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At least 523 records · Page 29Linked to original sources
PubMed2004

The population structure of African cultivated rice oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation.

Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown (1) by a lack of decay in LD among markers on the same chromosome and (2) by a strictly increasing composite likelihood function for the recombination parameter. This suggested that the elevation in LD was due not to physical linkage but to other factors, such as population structure. A Bayesian clustering analysis confirmed this hypothesis, indicating that the sample of O. glaberrima in this study was subdivided into at least five cryptic subpopulations. Two of these subpopulations clustered with control samples of O. sativa, subspecies indica and japonica, indicating that some O. glaberrima accessions represent admixtures. The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits-possibly reflecting ecological adaptation to different growing environments.

Acclimatization↗
PubMed2000

Species relationships and population structure of Littorina saxatilis Olivi and L. tenebrosa Montagu in Ireland using single-strand conformational polymorphisms (SSCPs) of cytochrome b fragments.

Littorina saxatilis is a ubiquitous snail of intertidal habitats in the North Atlantic. Shell type in littorinids is extremely polymorphic and defined by habitat. Taxonomy based upon shell type has been revised in the light of anatomic and genetic information, but uncertainties remain. In this study, the population structure of L. saxatilis and L. tenebrosa was studied at 11 sites in Ireland using single-strand conformational polymorphisms of a 375-bp portion of the cytochrome b gene, and the status of L. tenebrosa, the small, fragile-shelled, brackish water type, was considered. The genetic patterns among L. saxatilis and L. tenebrosa populations were examined over varying distances and L. tenebrosa was compared with adjacent L. saxatilis populations at four sites on the west coast of Ireland and one site on the east coast. Haplotype diversity was high with 32 haplotypes present among 995 individuals. Pairwise tests suggest gene flow over small scales among and between habitat types and may reflect the stochastic legacy of postglacial recolonization over larger scales. In AMOVA tests, geography explained nearly twice as much of the variance (30%) as habitat type (18%), indicating that gene flow is more restricted by distance than by habitat type, and supporting the status of L. tenebrosa as an ecotype of L. saxatilis rather than a separate species.

Analysis of Variance↗
PubMed2003

Host specificity and population structure of two exotic helminths, Camallanus cotti (Nematoda) and Bothriocephalus acheilognathi (Cestoda), parasitizing exotic fishes in Waianu Stream, O'ahu, Hawai'i.

Introduction of exotic fishes into Hawai'ian streams has resulted in the simultaneous introduction of exotic parasites. Camallanus corti (Nematoda) and Bothricephalus acheilognathi (Cestoda) are the most prevalent and abundant fish helminths in Hawai'ian streams. The population structure and host specificity of C. cotti and B. acheilognathi in exotic poeciliids were examined during May and June 1995 in Waianu Stream, O'ahu, Hawai'i. Prevalence and mean abundance of C. cotti were significantly different among Poecilia reticulata (65.2%, 1.05), Poecilia mexicana (49.0%, 0.87), and Xiphophorus helleri (32.3%, 0.44). Prevalence of B. acheilognathi was significantly higher in P. mexicana (6.1%) than in P. reticulata (2.1%) and X. helleri (1.6%). However, tapeworm differences in mean abundance were not significant among P. mexicana (0.08), P. reticulata (0.04), or X. helleri (0.03). Nematode and tapeworm prevalence and mean abundance were not significantly different with regard to fish sex. Camallanus cotti prevalence and mean abundance increased as P. mexicana body size increased (r2 = 0.84 and r2 = 0.72, respectively), whereas B. acheilognathi displayed no significant trend with respect to poeciliid body size.

Analysis of Variance↗
PubMed1995

Developing microsatellite markers for insect population structure: complex variation in a checkerspot butterfly.

