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At least 415 records · Page 23Linked to original sources
PubMed1999

Microgeographic population genetic structure in the northern water snake, Nerodia sipedon sipedon detected using microsatellite DNA loci.

We describe the isolation and genetic characterization of eight microsatellite DNA loci from the northern water snake, Nerodia sipedon sipedon and use these loci to analyse levels of genetic differentiation between local (< 2 km apart) populations of these snakes in Ontario. These loci are variable, with expected heterozygosities ranging from 0.28 to 0.91, and can correctly exclude nonsires in parentage analyses with a high probability (0.998). Population analyses reveal significant deviation from expected heterozygosity levels for one population, probably a result of a null allele(s) at a single locus and small but significant levels of genetic differentiation among all three populations. This demonstrates that microgeographic genetic structure exists in this species, possibly due to limited dispersal.

Alleles↗
PubMed2004

Genetic structure and affinities among tribal populations of southern India: a study of 24 autosomal DNA markers.

We describe the genetic structure and affinities of five Dravidian-speaking tribal populations inhabiting the Nilgiri hills of Tamil Nadu, in south India, using 24 autosomal DNA markers. Our goals were: (i). to examine what evolutionary forces have most significantly impacted south Indian tribal genetic variation, and (ii). to test whether the phenotypic similarities of some south Indian tribal groups to Africans represent a signature of close relationship to Africans or are due to convergence. All loci were polymorphic and average heterozygosities were substantial (range: 0.347-0.423). Genetic differentiation was high (Gst= 6.7%) and genetic distances were not significantly correlated with geographic distances. Genetic drift therefore probably played a significant role in shaping the patterns of genetic variation observed in southern Indian tribal populations. Otherwise, analyses of population relationships showed that Indian populations are closely related to one another, regardless of phenotypic characteristics, and do not show particular affinities to Africans. We conclude that the phenotypic similarities of some Indian groups to Africans do not reflect a close relationship between these groups, but are better explained by convergence.

Adult↗
PubMed1995

Surname sampling for the study of the genetic structure of an Italian province.

Italian provinces may constitute a basic geographic unit that is big enough to be genetically structured but small enough to be analyzed intensively. In the present study surnames starting with three different letters of the alphabet were sampled from the telephone directory and used as a relatively simple and efficient way to cast light on the genetic and demographic pattern of the province and to prove the sampling efficiency. The 189 communes of the province of Pavia were grouped into 13 subregions composed of geographically clustered communes, and the relationships among them were examined using principal components analysis (PCA) and cluster analysis. The three samples show a concordant pattern: The Po and Ticino rivers are geographic barriers and subdivide the province into three regions (Lomellina, Pavese, and Oltrepó), which therefore appear to be genetifally differentiated. Both PCA and cluster analysis indicate that the main division is between the Oltrepó and the Pavese-Lomellina clusters and that it corresponds to the separation created by the Po River. The second split separates Lomellina from Pavese and thus parallels the Ticino River. The Lomellina subregions are more clustered than those of Pavese or Oltrepó. Furthermore, Lomellina has the highest number of surnames that are found only in a single area. This finding is possible due to endogamy dating back to an ancient border (valid until 1860) that separated Lomellina from the rest of Lombardy. Furthermore, Lomellina shows the highest frequency of surnames present only in one of the 13 subregions and the lowest percentage of unique surnames; both facts may describe genetic isolation of the area. A correlation is also seen between the percentage of surnames present only once in each of the 13 subregions and the census immigration rate: Both indicate the tendency of reduced immigration into the bigger towns. Particular discordances between the two estimates may reflect local or tourism-related migration.

Demography↗
PubMed2004

Bayesian models for the analysis of genetic structure when populations are correlated.

MOTIVATION: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. RESULTS: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework. CONTACT: fur@ohsu.edu.

Bayes Theorem↗
PubMedDate not supplied

[An analysis of the genetic structure of a hybrid population of green frogs, Rana esculenta complex, from the flats of the Danube].

Analysis of genetic structure of geographically isolated population of hybrid complex Rana esculenta L. from Danube delta according to a complex of biochemical gene markers was conducted. A parental species of Rana ridibunda and hybrids ridibunda-lessonae of the first generation only were found in the population. The complete absence of genetic recombination and introgression of genes from the locus Ldh-B, which was found in Dnieper populations, is characteristic of the population. The differences observed may be explained by genetic nonuniformity of geographical forms of R. lessonae. This forms may have taxonomic differences.

Alleles↗
PubMed1994

Genetic structure of the Utah Mormons: comparison of results based on RFLPs, blood groups, migration matrices, isonymy, and pedigrees.

