spatial autocorrelation techniques. These studies mostly provided qualitative descriptions of SGS, rendering quantitative comparisons among studies difficult. The theory of isolation by distance can predict the pattern of SGS under limited gene dispersal, suggesting new approaches, based on the relationship between pairwise relatedness coefficients and the spatial distance between individuals, to quantify SGS and infer gene dispersal parameters. Here we review the theory underlying such methods and discuss issues about their application to plant populations, such as the choice of the relatedness statistics, the sampling scheme to adopt, the procedure to test SGS, and the interpretation of spatial autocorrelograms. We propose to quantify SGS by an 'Sp' statistic primarily dependent upon the rate of decrease of pairwise kinship coefficients between individuals with the logarithm of the distance in two dimensions. Under certain conditions, this statistic estimates the reciprocal of the neighbourhood size. Reanalysing data from, mostly, published studies, the Sp statistic was assessed for 47 plant species. It was found to be significantly related to the mating system (higher in selfing species) and to the life form (higher in herbs than trees), as well as to the population density (higher under low density). We discuss the necessity for comparing SGS with direct estimates of gene dispersal distances, and show how the approach presented can be extended to assess (i) the level of biparental inbreeding, and (ii) the kurtosis of the gene dispersal distribution.

Demography↗
PubMed1976

Genetic structure and heterozygosity in the kuru region, eastern highlands of New Guinea.

Genetic structure of 20 of the 37 linguistic groups in the Eastern Highlands of New Guinea including the kuru region is analyzed using information on blood groups and serum protein polymorphisms. The average individual is heterozygous at 28.6% of loci and the average number of alleles per locus is 1.234. Coefficients of kinship for linguistic groups range from 0.005 for the sweet potato cultivating North Fore to 0.075 for the isolated Pawaians whose dietary staple is sago and who depend more on hunting and gathering. As one selects linguistic groups with smaller and smaller population size and increasing isolation, one finds that kinship coefficients rise as much as tenfold, but there is no concomitant loss of heterozygosity or trend toward fixation of alleles. Genetic relationships established by genetic distance trees and by principal components analysis are comparable and are consistent with other anthropological observations.

Alleles↗
PubMed1985

[Polymorphic biochemical systems in a population of newly arrived inhabitants of the northeastern USSR. IV. The characteristics of the genetic structure of persons with chronic pathological processes].

Analysis of properties of the genetic structure in 2847 individuals with different chronic diseases (1261 men and 1586 women) for 14 polymorphic loci (AcP, PGM1, PGD, GPT, GLO-I, EsD, AK, Pp, E2, Hp, Gc, Tf, AB0 and Rh) is presented. Discrepancy between the observed and expected phenotype frequencies for PGM1, GLO-I, EsD and AB0 loci is observed in a sample of patients Deviation from the expected frequencies is unequal for the representatives of different sex. Male and female portions of the sample differ significantly from each other for AcP, GPT, GLO-I, AK, EsD, Tf and AB0 loci, i. e. for 7 from 14 systems analysed. Highly significant differences between healthy and sick individuals have been detected: in general samples for 8 loci (AcP, PGM1, GPT, GLO-I, AK, Pp, Hp, AB0); in men for 8 loci (AcP, GPT, AK, PGD, Pp, Tf, AB0); in women for 5 loci (PGD, Pp, Gc, Tf, AB0). The difference between sick and healthy individuals of different sex is not only of qualitative but also of quantitative expression. The difference between sick and healthy men is much stronger, as compared to that between women. A decline in the average heterozygosity is noted in sick individuals. From the results obtained it is possible to conclude that the group of different pathologic conditions for the complex of genetic parameters differs significantly from that of healthy individuals. This may be a reflection of adaptation and disadaptation processes under the extreme environmental conditions.

ABO Blood-Group System↗
PubMed1992

Genetic structures in the Po Delta: principal components, systemic functions and the relative age of the beta-thalassemia polymorphism.

The principal component representations of the genetic structure of the human population of the Po Delta, obtained from 7 polymorphic loci, are compared with the representations obtained from the systemic function of gene frequencies devised by Womble 1951. It is noted that, when tridimensional representations are used, some consistency is visible in the results of the two methods for the description of the genetic population structure in the area under study. Both methods indicate that the present structure of the balanced polymorphism for beta-thalassemia in the area appears to be more recent than the structure of the neutral polymorphisms studied.

