Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “population structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6Linked to original sources
PubMed2002

Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers.

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

Animals↗
PubMed1990

Examining population structure through the use of surname matrices: methodology for visualizing nonrandom mating.

The analysis of nonrandom mating using the frequency of marital isonymy indirectly measures the degree of population structure. However, population structure is the result of all matings in a population. Difficulties with large surname matrices have resulted in data being summarized into a single statistic or collapsed into brief tables, with considerable loss of information. By using sophisticated computer graphing procedures and displays, it is possible to directly analyze the mating structure of a community. If P is a vector of proportions for each male surname i (i = 1, 2, 3, ..., n), Q a similar vector of female surnames j(j = 1, 2, 3, ...,m), then the expected frequency matrix E of each possible mating is P x Q. The difference D between the observed frequency matrix O and the expected matrix is O-E. The D matrix is graphed with the x axis containing the male surnames, the y axis the female surnames, and the z axis the difference values dij. Negative values represent negative nonrandom mating and positive values positive nonrandom mating. From 5417 marriages (1840-1963) in the Midlands of Tasmania, those between spouses having 1 of 194 core names were extracted. We analyze these marriages utilizing the new technique and examine the surface of the graph and statistical analysis of its finer structure. Among the results was the demonstration of frequency-dependent selection of surnames. This finding has significant implications for microevolution of human populations, as surnames have existed for possibly 700 years.

Computer Simulation↗
PubMed2001

The effects of mode of development on phylogeography and population structure of North Atlantic Crepidula (Gastropoda: Calyptraeidae).

The mode of development of marine invertebrates is thought to influence levels of population structure and the location of species range endpoints via differences in dispersal ability. To examine these effects, populations of three sympatric clades of sedentary, marine gastropods in the genus Crepidula were sampled along the Atlantic and Gulf coasts of North America. A haplotype tree was constructed for each clade based on 640 bp sequences of mitochondrial cytochrome oxidase c subunit I. Examination of the tree topology, and AMOVA analysis show that species with direct development (those hatching as benthic juveniles) have higher levels of population structure than do species with planktonic development. Both species in the direct-developing C. convexa clade have high levels of geographical differentiation, with most populations representing a discrete clade of haplotypes. The planktotrophic species C. fornicata contains two major haplotype clades, both of which include samples from throughout the Atlantic coast. In this species there is no geographical differentiation among haplotypes but AMOVA analysis detects a small but statistically significant level of geographical structure. The population structure within the C. plana species complex appears also to vary with mode of development: C. atrasolea, a direct-developing species, has higher levels of population structure than does C. depressa, a sympatric planktotrophic species. The coincident occurrence of range endpoints and genetic breaks along the east coast of Florida in both direct-developing species and species with planktonic development indicates that this biogeographic break is not due to development-specific mechanisms such as hydrographic effects on larval recruitment.

Animals↗
PubMed2006

Population structure of an island malaria vector.

The impact of islands on the population structure of Anopheles flavirostris (Ludlow) (Diptera: Culicidae), the primary malaria vector in the Philippines, was assessed. A phylogenetic analysis of 16 cytochrome oxidase subunit 1 (CO1) haplotypes revealed three clades: one basal clade containing genetically disparate haplotypes from Mindanao, and two derived clades, one of which was largely confined to the largest island, Luzon, and one that was widespread except for Luzon. For the Luzon clade, nested clade analysis revealed an isolation-by-distance effect, and a mismatch distribution analysis diagnosed a recent demographic expansion (sum of squared deviation, SDD = 0.0093, P= 0.075), which mirrors demographic attributes found in mainland primary malaria vectors and could inflate estimates of gene flow from F(ST). For the widespread clade, evidence of range expansion and past fragmentation and/or long distance colonization from the Visayas or Mindanao to Palawan is suggested. A south-to-north range expansion of An. flavirostris is suggested; estimates of coalescence for the Luzon clade was 214 000 years ago (ya) (95% confidence interval 35 600-298 000 ya), i.e. late Pleistocene. Present day rather than Pleistocene island association and some, but not all, sea barriers appeared to be important for An. flavirostris population structure. Our results suggest that endemic island malaria vector species need to be considered before any generalizations are made about the population structure of primary and secondary vectors.

