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At least 379 records · Page 21Linked to original sources
PubMed1997

The number of segregating sites in a sample of DNA sequences from a geographically structured population.

The distribution of the number of segregating sites among randomly sampled DNA sequences from a geographically structured population is studied. We assume the infinitely-many-sites model of neutral genes and no recombination. Employing the genealogical process, we derive an equation for the generating function of the distribution of the number of segregating sites. First we study the strong-migration limit and prove that the distribution converges to that for a panmictic population. We also study the case of two sampled DNA sequences in the d-dimensional torus model with homogeneous migration.

DNA↗
PubMed2005

The Chapman-Enskog procedure for an age-structured population model: initial, boundary and corner layer corrections.

We consider a mathematical model of an age-structured population of some fisheries (for example, anchovies, sardines or soles). Two time scales are involved in the problem: the fast time scale for the migration dynamics and the slow time scale for the demographic process. At a first step, we study the so called 'aggregated' system by means of the semigroups theory. Then, we study the asymptotic behaviour of the model by using the Chapman-Enskog procedure. In particular, we study initial, boundary and corner layer effects in order to obtain the exact initial and boundary conditions the approximated solution has to satisfy.

Animals↗
PubMed1991

The population structure and transmission of Escherichia coli in an isolated human community; studies on an Antarctic base.

The population structure and transmission of Escherichia coli in a small group of individuals isolated for 26 weeks on an Antarctic base were studied by multilocus electrophoresis of eight enzymes and plasmid analysis. Two hundred and sixty-nine strains were isolated. They were grouped into 60 allozyme types (ETs). Half of these ETs were only isolated once; others were repeatedly isolated from single subjects. Eleven were found in more than one subject and the pattern of the occurrence of some of them was considered to provide evidence of their spread from subject to subject.

Adult↗
PubMed2005

Low genetic diversity and significant population structuring in the relict Amentotaxus argotaenia complex (Taxaceae) based on ISSR fingerprinting.

Amentotaxus, a genus of the Taxaceae, represents an ancient lineage that has long existed in Eurasia. All Amentotaxus species experienced frequent population expansion and contraction over periodical glaciations in Tertiary and Quaternary. Among them, Amentotaxus argotaenia complex consists of three morphologically alike species, A. argotaenia, Amentotaxus yunnanensis, and Amentotaxus formosana. This complex is distributed in the subtropical region of mainland China and Taiwan where many Pleistocene refugia have been documented. In this study, genetic diversity and population structuring within and between species were investigated based on the inter-simple sequence repeats (ISSR) fingerprinting. Mean genetic diversity within populations was estimated in three ways: (1) the percentage of polymorphic loci out of all loci (P) (2) Nei's unbiased expected heterozygosity (He), and (3) Shannon's index of phenotypic diversity. For a total of 310 individuals of 15 populations sampled from the three species, low levels of ISSR genetic variation within populations were detected, with P=4.66-16.58%, He=0.0176-0.0645 and Hpop=0.0263-0.0939, agreeing with their seriously threatened status. AMOVA analyses revealed that the differences between species only accounted for 27.38% of the total variation, whereas differences among populations and within populations were 57.70 and 14.92%, respectively, indicating substantial isolation between the patch-like populations. A neighbor-joining tree identified a close affinity between A. yunnanensis and A. formosana. Genetic drift due to small population size, plus limited current gene flow, resulted in significant genetic structuring. Low levels of intra-populational genetic variation and considerable inter-populational divergence were also attributable to demographic bottlenecks during and/or after the Pleistocene glaciations.

Minisatellite Repeats↗
PubMed2003

Theory of the effects of population structure and sampling on patterns of linkage disequilibrium applied to genomic data from humans.

We develop predictions for the correlation of heterozygosity and for linkage disequilibrium between two loci using a simple model of population structure that includes migration among local populations, or demes. We compare the results for a sample of size two from the same deme (a single-deme sample) to those for a sample of size two from two different demes (a scattered sample). The correlation in heterozygosity for a scattered sample is surprisingly insensitive to both the migration rate and the number of demes. In contrast, the correlation in heterozygosity for a single-deme sample is sensitive to both, and the effect of an increase in the number of demes is qualitatively similar to that of a decrease in the migration rate: both increase the correlation in heterozygosity. These same conclusions hold for a commonly used measure of linkage disequilibrium (r(2)). We compare the predictions of the theory to genomic data from humans and show that subdivision might account for a substantial portion of the genetic associations observed within the human genome, even though migration rates among local populations of humans are relatively large. Because correlations due to subdivision rather than to physical linkage can be large even in a single-deme sample, then if long-term migration has been important in shaping patterns of human polymorphism, the common practice of disease mapping using linkage disequilibrium in "isolated" local populations may be subject to error.