Alleles↗
PubMed1998

Phenotypic and genetic structure of traits delineating personality disorder.

BACKGROUND: The evidence suggests that personality traits are hierarchically organized with more specific or lower-order traits combining to form more generalized higher-order traits. Agreement exists across studies regarding the lower-order traits that delineate personality disorder but not the higher-order traits. This study seeks to identify the higher-order structure of personality disorder by examining the phenotypic and genetic structures underlying lower-order traits. METHODS: Eighteen lower-order traits were assessed using the Dimensional Assessment of Personality Disorder-Basic Questionnaire in samples of 656 personality disordered patients, 939 general population subjects, and a volunteer sample of 686 twin pairs. RESULTS: Principal components analysis yielded 4 components, labeled Emotional Dysregulation, Dissocial Behavior, Inhibitedness, and Compulsivity, that were similar across the 3 samples. Multivariate genetic analyses also yielded 4 genetic and environmental factors that were remarkably similar to the phenotypic factors. Analysis of the residual heritability of the lower-order traits when the effects of the higher-order factors were removed revealed a substantial residual heritable component for 12 of the 18 traits. CONCLUSIONS: The results support the following conclusions. First, the stable structure of traits across clinical and nonclinical samples is consistent with dimensional representations of personality disorders. Second, the higher-order traits of personality disorder strongly resemble dimensions of normal personality. This implies that a dimensional classification should be compatible with normative personality. Third, the residual heritability of the lower-order traits suggests that the personality phenotypes are based on a large number of specific genetic components.

Adolescent↗
PubMed2003

Nuclear and chloroplast genetic structure indicate fine-scale spatial dynamics in a neotropical tree population.

Dicorynia guianensis is a canopy tree, endemic to the tropical rain forest of French Guiana. We compared generational and spatial genetic structure for maternally and biparentally inherited markers in two cohorts (adult and seedling) in order to infer processes shaping the distribution of genetic diversity. The study was conducted on a 40 ha study plot located at Paracou near Kourou, where 172 adults trees and 375 saplings were sampled. Aggregation of trees was therefore suggested at different distances, ranging from 100 to 400 m. There was a strong link between demographic and genetic spatial structures at small distances (less than 100 m) that is likely to be the consequence of restricted seed dispersal. Genetic differentiation was more pronounced between spatial aggregates than between cohorts. Despite the spatial differentiation, the species was able to maintain high levels of diversity for maternal genomes, suggesting rapid turnover of aggregates. Spatial autocorrelation was larger for chloroplast than nuclear markers indicating a strong asymmetry between pollen and seed flow. Fixation indices indicated a lower heterozygote deficiency for the adults, maybe because of gradual elimination of selfed trees. Genetic relatedness at lower distances was higher in adult trees than in saplings, as a result of generation overlapping in the adult cohort. Overall, our results confirm earlier biological knowledge about the dispersion mechanisms of the species, and lead to an enhanced role of spatial processes in the dynamics of genetic diversity of D. guianensis.

Cell Nucleus↗
PubMed2004

[Population genetic structure of Pelophylax nigromaculata in Chinese mainland based on mtDNA control region sequences].

Molecular genetic data were used to investigate population genetic structure and differentiation of Pelophylax nigromaculata (Anura: Ranidae). Frogs were collected from 12 localities across Chinese mainland. Sample sizes of up to 10 frogs per population were assayed for mitochondrial control region sequence variation. The aligned 685 bp of the 5'CR include 111 variable sites. Sixty-seven haplotypes were defined. Most of the haplotypes are unique to local populations, only 7 of the 67 are shared among a few local populations. The overall species haplotype diversity is quite high (h = 0.98 +/- 0.005), and the nucleotide diversity is also high (pi = 0.0303 +/- 0.0029). This is corresponding to huge population size and extensive distribution of Pelophylax nigromaculata throughout Palaearctic and Oriental Regions. Phylogenetic tree of mtDNA control region haplotypes based on maximum parsimony algorithm and reconstructed phylogenetic relationships among the local populations based on neighbor joining algorithm all suggest that the haplotypes of Jiling and Liaoning populations in northeastern China have a sister relationship with 10 local populations in northern, central, southern and southwestern China. The analysis of molecular variance (AMOVA), the pairwise FST values and nucleotide divergence all support significant population subdivision between the Jilin-Liaoning group and multi-population group. The most possible cause of the significant genetic subdivision between the two groups might be referred to the effect of Quaternary glaciation. The possible reasons for the lack of obvious geographic structure on the whole in the multi-population group and the genetic differentiation in some local populations of the multi-population group were also discussed.

