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[Parasitic systems and the population structure of parasitic organisms].

The analysis of population systems is carried out on the basis of the classification of spatial and functional structure of populations developed by V. N. Beklemishev. Two aspects of the structure of population systems are established. Firstly, population systems are composed of the smaller groups characterised by different self-maintenance ability. Secondly, different functional parts are included into these systems in accordance with different stages (phases) of a life cycle. Peculiarities of the population systems are discussed from these points of view. The population system is a functional part of a particular community. Steady interrelationships between population systems in the community ("community links") are the basis on which the complexes of population systems in different species are formed. A prominent example of this is the parasitic systems, that is the population system of a parasite and all connected populations of its hosts. The structure of a parasitic system is examined. In general, it is characterised by a) peculiarities of the life cycle of the parasite, since its population systems are the organising component of the parasitic system; b) subdivision of the environment for parasites. The first trait is discussed from the standpoint of phase structure of populations which is could be clearly seen in parasites, and the second one-from the viewpoint of the availability of distinct microbiotopes connected with different parts of the population system of parasites. It is the subdivision of the parasites' environment and its organisation according to the scale (interspecies, interpopulation or intrapopulation) variability of the hosts, that make it possible to recognise spatial and functional parts in the framework of the parasitic system. The critical review of the terminology used in the population parasitology is presented.

Animals↗
PubMed2006

Genetic diversity and population structure of yellow camellia (Camellia nitidissima) in China as revealed by RAPD and AFLP markers.

Camellia nitidissima, a rare plant but a useful genetic resource for commercial cultivation of ornamental camellias, is distributed in a narrow region of South China and North Vietnam. In this study, RAPD and AFLP markers were used to assess the genetic diversity and population structure of six natural populations of C. nitidissima from Guangxi in South China. Twenty RAPD primers amplified 183 bands, of which 143 bands were polymorphic, and 8 AFLP primer pairs produced 502 bands, of which 364 were polymorphic. Independent as well as combined analyses of the cluster analyses of the RAPD and AFLP fragments showed that the six populations could be classified into two major genetic groups corresponding to the Nanning and Fangcheng areas. The Mantel test revealed significant correlation between the genetic and geographic distances of C. nitidissima populations (r = 0.953, p = 0.036). AMOVA analysis allowed the partitioning of the genetic variation between groups (36.09%), among populations within groups (25.78%), and within populations (38.14%). An understanding of both the genetic diversity and the population structure of C. nitidissima in China can also provide insight into the conservation and management of this endangered species.

Base Sequence↗
PubMed2002

The evolution of alternative cryptic female choice strategies in age-structured populations.

Cryptic female choice is a potentially important aspect of the sexual selection process. According to the theory of sexual dialectics, postcopulation manipulation of relative male fertilization success can provide an avenue by which females can circumvent attempts by males to control female reproduction. Here I use stochastic models to investigate the evolution of cryptic female choice in populations with and without age structure. In populations without age structure, cryptic female choice will evolve only when (1) precopulatory mate choice by females is inefficient, (2) variation in male fitness is correlated with a trait upon which a female can base her choice of mates, and (3) the cost of multiple mating is not too high. In populations with age structure, similar conditions apply. However, selection sometimes favors females that employ alternative strategies of female choice at different ages. These results help to define the types of biological systems in which we should expect to see the evolution of cryptic female choice. They also illustrate that the evolution of choice strategies in females may be complex and may mirror in some important respects the evolution of alternative mating tactics in males.

Age Factors↗
PubMed1987

Equilibrium and local stability in a logistic matrix model for age-structured populations.

A logistic matrix model for age-structured population dynamics is constructed. This model discretizes a continuous, density-dependent model with age structure, i.e. it is an extension of the logistic model to the case of age-dependence. We prove the existence and uniqueness of its equilibrium and give a necessary and sufficient condition for the local stability of the equilibrium.

Aging↗
PubMed1976

Population structure of Barra (Outer Hebrides).

Historical demography, surname concordance (isonymy), migration, and genealogy give a consistent description of population structure. The census size has averaged about 1400 over the last five centuries. Conjoined with an effective migration rate of 3-05 per generation as estimated by three different methods, this gives an evolutionary size of 638, random kinship of 0-008 and inbreeding of 0-007 relative to the rest of Britain. The population structure of Barra is similar to other British isolates in the recent past, but an order of magnitude less inbred than slash-and-burn agriculturalists and Pacific Islanders. Some consequences for rare genes and polymorphisms are discussed.

