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PubMed1999

Microspatial genetic structure in the land snail helix aspersa (Gastropoda: helicidae)

The microspatial genetic structure of allele frequencies at seven isozyme loci was examined for 15 populations of the land snail Helix aspersa sampled in a village from Brittany (north-western France). Spatial heterogeneity of allele frequencies was highly significant (P < 0.001). Fixation indices reflected nonrandom mating within neighbourhoods and a slight but consistent differentiation between colonies (FST=0.044; P < 0.01). Analyses of gene flow or genetic distances failed to reveal a significant relationship with geographical distance, probably because of the complexity of environmental heterogeneity. However, matrix comparisons between genetic distances and connectivity networks among adjacent colonies (Gabriel-connected graph) yielded a significant correlation in every case, indicating a 'step-by-step' relationship between neighbouring localities. Moreover, most of the allozymes were spatially structured and showed (i) a gradual isolation of colonies with increasing geographical distances, and (ii), for some correlogram profiles, a circular gradient illustrating a multidirectional colonization of the village. The probable existence of disperser individuals allowed us to suggest a metapopulation model which would explain the maintenance of such animals in fragmented habitats where anthropogenic disturbances and extinction/recolonization events are commonly observed.

Journal Article↗
PubMedDate not supplied

Male/female ratio in centenarians: a possible role played by population genetic structure.

All the demographic surveys on the centenarians have highlighted that females outnumber males. The centenarians' male/female (M/F) ratio reported by most studies ranges between 1:4 and 1:7. A puzzling 1:2 ratio was observed in Calabria, a Southern Italian region. To our knowledge only in Sardinia a similar phenomenon had been previously observed. We have therefore used the data of the Italian Institute of Statistics to figure out the centenarians' M/F ratio in the Italian regions. We found that this ratio gradually decreases from South to North. Such a result is certainly due to many factors. Thus, we have explored the possibility, it is also influenced by the genetic structure of the Italian population. In fact, the distribution of the centenarians' M/F ratio turned out to be significantly correlated with the genetic structure of the Italian population as outlined by the principal component analysis.

Aged↗
PubMed1997

Genetic structure of the indigenous populations of Siberia.

This study explores the genetic structure of Siberian indigenous populations on the basis of standard blood group and protein markers and DNA variable number of tandem repeats (VNTR) variation. Four analytical methods were utilized in this study: Harpending and Jenkin's R-matrix; Harpending and Ward's method of correlating genetic heterozygosity (H) to the distance from the centroid of the gene frequency array (rii); spatial autocorrelation, and Mantel tests. Because of the underlying assumptions of the various methods, the numbers of populations used in the analyses varied from 15 to 62. Since spatial autocorrelation is based upon separate correlations between alleles, a larger number of standard blood markers and populations were used. Fewest Siberian populations have been sampled for VNTRs, thus, only a limited comparison was possible. The four analytical procedures employed in this study yielded complementary results suggestive of the effects of unique historical events, evolutionary forces, and geography on the distribution of alleles in Siberian indigenous populations. The principal components analysis of the R-matrix demonstrated the presence of populational clusters that reflect their phylogenetic relationship. Mantel comparisons of matrices indicate that an intimate relationship exists between geography, languages, and genetics of Siberian populations. Spatial autocorrelation patterns reflect the isolation-by-distance model of Malecot and the possible effects of long-distance migration.

ABO Blood-Group System↗
PubMed1994

Genetic Structure of Rhizobium leguminosarum biovar trifolii and viciae Populations Found in Two Oregon Soils under Different Plant Communities.