Animals↗
PubMed2001

Genetic structure and distinctness of Apis mellifera L. populations from the Canary Islands.

The genetic structure of Apis mellifera populations from the Canary Islands has been assessed by mitochondrial (restriction fragment length polymorphisms of the intergenic transfer RNAleu-COII region) and nuclear (microsatellites) studies. These populations show a low level of genetic variation in terms of average number of alleles and degree of heterozygosity. Significant differences in the distribution of alleles were found in both data sets, confirming the genetic differentiation among some of the islands but not within them. Two mitochondrial haplotypes characteristic of the Canary Islands are found at high frequencies, although populations are introgressed by imported honeybees of eastern European C lineage. This introgression is rather high on Tenerife and El Hierro and low on Gran Canaria and La Gomera, whereas on La Palma it has not been recorded. The finding of microsatellite alleles characteristic of the eastern European lineage corroborates the genetic introgression. Phylogenetic analyses indicate that the Canarian honeybees are differentiated from other lineages and provide genetic evidence of their African origin.

Alleles↗
PubMed2004

Effects of habitat fragmentation on the genetic structure of the monophagous butterfly Polyommatus coridon along its northern range margin.

Population genetic patterns of species at their range margin have important implications for species conservation. We performed allozyme electrophoresis of 19 loci to investigate patterns of the genetic structure of 17 populations (538 individuals) of the butterfly Polyommatus coridon, a monophagous habitat specialist with a patchy distribution. The butterfly and its larval food plant Hippocrepis comosa reach their northern distribution margin in the study region (southern Lower Saxony, Germany). Butterfly population size increased with host plant population size. The genetic differentiation between populations was low but significant (FST = 0.013). No isolation-by-distance was found. Hierarchical F-statistics revealed significant differentiation between a western and an eastern subregion, separated by a river valley. The combination of genetic and ecological data sets revealed that the expected heterozygosity (mean: 18.5%) decreased with increasing distance to the nearest P. coridon population. The population size of P. coridon and the size of larval food plant population had no effect on the genetic diversity. The genetic diversity of edge populations of P. coridon was reduced compared to populations from the centre of its distribution. This might be explained by (i). an increasing habitat fragmentation towards the edge of the distribution range and/or (ii). a general reduction of genetic variability towards the northern edge of its distribution.

Animals↗
PubMed2000

The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data.

Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean FST approximately 0.08; P < 0.01). Atlantic breeds clearly form a separate cluster from the Balearic Islands breeds and among the former only two form a clear clustering, while the rest of Atlantic breeds (Jaca Navarra, Caballo Gallego and Pottoka) are not consistently differentiated. Multivariate analysis showed that Asturcon populations, Losina and Balearic Islands breeds are clearly separated from each other and from the rest of the breeds. In addition to this, the use of the microsatellites proved to be useful for breed assignment.

Animals↗
PubMed2003

Population genetic structure and cladistic analysis of Trypanosoma brucei isolates.

Using a novel multilocus DNA marker analysis method, we studied the population genetic structure of Trypansoma brucei stocks and derived clones isolated from animal and rhodesiense sleeping sickness patients during a national sleeping sickness control program in Mukono district, Uganda. We then performed a cladistic analysis to trace relationships and evolution, using stocks and clones recovered from geographically and temporally matched hosts, including inter-strain comparisons with T. b. gambiense stocks and clones. Our results show that while there was close genetic relatedness among parasite populations from the same geographical region, micro-heterogeneities exist between different stocks. Data are presented that indicate that not every human sleeping sickness focus may be associated with a particular human-infective trypanosome strain responsible for long-term stability of the reference focus. We provide evidence of genetic sub-structuring among type 1 T. b. gambiense stocks, which has potentially important implications for molecular epidemiology of T. brucei.

Animals↗