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At least 217 records · Page 12Linked to original sources
PubMed2001

Is the impact of environmental noise visible in the dynamics of age-structured populations?

Climate change has ignited lively research into its impact on various population-level processes. The research agenda in ecology says that some of the fluctuations in population size are accountable for by the external noise (e.g. weather) modulating the dynamics of populations. We obeyed the agenda by assuming population growth after a resource-limited Leslie matrix model in an age-structured population. The renewal process was disturbed by superimposing noise on the development of numbers in one or several age groups. We constructed models for iteroparous and semelparous breeders so that, for both categories, the population growth rate was matching. We analysed how the modulated population dynamics correlates with the noise signal with different time-lags. No significant correlations were observed for semelparous breeders, whereas for iteroparous breeders high correlations were frequently observed with time-lags of 71 year or longer. However, the latter occurs under red-coloured noise and for low growth rates when the disturbance is on the youngest age group only. It is laborious to find any clear signs of the (red) noise- and age group-specific fluctuations if the disturbance influences older age groups only. These results cast doubts on the possibility of detecting the signature of external disturbance after it has modulated temporal fluctuations in age-structured populations.

Age Factors↗
PubMed2004

Genetic diversity and population structure of Aeromonas hydrophila, Aer. bestiarum, Aer. salmonicida and Aer. popoffii by multilocus enzyme electrophoresis (MLEE).

Genetic diversity, genetic relationship, identification and population structure of 120 Aeromonas strains (including Aer. hydrophila, Aer. bestiarum, Aer. salmonicida and Aer. popoffii) isolated from various sources were studied by analysis of 15 genetic loci by multilocus enzyme electrophoresis (MLEE). All 15 loci were polymorphic, with an average of 9.4 alleles per locus and a mean genetic diversity (H) of 0.64. Cluster analysis defined at H < or = 0.7 differentiated most of the taxa analysed except the Aer. popoffii and Aer. bestiarum strains, which showed a close genetic relationship. Allelic frequencies of five loci (EST1, HEX, IDH, LDH1 and MDH) identified 94% of the strains. The index of association (IA) for the total sample was 2.38 and IA values calculated for the different populations were always significantly different from zero. These results suggest that the population structure of this Aeromonas sample is strongly clonal, confirm the taxonomic status of the analysed species in population genetics terms, and show the usefulness of MLEE for identifying Aeromonas species.

Aeromonas↗
PubMed2003

On the concept of attractor for community-dynamical processes II: the case of structured populations.

In Part I of this paper Jacobs and Metz (2003) extended the concept of the Conley-Ruelle, or chain, attractor in a way relevant to unstructured community ecological models. Their modified theory incorporated the facts that certain parts of the boundary of the state space correspond to the situation of at least one species being extinct and that an extinct species can not be rescued by noise. In this part we extend the theory to communities of physiologically structured populations. One difference between the structured and unstructured cases is that a structured population may be doomed to extinction and not rescuable by any biologically relevant noise before actual extinction has taken place. Another difference is that in the structured case we have to use different topologies to define continuity of orbits and to measure noise. Biologically meaningful noise is furthermore related to the linear structure of the community state space. The construction of extinction preserving chain attractors developed in this paper takes all these points into account.

Algorithms↗
PubMed2006

Genetic diversity and population structure of Elytrigia pycnantha (Godr.) (Triticeae) in Mont Saint-Michel Bay using microsatellite markers.

During the last decade, an invasive wheatgrass species (Elytrigia pycnantha) has colonized the low salt marshes of the Mont Saint Michel Bay resulting in an accelerated change in the vegetation. This study was conducted using microgeographical genetic diversity in order to understand the genetic structure of this invasive and clonal species. Genetic variation and population structure of fifteen populations collected in high and low marsh habitats around the Bay were analyzed using five microsatellite loci. Because E. pycnantha is an allohexaploid, the application of standard genetic diversity statistics was not possible; we chose to summarize genetic diversity using statistics calculated from banding phenotypes. The mean number of alleles per locus was 10.2, the mean number of different alleles per sample was 6.87. The mean number of allelic phenotypes across all populations was 7.21. The mean value of genetic diversity for the species, calculated as the average number of alleles by which pairs of individuals differ, was H's = 1.91 and H't = 2.04. Little genetic differentiation among populations was detected (0.067). The association between pairwise genetic differentiation and geographic distances exhibited no evidence for isolation by distance. A geographical pattern of population differentiation, where a single population GI was clearly separated from the remaining population groups (considered as a metapopulation), was revealed by principal component analysis (PCA), and we propose that this is because GI represents a new genotype.

