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PubMed1990

[The concept of open stable population: an application to the study of changes in population structure].

"The open stable population model is an extension of the stable population model. It is based upon a new immigration index. The model is used to study the impact of demographic phenomena on the population's structure by age and place of birth. For a given increase in the rate of growth, a fertility increase has more impact on the rejuvenation of the age structure than an immigration increase. With an average of 1.75 children per woman, the minimum immigration level required to avoid a decrease in population would result in a percentage of foreign-born similar to the maximum observed in any developed country...." The geographical focus is on developed countries, particularly Canada. (SUMMARY IN ENG AND SPA)

Age Distribution↗
PubMed1994

Obtaining birth and mortality patterns from structured population trajectories.

"A method is presented for unravelling the demographic equation for structured populations. A solution to the McKendrick-von Foerster equation is constructed using spline functions and this is fitted to stage-structured population data in such a way that the solution is smooth, positive, and does not imply negative death rates. The smoothness of the surface, and hence the complexity of the population model, is determined in a statistically optimum manner using cross validation. Time- and age-dependent death rates can be obtained as well as time-dependent birth rates. Confidence intervals are obtained for population size and death rates that give a 95% probability that the true population dynamics are within the intervals. Practical application of the method is demonstrated, and comparison made with three alternative methods."

Demography↗
PubMed1999

Analysis of the population structure in Oman.

Knowledge of a population structure can be a unique aid in planning genetic services. In order to facilitate the development of genetic services in the Sultanate of Oman, a tribal data base has been developed. The historic records of the beginning of the 19th century were used as the basis and were updated with contemporary information. The tribal data base includes tribal names, locations, and the main 185 major tribes and their subsections. Tribal data can be used for health care planning and the development of disease-specific genetic registers if the hospital records also include the tribal name. They may also provide a useful aid in genetic screening and disease prevention programmes, as when specific mutations are found in rare diseases, it is likely that these will be found to be exclusive to specific tribes, and laboratory testing will be greatly simplified. It is likely that similar data bases could be developed elsewhere in the Middle East and in the immigrant communities in Western Europe.

Journal Article↗
PubMed2003

Biology of the amphioxus, Branchiostoma belcheri in the Ariake Sea, Japan I. Population structure and growth.

We investigated the population structure and growth of the amphioxus Branchiostoma belcheri for four years in the southern Ariake Sea, Japan. We counted 62-66 myotomes and 251-310 dorsal fin-ray chambers, and these results support that this species is an intermediate form of B. belcheri and its subspecies B. belcheri tsingtauense. The ratio of females to males was 1:1.12. Males were more numerous than females among small individuals (< 40 mm body length), but we found no significant differences among large animals (50 mm body length). Spawning occurred from mid June to early July. Groups of newly settled young appeared from January to June of their second year. We observed a large fluctuation between years in the numbers of newly settled young. The estimated size of one-year-old individuals was 19.4 mm in body length; within the next 12 months, they reached 32.1 mm. Three- and four-year-old individuals measured 38.6 mm and 45.8 mm, respectively. Few grew beyond 60 mm; the largest specimen collected was a 64 mm male.

Animals↗
PubMed2001

Population structure and dispersal in the Canary Island caddisfly Mesophylax aspersus (Trichoptera, Limnephilidae).

Population genetic structure of the circum-Mediterranean caddisfly Mesophylax aspersus (Trichoptera, Limnephilidae) on the Canary Islands was investigated by studying allozyme variation at nine putative loci in five populations. Genetic variability, population structure and gene flow were compared with data in the literature for continental taxa to assess the effect of isolation of island populations on the genetic structure. Larvae were collected from streams on the islands of Tenerife (one population), La Gomera (two populations in the same catchment) and La Palma (two populations in different catchments). Genetic variability within populations was high relative to that recorded previously for continental Trichoptera, e.g. mean heterozygosity was 0.119--0.336 (0.035--0.15 in continental taxa). Highly significant population structuring was observed (mean F(ST)=0.250), and there was significant within-population structuring (mean F(IS)=0.098). Populations from the same catchment or island were no more similar than populations from different islands, which suggests that occasional long-distance dispersal, both between and within islands, is the predominant influence on the population structure. This dispersal ability has contributed to the colonization of most permanent streams on the Canary Islands by M. aspersus.

