SEARCH · Search PubMed

Results for “population structure”

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

SourceResearch connectionFrom yearThrough year

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

At least 469 records · Page 26Linked to original sources

PubMed2001

Speciation and population structure in the morphospecies Lutzomyia longipalpis (Lutz & Neiva) as derived from the mitochondrial ND4 gene.

Recent studies have suggested that the phlebotomine sand fly Lutzomyia longipalpis (Diptera: Psychodidae), the principal vector of visceral leishmaniasis in the Neotropics, may consist of several allopatric sibling species. Phylogenetic and population genetic analyses of nucleotide variation in a 618-bp fragment of the mitochondrial ND4 gene were carried out on specimens of Lu. longipalpis from several locations in Central and South America. The analyses were concordant with previous findings, indicating that certain allopatric populations of Lu. longipalpis have become sufficiently differentiated as to represent sibling species. Phylogenetic analyses revealed deep genetic divisions between four clades represented by specimens from northern South America, Brazil, Central America, and an isolated Colombian population. Strong differentiation also was observed between certain populations within the first two clades. Partitioning of genetic diversity within and between Central American populations did not show the presence of more than one species in the region. However, distance, even within the 70-km range of the Honduran collection sites, was found to have a remarkably strong effect on gene flow. The highly subdivided population structure may be due to the patchiness of their distribution. F(ST) values comparing a Guatemalan population with several Honduran populations revealed a level of differentiation associated with a negligible rate of gene flow.

Alleles↗

PubMed2006

Transgenic maize in the presence of ampicillin modifies the metabolic profile and microbial population structure of bovine rumen fluid in vitro.

Recently, transgenic crops have been considered as possible donors of transgenes that could be taken up by micro-organisms under appropriate conditions. In an in vitro rumen simulation system, effects of ampicillin on microbial communities growing either on rumen contents with transgenic maize carrying a gene that confers resistance to ampicillin or its isogenic counterpart as substrates were examined continuously over 13 d. Rate of production of SCFA was measured to determine functional changes in the rumen model and single-strand conformational polymorphism was used to detect alterations in structure of the microbial community. Rumen contents treated with ampicillin displayed a marked decrease in the rate of production of SCFA and diversity of the microbial community was reduced severely. In the presence of transgenic maize, however, the patterns of change of rumen micro-organisms and their metabolic profiles were different from that of rumen fluid incorporating maize bred conventionally. Recovery of propionate production was observed both in the rumen fluid fed transgenic and conventional maize after a delay of several days but recovery occurred earlier in fermenters fed transgenic maize. Alterations in the microbial population structures resulting from the ampicillin challenge were not reversed during the experimental run although there was evidence of adaptation of the microbial communities over time in the presence of the antibiotic, showing that populations with different microbial structures could resume a pre-challenge metabolic profile following the introduction of ampicillin, irrespective of the source of the plant material in the growth medium.

Ampicillin↗

PubMed2006

Genetic variation and population structure of oriental migratory locust, Locusta migratoria manilensis, in China by allozyme, SSRP-PCR, and AFLP markers.

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5-98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6-66.7%). The genetic distances between the populations were relatively low. Shannon's index and Nei's gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.

Animals↗

PubMed2004

Helicobacter pylori: recombination, population structure and human migrations.

Helicobacter pylori shows extensive genetic diversity and variability due to frequent intraspecific recombination during mixed infection. In the last years, modern genetic and genomic technology as well as cutting-edge population genetic analysis have been used to investigate the population structure and genetic variability of this pathogen. This review article summarizes recent developments in this rapidly moving field.

Ecosystem↗

PubMed2003

Bistability in a size-structured population model of cannibalistic fish--a continuation study.