Animals↗
PubMed2006

Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry.

The identification of geographic population structure and genetic ancestry on the basis of a minimal set of genetic markers is desirable for a wide range of applications in medical and forensic sciences. However, the absence of sharp discontinuities in the neutral genetic diversity among human populations implies that, in practice, a large number of neutral markers will be required to identify the genetic ancestry of one individual. We showed that it is possible to reduce the amount of markers required for detecting continental population structure to only 10 single-nucleotide polymorphisms (SNPs), by applying a newly developed ascertainment algorithm to Affymetrix GeneChip Mapping 10K SNP array data that we obtained from samples of globally dispersed human individuals (the Y Chromosome Consortium panel). Furthermore, this set of SNPs was able to recover the genetic ancestry of individuals from all four continents represented in the original data set when applied to an independent, much larger, worldwide population data set (Centre d'Etude du Polymorphisme Humain-Human Genome Diversity Project Cell Line Panel). Finally, we provide evidence that the unusual patterns of genetic variation we observed at the respective genomic regions surrounding the five most informative SNPs is in agreement with local positive selection being the explanation for the striking SNP allele-frequency differences we found between continental groups of human populations.

Algorithms↗
PubMed1998

Global matrilineal population structure in sperm whales as indicated by mitochondrial DNA sequences.

The genetic variability and population structure of worldwide populations of the sperm whale was investigated by sequence analysis of the first 5'L 330 base pairs in the mitochondrial DNA (mtDNA) control region. The study included a total of 231 individuals from three major oceanic regions, the North Atlantic, the North Pacific and the Southern Hemisphere. Fifteen segregating nucleotide sites defined 16 mtDNA haplotypes (lineages). The most common mtDNA types were present in more than one oceanic region, whereas ocean-specific types were rare. Analyses of heterogeneity of mtDNA type frequencies between oceans indicated moderate (GST = 0.03) but statistically significant (p = 0.0007) genetic differentiation on a global scale. In addition, strong genetic differentiation was found between potential social groups (GST = 0.03-0.6), indicating matrilineal relatedness within groups. The global nucleotide diversity was quite low (pi = 0.004) implying a recent common mtDNA ancestry (< 100,000) years ago) and a young global population structure. However, within this time period, female dispersal has apparently been limited enough to allow the development of global mtDNA differentiation. The results are consistent with those from observational studies and whaling data indicating stable social affiliations, some degree of area fidelity and latitudinal range limitations in groups of females and juveniles.

Animals↗
PubMed1997

Application of HLA class II polymorphism analysis to the study of the population structure of the Island of Krk, Croatia.

The population structure of the northern Adriatic island of Krk, Croatia, was studied using PCR methodology and nonradioactive oligonucleotide hybridization for the analysis of HLA-DRB1, DRB3, DRB4, DRB5, DQA1, and DQB1 polymorphisms. Allele frequencies, genetic kinship (R), and genetic distances (E2) were computed, and correlations between distance (genetic, linguistic, geographic) and kinship (migration) matrices were examined. The results, reflecting past (micro-) evolutionary processes, indicate that ethnohistorical and sociocultural events rather than geographic distances are the primary determinants of today's population structure of the island.

Adult↗
PubMed1999

Importance of population structure at the time of toxicant exposure.

