Geographic distribution of surnames and genetic structure: the county of Ardeche at the beginning of the twentieth century

The analysis of the geographical distribution of surnames (whose transmission in the European societies is similar to that of the Y chromosome) allows to study in an exhaustive way the spatial and temporal human population structure and the influence of environmental variations on this structure. The genetic structure of the Ardèche county was analysed through a study of the surname characteristics (diversity, frequency, geographical dispersion, etc.) of individuals born between 1891 and 1915. The estimation of the intra-community average consanguinity and the inter-district genetic relationships reveals a clear differentiation between populations of the mountainous part (geographically isolated, highly inbred) and those of the Rh?ne valley (less isolated, weakly inbred). As predicted by the isolation by distance model, inter-population coefficients of kinship decreases as distance increases, confirming the presence of a spatial structure, characterized by neighborhood exchange and resulting from former migratory flow.     

Genetic structure through surnames in Campobasso Province, Italy

The population of Campobasso Province shows a level of inbreeding that is distinct from most Italian rural populations, regardless of their geographic location (Fr=0.0040; Fn=0.0102; Ft=0.0142). The genetic structure of the Italian-Greek communities of Lecce and Reggio Calabria Provinces does not appear to be affected by ethnicity. The level of inbreeding in Italian-Greeks of Reggio Calabria Province is similar to other Italians of Campobasso Province (Fr=0.0041; Fn=0.0127; Ft=0.0168). The Italian-Greeks of Lecce Province show random mating, and their inbreeding is in fact very low (Fr=0.0038; Fn=0.0024; Ft=0.0062).     

The structure of common genetic variation in United States populations

The common-variant/common-disease model predicts that most risk alleles underlying complex health-related traits are common and, therefore, old and found in multiple populations, rather than being rare or population specific. Accordingly, there is widespread interest in assessing the population structure of common alleles. However, such assessments have been confounded by analysis of data sets with bias toward ascertainment of common alleles (e.g., HapMap and Perlegen) or in which a relatively small number of genes and/or populations were sampled. The aim of this study was to examine the structure of common variation ascertained in major U.S. populations, by resequencing the exons and flanking regions of 3,873 genes in 154 chromosomes from European, Latino/Hispanic, Asian, and African Americans generated by the Genaissance Resequencing Project. The frequency distributions of private and common single-nucleotide polymorphisms (SNPs) were measured, and the extent to which common SNPs were shared across populations was analyzed using several different estimators of population structure. Most SNPs that were common in one population were present in multiple populations, but SNPs common in one population were frequently not common in other populations. Moreover, SNPs that were common in two or more populations often differed significantly in frequency from one population to another, particularly in comparisons of African Americans versus other U.S. populations. These findings indicate that, even if the bulk of alleles underlying complex health-related traits are common SNPs, geographic ancestry might well be an important predictor of whether a person carries a risk allele.     

Finding the most significant common sequence and structure motifs in a set of RNA sequences.

We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints. In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections. The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The algorithm finds the multiple alignments using a greedy approach and has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. The choice of scoring system and the method of progressively constructing the final solution are important considerations that are discussed. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structures identical to published ones.     

Functional synergism between the most common polymorphism in human alanine:glyoxylate aminotransferase and four of the most common disease-causing mutations

The autosomal recessive disorder primary hyperoxaluria type 1 (PH1) is caused by a deficiency of the liver-specific pyridoxal-phosphate-dependent enzyme alanine:glyoxylate aminotransferase (AGT). Numerous mutations and polymorphisms in the gene encoding AGT have been identified, but in only a few cases has the causal relationship between genotype and phenotype actually been demonstrated. In this study, we have determined the effects of the most common naturally occurring amino acid substitutions (both normal polymorphisms and disease-causing mutations) on the properties, especially specific catalytic activity, of purified recombinant AGT. The results presented in this paper show the following: 1) normal human His-tagged AGT can be expressed at high levels in Escherichia coli and purified in a correctly folded, dimerized and catalytically active state; 2) presence of the common P11L polymorphism decreases the specific activity of purified recombinant AGT by a factor of three; 3) AGTs containing four of the most common PH1-specific mutations (G41R, F152I, G170R, and I244T) are all soluble and catalytically active in the absence of the P11L polymorphism, but in its presence all lead to protein destabilization and aggregation into inclusion bodies; 4) naturally occurring and artificial amino acid substitutions that lead to peroxisome-to-mitochondrion AGT mistargeting in mammalian cells also lead to destabilization and aggregation in E. coli; and 5) the PH1-specific G82E mutation abolishes AGT catalytic activity by interfering with cofactor binding, as does the artificial K209R mutation at the putative site of cofactor Shiff base formation. These results are discussed in the light of the high allelic frequency ( approximately 20%) of the P11L polymorphism and its importance in determining the phenotypic manifestations of mutations in PH1.     