Emigration and Immigration↗
PubMed2001

Density and population structure of owl monkeys (Aotus azarai) in the Argentinean Chaco.

Owl monkeys are small monogamous primates ranging over a wide area extending from Panama to the Chaco region of northern Argentina. The Chaco, an alluvial plain covering over one million km2 of Argentina, Bolivia, Brazil, and Paraguay, consists of a mosaic of grasslands, savannas, xeric thorn forests, and gallery forests. The region shows significant seasonal variation in climate, rainfall, and food availability. The goal of this study was to determine the density, size, and structure of a population of Aotus azarai in the seasonal gallery forests of the eastern Argentinean Chaco. Reported population density, as well as group size and composition are based on data collected from 11 groups contacted on approximately 900 occasions, and observed for over 2,000 hours during a three-year period. Group and individual densities were 16 groups/km2 and 64 individuals/km2, respectively. Approximately half of the groups (n = 5) were small groups which had three individuals most of the time and never more than four, whereas the remaining groups were large groups composed of four or five individuals, and sometimes even six or seven individuals. This is the first study of A. azarai based on monitoring of a relatively large number of distinct groups. Our data suggest that owl monkeys in the seasonal subtropical forests of Formosa live at a density as high as those reported for owl monkey populations observed in tropical forests. The data also show that the social groups in the owl monkey population are of comparable size and composition to those characteristic of populations in the tropics.

Animals↗
PubMed2005

Y-chromosome and mitochondrial DNA studies on the population structure of the Christmas Island community.

Christmas Island is a remote Australian territory located close to the main Indonesian island of Java. Y-chromosome and mitochondrial DNA (mtDNA) markers were used to investigate the genetic structure of the population, which comprises communities of mixed ethnic origin. Analysis of 12 Y-chromosome biallelic polymorphisms revealed a high level of gene diversity and haplotype frequencies that were consistent with source populations in southern China and Southeast Asia. mtDNA hypervariable segment I (HVS-I) sequences displayed high levels of haplotype diversity and nucleotide diversity that were comparable to various Asian populations. Genetic distances revealed extremely low mtDNA differentiation among Christmas Islanders and Asian populations. This was supported by the relatively high proportion of sequence types shared among these populations. The most common mtDNA haplogroups were M* and B, followed by D and F, which are prevalent in East/Southeast Asia. Christmas Islanders of European descent were characterized by the Eurasian haplogroup R*, and a limited degree of admixture was observed. In general, analysis of the genetic data indicated population affinities to southern Chinese (in particular from the Yunnan Province) and Southeast Asia (Thailand, Malaysia, and Cambodia), which was consistent with historical records of settlement. The combined use of these different marker systems provides a useful and appropriate model for the study of contemporary populations derived from different ethnic origins.

Asian People↗
PubMed1990

Evolution of increased susceptibility to infectious diseases in age structured populations.

Current theory on the epidemiology of infectious diseases in genetically heterogeneous host populations ignores age structure. Thus, the possibility that microparasites might have negative effects on fitness in different ways during different phases of the lives of their hosts is not accounted for. For example, infections causing mortality and morbidity among juveniles might also have an impairing effect on reproduction among adults, as is the case in many so called childhood diseases. I demonstrate that when this is the case there may be a selective pressure for the host to evolve a higher level of susceptibility to an infection, provided it has the following properties: it should (i) provide life-long immunity, (ii) have a negative effect on reproduction and (iii) not cause too many mortalities.

Adult↗
PubMed2000

Population structure of Aedes albopictus (Skuse): the mosquito which is colonizing Mediterranean countries.

Multilocus electrophoresis analysis has been used to study the genetic structure of 18 populations of Aedes albopictus newly introduced to Italy, in comparison with two populations in the United States, four in Japan, and four in Indonesia. Allozyme analysis revealed that 15 out of the 18 studied loci were polymorphic among the 28 populations. No significant deviations from Hardy-Weinberg equilibrium were found at polymorphic loci. High genetic affinity was observed between the Italian populations and those from the United States and Japan. The analysis of variance in allele frequencies showed that variance among subpopulations accounted for most of the total variance, suggesting that isolation of the Italian populations is not related to distance. Analysis of linkage disequilibrium using Ohta's method shows that the variance in the frequency of allele combinations could be explained by the action of the genetic drift which accompanies the establishment of new populations. The colonization process of Ae. albopictus in Italy is following a trend similar to that previously observed in the U.S. A., probably because both infestations derive from several successive introductions, each with large numbers of individuals.

Aedes↗
PubMed2003

Population structure of the pumpkin fruit fly Bactrocera depressa (Tephritidae) in Korea and Japan: Pliocene allopatry or recent invasion?