We isolated and characterized two microsatellite markers from the genome of the endangered checkerspot butterfly Melitaea cinxia L. In Finland, this species only survives on the Aland islands, where it exhibits a highly fragmented metapopulation structure on small meadows. Four alleles were observed at the locus CINX1 and nine at CINX4; the total gene diversities at the two loci were HT = 0.34 and 0.80, respectively. A pilot survey showed moderate gene frequency differentiation among meadows (local populations; FLM = 0.1) and among metapopulations c. 30 km apart (FMT = 0.2). Contrary to prior expectation, distinct feeding larval groups collected in the spring did not represent offspring of single females. There was a conspicuous excess of homozygotes within local populations (FIL = 0.35), which can hardly be attributed to population structure alone; this urges caution in straightforward interpretation of microsatellite phenotype data.

Animals↗
PubMed2005

A second look at mitochondrial DNA variability in European anchovy (Engraulis encrasicolus): assessing models of population structure and the Black Sea isolation hypothesis.

Genetic architectures of marine fishes are generally shallow because of the large potential for gene flow in the sea. European anchovy, however, are unusual among small pelagic fishes in showing large differences among sub-basins and in harbouring two mtDNA phylogroups ('A' & 'B'), representing 1.1-1.85 million years of separation. Here the mtDNA RFLP dataset of Magoulas et al. [1996, Mol. Biol. Evol. 13: 178-190] is re-examined to assess population models accounting for this subdivided population structure and to evaluate the zoogeographical origins of the two major phylogroups. Haplotype and nucleotide diversities are highest in the Ionian Sea and lowest in the Aegean and Black seas. However, this gradient is absent when 'A' and 'B' haplotypes are examined separately. Neither the self-sustaining nor the basin population models adequately describe anchovy population behaviour. Tests for neutrality, mismatch and nested clade analyses are concordant in depicting recent expansions of both phylogroups. Unimodel mismatch distributions and haplotype coalescences dating to the last (Eemian) interglacial ('B') and the Weichselian pleniglacial period ('A') indicate separate colonizations of the Mediterranean Basin. Phylogroup 'A' is unlikely to have arisen through continuous long-term isolation in the Black Sea because of climate extremes from displaced subpolar weather systems during the ice ages. Ancestors of both groups appear to have colonized the Mediterranean from the Atlantic in the late Pleistocene. Hence, zoogeographic models of anchovy in the Mediterranean must also include the eastern (and possibly southern) Atlantic.

Animals↗
PubMed2001

Predicting the dynamics of antiviral cytotoxic T-cell memory in response to different stimuli: cell population structure and protective function.

This paper examines the numerical and functional consequences of various stimuli on antiviral CD8+ T-cell memory using a mathematical model. The model is based upon biological evidence from the murine model of infection with lymphocytic choriomeningitis virus (LCMV) that the phenotype of immunological memory represents low-level responses driven by various stimuli, and the memory CTL population is partitioned between resting, cycling and effector cells. These subpopulations differ in their lifespan, their potential to mediate antiviral protection and in the stimuli needed for their maintenance. Three types of maintenance stimuli are examined: non-antigen-specific (bystander) stimulation, persisting antigen stimulation and reinfection-mediated stimulation. The modelling predicts that: (i) stable persistence of CTL memory requires the presence of either bystander or antigen-specific stimulation above a certain threshold depending on the sensitivity of memory CTL to stimulation and their life-span; (ii) a relatively low level of stimuli (approximately 10(4) fold less on a per CTL basis compared to acute infection) is needed to stabilize the expanded memory CTL population; (iii) the presence of CTL subsets in the memory pool of different activation states and lifespans ensures the robustness of memory persistence in the face of temporal variation in the low-level stimuli and; (iv) an 'optimal' population structure of the memory CTL pool, in terms of immediate protection, requires the presence of both activated cycling and effector CTL. For this, persisting antigen alone or synergistically with bystander signals provide the appropriate stimulation, so that the stimuli equivalent to approximately 30 p.f.u. of LCMV in the spleen are sufficient to maintain approximately 10(5)-10(6) specific CTL in the memory pool. These observations are relevant both to our understanding of natural protective immunity and to vaccine design.

Animals↗
PubMed2005

Extreme population structure and high interspecific divergence of the Silene Y chromosome.