Populations in nature often consist of a mixture of stages and ages, yet toxicological studies even demographic studies, usually evaluate one starting life stage. In this study it was asked whether the starting age/stage structure of a population at the time of initial pesticide exposure influenced the impact that pesticides have on population growth rates. This question was answered by exposing differently structured populations of two terrestrial arthropod species, the two-spotted spider mite, Tetranychus urticae (Koch), and the pea aphid, Acrythosiphon pisum (Harris), to pesticides. The three structured populations tested were (1) eggs or neonates for A. pisum and T. urticae, respectively, (2) stable age distribution, and (3) young adult females only. Instantaneous rates of population increase (ri) for the three structured populations were determined over time without exposure to pesticides (control) and after exposure to pesticides. Populations of T. urticae were exposed to 100 ppm of the pesticide dicofol; populations of A. pisum were exposed to 200 ppm Neemix. The ri for the three control populations of T. urticae and A. pisum converged in a closed system 16 and 17 days after the start of the study, respectively. Unlike the control populations, the ri of the three treated populations did not converge by Day 16 for the mite species or Day 17 for the aphid species after exposure to pesticides. Growth rates of populations started as eggs (mites) or neonates (aphids) remained significantly lower than those of the adult or mixed-age populations (P</=0.05). Acute mortality data indicated that exposure to 100 ppm dicofol was equivalent to the LC21 for the egg stage, the LC59 for immatures, and the LC69 for adult T. urticae. Thus, even though the egg stage was the least susceptible stage of T. urticae, populations started as eggs were significantly more susceptible than populations started as the stable age distribution or as adults. It was concluded that the initial structure of a population does have an influence on the impact that pesticides will have on populations and that age/stage structure should be given serious consideration when evaluating toxicant effects.

Age Factors↗
PubMed1994

Evolutionarily stable growth rates in size-structured populations under size-related competition.

The competitive interactions between individuals in size-structured populations usually change as a function of the individuals' sizes. A general model of a density-dependent size-structured population is used to investigate the size-specific birth and death rates that result when growth rates can be adjusted adaptively. If there is no cost associated with faster growth, the evolutionarily stable growth rates result in an ideal free distribution of individuals among size classes, provided that competition within size classes is stronger than competition between size classes. When the population is stationary, this ideal free distribution is characterized by identical ratios of expected number of offspring per unit time to probability of death per unit time for all size classes with growth rates less than the physiologically maximum level. If more rapid growth reduces birth rate or increases death rate, the size-specific ratios of births to mortality increase with the organism's size. If the population is growing in a density independent manner, but there is a cost to growth, there should be an increase with size in the ratio of reproductive output to the quantity (population growth rate minus survival probability). Available evidence about size-specific birth and death rates in some size-structured populations is discussed.

Animals↗
PubMed1986

Hierarchical selection theory and sex ratios. I. General solutions for structured populations.

Models of sex-ratio evolution in structured populations are derived with G.R. Price's covariance form for the hierarchical analysis of natural selection (1970, Nature 227, 520-521). Previous work on competition among related males for mates (local mate competition), competition among related females for a limiting resource (local resource competition), inbreeding, group selection, and asymmetry of genetic inheritance between males and females, are subsumed under a general formulation for sex-ratio biases in structured populations. I found that the evolutionarily stable strategy sex ratio (males:females) for diploids is 1 - rho m:1 - rho f, where rho m is the regression coefficient of relatedness of the controlling genotypes on males competing for mates, rho f is the regression of controlling genotypes on females that compete for a fixed, limiting resource, and there is no inbreeding. For inbreeding and no competition among females, the evolutionarily stable strategy is 1 - rho m:1 + rho mf, where rho mf is the regression of controlling genotypes on females' mates.

Animals↗
PubMed2001

Allozyme diversity and population structure of Japanese and Korean populations of wild radish, Raphanus sativus var. hortensis f. raphanistroides (Brassicaceae).