Emigration and Immigration↗
PubMed2005

Recombination hotspots and population structure in Plasmodium falciparum.

Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasite's short generation time, coupled with a high cross-over rate, can cause rapid LD break-down. However, observations of low genetic variation have led to suggestions of effective clonality: selfing, population admixture, and selection may preserve LD in populations. Indeed, extensive LD surrounding drug-resistant genes has been observed, indicating that recombination and selection play important roles in shaping recent parasite genome evolution. These studies, however, provide only limited information about haplotype variation at local scales. Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been sequenced previously. The parasites are clustered according to continental origin, but alternative groupings were obtained using SNPs at 37 putative transporter genes that are potentially under selection. Geographic isolation and highly variable multiple infection rates are the major factors affecting haplotype structure. Variation in effective recombination rates is high, both among populations and along the chromosome, with recombination hotspots conserved among populations at chromosome ends. This study supports the feasibility of genome-wide association studies in some parasite populations.

Africa↗
PubMed2005

Population structure of the Brazilian southern green stink bug, Nezara viridula.

The Southern Green Stink Bug, Nezara viridula (L.) (Heteroptera: Pentatomidae), is a cosmopolitan and economically important pest to several crops. Studies on N. viridula migration and population structure have been neglected. We studied geographically distinct Brazilian N. viridula populations to assess their variability and to determine gene flow among them. DNA from specimens collected on soybean fields were subjected to RAPD analysis to determine genetic similarity and population structure parameters. All N. viridula populations studied were genetically distinct from the others. The maximum similarity occurred between populations from Londrina and Sertanópolis (Parana State). The Cruz Alta population was the most divergent from the others. Despite the short distance between Cambé and Londrina (ca. 29 km), and the absence of geographic barriers, both populations clustered in different groups and the estimated gene flow index (Nm) among them was 2.02, indicating relatively restricted migration. The estimated overall index, Nm was 1.41 suggesting that N. viridula is a better flier than the Neotropical Brown stink bug, Euschistus heros (Nm =0.83).

Animals↗
PubMed2005

Population structure, differential bias and genomic control in a large-scale, case-control association study.

The main problems in drawing causal inferences from epidemiological case-control studies are confounding by unmeasured extraneous factors, selection bias and differential misclassification of exposure. In genetics the first of these, in the form of population structure, has dominated recent debate. Population structure explained part of the significant +11.2% inflation of test statistics we observed in an analysis of 6,322 nonsynonymous SNPs in 816 cases of type 1 diabetes and 877 population-based controls from Great Britain. The remainder of the inflation resulted from differential bias in genotype scoring between case and control DNA samples, which originated from two laboratories, causing false-positive associations. To avoid excluding SNPs and losing valuable information, we extended the genomic control method by applying a variable downweighting to each SNP.

Adolescent↗
PubMed2006

Seascape genetics: a coupled oceanographic-genetic model predicts population structure of Caribbean corals.

Population genetics is a powerful tool for measuring important larval connections between marine populations [1-4]. Similarly, oceanographic models based on environmental data can simulate particle movements in ocean currents and make quantitative estimates of larval connections between populations possible [5-9]. However, these two powerful approaches have remained disconnected because no general models currently provide a means of directly comparing dispersal predictions with empirical genetic data (except, see [10]). In addition, previous genetic models have considered relatively simple dispersal scenarios that are often unrealistic for marine larvae [11-15], and recent landscape genetic models have yet to be applied in a marine context [16-20]. We have developed a genetic model that uses connectivity estimates from oceanographic models to predict genetic patterns resulting from larval dispersal in a Caribbean coral. We then compare the predictions to empirical data for threatened staghorn corals. Our coupled oceanographic-genetic model predicts many of the patterns observed in this and other empirical datasets; such patterns include the isolation of the Bahamas and an east-west divergence near Puerto Rico [3, 21-23]. This new approach provides both a valuable tool for predicting genetic structure in marine populations and a means of explicitly testing these predictions with empirical data.

Animals↗
PubMed1999

Dispersal, gene flow, and population structure.