An investigation was carried out to determine the genetic structure in soil populations of Rhizobium leguminosarum bv. trifolii and viciae at each of two Oregon sites (A and C) that were 1 km apart. Although the soils were similar, the plant communities were quite different because grazing by domestic animals had been allowed (site A) or prevented (site C). Analysis of allelic variation at 13 enzyme-encoding loci by multilocus enzyme electrophoresis delineated 202 chromosomal types (ETs) among a total of 456 isolates representing two populations of R. leguminosarum bv. trifolii (AT and CT) and two populations of R. leguminosarum bv. viciae (AV and CV). Regardless of their site of origin or biovar affiliation, isolates of the same ET were confirmed to be more closely related to each other than to isolates of other ETs by repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus sequences and the PCR technique. Despite the wide range in densities of the Rhizobium populations (<10 to >10/g of soil), their overall genetic diversities were similar (mean genetic diversity, 0.45 to 0.51), indicating that low-density populations of soil-borne bacterial species are not necessarily of little genetic diversity. Linkage disequilibrium analysis revealed significant multilocus structure (nonrandom associations of alleles) within each of the four populations. From a combination of cluster and linkage disequilibrium analyses, a total of eight distinct groups of ETs were defined in the four populations. Two groups (I and III) contributed significant numbers of ETs and isolates to each population. The two populations of R. leguminosarum bv. viciae (AV and CV) exhibited similar genetic structures despite existing at different densities, in different plant communities, and in the presence (CV) or absence (AV) of their local Vicia hosts. In contrast, total linkage disequilibrium was partitioned differently in two biovar populations occupying the same soil (AV and AT), with disequilibrium in the latter being due entirely to the presence of group V.

Journal Article↗
PubMedDate not supplied

Allozyme diversity and genetic structure of the leafy cactus (Pereskia guamacho [Cactaceae]).

We examined levels of genetic variation and genetic structure in the leafy cactus (Pereskia guamacho) in arid and semiarid zones in Venezuela. We surveyed genetic diversity within 17 populations using 19 allozyme loci. Genetic diversity was relatively high at both the species (P(s) = 89%, A(s) = 3.26, AP(s) = 3.53, H(es) = 0.24) and population (P(p) = 63%, A(p) = 1.90, AP(p) = 2.42, H(ep) = 0.20) levels. A significant deficit of heterozygote individuals was detected within populations in the Paraguana Peninsula region (F(IS) = 0.301). Relatively low levels of population differentiation were detected at macrogeographic (G(ST) = 0.112) and regional levels (G(ST) = 0.044 for peninsula region and G(ST) = 0.074 for mainland region), suggesting substantial genetic exchange among populations; however, gene flow in this species seems to be regulated by the distance among populations. Overall, estimates of genetic diversity found in P. guamacho are concordant with the pattern observed for other cacti surveyed, namely high levels of polymorphism and genetic diversity with one common allele and several rare alleles per locus. Differences in gene dispersal systems between this species and other cacti studied were not reflected in the patterns of genetic diversity observed. The concentration of the highest estimates of genetic variation in northwestern Venezuela suggests a potential reservoir of plant genetic diversity within xerophilous ecosystems in northern South America.

Cactaceae↗
PubMed1994

[Analysis of maintenance of redundant genetic structures in the yeast Saccharomyces cerevisiae: disomy and spontaneous mitochondrial rho(-)-mutability].

With the postmeiotic progeny of triploids used as initial material, n + 1 disomics at chromosomes II, III, VII, VIII, and X were isolated. Disomy at the chromosomes listed (as well as for chromosomes IV and XIV, as demonstrated previously) is associated with decreased spontaneous rho- mitochondrial mutability. This suggests that a disturbance of the chromosome balance itself as such can lead to considerable changes in the spontaneous variability of the mitochondrial genome. From crosses between n + 1 disomics at chromosome IV and for each of the remaining above-mentioned six chromosomes, double n + 2 disomics were isolated, carrying nonchromologous pairs of extra chromosomes. Analysis of mitotic stability of the chromosome IV and spontaneous rho- mutability in double disomics shows that the effect of disomy on spontaneous rho- mutability most probably cannot be explained by direct competition between different genetic structures maintained in Saccharomyces cerevisiae cells. Disturbance of the chromosome balance in disomy is accompanied by essential qualitative changes in processes mediating the maintenance of genetic structures in yeast cells.