Alleles↗
PubMedDate not supplied

Population structure and anthropometric variation in rural western Ireland: migration and biological differentiation.

Models of population structure can be investigated using data on anthropometric variation among local populations. Anthropometric data collected by Dupertuis and Dawson during the 1930s were analysed from 347 males and 261 females in 12 towns in three counties of western Ireland. We hypothesized that recent migration would decrease the degree of among-group variation. To test this hypothesis, two additional samples were created by excluding known inter-county migrants from both male and female samples. Based on ethnographic data, a fifth sample was created using unmarried females only, in order to control partially for local migration upon marriage. Univariate and multivariate measures of relative differentiation were developed to compare different levels of migration and differences among the sexes. We found that the degree of among-group variation decreased as the amount of migration increased, in accordance with spatial models of population structure. Using non-parametric correlations of geographic and anthropometric distance, the observed patterns of differentiation were closely related to geography, suggesting a spatial model of gene flow to be appropriate in interpreting among-group variation. The female samples showed greater differentiation and higher correlations with geography than the males. It seems that this results from the sensitivity of males to developmental and local environmental influences, causing an increase in the relative amount of within-group variation.

Age Factors↗
PubMed2001

Effect of race, genetic population structure, and genetic models in two-locus association studies: clustering of functional renin-angiotensin system gene variants in hypertension association studies.

Previous genetic association studies have overlooked the potential for biased results when analyzing different population structures in ethnically diverse populations. The purpose of the present study was to quantify this bias in two-locus association studies conducted on an admixtured urban population. We studied the genetic structure distribution of angiotensin-converting enzyme insertion/deletion (ACE I/D) and angiotensinogen methionine/threonine (M/T) polymorphisms in 382 subjects from three subgroups in a highly admixtured urban population. Group I included 150 white subjects; group II, 142 mulatto subjects, and group III, 90 black subjects. We conducted sample size simulation studies using these data in different genetic models of gene action and interaction and used genetic distance calculation algorithms to help determine the population structure for the studied loci. Our results showed a statistically different population structure distribution of both ACE I/D (P = 0.02, OR = 1.56, 95% CI = 1.05-2.33 for the D allele, white versus black subgroup) and angiotensinogen M/T polymorphism (P = 0.007, OR = 1.71, 95% CI = 1.14-2.58 for the T allele, white versus black subgroup). Different sample sizes are predicted to be determinant of the power to detect a given genotypic association with a particular phenotype when conducting two-locus association studies in admixtured populations. In addition, the postulated genetic model is also a major determinant of the power to detect any association in a given sample size. The present simulation study helped to demonstrate the complex interrelation among ethnicity, power of the association, and the postulated genetic model of action of a particular allele in the context of clustering studies. This information is essential for the correct planning and interpretation of future association studies conducted on this population.

Alleles↗
PubMed2004

Joint effects of self-fertilization and population structure on mutation load, inbreeding depression and heterosis.

Both the spatial distribution of organisms and their mode of reproduction have important effects on the change in allele frequencies within populations. In this article, we study the combined effect of population structure and the rate of partial selfing of organisms on the efficiency of selection against recurrent deleterious mutations. Assuming an island model of population structure and weak selection, we express the mutation load, the within- and between-deme inbreeding depression, and heterosis as functions of the frequency of deleterious mutants in the metapopulation; we then use a diffusion model to calculate an expression for the equilibrium probability distribution of this frequency of deleterious mutants. This allows us to derive approximations for the average mutant frequency, mutation load, inbreeding depression, and heterosis, the simplest ones being Equations 35-39 in the text. We find that population structure can help to purge recessive deleterious mutations and reduce the load for some parameter values (in particular when the dominance coefficient of these mutations is <0.2-0.3), but that this effect is reversed when the selfing rate is above a given value. Conversely, within-deme inbreeding depression always decreases, while heterosis always increases, with the degree of population subdivision, for all selfing rates.