By numerical continuation of equilibria, we study a size-structured model for the dynamics of a cannibalistic fish population and its alternative resource. Because we model the cannibalistic interaction as dependent on the ratio of cannibal length and victim length, a cannibal experiences a size distribution of potential victims which depends on its own body size. We show how equilibria of the resulting infinite-dimensional dynamical system can be traced with an existing method for numerical continuation for physiologically structured population models. With this approach we found that cannibalism can induce bistability associated with a fold (or, saddle-node) bifurcation. The two stable states can be qualified as 'stunted' and 'piscivorous', respectively. We identify a new ecological mechanism for bistability, in which the energy gain from cannibalism plays a crucial role: Whereas in the stunted population state cannibals consume their victims, on average, while they are very small and yield little energy, in the piscivorous state cannibals consume their victims not before they have become much bigger, which results in a much higher mean yield of cannibalism. We refer to this mechanism as the 'Hansel and Gretel' effect. It is not related to any individual 'choice' or 'strategy', but depends purely on a difference in population size distribution. We argue that studying dynamics of size-structured population models with this new approach of equilibrium continuation extends the insight that can be gleaned from numerical simulations of the model dynamics.

Animals↗

PubMed2026

Genomic analysis of breed composition and population structure in Montana composite cattle.

The Montana composite was developed in Brazil from crosses between Bos indicus and Bos taurus and structured into four biological types: Zebu (N), adapted taurine (A), British taurine (B), and continental taurine (C). This study aimed to characterize the genetic diversity and population structure of the Montana composite using genomic data through principal component analysis (PCA), admixture analysis, and Wright's FST statistic. The PCA revealed a clear separation between Bos indicus and Bos taurus groups, with Montana animals distributed in an intermediate position. The first two principal components explained 69.48% and 3.45% of the total variation, respectively. Supervised admixture estimates indicated a predominance of taurine contribution, with type A accounting for 34.47%, 52.64%, and 51.71% at K = 4, 9, and 11, respectively. Increasing the ancestry resolution refined the contribution of individual founder breeds without changing the overall predominance of taurine ancestry. Comparisons between breed proportions obtained from pedigree and genomic data revealed significant differences, for most biological types and ancestry models (P < 0.001), indicating that realized breed composition deviates from theoretical expectations. Estimates of genetic differentiation confirmed greater divergence between Zebu and taurine groups, as well as reduced distances among populations sharing common ancestry. Specific relationships were identified between the composite and some of its founder breeds, particularly Belmont Red, Senepol, and Tuli. Overall, the results demonstrate that the Montana composite has a complex genomic structure, with genomic ancestry varying according to the resolution adopted and differing from pedigree-based expectations.

Animals↗

PubMed2004

Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites.

In this paper, data on 20 X-chromosomal microsatellite polymorphisms from the HGDP-CEPH cell line panel are used to infer human population structure. Inferences from these data are compared to those obtained from autosomal microsatellites. Some of the major features of the structure seen with 377 autosomal markers are generally visible with the X-linked markers, although the latter provide less resolution. Differences between the X-chromosomal and autosomal results can be explained without requiring major differences in demographic parameters between males and females. The dependence of the partitioning on the number of individuals sampled from each region and on the number of markers used is discussed.

Analysis of Variance↗

PubMed2000

Oncomelania hupensis (Gastropoda: rissooidea) in eastern China: molecular phylogeny, population structure, and ecology.

The rissooidean snail genus Oncomelania is of medical interest as various taxa are hosts for the human blood fluke Schistosoma and the lung fluke Paragonimus; because of close co-evolved host-parasite-relationships, snail diversity may reflect parasite diversity. There is a considerable amount of confusion regarding the identity of smooth- and ribbed-shelled populations of Oncomelania hupensis in eastern China. We therefore studied the genetic variation, population structure, phylogenetic relationships and ecology of five smooth- and five ribbed-shelled populations in Hubei, Hunan, Anhui, Zhejiang, and Jiangsu provinces. Based on sequencing data of a fragment of the mitochondrial gene for cytochrome oxidase I from 80 individuals, we found little genetic variability within the ingroup-individuals studied here (average pi=0.01922). Moreover, within the ingroup, smooth-shelled individuals cluster together with ribbed-shelled individuals. We therefore consider all smooth- and ribbed-shelled populations of Oncomelania throughout the lower Yangtze River basin to belong to the subspecies O. hupensis hupensis. Our data indicate that ribbing in O. h. hupensis is associated with the annual floods of the Yangtze River. The greatest haplotype (d(H)) and nucleotide diversities (pi) are found in aggregates of ribbed-shelled snails along areas of the Yangtze River drainage subject to flooding. In areas not affected by flooding, the shells are smooth and genetic diversity decreases significantly.