The genetic structure of the Utah Mormon population is examined using 25 blood group and 47 RFLP alleles obtained from 442 subjects living in 8 geographic subdivisions. Nei's GST was 0.013 (p < 0.002) for the RFLP data and 0.012 (p > 0.4) for the blood group data, showing that only 1% of the genetic variance in this population can be attributed to subdivision effects. A comparison of intersubdivision distance matrices based on blood groups, RFLPs, migration matrices, isonymy, and pedigrees shows that genetic distances have relatively low and nonsignificant correlations with the other three types of data. However, the correlations based on RFLPs are considerably higher than those based on blood groups. Relationship matrices based on interindividual allele sharing were compared with known genealogical kinship coefficients between each pair of individuals. The correlation between the blood group and RFLP relationship matrices was small but marginally significant using the Mantel test (r = 0.014, p < 0.06). The RFLP relationship matrix correlated more highly with genealogical kinship than did the blood group relationship matrix (r = 0.023, p < 0.0001 and r = 0.012, p < 0.001, respectively). These correlations increased by approximately one order of magnitude when pairs of subjects having zero kinship coefficients were excluded. These results show that genetic distances derived from RFLPs correlate more strongly with other types of kinship than do distances based on blood groups. This probably reflects the fact that RFLPs are more neutral, have frequencies that are more accurately estimated, and contain more information about DNA sequence variation.

Blood Group Antigens↗
PubMed2001

Impact of landscape management on the genetic structure of red squirrel populations.

Landscape management practices that alter the degree of habitat fragmentation can significantly affect the genetic structure of animal populations. British red squirrels use "stepping stone" patches of habitat to move considerable distances through a fragmented habitat. Over the past few decades, the planting of a large conifer forest has connected groups of forest fragments in the north of England with those in southern Scotland. This "defragmentation" of the landscape has resulted in substantial genetic mixing of Scottish and Cumbrian genes in squirrel populations up to 100 kilometers from the site of the new forest. These results have implications for the conservation management of animal and plant species in fragmented landscapes such as those found in Britain.

Animals↗
PubMed2002

Genetic structure of Fundulus heteroclitus from PAH-contaminated and neighboring sites in the Elizabeth and York Rivers.

Population genetic characteristics of mummichog, Fundulus heteroclitus, from the heavily industrialized Elizabeth River and nearby York River (Virginia USA) were assessed relative to sediment PAH concentrations. Allozyme genotype frequencies for all loci were consistent with random mating expectations at each locality and age class. Fish from all sites had comparable levels of enzyme polymorphism and heterozygosity regardless of the associated sediment PAH concentrations. Allozyme frequencies for 12 of 15 loci were homogeneous for mummichog from all localities except that allozyme frequencies were significantly different for the Idh-2 locus of (adult and juvenile) mummichog at the heavily-contaminated Atlantic Wood site relative to all other sites. Additionally, allele frequency differences were noted for Ldh-C and Gpi-1 among juvenile mummichog. Values for F(st) were 0.0254 and 0.0141 in the juvenile and adult samples, respectively, indicating greater among-locality genetic differentiation for juvenile mummichog than for adults. Juvenile mummichog are more likely to remain in their natal area while adult samples reflect movement of fish during two or more winter seasons. Correlation analysis suggested that genetic differentiation was not correlated with geographic distance at the spatial scale studied here; however, there was a significant correlation between genetic distance and differences among sites in organic carbon-normalized PAH concentrations. Mummichog collected at the heavily PAH-contaminated AW locality were genetically distinct from those at neighboring sites.

Animals↗
PubMed2004

Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae).

We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and theta(B); (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Information Criterion (DIC) as a model choice criterion for determining whether there is evidence for inbreeding within populations or genetic differentiation among populations; and (iv) use of samples from the posterior distributions for f and theta(B) derived from different data sets to determine whether the estimates are consistent with one another. We illustrate each of these extensions by applying them to data derived from previous allozyme and random amplified polymorphic DNA surveys of an endangered orchid, Platanthera leucophaea, and we conclude that differences in theta(B) from the two data sets may represent differences in the underlying mutational processes.

Bayes Theorem↗
PubMed2000

Population genetic structure of brown trout (Salmo trutta L.) within a northern boreal forest stream.

Brown trout (Salmo trutta L.) population genetic structure and its temporal stability were studied within a small forest stream in central Sweden using five microsatellite loci. Both resident and migrating brown trout are present in the watershed. Tissue samples were collected from seven sections of the stream during two consecutive years. No differences were found in multilocus FST estimates between years within sections except in one case. Moreover, differences between age cohorts within sample sections were rare. The low interannual variation and the low heterogeny between cohorts is interpreted as indications of temporal stability. Pairwise multilocus FST estimates increased with increasing geographic distance, indicating isolation by distance. It is argued that the brown trout of the Färsån stream represent a population complex. The structure is probably maintained by precise natal homing and a limited, but important, amount of gene flow between closely situated sections within the stream supporting a stepping-stone model of gene flow.