Crosses, Genetic↗
PubMed2005

Age, phylogeography and population structure of the microendemic banded spring snail, Mexipyrgus churinceanus.

Recent theoretical and empirical studies of phylogeography and population structure indicate that many processes influence intraspecific evolutionary history. The present study represents the first examination of various forces influencing the spatial and temporal patterns of sequence variation in the freshwater Mexican banded spring snail, Mexipyrgus churinceanus. This snail occurs in one of the most critically endangered centres of freshwater endemism, the desert ecosystem of Cuatro Ciénegas. From cytochrome b mtDNA sequence variation, there is strong evidence of long-term isolation of three regions, suggesting that these regions represent evolutionarily distinct lineages. Molecular clock estimates of clade age indicate a time to most recent common ancestor of approximately 2.5 million years ago (Ma). The three regions differ considerably in the historical and demographic forces affecting population structure. The western populations have extremely low mtDNA diversity consistent with a severe bottleneck dating to 50,000 years before present (bp). The nearby Rio Mesquites drainage is characterized by fragmentation events, restricted gene flow with isolation by distance, and higher levels of mtDNA polymorphism. These patterns are consistent with the long-term stability of this drainage along with habitat heterogeneity and brooding contributing to population isolation and restricted gene flow. Southeastern populations show evidence of range expansion and a strong influence of genetic drift. Migration rates between drainages indicate very little gene flow between drainages except for asymmetric migration from the Rio Mesquites into both western and southeastern drainages.

Animals↗
PubMed2004

Population structure of pathogenic bacteria revisited.

This minireview summarizes the historical development of bacterial population genetic concepts since the early 1980s. Initially multilocus enzyme electrophoresis was used to determine population structures but this technique is poorly portable between laboratories and was replaced in 1998 by multilocus sequence typing. Diverse population structures exist in different bacterial species. Two distinctive structures are described in greater detail. "Young" organisms, such as Yersinia pestis, have evolved or undergone a severe bottleneck in recent millennia and have not yet accumulated much sequence diversity. "genoclouds" in subgroup III Neisseria meningitidis arise because of the accumulation of diversity due to herd immunity, which is then purified during subsequent epidemic spread.

Bacteria↗
PubMed2003

Population structure of São Miguel Island, Azores: a surname study.

The knowledge of a population structure may constitute a powerful tool for mapping genes underlying susceptibility to Mendelian and complex diseases. To obtain a better understanding of the population structure of São Miguel Island (Azorean Archipelago, Portugal), we carried out a surname survey using the surnames listed in the most recent telephone book (2001). We identified 1315 different surnames in a total of 27,621 subscribers. The frequency of the different surnames was used to calculate the following parameters: isonymy (I), random component of inbreeding (FST), genetic diversity according to Fisher (alpha), migration rate according to Karlin-McGregor (v) and Nei's genetic distance. Eleven localities were selected, according to population size and geographic distribution, for analysis using the above parameters. Our results show that 51% of Salga's population and 52% of Sete Cidades's population are represented by six and eight surnames, respectively. These figures demonstrate the effective isolation of these two small places, which are located at opposite ends of São Miguel Island. Salga, Achada, and Sete Cidades present the lowest values of Fisher's alpha, indicating less genetic diversity. In contrast, the capital, Ponta Delgada, presents the highest value of alpha (78.13), indicating more genetic diversity. Our data indicate that the clustering of the localities corresponds to the geographic features of the island, where localities close together tend to share similar surnames. In conclusion, the population of São Miguel is relatively homogeneous and may constitute an ideal model for genetic mapping studies.

Azores↗
PubMed2004

Population structure of Salmonella investigated by amplified fragment length polymorphism.