Animals↗

PubMed2006

Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil.

Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term N(e) varied from 92.4 individuals under the linkage disequilibrium model to infinity under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance.

Animals↗

PubMed2004

Population structure of the beetle pests Phyllodecta vulgatissima and P. vitellinae on UK willow plantations.

Phyllodecta (= Phratora) vulgatissima and P. vitellinae (Coleoptera: Chrysomelidae) are important pests of willows and poplars. Their differences in host species preference may provide a non-chemical control strategy for pest control. However, little is known about population structure with respect to hosts, regions or seasons. Using five microsatellites, 850 P. vulgatissima and 1100 P. vitellinae individuals, comprising 17 and 22 UK samples, respectively, were genotyped. High diversity was observed at all loci. Migrant numbers exchanged per generation (Nm) were high (2.1-12.6 for P. vulgatissima and 0.9-12.2 for P. vitellinae), suggesting high genetic exchange between samples. Estimates of population differentiation (FST) and analyses of the data using Bayesian methods (Partition and Structure) showed little evidence of subdivision in relation to geography, sampling time or host.

Animals↗

PubMed1994

Epidemiologic effects of vaccines with complex direct effects in an age-structured population.

Vaccines can alter the dynamic interaction of an infectious agent with a host in complex ways. The effect of routine childhood immunization on age-specific cases was studied in an age-structured population, assuming different vaccine effects at the individual level. Assumptions about vaccine efficacy include partial protection to infection and disease, reduction in infectiousness, waning of protection, and boosting of the level and duration of protection by natural infection. The concept of relative pathogenicity is introduced to describe the effect of a vaccine on the development of disease conditional on being infected. The concepts of the immunologically naive susceptible, naive susceptible equivalent, and relative residual infection potential are introduced in the context of defining the reproduction number of a population vaccinated with a partially protective vaccine. Sensitivity to boosting has a particularly pronounced effect in reducing the number of older vaccinated cases. Near the threshold for eliminating transmission, the dynamic behavior and number as well as age distribution of cases is very sensitive to the degree of protection and relative residual infectiousness. The number of unvaccinated cases is more sensitive to the level of coverage than to the type of vaccine, while the number of vaccinated cases is very sensitive to assumptions about vaccine efficacy.

Adolescent↗

PubMed1998

Population structure and diversity of avian isolates of Pasteurella multocida from Australia.

A total of 110 isolates of Pasteurella multocida from Australian poultry and reference strains for the 16 somatic serovars plus the three subspecies (gallicida, multocida, septica) were analysed to examine their population structure and diversity. The 81 field isolates examined by multilocus enzyme electrophoresis (MLEE) were diverse, being divided into 56 electrophoretic types (ETs), with the 19 reference strains in another 15 ETs. The population was clonal and somatic serotyping was not particularly useful in establishing relationships between isolates. The 71 ETs formed three distinct subclusters (A, B and C) at a genetic distance of 0.36. Biovars tended to be associated with these subclusters: A with biovars 1, 3, 4, 5 and 8 and B with biovars 2, 6, 7, 9 and 10. Ribotyping, performed on all 110 isolates using Hpall, recognized 21 ribotypes forming nine clusters (R1-R9). The isolates in ribotype cluster R1 were almost identical to those in MLEE cluster B. Using both MLEE and ribotyping, the 19 non-Australian reference strains were found to be distributed over the full diversity of the Australian isolates of P. multocida. This study has shown that a range of P. multocida clones are associated with fowl cholera in Australia and that many of the Australian isolates are similar to non-Australian reference strains. Both the MLEE results and the ribotyping data identified a previously unrecognized subset of P. multocida strains.