Ecosystem↗
PubMed1995

Genetic characterization of isolates of Giardia duodenalis by enzyme electrophoresis: implications for reproductive biology, population structure, taxonomy, and epidemiology.

The nature and extent of genetic variation in Giardia was used to infer its mode of reproduction, population structure, taxonomy, and zoonotic potential. Ninety-seven isolates of Giardia duodenalis, from a defined area in Western Australia and throughout Australia and overseas, were obtained from humans, cats, cattle, sheep, dogs, goat, beaver, and rats. Enzyme electrophoresis revealed extensive genetic variation with 47 different zymodemes. The widespread occurrence of certain zymodemes and the similarity of relationships among isolates inferred from independent genetic markers suggests a clonal population structure for G. duodenalis, although occasional bouts of genetic exchange may occur. The 47 zymodemes clustered similarly in phenetic (UPGMA) and phylogenetic (Fitch-Margoliash) analyses. The level of genetic diversity in isolates from a defined geographical area in Western Australia was similar to the level of diversity in isolates from throughout Australia. These data suggest that clonal lineages within G. duodenalis are evolutionarily independent. Although there was a significant overall correlation between genetic distance separating zymodemes and occurrence in different host species, we found genetically identical isolates from humans and other animals and extensive genetic diversity between isolates from humans. We interpret this as evidence for zoonotic transmission of the parasite.

Animals↗
PubMed2004

Population structure and genetic variability within isolates of Grapevine fanleaf virus from a naturally infected vineyard in France: evidence for mixed infection and recombination.

The nematode-borne Grapevine fanleaf virus, from the genus Nepovirus in the family Comoviridae, causes severe degeneration of grapevines in most vineyards worldwide. We characterized 347 isolates from transgenic and conventional grapevines from two vineyard sites in the Champagne region of France for their molecular variant composition. The population structure and genetic diversity were examined in the coat protein gene by IC-RT-PCR-RFLP analysis with EcoRI and StyI, and nucleotide sequencing, respectively. RFLP data suggested that 55 % (191 of 347) of the isolates had a population structure consisting of one predominant variant. Sequencing data of 51 isolates representing the different restrictotypes confirmed the existence of mixed infection with a frequency of 33 % (17 of 51) and showed two major predominant haplotypes representing 71 % (60 of 85) of the sequence variants. Comparative nucleotide diversity among population subsets implied a lack of genetic differentiation according to host (transgenic vs conventional) or field site for most restrictotypes (17 of 18 and 13 of 18) and for haplotypes in most phylogenetic groups (seven of eight and six of eight), respectively. Interestingly, five of the 85 haplotypes sequenced had an intermediate divergence (0.036-0.066) between the lower (0.005-0.028) and upper range (0.083-0.138) of nucleotide variability, suggesting the occurrence of homologous RNA recombination. Sequence alignments clearly indicated a mosaic structure for four of these five variants, for which recombination sites were identified and parental lineages proposed. This is the first in-depth characterization of the population structure and genetic diversity in a nepovirus.

Base Sequence↗
PubMed1984

Evidence for clonal population structure in Escherichia coli.

Genotypes of 142 K1 isolates of four O serogroups of Escherichia coli from human hosts in Europe and the United States were characterized by an electrophoretic analysis of allozymic variation in 12 chromosomally encoded enzymes. The genetic structure of natural populations revealed by this analysis is closely similar to that indicated in earlier studies by Achtman and colleagues of the electrophoretic migration pattern for four outer membrane proteins and the chemical structure of the cell-wall lipopolysaccharides. The combined evidence demonstrates that most of the K1 isolates belong to a small number of geographically widespread clones. The distribution of O serogroups among the isolates does not consistently correspond to the clonal structure; O1:K1 isolates represent at least two distantly related, geographically widespread clones, one of which is genetically similar to a clone of the O18:K1 serotype. These findings for K1 isolates add to a growing body of evidence supporting the hypothesis that the genetic structure of natural populations of E. coli is basically clonal, with very limited recombination of chromosomal genes. Clonal structure has important implications for the study of the determinants of pathogenicity and disease specificity in E. coli.