AIMS: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. METHODS AND RESULTS: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination that is novel in Salmonella. Both species S. bongori and S. enterica and all subsp. of S. enterica were represented with emphasis on S. enterica subsp. enterica using a local strain collection and strains from the Salmonella Reference Collection B (SARB). The amplified fragments were used in a band-based cluster analysis. The tree resulting from the subgroup analysis clearly separated all subgroups with high bootstrap values with the species S. bongori being the most distantly related of the subgroups. The tree resulting from the analysis of the SARB collection showed that some serotypes are very clonal whereas others are highly divergent. CONCLUSIONS: AFLP clearly clustered strains representing the subgroups of Salmonella together with high bootstrap values and the serotypes of subspecies enterica were divided into polyphyletic or monophyletic types corresponding well with multilocus enzyme electrophoresis (MLEE) and sequence-based studies of the population structure in Salmonella. SIGNIFICANCE AND IMPACT OF THE STUDY: AFLP with the enzyme combination BglII and BspDI allows discrimination of individual strains and provides evidence for the usefulness of AFLP in studies of population structure in Salmonella.

Base Sequence↗
PubMed2024

Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia.

The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are receiving immigrants from the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). Using clustering and phylogenetic analyses we found three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as an evolutionary significant unit in Patagonia.

Humans↗
PubMed2000

Postsealing genetic variation and population structure of two species of fur seal (Arctocephalus gazella and A. tropicalis).

Commercial sealing in the 18th and 19th centuries had a major impact on the Antarctic and subantarctic fur seal populations (Arctocephalus gazella and A. tropicalis) in the Southern Ocean. The intensive and unrestricted nature of the industry ensured substantial reductions in population sizes and resulted in both species becoming locally extinct at some sites. However, both species are continuing to recover, through the recolonization of islands across their former range and increasing population size. This study investigated the extent and pattern of genetic variation in each species to examine the hypothesis that higher levels of historic sealing in A. gazella have resulted in a greater loss of genetic variability and population structure compared with A. tropicalis. A 316-bp section of the mitochondrial control region was sequenced and revealed nucleotide diversities of 3.2% and 4.8% for A. gazella and A. tropicalis, respectively. There was no geographical distribution of lineages observed within either species, although the respective PhiST values of 0.074 and 0.19 were significantly greater than zero. These data indicate low levels of population structure in A. gazella and relatively high levels in A. tropicalis. Additional samples screened with restriction endonucleases were incorporated, and the distribution of restriction fragment length polymorphism (RFLP) and sequence haplotypes were examined to identify the main source populations of newly recolonized islands. For A. tropicalis, the data suggest that Macquarie Island and Iles Crozet were probably recolonized by females from Marion Island, and to a lesser extent Ile Amsterdam. Although there was less population structure within A. gazella, there were two geographical regions identified: a western region containing the populations of South Georgia and Bouvetoya, which were the probable sources for populations at Marion, the South Shetland and Heard Islands; and an eastern region containing the panmictic populations of Iles Kerguelen and Macquarie Island. The latter region may be a result of a pronounced founder effect, or represent a remnant population that survived sealing at Iles Kerguelen.

Animals↗
PubMed1999

Temporal trends in the population structure of Bordetella pertussis during 1949-1996 in a highly vaccinated population.

The population structure of Bordetella pertussis in The Netherlands in 5 successive periods, encompassing 1949-1996, was analyzed by DNA typing ("fingerprinting"). In 10 years following the introduction of wide-scale vaccination in 1953, a decrease in genotypic diversity (GD) was observed, suggesting clonal expansion of strains that were adapted to vaccine-induced immunity. In subsequent periods, GD increased to prevaccination levels, probably reflecting a gradual adaptation of the B. pertussis population involving many lineages. In the 1990s, GD decreased again. This decrease coincided with an antigenic shift in the surface protein pertactin. No evidence was found for changes in DNA types or GD in 1996, when a large pertussis epidemic occurred. Thus, gradual changes in the bacterial population previous to 1996 were probably the cause of the 1996 epidemic. The results herein suggest that vaccination has selected for strains that are adapted to a highly vaccinated population. Similar changes may have occurred in other countries, explaining the reemergence of pertussis in vaccinated populations.