Chromosome Aberrations↗
PubMed2004

First microsatellite loci of red mullet (Mullus barbatus) and their application to genetic structure analysis of Adriatic shared stock.

In order to study the genetic structure of the Adriatic shared stock of red mullet (Mullus barbatus), we developed a set of dinucleotide microsatellite markers. A dinucleotide-enriched genomic library was obtained, and 6 polymorphic dinucleotide loci were successfully optimized. The markers showed high expected heterozygosity (from 0.68 to 0.92) and allele number (from 12 to 33); thus they appear to be suitable for detecting genetic differences in the population of red mullet. Four Adriatic samples were subsequently analyzed for microsatellite variation, and the results showed subtle but statistically significant genetic differentiation, indicating that the Adriatic red mullet may group into local, genetically isolated populations. No correlation between geographic distance and genetic differentiation was observed. In addition, the evidence of recent bottlenecks in the Adriatic samples indicates that the observed population subdivision might reflect random local allelic variations, generated by reproductive success, survival rates, or fishing pressure.

Animals↗
PubMed2003

[RAPD-polymerase chain reaction analysis of the genetic structure of tumor hepatocyte population MH-22A].

The viability and genetic variability of mouse hepatoma MH-22a were studied by RAPD-PCR method using 3 primers, and the genetic structure of the tumor hepatocyte population based on the number of clonal fingerprint rearrangements was identified: 56% of hepatocytes made up clones with 0-3 rearrangements (the stem line of the population); 32%--the variable part with 4-7 rearrangements per clone and 12%--the aberrant part with 8-12 rearrangements per clone. The stem line appeared the most viable featuring zero or least genetic variability while the clones characterized by the greatest genetic variability were least viable.

Animals↗
PubMed2000

Mating frequency and genetic structure of the Argentine ant Linepithema humile.

The nest and population genetic structures of the Argentine ant, Linepithema humile were investigated using eight microsatellite loci. Genotypes of the sperm from spermathecae of 87 queens were consistent with all queens being singly inseminated. The probability of a double mating remaining undetected was low (0.012) suggesting that no queens or only a very low proportion mate multiply. The relatedness between the queens and their mates was negative (R = -0.164 +/- 0.044) and significantly different to zero (P = 0.020). However, the high negative relatedness value was caused by a significant allele frequency difference between the sexes at a single locus (Lhum-28). When this locus was removed from the analyses, the relatedness was not significantly different from zero (R = 0.013 +/- 0.050, P = 0.812). Analysis of 10 nests revealed that the genetic differentiation among nests was weak (FST = 0.003) and not distinguishable from zero (P = 0.468). Similarly, the overall relatedness among nestmate females was not significantly different from zero (R = 0.007 +/- 0.018, P = 0.706). These results are consistent with the lack of distinct nest boundaries and the large number of queens per nest in the population studied. Although mating takes place inside the nest, the inbreeding coefficient was close to zero (F = 0.007 +/- 0.025, P = 0.786). Overall, these data indicate substantial local gene flow mediated by movement of reproductives among colonies.

Animals↗
PubMed1995

Genetic structure of four species of Triatoma (Hemiptera: Reduviidae) from Argentina.

The genetic structure of Triatoma guasayana Wygodzinsky & Abalos, T. sordida (Stål), T. platensis Neiva, and T. infestans (Klug) was compared by starch gel electrophoresis. In total, 17 enzyme loci were analyzed in T. infestans and 14 loci in the other three species. Zymograms were useful in species identification. Icdh-2 and Hk-1 are diagnostic loci, and Icdh-1, Hk-2, Es-1, and Es-2 are helpful in distinguishing these species. The proportion of polymorphic loci for the four species (range, 52.9 to 58.3%) was somewhat higher than that expected from reports for other insects. Mean heterozygosity per locus (range, 0.062 to 0.156) was within the range reported for insects in the literature. The level of heterozygosity was highest for T. guasayana and lowest for T. sordida. Values of genetic distance (Nei's D), identity (Nei's I), and similarity (Rogers's S) indices indicate that the four species are well-defined taxa. T. infestans and T. platensis are the closest (D = 0.45, S = 0.62). T. guasayana and T. sordida (D = 0.77, S = 0.46) form another pair of related species.