Cloning, Molecular↗
PubMed1991

Determining the initial age distribution for an age structured population.

"This paper deals with an inverse problem in age-structured population dynamics; the recovery of an unknown initial age distribution. We attempt to recover this function from overposed data which consists of either the total population over a time interval equal to the maximum life span of the species or the age structure of the population at a fixed later time. Existence, uniqueness and continuous dependence of the initial distribution function on the data are addressed. Some numerical simulations are presented to illustrate the feasibility of recovery using the methods of the paper."

Age Distribution↗
PubMed1985

[Population structure of the forest Nentsi. V. F-statistics, genetic distances and the average heterozygosity (compared to the Nganasani)].

Aspects of population structure within two of the least disintegrated "anthropological isolates" in north-western (forest Nentsi) and north-central (Nganasani) Siberia were analysed on the basis of 14 polymorphic loci. The mean FIS values were found to be 0.008 in the forest Nentsi and -0.038 in the Nganasani. The negative FIS in the latter may be due to avoidance of close inbreeding. This is not the case with the Forest Nentsi who prefer matings of the uncle-niece and first cousin's type. The mean RST(FST) values of 0.026 for the forest Nentsi and 0.009 for less heterogeneous Nganasani fall within the range of values found in subdivided human groups with a similar pattern of material culture and economy. Analysis of covariance and variance matrices containing gene frequencies for seven forest Nentsi and three Nganasani subdivisions indicate that the population structure of both groups is the product of the counterbalancing action of genetic drift and migration. Pairwise genetic and geographic distance matrices between subpopulations within both groups are highly correlated, allowing us to ascribe more than 90 percent of variation among subdivisions of the Nganasani and almost 70 percent in the forest Nentsi to the effects of geographic barriers, namely distance. Mean locus heterozygosity was found to be higher in the forest Nentsi (0.332) than in the Nganasani (0.286) reflecting pronounced difference in their histories.

Alleles↗
PubMed1985

Genetic and population structure of four Sardinian villages.

Data on microgeographic population structure on four neighbouring villages of Sardinia island (Italy) are presented and discussed. Two villages are located in the lowlands where malaria from Plasmodium falciparum was endemic until the eradication of paludism. The other two villages are located in the highlands and they were malaria-free because of the altitude. Census data, inbreeding, migration matrices and surname distributions have been collected. The genetic differentiation of the four villages, tested for 31 genetic polymorphisms (106 alleles), is only in part compatible with migration rates inferred from demographic data. The possible adaptive nature of some genetic markers with respect to malarial resistance is discussed. Ambiguous results from population genetics quantitative methods do not support definite answers.

Blood Group Antigens↗
PubMed2006

Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium.

The existence of a large-scale population structure was investigated in Arabidopsis thaliana by studying patterns of polymorphism in a set of 71 European accessions. We used sequence polymorphism surveyed in 10 fragments of approximately 600 nucleotides and a set of nine microsatellite markers. Population structure was investigated using a model-based inference framework. Among the accessions studied, the presence of four groups was inferred using genetic data, without using prior information on the geographical origin of the accessions. Significant genetic isolation by geographical distance was detected at the group level, together with a geographical gradient in allelic richness across groups. These results are discussed with respect to the previously proposed scenario of postglacial colonization of Europe from putative glacial refugia. Finally, the contribution of the inferred structure to linkage disequilibrium among 171 pairs of essentially unlinked markers was also investigated. Linkage disequilibrium analysis revealed that significant associations detected in the whole sample were mainly due to genetic differentiation among the inferred groups. We discuss the implication of this finding for future association studies in A. thaliana.

Arabidopsis↗
PubMed2005

The effect of host heterogeneity and parasite intragenomic interactions on parasite population structure.