Analysis of marital structure in Massachusetts using repeating pairs of surnames.

Analysis of surnames from marriages is now a well-established method in the study of marital and genetic structure. Traditional methods of partitioning inbreeding into random and nonrandom components rely on the total number of isonymous marriages. Because this number is often low, standard errors of inbreeding estimates tend to be high. Lasker and Kaplan (1985) devised a method that circumvents this problem by focusing on the total number of repeating pairs (RP) of surnames among marriages. The observed value of RP can be compared with the value expected at random (RPr) to assess patterns of subdivision within a population. The RP method is applied here to data from 3431 marriages that took place from 1800 to 1849 in 4 Massachusetts towns. The level of excess RP [(RP-RPr)/RPr] is positively associated with population size and exogamy rate. These results indicate a tendency for greater relative subdivision in larger, more exogamous populations. One possible reason for increased subdivision is preferential marriage by social class, although adequate data are not available for a test of this hypothesis.     

Fine-scale genetic structure and dispersal in the common vole (Microtus arvalis)

The genetic structure and demography of local populations is tightly linked to the rate and scale of dispersal. Dispersal parameters are notoriously difficult to determine in the field, and remain often completely unknown for smaller organisms. In this study, we investigate spatial and temporal genetic structure in relation to dispersal patterns among local populations of the probably most abundant European mammals, the common vole (Microtus arvalis). Voles were studied in six natural populations at distances of 0.4-2.5 km in three different seasons (fall, spring, summer) corresponding to different life-history stages. Field observations provided no direct evidence for movements of individuals between populations. The analysis of 10 microsatellite markers revealed a persistent overall genetic structure among populations of 2.9%, 2.5% and 3% FST in the respective season. Pairwise comparisons showed that even the closest populations were significantly differentiated from each other in each season, but there was no evidence for temporal differentiation within populations or isolation by distance among populations. Despite significant genetic structure, assignment analyses identified a relatively high proportion of individuals as being immigrants for the population where they were captured. The immigration rate was not significantly lower for females than for males. We suggest that a generally low and sex-dependent effective dispersal rate as the consequence of only few immigrants reproducing successfully in the new populations together with the social structure within populations may explain the maintenance of genetic differentiation among populations despite migration.     

Estimating seed vs. pollen dispersal from spatial genetic structure in the common ash

Spatial genetic structure was analysed with five highly polymorphic microsatellite loci in a Romanian population of common ash (Fraxinus excelsior L.), a wind-pollinated and wind-dispersed tree species occurring in mixed deciduous forests over almost all of Europe. Contributions of seed and pollen dispersal to total gene flow were investigated by analysing the pattern of decrease in kinship coefficients among pairs of individuals with geographical distance and comparing it with simulation results. Plots of kinship against the logarithm of distance were decomposed into a slope and a shape component. Simulations showed that the slope is informative about the global level of gene flow, in agreement with theoretical expectations, whereas the shape component was correlated with the relative importance of seed vs. pollen dispersal. Hence, our results indicate that insights into the relative contributions of seed and pollen dispersal to overall gene flow can be gained from details of the pattern of spatial genetic structure at biparentally inherited loci. In common ash, the slope provided an estimate of total gene dispersal in terms of Wright's neighbourhood size of Nb = 519 individuals. No precise estimate of seed vs. pollen flow could be obtained from the shape because of the stochasticity inherent to the data, but the parameter combinations that best fitted the data indicated restricted seed flow, sigmas pound 14 m, and moderate pollen flow, 70 m pound sigmap pound 140 m.     