Alleles↗
PubMed1996

Genetic structure of autochthonous populations of Meso-America: Mexico.

We analyze the possible effect of gene flow on the genetic structure of present-day Mexicans. For this purpose we reviewed previous admixture estimates for various Indian and Mestizo groups. Several facts seem clear: (1) There are no pure Indian groups in Mexico, because all Indian groups show variable degrees of admixture, mostly with whites (range, 0.088 in the Huichol to 0.373 in the Huasteco); (2) the main ancestral contribution to the noncoastal lower middle class Mestizo populations is Indian (above 50%) so that from a genetic standpoint Indians and lower middle class Mestizos are not much different; and (3) black ancestry is quite high on the coasts, ranging from 0.127 to 0.405 on the east coast, and is present in other Mestizos, ranging in large urban centers from 0.027 in Oaxaca to 0.107 in Puebla and in smaller cities from 0.08 in Tlaxcala to 0.181 in Cuanalán.

Emigration and Immigration↗
PubMedDate not supplied

Genetic structure of Algerian populations.

Blood samples were collected in Algeria from 4,444 army recruits and tested for 10 genetic polymorphic systems. These samples were collected from territorial Wilayas (administrative units of Algeria) from which the young soldiers had originated. Based on similar geography and economic and political history, these Wilayas were clustered into 10 regions. These regions, not part of the governmental administrative units, were characterized by allelic frequencies, and analyzed using R-matrix principal components, Wright's F(ST), spatial autocorrelation, and Mantel tests. Hierarchical relationships between the culturally defined regions were examined using two different analytical methods of phylogenetic tree constructions: neighbor-joining, and unweighted pair group average arithmetic (UPGMA). These results indicated the predominance of genetic homogeneity due to the gene flow between regions, but with some migration emanating from sub-Saharan Africa and Mediterranean Europe. Wright's F(ST) value of 0.0063, based on 16 alleles, suggested a relatively small genetic microdifferentiation of the regions. In Algeria, gene flow apparently swamped most of the effects of stochastic processes and disrupted the relationship between geography and genetics, as characterized by the isolation-by-distance model. Some genetic differences and similarities were observed between regions or clusters of regions. The resulting genetic structure of the Algerian populations is best explained by a combination of gene flow, ecology, and history.

Algeria↗
PubMed2001

Population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at microsatellite loci.

We report the population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at 10 microsatellite loci. Additionally, we compare heterozygosity and inbreeding estimates for continuous and fragmented populations and discuss the consequences for conservation. For a total of 314 individuals over 10 populations, the number of alleles per locus ranged from 20 to 27 and expected and observed heterozygosity varied from 0.129 to 0.924 and 0.067 to 1.000, respectively. Significant values of theta and R(ST) showed important genetic differentiation among populations. theta was much lower than R(ST), suggesting that identity by state and identity by descent have diverged in these populations. Although a significant amount of inbreeding was found under the identity by descent model (f = 0.11), an estimate of inbreeding for microsatellite markers based on a more adequate stepwise mutation model showed no evidence of nonrandom mating (R(IS) = 0.04). Differentiation (pairwise F(ST)) was positively correlated with geographical distance, as expected under the isolation by distance model. No effect of fragmentation on heterozygosity or inbreeding could be detected. This is most likely due to the fact that Cerrado fragmentation is a relatively recent event (approximately 60 years) compared to the species life cycle. Also, the populations surveyed from both fragmented and disturbed areas were composed mainly of adult individuals, already present prior to ecosystem fragmentation. Adequate hypothesis testing of the effect of habitat fragmentation will require the recurrent analysis of juveniles across generations in both fragmented and nonfragmented areas.

Brazil↗
PubMed1994

Genetic structure of populations of beta-haemolytic Lancefield group C streptococci from horses and their association with disease.

The genetic structure of beta-haemolytic Lancefield group C streptococci isolated from horses in Australia was examined by multilocus enzyme electrophoresis. The 249 isolates comprised 70 classified phenotypically as Streptococcus equi subspecies equi, 177 classified as S equi subspecies zooepidemicus and two which were unclassifiable. Forty-one electrophoretic types were identified which could be classified into three major clusters, A, B and C. Of the isolates, 178 fell into cluster B (types 4 to 22) and lay within a genetic distance of 0.36. Sixty-nine of the 70 S equi subspecies equi isolates fell into type 12, which suggests that they were members of a single clone, and the isolates from abscesses were significantly more likely to belong to type 12 than those from horses with no clinical signs (P < 0.001). There were no other significant associations between electrophoretic types or clusters and the isolation of the organism from particular sites. These data suggested that S zooepidemicus may be the archetypal species from which the clone designated subspecies equi has been derived. If isolates of the subspecies equi from other geographical regions also prove to be members of electrophoretic type 12, this hypothesis would be strengthened.