The accuracy of gene flow estimates is unknown in most natural populations because direct estimates of dispersal are often not possible. These estimates can be highly imprecise or even biased because population genetic structure reflects more than a simple balance between genetic drift and gene flow. Most of the models used to estimate gene flow also assume very simple patterns of movement. As a result, multiple interpretations of population structure involving contemporary gene flow, departures from equilibrium, and other factors are almost always possible. One way to isolate the relative contribution of gene flow to population genetic differentiation is to utilize comparative methods. Population genetic statistics such as FST, heterozygosity and Nei's D can be compared between species with differing dispersal abilities if these species are otherwise phylogenetically, geographically and demographically comparable. Accordingly, the available literature was searched for all groups that meet these criteria to determine whether broad conclusions regarding the relationships between dispersal, population genetic structure, and gene flow estimates are possible. Allozyme and mtDNA data were summarized for 27 animal groups in which dispersal differences can be characterized. In total, genetic data were obtained for 333 species of vertebrates and invertebrates from terrestrial, freshwater and marine habitats. Across these groups, dispersal ability was consistently related to population structure, with a mean rank correlation of -0.72 between ranked dispersal ability and FST. Gene flow estimates derived from private alleles were also correlated with dispersal ability, but were less widely available. Direct-count heterozygosity and average values of Nei's D showed moderate degrees of correlation with dispersal ability. Thus, despite regional, taxonomic and methodological differences among the groups of species surveyed, available data demonstrate that dispersal makes a measurable contribution to population genetic differentiation in the majority of animal species in nature, and that gene flow estimates are rarely so overwhelmed by population history, departures from equilibrium, or other microevolutionary forces as to be uninformative.

Animals↗
PubMed2002

Population structure and genetic diversity in insular populations of Nasutitermes takasagoensis (Isoptera: Termitidae) analyzed by AFLP markers.

Dispersal ability and degree of inbreeding in a population can indirectly be assessed using genetic markers. In general, it was suggested that winged termites are not able to fly distances greater than several hundred meters. Here, amplified fragment length polymorphism (AFLP) was used to analyze genetic diversity, population substructure, and gene flow among insular populations of the termite Nasutitermes takasagoensis (Isoptera: Termitidae) in the Yaeyama Islands, Okinawa, Japan. Samples were collected from 77 nests on seven islands of the Yaeyama Group. Using three primer combinations a total of 155 bands were generated with 78 (50%) polymorphic bands. Genetic distance and G(st) values among insular populations were calculated. Relatively high genetic diversity and low values of G (st), suggest there is moderate subpopulation structure. Based on these results, we discussed two possibilities; first, winged termites are able to fly over distances of several kilometers, and second, these results were obtained because insular populations share a recent common origin.

Animals↗
PubMed1993

Randomly amplified polymorphic DNA analysis of clonal population structure and geographic variation in a freshwater bryozoan.

The randomly amplified polymorphic DNA (RAPD) assay was used to identify genetic polymorphisms in three clonal populations of the freshwater bryozoan, Cristatella mucedo, a species with few useful biochemical genetic markers. Of the 19 decamer oligonucleotide primers screened, 13 gave clear, reproducible RAPD profiles. Clonal population structure was evident, and one clone was dominant at each site. Cluster analysis grouped populations from more distant localities separately (Thames Valley and Norfolk), whereas populations from the Thames Valley clustered together. However, even at the regional scale a high degree of relatedness pertained. This work is one of the first RAPD studies of natural populations, and demonstrates the suitability of the technique for examining population structure and geographic variation in clonal taxa.

Animals↗
PubMed2006

Assessment of population structure by single nucleotide polymorphisms (SNPs) in goat breeds.

Single nucleotide polymorphisms (SNPs) may be used in biodiversity studies and commercial tasks like traceability, paternity testing and selection for suitable genotypes. Twenty-seven SNPs were characterized and genotyped on 250 individuals belonging to eight Italian goat breeds. Multilocus genotype data were used to infer population structure and assign individuals to populations. To estimate the number of groups (K) to test in population structure analysis we used likelihood values and variance of the bootstrap samples, deriving optimal K from a drop in the likelihood and a rise in the variance plots against K.

Animals↗
PubMed2002

Genetic diversity and population structure of Plasmodium falciparum isolates from Dakar, Senegal, investigated from microsatellite and antigen determinant loci.