Alleles↗
PubMed1997

[Genetic structure of the population of Guarico, Venezuela, studied through isonymy].

The genetic structure of the State of Guárico, Venezuela, was studied through the distribution of surnames from individuals above 40 years of age, obtained from the register of electors. The sample studied consisted in 109,200 individuals and 14,138 different surnames. For each of the 32 counties of the State, the following estimators were calculated: percentage of the population included in surnames which appear only once (estimator A), percentage of the population included in the seven most frequent surnames (estimator B), the coefficient of consanguinity due to random isonymy (n phi ii), and Karlin and McGregors ni nu, an estimator of migration. The correlation between n phi ii and B was 0.97, indicating that 94% of the variation observed in the coefficient of consanguinity due to random isonymy is due to the seven most frequent surnames. The correlation between A and ni was 0.93, so that 86% of the variation observed in ni, is due to surnames which appear only once. On the other hand, correlations between A and B, and between n phi ii and nu were non significant (0.25 and 0.01 respectively), meaning that they are measuring different features of population structure: B and n phi ii, and v were non significant (0.25 and 0.01 respectively), meaning that they are measuring different features of population structure: B and n phi ii, isolation, and A and nu, migration. The most isolated counties of Guárico, according to n phi ii and B, are Santa Rita, Espino, El Calvario, Ortiz and Santa María de Ipire. Microdifferentiation of the State was studied through the estimation of RST, which gave a value of 0.0008. Comparing this value with those obtained in other Venezuelan States, it is found that Guárico, with Aragua and Yaracuy, are among the least differentiated States, probably because of the absence of important geographical barriers and the nearness to the Capital City of our country.

Adult↗
PubMed2000

[Impacts of stochastic migration of seed and pollen on differentiation of plant population genetic structure].

The island model was extended to plant population with incorporation of the effects of stochastic migration of seed and pollen grain. Exact mean and variance of gene frequencies were formulated for each of three genomes with different modes of inheritance (bi-parental, paternal and maternal). Theoretical results indicate that stochastic migration in both seed and pollen may increase the variance of gene frequencies among populations, depending upon how large the variations of migration rate and/or migrant gene frequency are. Fluctuation in migration rate or in migrant gene frequencies of seed and pollen grain is also an important factor influencing population genetic structure, perhaps as important as the absolute value of migration rate. One important result is that the combined effect induced by the fluctuation of both migration rate and migrant gene frequency of seed and pollen can greatly intensify differentiation of population genetic structure. Application of these theoretical results in practical work was discussed in detail.

Demography↗
PubMed2001

[Analyses of population genetic structure by using dominant markers].

Dominant markers tend to under-estimate the amount of genetic diversity relative to codominant systems when applying in population genetics. In order to compare various existing methods for analysis of genetic structure, RAPD markers were used to detect genetic variability of 5 populations of Oryza granulata from China. The results indicated that both Shannon index of diversity and Nei gene diversity were superior to percentage of polymorphic bands (PPB) because the latter lacked of ability to describe frequency difference of polymorphic bands. Mantel test showed significant relation (r > 0.95, t > t0.01) among matrice of 17 different genetic similarities, which indicated that all of them could be used in analysis of genetic relations of individuals of Oryza granulata. Both AMOVA analysis based on phi st distance and analysis of Nei's distance showed consistent results in defining relationship among the 5 populations, and Lynch-Milligan pruning should be used to improve the estimation of population parameters. All of AMOVA, Gst and Shannon diversity analyses obtained similar results with majority of genetic variation occurring between Yunnan and Hainan, and low levels of genetic diversity resided within regions and populations.

Genetic Markers↗
PubMed2006

Effects of management regime and plant species on the enzyme activity and genetic structure of N-fixing, denitrifying and nitrifying bacterial communities in grassland soils.