Raphanus satiuus var. hortensis f. raphanistroides (wild radish: Brassicaceae) is an insect-pollinated wild plant that grows mainly on beaches in East Asia. Starch gel electrophoresis was used to investigate the allozyme diversity and genetic structure of 25 Japanese and 9 Korean populations of this plant. Although the Korean populations were small, isolated, and patchily distributed, they maintained a high level of genetic diversity; the average percentage of polymorphic loci was 63.1%, the mean number of alleles per locus was 2.27, and the average heterozygosity was 0.278. The corresponding estimates for these parameters in the Japanese populations were 53.3%, 2.26, and 0.278. These estimates are considerably higher than those from species with similar life history and ecological characteristics, but they are lower than those from R. raphanistrum, the wild radish that grows in Europe and the U.S.A. The combination of an insect-pollinated, outcrossing breeding system, large population sizes, gene flow from cultivated radish population, and a propensity for high fecundity may explain the high level of genetic diversity within wild populations.

Alleles↗
PubMed2001

Recombination and the population structures of bacterial pathogens.

The population structures of bacterial species are complex and often controversial. To a large extent, this is due to uncertainty about the frequency and impact of recombination in bacteria. The existence of clones within bacterial populations, and of linkage disequilibrium between alleles at different loci, is often cited as evidence for low rates of recombination. However, clones and linkage disequilibrium are almost inevitable in species that divide by binary fission and can be present in populations where recombination is frequent. In recent years, it has become possible to directly compare rates of recombination in different species. These studies indicate that in many bacterial species, including Neisseria meningitidis, Streptococcus pneumoniae, and Staphylococcus aureus, evolutionary change at neutral (housekeeping) loci is more likely to occur by recombination than mutation and can result in the elimination of any deep-rooted phylogenetic signal. In such species, the long-term evolution of the population is dominated by recombination, but this does not occur at a sufficiently high frequency to prevent the emergence of adaptive clones, although these are relatively short-lived and rapidly diversify.

Bacterial Physiological Phenomena↗
PubMed1999

Evolution of cooperation in spatially structured populations

Using a spatial lattice model of the Iterated Prisoner's Dilemma we studied the evolution of cooperation within the strategy space of all stochastic strategies with a memory of one round. Comparing the spatial model with a randomly mixed model showed that (1) there is more cooperative behaviour in a spatially structured population, (2) PAVLOV and generous variants of it are very successful strategies in the spatial context and (3) in spatially structured populations evolution is much less chaotic than in unstructured populations. In spatially structured populations, generous variants of PAVLOV are found to be very successful strategies in playing the Iterated Prisoner's Dilemma. The main weakness of PAVLOV is that it is exploitable by defective strategies. In a spatial context this disadvantage is much less important than the good error correction of PAVLOV, and especially of generous PAVLOV, because in a spatially structured population successful strategies always build clusters. Copyright 1999 Academic Press.

Journal Article↗
PubMed2004

Strong population structure in the marine sponge Crambe crambe (Poecilosclerida) as revealed by microsatellite markers.

Different categories of molecular markers have been used so far to study the population structure of sponges. However, these markers often did not have the resolution power to address precisely questions on structuring processes, especially at the intrapopulational level. In this study we show that microsatellites fulfil these expectations, allowing a fine description of population structure at different geographical scales in the marine sponge Crambe crambe. Specimens were collected in 11 locations, representing most of the Atlanto-Mediterranean range of the species, and were analysed at six loci. As expected for a sessile invertebrate with lecitotrophic larvae, high levels of between-population structure were found (FST = 0.18) and a significant isolation-by-distance pattern was observed. A strong genetic structure was also found within sampled sites (FIS = 0.21) that may be explained by several factors including inbreeding, selfing and the Wahlund effect. In spite of a sampling design planned to avoid the sampling of clones, genotypically identical individuals for the six loci were found in some locations. The significance of these potential clones is discussed and their effect on the observed pattern of population structure assessed. Patterns of allelic distribution within populations suggest the possibility of a recent colonization of the Atlantic range from the Mediterranean Sea.

Animals↗
PubMed1987

Partial correlation of distance matrices in studies of population structure.