Previous studies have demonstrated that the diversity of Y-linked genes is substantially lower than that of their X-linked homologs in the plant Silene latifolia. This difference has been attributed to selective sweeps, Muller's ratchet, and background selection, processes that are predicted to severely affect the evolution of the nonrecombining Y chromosome. We studied the DNA diversity of a noncoding region of the homologous genes DD44Y and DD44X, sampling S. latifolia populations from a wide geographical area and also including the closely related species S. dioica, S. diclinis, and S. heuffelii. On the Y chromosome of S. latifolia, we found substantial DNA diversity. Geographical population structure was far higher than on the X chromosome and differentiation between the species was also higher for the Y than for the X chromosome. Our findings indicate that the loss of genetic diversity on the Y chromosome in Silene occurs within local populations rather than within entire species. These results are compatible with background selection, Muller's ratchet, and local selective sweeps, but not with species-wide selective sweeps. The higher interspecific divergence of DD44Y, compared to DD44X, supports the hypothesis that Y chromosome differentiation between incipient species precedes reproductive isolation of the entire genome, forming an early stage in the process of speciation.

Base Sequence↗
PubMed2002

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis.

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.

Alleles↗
PubMed2006

Epidemiological dynamics of antimonial resistance in Leishmania donovani: genotyping reveals a polyclonal population structure among naturally-resistant clinical isolates from Nepal.

Pentavalent antimonials (SbV) are the first line drug against leishmaniasis worldwide, but drug resistance is increasingly reported, particularly in the Indian sub-continent, where it represents a major threat for the control of anthroponotic visceral leishmaniasis (VL). In order to understand the epidemiological dynamics of antimonial resistance in anthroponotic VL, we analysed here the population structure of 24 Leishmania donovani stocks isolated from anthroponotic VL-patients from Eastern Nepal: 13 SbV-naturally resistant and 11 SbV-sensitive, as demonstrated by in vitro drug susceptibility assays. The parasites were genotyped by PCR-RFLP analysis of kDNA minicircles and by microsatellite analysis and the encountered polymorphism revealed a polyclonal structure among resistant isolates. Furthermore, analysis of paired samples obtained from the same patients before treatment and after failure revealed primary as well as acquired resistance. The hypothesis of independent events of drug resistance emergence is proposed and confronted to alternative explanations. Our results show the dynamics of drug resistance epidemiology and highlight the importance of surveillance networks.

Amphotericin B↗
PubMed2004

Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle.

The East Indies triangle, bordered by the Phillipines, Malay Peninsula and New Guinea, has a high level of tropical marine species biodiversity. Pristipomoides multidens is a large, long-lived, fecund snapper species that is distributed throughout the East Indies and Indo-Pacific. Samples were analysed from central and eastern Indonesia and northern Australia to test for genetic discontinuities in population structure. Fish (n = 377) were collected from the Indonesian islands of Bali, Sumbawa, Flores, West Timor, Tanimbar and Tual along with 131 fish from two northern Australian locations (Arafura and Timor Seas) from a previous study. Genetic variation in the control region of the mitochondrial genome was assayed using restriction fragment length polymorphism and direct sequencing. Haplotype diversity was high (0.67-0.82), as was intraspecific sequence divergence (range 0-5.8%). F(ST) between pairs of populations ranged from 0 to 0.2753. Genetic subdivision was apparent on a small spatial scale; F(ST) was 0.16 over 191 km (Bali/Sumbawa) and 0.17 over 491 km (Bali/Flores). Constraints to dispersal that contribute to, and maintain, the observed degree of genetic subdivision are experienced presumably by all life history stages of this tropical marine finfish. The constraints may include (1) little or no movement of eggs or larvae, (2) little or no home range or migratory movement of adults and (3) loss of larval cohorts due to transport of larvae away from suitable habitat by prevailing currents.

Analysis of Variance↗
PubMed2006

Genetic population structure of the soil bacterium Myxococcus xanthus at the centimeter scale.

Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history of social swarming, social predation, and multicellular fruiting body formation. Very little is known about genetic diversity within this species or how social strategies might vary among neighboring strains at small spatial scales. To investigate the small-scale population structure of M. xanthus, 78 clones were isolated from a patch of soil (16 by 16 cm) in Tübingen, Germany. Among these isolates, 21 genotypes could be distinguished from a concatemer of three gene fragments: csgA (developmental C signal), fibA (extracellular matrix-associated zinc metalloprotease), and pilA (the pilin subunit of type IV pili). Accumulation curves showed that most of the diversity present at this scale was sampled. The pilA gene contains both conserved and highly variable regions, and two frequency-distribution tests provide evidence for balancing selection on this gene. The functional domains in the csgA gene were found to be conserved. Three instances of lateral gene transfer could be inferred from a comparison of individual gene phylogenies, but no evidence was found for linkage equilibrium, supporting the view that M. xanthus evolution is largely clonal. This study shows that M. xanthus is surrounded by a variety of distinct conspecifics in its natural soil habitat at a spatial scale at which encounters among genotypes are likely.

Bacterial Proteins↗
PubMed2006

Late Chachapoya population structure prior to Inka conquest.

Archaeological and ethnohistorical documents suggest that the Chachapoya region was inhabited by a number of distinct sociopolitical groups that only united in the face of their common enemy, the Inka. The purpose of this research is to quantify the amount of internal genetic differentiation and levels of extraregional gene flow during the Late Chachapoya period, in order to obtain a better understanding of the genetic relationship between these presumed ethnic groups. Craniometric data were collected from three Late Chachapoya samples (Laguna Huayabamba, Kuelap, and Laguna de los Cóndores), in order to understand the genetic relationships between the groups and facilitate our understanding of Late Chachapoya population structure. Genetic differentiation among these series ranged from 0.047 (heritability = 1.0) to 0.090 (heritability = 0.55). The Relethford-Blangero residuals indicate that the Laguna Huayabamba and Laguna de los Cóndores populations were receiving greater than average external gene flow, while Kuelap was receiving less than average external gene flow. The correspondence between biological and archaeological data in the investigation of prehistoric ethnic identity is discussed.

Anthropology, Cultural↗
PubMed2004

Age-structured population growth rates in constant and variable environments: a near equilibrium approach.

General measures summarizing the shapes of mortality and fecundity schedules are proposed. These measures are derived from moments of probability distributions related to mortality and fecundity schedules. Like moments, these measures form infinite sequences, but the first terms of these sequences are of particular value in approximating the long-term growth rate of an age- structured population that is growing slowly. Higher order terms are needed for approximating faster growing populations. These approximations offer a general nonparametric approach to the study of life-history evolution in both constant and variable environments. These techniques provide simple quantitative representations of the classical findings that, with fixed expected lifetime and net reproductive rate, type I mortality and early peak reproduction increase the absolute magnitude of the population growth rate, while type III mortality and delayed peak reproduction reduce this absolute magnitude.

Environment↗
PubMed2001

On the formulation and analysis of general deterministic structured population models. II. Nonlinear theory.

This paper is as much about a certain modelling methodology, as it is about the constructive definition of future population states from a description of individual behaviour and an initial population state. The key idea is to build a nonlinear model in two steps, by explicitly introducing the environmental condition via the requirement that individuals are independent from one another (and hence equations are linear) when this condition is prescribed as a function of time. A linear physiologically structured population model is defined by two rules, one for reproduction and one for development and survival, both depending on the initial individual state and the prevailing environmental condition. In Part I we showed how one can constructively define future population state operators from these two ingredients. A nonlinear model is a linear model together with a feedback law that describes how the environmental condition at any particular time depends on the population size and composition at that time. When applied to the solution of the linear problem, the feedback law yields a fixed point problem. This we solve constructively by means of the contraction mapping principle, for any given initial population state. Using subsequently this fixed point as input in the linear population model, we obtain a population semiflow. We then say that we solved the nonlinear problem.

Animals↗
PubMed2000

Sequence diversity of Pseudomonas aeruginosa: impact on population structure and genome evolution.