Because of their widespread agricultural impact and rapid range expansions, true fruit flies (Tephritidae) are the subject of quarantine and control efforts worldwide. Among these flies, the pumpkin fruit fly Bactrocera depressa, which infests squash and other cucurbitaceous plants in Korea, Japan and Taiwan, was recently isolated from produce shipments entering Japan and identified as a regulatory target. This species was described in 1933 from collections in Japan and discovered in 1974 in Korea, suggesting that it may have recently invaded mainland Asia. We analysed the genetic structure of Asian populations of B. depressa using sequence variation for mitochondrial gene cytochrome-oxidase I and three nuclear loci: elongation factor 1alpha, tubulinbeta1 and tubulinbeta3, using frequency-based approaches, nested clade analysis and assignment tests. Contrary to the hypothesis of recent invasion, high levels of genetic subdivision were found among five Korean and three Japanese populations. Nested clade analysis suggested a variety of processes operating over different time scales, including ancient isolation between Korea and Japan and more recent range expansions within each country. Contrary to a priori expectations, the results also suggested the recent introduction of a mitochondrial haplotype into Yokohama, Japan that is related closely to a widespread haplotype found throughout Korea. Assignment tests also supported these conclusions. The combination of a genealogical approach and probabilistic assignments of individuals to populations of origin was able to provide statistical support for the identification of cryptic introductions within an otherwise widespread indigenous species.

Animals↗
PubMedDate not supplied

Population structure and immigration; a study of the Valserine valley (French Jura) from the 17th century until the present.

The establishment of the genealogies and biographies of inhabitants of selected villages from the Haut-Jura from the 17th century up to the present day has enabled us to demonstrate the major role of immigration on the genetic structure of a population. The evaluation of the effective descendance of native versus immigrant couples shows the imbalance of demographic contribution in favour of the first category. Immigrant couples account for 26% of all couples with at least one offspring in the valley, but account for 7.2% of all couples with an effective descendance. In our opinion, this effective immigration reflects in a much better way the measurement of immigration impact on population genetic parameters, especially the genetic 'opening' of the population due to immigration. This measurement of the effective descendance divides the population into two major groups: a core of stable lineage characterized by 70% of couples with an effective descendance, 'surrounded' by an unstable group from which only 30% of couples have an effective descendence in the population. Furthermore, from any given point in time this difference between the two groups can be observed among their descendants during the following generations. The existence of such a core can be explained by the social history of the valley, and shows that any specific unfavorable genetic fostered by the core can be locked within the population and transmitted throughout generations.

Demography↗
PubMed2000

Investigations into the Genetic Variation, Population Structure, and Breeding Systems of the Fern Asplenium trichomanes subsp. quadrivalens.

The genetic structure of five populations of the tetraploid fern Asplenium trichomanes subsp. quadrivalens in northern Switzerland was analyzed. Asplenium trichomanes subsp. quadrivalens is one of the most common and most widespread ferns in Europe. In this study we have combined genetic investigations, spatial autocorrelation, and breeding experiments to investigate in detail five populations from natural rock faces. Enzyme electrophoresis revealed very low genetic variability within and among the populations. The small amount of variation was partitioned mainly among the localities, indicated by high Fst values up to 0.764. Overall means of the proportion of polymorphic loci (P=0.076), the mean number of alleles per locus (A=1.086), and the mean expected heterozygosity (H=0.018) were low compared with other ferns (e.g., Kirkpatrick et al. 1990). Very few heterozygous individuals were found. Values of the fixation index (F) were high, ranging between 0.732 and 1.000 and indicating substantial inbreeding. Spatial autocorrelation showed different patterns of substructure in populations of A. trichomanes subsp. quadrivalens with a tendency for patches in short distances (up to 1.5 m). The breeding experiments with isolated prothalli and prothalli pairs showed that a mean of 56.4% of the isolated prothalli were successful in sporophyte formation. The highest rate in one population was 83.3%. We conclude that genetic load must be low in A. trichomanes subsp. quadrivalens. Sporophyte formation was statistically more successful in the experiments with gametophyte pairs than in isolates, indicating that additional cross-fertilization occurred. The latter agreed with the occurrence of few heterozygote samples and the small number of multilocus phenotypes found in natural habitats. Asplenium trichomanes subsp. quadrivalens is shown to be a highly inbreeding taxon with the capability of single spore colonization and subsequent founding of new populations. Such features can be hypothesized to have contributed to the postglacial colonization and the widespread distribution of this taxon in Europe.

Journal Article↗
PubMed2005

Genetic variation and population structure of an isolate of Citrus exocortis viroid (CEVd) and of the progenies of two infectious sequence variants.