Populations genetic structure of the razor clam Sinonovacula constricta from China,Korea and Vietnam

The population genetic structure of the razor clam Sinonovacula constricta was investigated between populations collected from China, Korea and Vietnam using cytochrome oxidase subunit 1 (COI) mtDNA and internal transcribed spacer 2 (ITS2) rDNA markers. A total of 622 bp of COI and 495 bp of ITS2 were sequenced. Highly significant Fst values and low rates of migration were observed from populations between Vietnam and China, (Fst = 0.7578, P < 0.001, Nm = 0.05 for COI; Fst = 0.91389, P < 0.001, Nm = 0.07 for ITS2) and Korea (Fst = 0.79783, P < 0.001, Nm = 0.07 for COI; Fst = 0.74143, P < 0.001, Nm = 0.03 for ITS2). However, lower Fst values and higher gene flow were detected between populations from China and Korea (Fst = 0.25733, P < 0.001, Nm = 0.73) based on COI analysis. The similar pattern was also captured by ITS2 rDNA marker. In addition, Neighbor-joining phylogenetic tree analysis of the two markers resulted in one cluster consisting of haplotypes from Vietnam, and a second group comprising haplotypes from China and Korea. This research revealed a closer genetic relationship between clam population from China and Korea but less similarity to population from Vietnam.     

Population genetic analysis of 6 Y-STR loci in Chinese northwestern Qinchuan yellow cattle breed

Six Y-STR loci (UMN0929, UMN0108, UMN0920, INRA124, UMN2404 and UMN0103) were analyzed using 576 healthy and unrelated males and 10 females of the Qinchuan cattle population in Chinese Shaanxi Province. Allele frequency, gene diversity, the polymorphic information content, and the number of effective gene were calculated. All loci were in accordance with the Hardy–Weinberg equilibrium (P > 0.05). The population data were compared with published data of other cattle breeds, suggesting that Qinchuan cattle were originated primarily from Bos Taurus. Results are valuable for individual identification, paternity testing, and origin analysis of Qinchuan cattle breed.     

Genetic structure of La Cabrera, Spain, from surnames and migration matrices

The genetic structure of La Cabrera (province of Léon, Spain), a highly isolated and inbred population (alpha3 = 0.00482), is analyzed by applying multivariate methods (nonmetric multidimensional scaling, Mantel test, Monmonier's algorithm) to different biodemographic data sets. Isonymy, parent-offspring migration (total, males, females), and marital migration matrices were obtained from 5,714 marriages recorded in 37 parishes (clustered in 4 municipalities) between 1880 and 1989. The aim of the study is to investigate the relationships between the genetic and geographic structures of the area. Endemicity values (diagonal of parent-offspring migration matrices), calculated for both sexes at two hierarchical levels (parishes and municipalities), show that female mobility follows the virilocal migration model at the higher (municipalities) level and the uxorilocal model at the parish level. Analysis of isonymy and parent-offspring migration matrices shows high correspondence between the genetic structure and geographic location of the parishes. In fact, the main reproductive barriers, constructed using Monmonier's algorithm, generally coincide with geographic barriers, highlighting increasing isolation patterns from northwest to southeast. Moreover, the analysis of isonymous relationships, which are influenced by earlier population movements, identifies three parishes whose outlier positions are explained by historical-cultural or geographic reasons. The positive and highly significant values (0.32 < or = r < or = 0.51;p < or = 0.001) given by the Mantel tests underline the dependence of the genetic structure on geographic distance. In confirmation of the endemicity results, the lowest correlation value (r = 0.32) is given by the female migration matrix. When the outlier parishes are omitted from the analysis, the correlation between isonymy and geographic distance increases from 0.35 to 0.46, and the values from the other migration matrices remain unchanged. In conclusion, the combination of different data sets and methods allows a wider and more coherent reconstruction of the historical changes in the genetic structure of the La Cabrera population.