Animals↗

PubMed2005

Population structure and properties of Candida albicans, as determined by multilocus sequence typing.

We submitted a panel of 416 isolates of Candida albicans from separate sources to multilocus sequence typing (MLST). The data generated determined a population structure in which four major clades of closely related isolates were delineated, together with eight minor clades comprising five or more isolates. By Fisher's exact test, a statistically significant association was found between particular clades and the anatomical source, geographical source, ABC genotype, decade of isolation, and homozygosity versus heterozygosity at the mating type-like locus (MTL) of the isolates in the clade. However, these associations may have been influenced by confounding variables, since in a univariate analysis of variance, only the clade associations with ABC type and anatomical source emerged as statistically significant, providing the first indication of possible differences between C. albicans strain type clades and their propensity to infect or colonize different anatomical locations. There were no significant differences between clades with respect to distributions of isolates resistant to fluconazole, itraconazole, or flucytosine. However, the majority of flucytosine-resistant isolates belonged to clade 1, and these isolates, but not flucytosine-resistant isolates in other clades, bore a unique mutation in the FUR1 gene that probably accounts for their resistance. A significantly higher proportion of isolates resistant to fluconazole, itraconazole, and flucytosine were homozygous at the MTL, suggesting that antifungal pressure may trigger a common mechanism that leads both to resistance and to MTL homozygosity. The utility of MLST for determining clade assignments of clinical isolates will form the basis for strain selection for future research into C. albicans virulence.

Analysis of Variance↗

PubMed1999

Discrete event versus continuous approach to reproduction in structured population dynamics.

The governing equations are derived for the dynamics of a population consisting of organisms which reproduce by laying one egg at the time, on the basis of a simple physiological model for the uptake and use of energy. Two life stages are assumed, the egg and the adult stage where the adults do not grow. These assumptions hold true, for instance, for rotifers. From the model for the life history of the individuals, a physiologically structured population model for a rotifer population is derived. On the basis of this discrete event reproduction population model a continuous reproduction population model is proposed. The population model together with the equation for the food result in chemostat equations which are solved numerically. We show that for the calculation of the transient population dynamic behaviour after a step-wise change of the dilution rate, an age structure suffices, despite the size and energy structure used to describe the dynamics of the individuals. Aggregation of the continuous reproduction population model yields an approximate lumped parameter model in terms of delay differential equations. In order to assess the performance of the models, experimental data from the literature are fitted. The main purpose of this paper is to discuss the consequences of discrete event versus continuous reproduction. In both population models death by starvation is taken into account. Unlike the continuous reproduction model, the discrete model captures the experimentally observed lack of egg production shortly after the step change in the dilution rate of the chemostat.

Age Factors↗

PubMed2000

Population structure of the pestiferous moth Helicoverpa armigera in the eastern Mediterranean using RAPD analysis.

The genetic structure of the cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), was studied in the eastern Mediterranean. Moths were sampled in six locations (five in Israel, and one in Turkey) and their genetic relationship was analysed using RAPD-PCR. Three 10-oligonucleotide primers revealed 84 presumptive polymorphic loci that were used to estimate population structure. Results reveal low level of genetic distances among Israeli and Turkish populations. The estimated values of FST and theta for the eastern Mediterranean populations were very low across all populations, indicating a high level of gene flow. Four distinct RAPD-product profile types were defined, and found in all Israeli and Turkish populations. Although no isolation by geographical distance was detected, topographical barriers may play a role in such isolation.

Alleles↗

PubMed2005

Electronic tagging and population structure of Atlantic bluefin tuna.