Animals↗
PubMed2006

Population genetic structure of the malaria vector Anopheles moucheti in south Cameroon forest region.

We used recently developed microsatellite DNA markers to explore the population genetic structure of the malaria vector, Anopheles moucheti. Polymorphism at 10 loci was examined to assess level of genetic differentiation between four A. moucheti populations from South Cameroon situated 65-400 km apart. All microsatellite loci were highly polymorphic with a number of distinct alleles per locus ranging from 9 to 17. Fst estimates ranging from 0.0094 to 0.0275 (P < 0.001) were recorded. These results suggest a very low level of genetic differentiation between A. moucheti populations. The recently available microsatellite loci revealed useful markers to assess genetic differentiation between geographical populations of A. moucheti in Cameroon.

Alleles↗
PubMed2006

Phylogeography and genetic structure of Hibiscus tiliaceus--speciation of a pantropical plant with sea-drifted seeds.

Phylogenetic relationships and the spatial genetic structure of a pantropical plant with sea-drifted seeds, Hibiscus tiliaceus L., and its allied species were investigated. The combined distribution range of these species is over almost the entire littoral area of the tropics worldwide, which might result from the dispersal of their sea-drifted seeds and from recurrent speciation in local populations. A phylogenetic tree constructed using the nucleotide sequences of a c. 7500-bp portion of chloroplast DNA suggested the possibility that recurrent speciation from H. tiliaceus has given rise to all of its allied species. Three major sequence haplotypes of H. tiliaceus had wide and overlapping distributions throughout the Pacific, Atlantic and Indian Ocean regions. This distribution pattern was also confirmed by PCR-SSCP (polymerase chain reaction amplification with single-strand conformation polymorphism) and PCR-SSP (PCR amplification with sequence specific primers) analyses performed on more than 1100 samples from 65 populations worldwide. Statistical analysis using F(ST) and analysis of molecular variance did not show significant genetic differentiation among the H. tiliaceus populations in the three oceanic regions. The results reported here suggested substantial gene flow occurred between populations in the different oceanic regions due to sea-drifted seeds. A strong genetic difference between the Pacific and Atlantic populations of Hibiscus pernambucensis Arruda was observed, which indicates that gene flow in this species between the two regions has been prevented. The wide and dominant distribution of a haplotype shared by H. pernambucensis and H. tiliaceus in the Atlantic region suggests significant introgression between the two species in this region.

DNA, Chloroplast↗
PubMedDate not supplied

Genetic structure of an Apis dorsata population: the significance of migration and colony aggregation.

Eight microsatellite loci were used to investigate the genetic structure of the giant honeybee (Apis dorsata) population in northeast India. This species migrates seasonally between summer and winter nesting sites, and queens appear to return to their previously occupied site. Furthermore, there is a strong tendency for colonies of this species to aggregate at perennially utilized nesting sites that may be shared by more than 150 colonies. These behavioral features suggest that colonies within aggregations should be more related than random colonies, but that the long-distance migration could act to minimize genetic differentiation both between geographical areas and within aggregations. Our genetic study supports these conjectures arising from natural history. A. dorsata aggregations are comprised of colonies that share more alleles than expected by chance. Although queens heading neighboring colonies are not close relatives, fixation indices show significant genetic differentiation among aggregation sites. However, there appears to be sufficient gene flow among aggregations to prevent high degrees of relatedness developing between colonies within aggregations. The results also suggest that there is significant population structuring between geographical regions, although the level of structuring caused by aggregation exceeds the differentiation attributable to geographic region.

Animal Migration↗
PubMed2006

Genetic structure of the forest pest Hylobius abietis on conifer plantations at different spatial scales in Europe.

The distribution of genetic variation within and among 20 European sites infested by the large pine weevil, Hylobius abietis, was analysed using dominant amplified fragment length polymorphism markers. Analysis of molecular variance was performed at the European, regional and local scales. Most of the genetic variability was found within rather than among populations and the global fixation index averaged over loci was low (0.07). We found no evidence of genetic drift, even in relatively isolated sites. This genetic pattern tends to confirm the high dispersal ability of the weevil and the influence of human-mediated expansion of its range through conifer plantations across Europe since the 19th century. Assignment tests demonstrated that the regional forest is a pertinent geographic scale for defining populations in the large pine weevil. Testing the potential influence of the larval host-plant identity (Scot Pine vs Norway Spruce) on the genetic structure revealed a weak but significant effect in two of the three regions tested (in Ardèche and in Limousin but not in Finland). One locus varied with host-plant use in the two French regions, indicating a potential role in host-plant adaptation. However, host-race formation is not observed in H. abietis; we discuss this result in the light of our current knowledge of this insect's biology. Altogether, this study shows that the use of different host plants for development does not constitute a strong barrier to gene flow for H. abietis and confirms the high dispersal ability of this forest pest.

Analysis of Variance↗