Management by combined grazing and mowing events is commonly used in grasslands, which influences the activity and composition of soil bacterial communities. Whether observed effects are mediated by management-induced disturbances, or indirectly by changes in the identity of major plant species, is still unknown. To address this issue, we quantified substrate-induced respiration (SIR), and the nitrification, denitrification and free-living N(2)-fixation enzyme activities below grass tufts of three major plant species (Holcus lanatus, Arrhenatherum elatius and Dactylis glomerata) in extensively or intensively managed grasslands. The genetic structures of eubacterial, ammonia oxidizing, nitrate reducing, and free-living N(2)-fixing communities were also characterized by ribosomal intergenic spacer analysis, and denaturing gradient gel electrophoresis (DGGE) or restriction fragment length polymorphism (RFLP) targeting group-specific genes. SIR was not influenced by management and plant species, whereas denitrification enzyme activity was influenced only by plant species, and management-plant species interactions were observed for fixation and nitrification enzyme activities. Changes in nitrification enzyme activity were likely largely explained by the observed changes in ammonium concentration, whereas N availability was not a major factor explaining changes in denitrification and fixation enzyme activities. The structures of eubacterial and free-living N(2)-fixing communities were essentially controlled by management, whereas the diversity of nitrate reducers and ammonia oxidizers depended on both management and plant species. For each functional group, changes in enzyme activity were not correlated or were weakly correlated to overall changes in genetic structure, but around 60% of activity variance was correlated to changes in five RFLP or DGGE bands. Although our conclusions should be tested for other ecosystems and seasons, these results show that predicting microbial changes induced by management in grasslands requires consideration of management-plant species interactions.

Agriculture↗
PubMed2004

[Multiple nonlinear statistical method of population genetic structure based on the allelic polymorphism data].

The distribution and structure of the allelic polymorphism data are analyzed and it is pointed out that the distribution of allelic polymorphism data reveals the characteristic of closed data (also named as compositional data or data of constant sum). It is interpreted that the correlation structure of the allelic polymorphism data contains null correlations introduced by "closure" and the statistical distribution of the data is not normal because of its constant row sum, which resulted in great difficulties in analyzing the data with traditional multiple linear statistical methods such as principal component analysis, factor analysis, cluster analysis and canonical correlation analysis. Based on the theory of compositional data analysis proposed by Aitchison in 1982, a multiple nonlinear statistical method originating from the "logratios" approach to the statistical analysis of compositional data is put forward in this paper. As an example, the "logratios" method was used to analyze the genetic structure of TH01 polymorphic loci in Chinese population and the results were compared with those of multiple linear methods such as component principal. It is concluded that the "logratios" multiple nonlinear principle component analysis is a better method with the virtue of sensitivity and specificity for analyzing the genetic structure of population from the data of allelic polymorphism.

Alleles↗
PubMed1982

Acute leukemia viruses E26 and avian myeloblastosis virus have related transformation-specific RNA sequences but different genetic structures, gene products, and oncogenic properties.