Comparative sequencing of Pseudomonas aeruginosa genes oriC, citS, ampC, oprI, fliC, and pilA in 19 environmental and clinical isolates revealed the sequence diversity to be about 1 order of magnitude lower than in comparable housekeeping genes of Salmonella. In contrast to the low nucleotide substitution rate, the frequency of recombination among different P. aeruginosa genotypes was high, leading to the random association of alleles. The P. aeruginosa population consists of equivalent genotypes that form a net-like population structure. However, each genotype represents a cluster of closely related strains which retain their sequence signature in the conserved gene pool and carry a set of genotype-specific DNA blocks. The codon adaptation index, a quantitative measure of synonymous codon bias of genes, was found to be consistently high in the P. aeruginosa genome irrespective of the metabolic category and the abundance of the encoded gene product. Such uniformly high codon adaptation indices of 0.55 to 0.85 fit the ubiquitous lifestyle of P. aeruginosa.

Biological Evolution↗
PubMed2006

Genetic diversity analyses of grapevine Rupestris stem pitting-associated virus reveal distinct population structures in scion versus rootstock varieties.

Grapevine Rupestris stem pitting-associated virus (GRSPaV) is a member of the genus Foveavirus within the family Flexiviridae. GRSPaV is closely associated with the disease Rupestris stem pitting and is frequently detected in grapevines worldwide. Previous research in several laboratories suggests that GRSPaV consists of a family of sequence variants. However, the genetic composition of GRSPaV variants in viral isolates from scion and rootstock varieties has not been studied extensively. In this report, the genetic diversity and population structure of GRSPaV isolates from scion and rootstock varieties were analysed using two pairs of primers targeting two different genomic regions encoding the helicase domain of the replicase and the capsid protein. In total, 190 cDNA clones derived from 24 isolates were sequenced and analysed. At least four major groups of GRSPaV variants were found to exist in grapevines. Interestingly, the majority of the scion varieties (9/10) that were analysed, regardless of their genetic background and geographical origin, harboured complex viral populations composed of two to four distinct viral variants. In contrast, the viral populations in isolates from rootstock varieties were homogeneous and comprised a single variant. The practice of grafting between scion and rootstock varieties commonly used in modern viticulture, coupled with the frequent regional and international exchange of propagating materials, may have played a major role in the ubiquitous distribution and mixed infections of distinct GRSPaV variants among scion varieties. The possible origin and evolution of GRSPaV are also discussed.

Cloning, Molecular↗
PubMed2006

Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum.

The Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of the D-loop mitochondrial region, samples collected at four different locations in the Southern Ocean, three in the Atlantic and one in the Pacific sector. Sampling was replicated in two different years at two locations. Sequence analysis showed a remarkably high polymorphism, with 110 haplotypes over the 256 investigated specimens, and about 80% of haplotypes occurring only once. Neutrality tests indicated that all samples were not at mutation-drift equilibrium, and suggested a past population expansion. This result was supported by the presence of a star-like topology in the D-loop gene tree, and by results of mismatch distribution. The start of the expansion was dated, using a specifically calibrated clock, between 111 and 126 thousand years ago. This value corresponds to the start of the cooling period that led to the last glaciation peak, and is in close agreement with a recently suggested range expansion for pelagic Antarctic ecosystems. Analysis of molecular variation indicated a small, though highly significant, value of differentiation between samples. This result, together with the lack of association between clades and geographical locations, indicates a weak population structure for the species.

Animals↗
PubMed1998

Probing the genetic population structure of Trypanosoma cruzi with polymorphic microsatellites.

We describe here the identification of eight polymorphic microsatellite loci with (CA)n repeats in the Trypanosoma cruzi genome based on the affinity capture of fragments using biotinylated (CA)12 attached to streptavidin-coated magnetic beads. The presence of two peaks in PCR amplification products from individual clones confirmed that T. cruzi is diploid. Hardy-Weinberg and linkage disequilibrium analyses suggested that sexual reproduction is rare or absent and that the population structure is clonal. Several strains, especially those isolated from nonhuman sources, showed more than two alleles in many loci demonstrating that they were multiclonal. The phylogenetic analysis of T. cruzi based on microsatellites revealed a great genetic distance among strains, although the strain dispersion profile in the Wagner network was in general agreement with the species dimorphism found by PCR amplification of the divergent region of the rRNA 24Salpha gene.

Animals↗