Understanding the processes that shape the genetic structure of parasite populations and the functional consequences of different parasite genotypes is critical for our ability to predict how an infection can spread through a host population and for the design of effective vaccines to combat infection and disease. Here, we examine how the genetic structure of parasite populations responds to host genetic heterogeneity. We consider the well-characterized molecular specificity of major histocompatibility complex binding of antigenic peptides to derive deterministic and stochastic models. We use these models to ask, firstly, what conditions favour the evolution of generalist parasite genotypes versus specialist parasite genotypes? Secondly, can parasite genotypes coexist in a population? We find that intragenomic interactions between parasite loci encoding antigenic peptides are pivotal in determining the outcome of evolution. Where parasite loci interact synergistically (i.e. the recognition of additional antigenic peptides has a disproportionately large effect on parasite fitness), generalist parasite genotypes are favoured. Where parasite loci act multiplicatively (have independent effects on fitness) or antagonistically (have diminishing effects on parasite fitness), specialist parasite genotypes are favoured. A key finding is that polymorphism is not stable and that, with respect to functionally important antigenic peptides, parasite populations are dominated by a single genotype.

Animals↗
PubMed1992

Population structure and mitochondrial DNA gene flow in Old World populations of Drosophila subobscura.

An extensive survey of mitochondrial DNA (mtDNA) restriction polymorphism in 156 isofemale lines from 29 different geographic populations of Drosophila subobscura distributed throughout the Old World was carried out. Ten restriction enzymes were used, five of which revealed restriction site polymorphism. Of the 31 restriction sites detected, 13 were found to be polymorphic. Comparisons with the mtDNA map of Drosophila yakuba indicate that the variable sites are mainly concentrated in protein genes, especially those corresponding to the NADH complex. A total of 13 different haplotypes were observed, two of which (haplotypes I and II) are quite frequent and widely distributed throughout the populations, whereas the other 11 with the exception of VIII, which deserves special attention, are each restricted to one population only and occur at low frequencies. The observed distribution of haplotypes, corroborated by a parsimonious unrooted tree, suggests an ancient origin of haplotypes I and II in the continent. In order to compare genetic structure according to mtDNA and allozymes, the 10 populations with higher population sizes were studied for 10 polymorphic allozymes also. One striking result is the high degree of population structure of the mtDNA when compared to that obtained for allozymes. If an island model is assumed, estimates of gene flow give values of 0.013 and 1.89 migrants per generation for mtDNA and allozymes, respectively. What is apparent from these estimates is that Drosophila subobscura populations are effectively subdivided for mtDNA genes at migration rates at which nuclear genes (allozymes) are almost panmictic.

Alleles↗
PubMed1994

Small perturbations in nonlinear age-structured population equations.

A non-linear age-structured population dynamic model described by partial integro-differential equations is considered, where the non-linear term reflects the interaction among individuals. This non-linear model is interpreted as a perturbed linear one. An approximation method based on the ideas of averaging, of a slow time transformation and a power series expansion is suggested. The asymptotic properties of the approximate solution are analyzed. It is shown that the approximate solution remains close to the true solution as t-->infinity.

Aging↗
PubMed2026

A genome-wide assessment of the population structure of thirteen admixed and pure Australian beef cattle breeds.

Knowledge of population structure is a key factor for successful multi-breed genomic prediction, especially in single-step analysis when metafounders are considered. In Australia, current assessments mostly focus on single breeds using a single-step genomic prediction method. However, the effective integration of pedigree, phenotypic, and genomic data in a multi-breed framework still requires further research, especially for combined analyses including admixed and multi-breed populations. This study began with 602,952 genotyped individuals with 8K SNPs in common from 13 beef cattle breeds (Alexandria, Angus, Brahman, Brangus, Charolais, Droughtmaster, Hereford, Kynuna, Limousin, Santa Gertrudis, Shorthorn, Speckle Park, and Wagyu). Due to different numbers of animals being genotyped in each breed, a representative subset of animals was chosen by employing a validated sampling strategy using Gaussian Mixture Models (GMM) complemented by Principal Component Analysis (PCA) within each breed. Subsequently, a specific number of animals in each cluster were randomly selected to capture the entire genetic diversity per breed, with a total of 260 animals from each breed. The first three principal components explained 59.89% of the total variation, with PC1 (33.54%) clearly separating Bos indicus from Bos taurus lineages. Admixture analysis identified stable ancestral components and defined the genetic makeup of both pure and composite populations. The results showed extensive genetic diversity in some breeds and highlighted distinct genetic differences between Bos indicus and Bos taurus breeds. In addition, six composite breeds' admixture levels confirmed their origin and breed history, revealing a directional shift in ancestry proportions by a longitudinal increase in Brahman ancestry within tropical composites over time. Thus, the findings pave the way for more effective utilization of genetic diversity both within and across populations and provide a framework for designing multi-breed genetic evaluations and breeding programs to improve productivity and profitability in Australian beef production.