Replication-defective acute leukemia viruses E26 and myeloblastosis virus (AMV) cause distinct leukemias although they belong to the same subgroup of oncogenic avian tumor viruses based on shared transformation-specific (onc) RNA sequences. E26 causes predominantly erythroblastosis in chicken and in quail, whereas AMV induces a myeloid leukemia. However, upon cultivation in vitro for >1 month, a majority of surviving hemopoietic cells of E26-infected animals bear myeloid markers similar to those of AMV-transformed cells. We have analyzed the genetic structure and gene products of E26 virus for a comparison with those of AMV. An E26/helper virus complex was found to contain two RNA species: a 5.7-kilobase (kb) RNA that hybridizes with cloned AMV-specific proviral DNA and hence is probably the E26 genome; and an 8.5-kb RNA that is unrelated to AMV and represents helper virus RNA. Thus, E26 RNA is smaller than 7.5-kb AMV RNA. Hybridization of size-selected poly(A)-terminating E26 RNA fragments with AMV-specific DNA indicated that the shared specific sequences are located in the 5' half of the E26 genome as opposed to a 3' location in AMV RNA. In nonproducer cells transformed in vitro by E26, a gag-related nonstructural 135,000-dalton protein (p135) was found. No gag(Pr76) or gag-pol (Pr180) precursors of essential virion proteins, which are present in AMV nonproducer cells, were observed. p135 was also found in cultured E26 virus producing cells of several leukemic chickens, and its intracellular concentration relative to that of the essential virion proteins encoded by the helper virus correlates with the ratio of E26 to helper RNA in virions released by these cells. p135 is phosphorylated but not glycosylated; antigenically it is not related to the pol or env gene products. It appears to be coded for by a partial gag gene and by E26-specific RNA sequences, presumably including those shared with AMV. Hence, AMV and E26 appear to use different strategies for the expression of related onc sequences: AMV is thought to encode a transforming protein via a subgenomic mRNA, whereas E26 codes for a gag-related polyprotein via genomic RNA. It is speculated that differences in the oncogenic properties of E26 and AMV are due to differences in their genetic structures and gene products.

Animals↗
PubMed2000

Fine-scale genetic structuring on Manacus manacus leks.

Leks have traditionally been considered as arenas where males compete to attract females and secure matings. Thus, direct fitness benefits mediated through competition between males to fertilize females have been considered to be the primary force driving the evolution of lekking behaviour. Inclusive fitness benefits mediated through kin selection may also be involved in lek formation and evolution, but to date this theory has been largely ignored. According to kin-selection theory, both reproducing and non-reproducing males may gain indirect inclusive fitness benefits. If females are attracted to larger leks, non-reproducing males add attractiveness to a lek, and therefore, in a genetically structured population, boost the reproductive success of kin. Theory predicts that the attractiveness of leks is plastic, and that males establish themselves on a lek in which the top male, in terms of reproductive success, is a close relative. Here we show that in white-bearded manakins (Manacus manacus), for which larger leks are more attractive to females and so secure the maximum number of matings, there is extraordinary fine-scale genetic structure, with leks being composed of clusters of related kin. We propose that males establish themselves where they find relatives to such an extent that they form groups within leks, and that such behaviour is consistent with kin-selection theory to maximize reproductive success of the group.

Alleles↗
PubMed1997

Micro- and macrogeographical genetic structure of colonies of naked mole-rats Heterocephalus glaber.

Patterns of genetic structure in eusocial naked mole-rat populations were quantified within and among geographically distant populations using multilocus DNA fingerprinting and mitochondrial DNA (mtDNA) sequence analysis. Individuals within colonies were genetically almost monomorphic, sharing the same mtDNA control region haplotype and having coefficients of band sharing estimated from DNA fingerprints ranging from 0.93 to 0.99. Family analysis of a hybrid captive colony of naked mole-rats with increased levels of genetic variability using multilocus DNA fingerprinting gave results consistent with Mendelian inheritance, and has revealed for the first time that multiple paternity can occur. In a survey of wild colonies from Ethiopia, Somalia and locations in northern and southern Kenya, we have examined mtDNA control region sequence variation in 42 individuals from 15 colonies, and together with multilocus DNA fingerprinting and mtDNA cytochrome-b sequence analysis in selected individuals have shown that these populations show considerable genetic divergence. Most of the variance in sequence divergence was found to be between geographical locations (phi ct = 0.68) and there was a significant correlation between sequence divergence and geographical separation of haplotypes. Six colonies from Mtito Andei in southern Kenya shared the same control region haplotype, suggesting a recent common maternal ancestor. In contrast, out of four colonies at Lerata in north Kenya, three haplotypes were identified, and phylogenetic analysis suggests that this area may be a zone where two distinct lineages are in close proximity. Genetic distances were maximal between Ethiopian and southern Kenyan populations at 5.8% for cytochrome-b, and are approaching interspecific values seen between other Bathyergids.

Animals↗