Electronic tags that archive or transmit stored data to satellites have advanced the mapping of habitats used by highly migratory fish in pelagic ecosystems. Here we report on the electronic tagging of 772 Atlantic bluefin tuna in the western Atlantic Ocean in an effort to identify population structure. Reporting electronic tags provided accurate location data that show the extensive migrations of individual fish (n = 330). Geoposition data delineate two populations, one using spawning grounds in the Gulf of Mexico and another from the Mediterranean Sea. Transatlantic movements of western-tagged bluefin tuna reveal site fidelity to known spawning areas in the Mediterranean Sea. Bluefin tuna that occupy western spawning grounds move to central and eastern Atlantic foraging grounds. Our results are consistent with two populations of bluefin tuna with distinct spawning areas that overlap on North Atlantic foraging grounds. Electronic tagging locations, when combined with US pelagic longline observer and logbook catch data, identify hot spots for spawning bluefin tuna in the northern slope waters of the Gulf of Mexico. Restrictions on the time and area where longlining occurs would reduce incidental catch mortalities on western spawning grounds.

Animal Identification Systems↗

PubMed2006

The recent history and population structure of five Mandarina snail species from subtropical Ogasawara (Bonin Islands, Japan).

The effect of Pleistocene climate change on the organisms of tropical and subtropical regions is rather poorly understood. We therefore studied the land snail genus Mandarina (Bradybaenidae) of oceanic Ogasawara (Bonin Islands, Japan), with the aim of using population genetic data to understand their recent history. Our analysis of a mitochondrial 16S ribosomal RNA region from more than 600 snails in five ground-living species suggests that populations on the small islands of Mukoujima, Anejima, Imotojima and Meijima, as well as on the low-lying southern and central parts of Hahajima, have probably undergone recent bottlenecks followed by subsequent expansions. Except between the main island of Hahajima and Mukouijima, there is almost no evidence for gene flow among islands even though the islands were connected repeatedly by land bridges through the Pleistocene. Within islands the population structure is severe, suggestive of a long-term, low level of gene flow (F(ST) is frequently greater than 0.5 among geographically close populations). Finally, there is a marked genetic patchiness, meaning that genetically close populations are sometimes separated by genetically distant populations. These patterns could be a consequence of expansion from bottlenecks, low active dispersal and founder effects caused by rare long-distance migrants. Unfortunately, the exact nature of the refugia and bottlenecks remains unknown because the palaeoclimate of this region is poorly understood. Dating the population size changes is also challenging because the molecular clock is uncertain. We suggest, however, that arid conditions or deforestation induced by decreased atmospheric CO(2) may have been the main factor in determining population size.

Animals↗

PubMed1999

Mitochondrial DNA population structure of roan and sable antelope: implications for the translocation and conservation of the species.

Mitochondrial DNA (mtDNA) control region sequences were analysed to determine the geographical genetic structure of Hippotragus niger (sable antelope) and H. equinus (roan antelope). Analyses by AMOVA, minimum evolution networks, parsimony, neighbour joining and maximum likelihood show that the roan antelope populations are geographically partitioned and that their phylogeography corresponds well with subspecific boundaries. In sharp contrast, however, our sequence data group all the sable antelope into two well-delineated maternal clades. One comprising specimens from the strictly east African H.n. roosevelti, and a second geographically diverse group which includes H.n. niger (South Africa, Zimbabwe), H.n. variani (Angola), and H.n. Kirkii (Zambia, Malawi). The differences in the genetic population structure suggest that distinct extrinsic and intrinsic factors have shaped the phylogeography of these two closely related antelope species. In the absence of obvious extrinsic barriers to gene flow, we suggest that behavioural differences may be responsible, at least in part, for the contrasting spatial patterns detected among geographical localities. Although our data reflect only the maternal phylogeny of these important game species, they nonetheless suggest that different management strategies should be applied. We recommend that roan antelope be translocated only within the currently defined subspecies boundaries, while in the case of sable antelope, conservation measures should focus on preserving the genetic integrity of the east African and southern African sable populations. Implicit in this is that translocations of animals between populations comprising these two distinct maternal genetic clades should be actively discouraged.

Africa↗