Bacterial Vaccines↗
PubMed2004

Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea.

Genetic population structure of turbot (Scophthalmus maximus L.) in the Northeast Atlantic was investigated using eight highly variable microsatellite loci. In total 706 individuals from eight locations with temporal replicates were assayed, covering an area from the French Bay of Biscay to the Aaland archipelago in the Baltic Sea. In contrast to previous genetic studies of turbot, we found significant genetic differentiation among samples with a maximum pairwise FST of 0.032. Limited or no genetic differentiation was found among samples within the Atlantic/North Sea area and within the Baltic Sea, suggesting high gene flow among populations in these areas. In contrast, there was a sharp cline in genetic differentiation going from the low saline Baltic Sea to the high saline North Sea. The data were explained best by two divergent populations connected by a hybrid zone; however, a mechanical mixing model could not be ruled out. A significant part of the genetic variance could be ascribed to variation among years within locality. Nevertheless, the population structure was relatively stable over time, suggesting that the observed pattern of genetic differentiation is biologically significant. This study suggests that hybrid zones are a common phenomenon for marine fishes in the transition area between the North Sea and the Baltic Sea and highlights the importance of using interspecific comparisons for inferring population structure in high gene flow species such as most marine fishes.

Animals↗
PubMed2006

Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers.

Population-based methods for the genetic mapping of adaptive traits and the analysis of natural selection require that the population structure and demographic history of a species are taken into account. We characterized geographic patterns of genetic variation in the model plant Arabidopsis thaliana by genotyping 115 genome-wide single nucleotide polymorphism (SNP) markers in 351 accessions from the whole species range using a matrix-assisted laser desorption/ionization time-of-flight assay, and by sequencing of nine unlinked short genomic regions in a subset of 64 accessions. The observed frequency distribution of SNPs is not consistent with a constant-size neutral model of sequence polymorphism due to an excess of rare polymorphisms. There is evidence for a significant population structure as indicated by differences in genetic diversity between geographic regions. Accessions from Central Asia have a low level of polymorphism and an increased level of genome-wide linkage disequilibrium (LD) relative to accessions from the Iberian Peninsula and Central Europe. Cluster analysis with the structure program grouped Eurasian accessions into K = 6 clusters. Accessions from the Iberian Peninsula and from Central Asia constitute distinct populations, whereas Central and Eastern European accessions represent admixed populations in which genomes were reshuffled by historical recombination events. These patterns likely result from a rapid postglacial recolonization of Eurasia from glacial refugial populations. Our analyses suggest that mapping populations for association or LD mapping should be chosen from regional rather than a species-wide sample or identified genetically as sets of individuals with similar average genetic distances.

Arabidopsis↗
PubMed2003

Human population structure and its effects on sampling Y chromosome sequence variation.

The excess of rare variants in global sequencing studies of the nonrecombining portion of the Y chromosome (NRY) has been interpreted as evidence for the effects of human demographic expansion. However, many NRY polymorphisms are geographically localized and the effect of different geographical sampling on patterns of NRY variation is unknown. We use two sampling designs to detect population structure and its effects on patterns of human NRY polymorphism. First, we sequence 26.5 kb of noncoding Y chromosome DNA from 92 globally distributed males representing 35 populations. We find that the number of polymorphisms with singleton variants is positively correlated with the number of populations sampled and that there is a significant negative correlation of Tajima's D (TD) and Fu and Li's D (FD) statistics with the number of pooled populations. We then sequence the same region in a total of 73 males sampled from 3 distinct populations and find that TD and FD values for the 3 pooled and individual population samples were much less negative than those in the aforementioned global sample. Coalescent simulations show that a simple splitting model of population structure, with no changes in population size, is sufficient to produce the negative values of TD seen in our pooled samples. These empirical and simulation results suggest that observed levels of NRY population structure may lead to an upward bias in the number of singleton variants in global surveys and call into question inferences of population expansion based on global sampling strategies.

Asian People↗