Anthropological studies of human population structure commonly compare various monogenic and polygenic (metric) distance matrices to distance matrices obtained from measures of geographical dispersion, linguistic differences, and migration patterns in an attempt to infer something about the effects of evolutionary factors (drift and differential selection, in particular). It is, though, commonly recognized that geography, language, and migration patterns may be intercorrelated due to the common effects of historical and social processes. Previous attempts to deal with the problems of assessing relative effects among such sets of intercorrelated factors using partial correlations have resulted in coefficients that are either not well defined or have no known sampling distribution or both. Here, we outline a general approach to partialling distance matrices that results in well-defined coefficients and valid significance testing procedures. Application of the matrix partialling methods to a variety of distance matrices obtained for a sample of eight ethnolinguistic groups from the Harvard Solomon Islands Expedition (Friedlaender et al., 1986) reveals a close association between language dissimilarity and dermatoglyphics controlling for geography, thus reinforcing earlier suggestions that dermatoglyphics, properly used, reflect historical relationships of groups in this region better than do anthropometry, odontometrics, or small batteries of blood polymorphisms.

Anthropology↗
PubMed2004

Red environmental noise and the appearance of delayed density dependence in age-structured populations.

Previous work suggests that red environmental noise can lead to the spurious appearance of delayed density dependence (DDD) in unstructured populations regulated only by direct density dependence. We analysed the effect of noise reddening on the pattern of spurious DDD in several variants of the density-dependent age-structured population model. We found patterns of spurious DDD in structured populations with either density-dependent fertility or density-dependent survival of the first age class, inconsistent with predictions from unstructured population models. Moreover, we found that nonspurious negative DDD always emerges in populations with deterministic chaotic dynamics, regardless of population structure or the type of environmental noise. The effect of noise reddening in generating spurious DDD is often negligible in the chaotic region of population deterministic dynamics. Our findings suggest that differences in species' life histories may exhibit different patterns of spurious DDD (owing to noise reddening) than predicted by unstructured models.

Age Factors↗
PubMed2004

Indirect protection obtained by Haemophilus influenzae type b vaccination: analysis in a structured population model.

We used a structured population model to study factors determining the magnitude of indirect protection in Haemophilus influenzae type b (Hib) vaccination. On a simulation platform mimicking the population of Finland, a Hib transmission and immunity model, including cross-reactive bacterial encounters, was formulated. Utilizing different vaccination coverages and vaccine types we could study how fast the incidence of Hib disease declined due to direct and indirect vaccination effects. With the Finnish vaccination schedule we could reproduce the observed disappearance of Hib cases. Our results show that an indirect effect was already significant with a relatively low vaccine coverage, even with a vaccine only partly reducing carriage acquisition. This suggests that the vaccination schedule and vaccine to be used should be chosen to result, in addition to immunological memory, in high antibody concentrations, sufficient to reduce carriage, the latter being the main factor behind successful elimination of transmission and disease.

Adolescent↗
PubMed1986

Life not lived due to disequilibrium in heterogeneous age-structured populations.

Three models of age-structured populations with demographically heterogeneous subpopulations are analyzed. In the first model, each subpopulation has its own age-specific vital rates which are fixed in time. In the second model, the vital rates of each subpopulation are uniformly inhibited by increasing total numbers of individuals. In the third, the vital rates of groups of subpopulations are inhibited by the total numbers of individuals in other groups of subpopulations with an intensity that depends on the interacting pair of groups. Three functions are defined to measure disequilibrium in the subpopulation frequencies, subpopulation age structures, and total population size. For the first model, we show that disequilibrium will shift the trajectory of the total numbers of individuals forward or backward in time by an asymptotic constant that is proportional to the sum of the disequilibrium measures. For the second model, we establish sufficient conditions for the existence of a globally stable equilibrium and we show that disequilibrium will result in a finite loss or gain in life which is proportional to the sum of the disequilibrium measures. For the last model, we show that the loss or gain in life for each group of subpopulations is a linear combination over all groups of the sums of the three disequilibrium measures. We illustrate these results with numerical examples and give possible biological interpretations of the models. We relate these new results to previous work on the cost of natural selection and measures of demographic disequilibrium.

Age Factors↗