Animals↗
PubMed2000

The population structure of ten Newfoundland outports.

Island populations are most informative in the study of the genetic structure of human aggregates. These populations are often of small size, thus violating the Hardy-Weinberg assumption of infinite size. Some geographically isolated island populations are further subdivided by religion, ethnicity, and socioeconomic factors, reducing their effective sizes and facilitating genetic changes due to stochastic processes. Because of extreme geographic and social isolation, fishing communities or outports of Newfoundland have been investigated for genetic microdifferentiation through the founder effect and genetic drift (Crawford et al. 1995). The purpose of this paper is to examine the population structure of 10 Newfoundland outports using the allelic frequencies derived from 12 red cell antigens. To achieve this goal, first we calculated gene frequencies using maximum-likelihood estimation procedures. Second, we used R-matrix methods to explore population differentiation. Third, we regressed mean per-locus heterozygosity on genetic distance from the gene frequency centroid to identify the most isolated populations. On the basis of this information, the three outports of Seal Cove, Island Harbor, and Tilting were found to be genetically differentiated from the other small populations. Moreover, religious and geographic subdivisions appear to explain the observed genetic variation.

Blood Group Antigens↗
PubMed2006

Isolation by distance within a river system: genetic population structuring of Atlantic salmon, Salmo salar, in tributaries of the Varzuga River in northwest Russia.

An important issue for designing any conservation programme aimed at preserving genetic diversity is estimation of the scale at which genetic structuring occurs. Additional relevant factors include distinguishing whether or not population structuring is expected to be stable as predicted by the member-vagrant hypothesis, or alternatively, whether populations are more prone to local extinction-recolonization processes, as predicted by the metapopulation evolutionary model. In this study, the population genetic structure of Atlantic salmon from 11 locations within or nearby the Varzuga River tributary system was assessed using 17 microsatellites. Mantel tests and spatial autocorrelation analyses revealed a significant isolation-by-distance signal within the tributary system as well as a negative association between the level of genetic diversity and waterway distance from the river mouth, indicating that dispersal is less likely to occur to populations deep in the tributary system. Individual-level spatial autocorrelation analyses indicated that the majority of migration occurred between populations situated within 20 km of each other. The relatively high level of genetic structuring and significant isolation-by-distance signal observed in the Varzuga tributaries are concordant with the predictions of the member-vagrant evolutionary model. However, one subpopulation in particular revealed signs of instability which may be due to its location in the tidal zone, or due to the fact that it is more affected by human impacts. The results suggest that preservation of a number of spawning sites spaced throughout the tributary system is recommendable for ensuring sustainable fishing tourism in the river.

Animals↗
PubMed1975

Population structure, gene flow and natural selection in populations of Euphydryas phaeton.

An examination of seven proteins, presumably encoded by seven structural gene loci, in three local populations of the supposedly sedentary and colonial butterfly, Euphydryas phaeton revealed that three (43 per cent) were polymorphic with three to five alleles each. In addition to this high level of heterozygosity, no statistically significant differences in allele frequencies were found at two of the three polymorphic loci. Since the effective breeding size in each population was estimated to range from as few as 20 to 200 individuals, it appears that some level of gene flow between populations must be invoked to explain the high levels of genetic variability maintained in local populations of this butterfly, despite its apparently colonial nature.

Alleles↗