The population structure and diversity within a Citrus exocortis viroid (CEVd) isolate was estimated by single strand conformation polymorphism (SSCP) and sequence analysis. A predominant sequence variant (V1) representing 52.8% of the overall population was identified. V1 and other additional variants presented a composition of the P domain characteristic of severe strains of CEVd. The nucleotide diversity of this CEVd population was lower than expected according to a model of neutral evolution, suggesting a strong negative selection. Citron plants were inoculated with dimeric clones of nine sequence variants and two resulted infectious inducing the severe symptoms characteristic of the original isolate. De novo populations were generated from these infectious variants and like in the original CEVd isolate, both populations presented V1 as the predominant variant but they evolved to a higher nucleotide diversity.

Base Sequence↗
PubMed1999

Genetic analysis of the population structure of socially organized oystercatchers (Haematopus ostralegus) using microsatellites.

On the island of Schiermonnikoog (The Netherlands), the breeding population of oystercatchers can be divided into two groups: 'residents' and 'leapfrogs', based on their distinct social characteristics and limited probabilities of status change between breeding seasons. In order to investigate whether this social organization has caused local genetic differentiation, leapfrogs and residents were compared at eight polymorphic microsatellite loci. No significant genetic subdivision between residents and leapfrogs was observed (theta = 0.0000; 95% confidence interval (CI), -0.0027-0.0033), indicating that the oystercatcher population on the island of Schiermonnikoog has to be considered as one panmictic unit. Investigation of three additional locations in the northern part of The Netherlands did not reveal significant genetic population subdivision either (theta = -0.0005; 95% CI, -0.0045-0.0037), despite the fact that adult osytercatchers show extreme fidelity to their breeding localities. These results indicate panmixis and considerable levels of gene flow within the northern part of The Netherlands. Thus, the results from genetical analyses do not seem to be in agreement with observational data on the dispersal behaviour of breeding individuals. It is argued that the lack of population structure, locally on Schiermonnikoog as well as across larger geographical distances, is to be attributed to high levels of gene flow through dispersal of juvenile birds.

Animals↗
PubMed2003

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.

Algorithms↗
PubMed2006

Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape.

Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in the few remaining high density populations in conservation areas, as well as individuals that occurred, with lower densities, in linear landscape elements, at two spatial scales. In a re-inventory of the landscape, after 3 years, both extinctions and colonizations of populations were observed. Contrary to expectations, no differences in genetic diversity between high and low density populations were observed. Both types of populations had relatively high levels of diversity. Overall genetic differentiation (theta) was 0.04 and significantly different from zero (P < 0.01). A significant isolation-by-distance pattern was found when all populations were simultaneously analysed (r = 0.24, P = 0.013). Isolation by distance was (marginally) significant at the small scale (r = 0.32, P = 0.06), whereas nonsignificant at the large spatial scale (r = -0.05, P = 0.66). A maximization-of-explained-variance procedure resulted in a threshold distance of 3.5 km above which populations were effectively genetically isolated. An additional partial exclusion Bayesian-based assignment test showed that overall 32.3% of the individuals were assigned to their population of origin, 48% were assigned to another population in the area and 19.7% were not assigned. Together, these results suggest high levels of gene flow. Seed dispersal contributes to the observed gene flow up to several hundred metres, which is higher than previously modelled using aerodynamic models on seed dispersal of H. radicata. We discuss the consequences of these results for an evaluation of the probability of persistence of this species in the fragmented landscape.

Asteraceae↗
PubMed2002

Populational structure of Schistosoma mansoni assessed by DNA microsatellites.

DNA microsatellites were used as molecular markers to analyse the population structure of the laboratory LE strain and of 10 field isolates of Schistosoma mansoni, the aetiologic agent of schistosomiasis. Out of 16,000 DNA sequences analysed in databases, 622 microsatellite loci were identified in 481 sequences (3.0%). The AT repetitions were the most frequent, followed by AAT and AC. Six loci showing perfect repetitions were selected and used in the polymerase chain reaction to evaluate polymorphisms in the number of repeats. Two groups of worms were studied. The first group consisted of 78 individuals, 39 of each sex, of the LE strain. The second group of worms consisted of 10 field isolates: seven from humans and three from snails. Four of the six loci were polymorphic, containing 11-17 alleles per locus. No linkage disequilibrium was observed among loci and none of the loci was sex linked. In both groups of worms, a significant deviation from Hardy-Weinberg equilibrium was observed. The observed heterozygosity was always lower than the expected one. The polymerase chain reaction primers were S. mansoni specific. The LE strain showed a lower total number of alleles or a lower average number of alleles/polymorphic locus than the field isolates, suggesting that 41 years of laboratory maintenance exerted selective pressure on the LE strain. The S. mansoni populations from the field were most genetically undifferentiated (R(ST)<0.027), suggesting a high gene flow among them. Our results showed the usefulness of microsatellites for population analysis of S. mansoni, offering a new alternative for a better understanding of schistosomiasis epidemiology.

Animals↗