We investigated the genetic diversity and the population structure of 32 Plasmodium falciparum blood sample isolates (25 from Dakar city and suburbs and seven from other localities in Senegal) with two different types of molecular markers, 19 microsatellite and four antigenic determinant loci. Under the same technical procedure, microsatellite loci showed a mean number of alleles greater than that of antigenic loci. Both markers revealed that 15.6% of blood samples were multi-infected. Mean expected heterozygosity calculated from microsatellites and antigens was similar, 0.74 and 0.70, respectively. Significant linkage disequilibrium was observed from microsatellite loci and antigenic determinant loci. This suggests a non-panmictic structure for this sample that could be explained by two non-exclusive hypotheses: (i) a particular mating system (i.e. clonality), and/or (ii) a population structure in P. falciparum (i.e. Wahlund effect). Urban samples could have been drawn from a heterogeneous set of foci with different level of parasitic transmission. Moreover, no relationship was found between multilocus genotypes and different parameters (i.e. age, sex and blood group of parasitized patients; number of trophozoites per microliter of blood). The results are discussed taking into account recently published studies on malaria population biology.

Adolescent↗
PubMed2004

Inferring the population structure and demography of Drosophila ananassae from multilocus data.

Inferring the origin, population structure, and demographic history of a species is a major objective of population genetics. Although many organisms have been analyzed, the genetic structures of subdivided populations are not well understood. Here we analyze Drosophila ananassae, a highly substructured, cosmopolitan, and human-commensal species distributed in the tropical, subtropical, and mildly temperate regions of the world. We adopt a multilocus approach (with 10 neutral loci) using 16 population samples covering almost the entire species range (Asia, Australia, and America). Analyzed with our recently developed Bayesian method, 5 populations in Southeast Asia are found to be central, while the other 11 are peripheral. These 5 central populations were sampled from localities that belonged to a single landmass ("Sundaland") during the late Pleistocene ( approximately 18,000 years ago), when sea level was approximately 120 m below the present level. The inferred migration routes of D. ananassae out of Sundaland seem to parallel those of humans in this region. Strong evidence for a population size expansion is seen particularly in the ancestral populations.

Animals↗
PubMed2007

Structured population dynamics: continuous size and discontinuous stage structures.

A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

Animals↗
PubMed2006

Concordant genetic estimators of migration reveal anthropogenically enhanced source-sink population structure in the river sculpin, Cottus gobio.

River systems are vulnerable to natural and anthropogenic habitat fragmentation and will often harbor populations deviating markedly from simplified theoretical models. We investigated fine-scale population structure in the sedentary river fish Cottus gobio using microsatellites and compared migration estimates from three FST estimators, a coalescent maximum-likelihood method and Bayesian recent migration analyses. Source-sink structure was evident via asymmetry in migration and genetic diversity with smaller upstream locations emigration biased and larger downstream subpopulations immigration biased. Patterns of isolation by distance suggested that the system was largely, but not entirely, in migration-drift equilibrium, with headwater populations harboring a signal of past colonizations and in some cases also recent population bottlenecks. Up- vs. downstream asymmetry in population structure was partly attributable to the effects of flow direction, but was enhanced by weirs prohibiting compensatory upstream migration. Estimators of migration showed strong correspondence, at least in relative terms, especially if pairwise FST was used as an indirect index of relative gene flow rather than being translated to Nm. Since true parameter values are unknown in natural systems, comparisons among estimators are important, both to determine confidence in estimates of migration and to validate the performance of different methods.

Animal Migration↗
PubMed1990

Effects of population structure on within-group variation in the Jirels of Nepal.

The impact of population structure on phenotypic differentiation is most frequently considered in terms of between-subdivision variation. However, the demographic and social structures of a population also induce changes in within-group variation. We analyze the intragenerational dynamics of within-group variation for the Jirels, a tribal population of eastern Nepal. In the analyses we utilized age- and sex-corrected cranial measures (head length, head breadth, bizygomatic diameter, minimum frontal diameter, and head circumference) available for 526 adults (ages 15-54 years). We used a multivariate measure of variance, the standardized generalized variance, to assess levels of within-village variability, quantifying the sampling variance for this statistic by using a jackknife methodology. To generate null expectations of within-group variation, we used permutation procedures, which permit robust testing of significance without distributional assumptions. We also compared the within-birthplace variation in adults to the observed within-residence variation to examine migration effects. Contrary to expectation, some villages with high rates of in-migration have less variability than those with few migrants. When differences between the sexes at birth are controlled for, females in some villages exhibit greater variance than males, reflecting known differences in sex-specific dispersal.

Adolescent↗