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At least 217 records · Page 12Linked to original sources
PubMed1993

Effective population size, genetic diversity, and coalescence time in subdivided populations.

A formula for the effective population size for the finite island model of subdivided populations is derived. The formula indicates that the effective size can be substantially greater than the actual number of individuals in the entire population when the migration rate among subpopulations is small. It is shown that the mean nucleotide diversity, coalescence time, and heterozygosity for genes sampled from the entire population can be predicted fairly well from the theory for randomly mating populations if the effective population size for the finite island model is used.

Animals↗
PubMed2005

Population genetic analysis of cat populations from Mexico, Colombia, Bolivia, and the Dominican Republic: identification of different gene pools in Latin America.

In this paper we identify new genetic profiles of eight Latin American cat populations. In addition, we combine data from the present study and previously published data on 70 other American and European populations to discuss (1) the points of introduction of mutant alleles for cat coat phenotypes from Europe into Latin America, (2) the heterozygosity levels at these loci in the current Latin American cat populations, (3) the level of genetic heterogeneity among Latin American cat populations, and how this compares with levels found in North American and European cat populations, and (4) how many different cat gene pools are currently present in Latin America. We also include in our purview historical records of human migrations from Europe to and within the Americas. Our analyses clearly support the view that the current genetic profiles and structuring of cat populations in Latin America can be largely explained by the historical migration patterns of humans.

Alleles↗
PubMed1991

Designs for population pharmacodynamics: value of pharmacokinetic data and population analysis.

Analyses of simulated data from pharmacokinetic/pharmacodynamic (PK/PD) studies varying with respect to the amount and timing of observations were undertaken to assess the value of these design choices. The simulation models assume mono- or biexponential drug disposition, and Emax-type pharmacodynamics. Data analysis uses a combined PK/PD population analysis or a hybrid, individual-PK/population-PD analysis. Assuming that the goal of the PK/PD studies is to estimate population PD, performance of designs is judged by comparing the precision of estimates of population mean PD parameters and of their interindividual variability. The simulations reveal that (i) PK data, even in small number (2 points per person from as few as 25-50% of persons) are very valuable for estimating population PD; (ii) designs involving more individuals, even if many are sparsely sampled, dominate designs calling for more complete study of fewer persons; (iii) the population analysis is generally superior to the hybrid analysis, especially when the PK model is misspecified (biexponential assumed to be monoexponential for analysis); (iv) varying sampling times and doses among subjects protects against the ill effects of model misspecification. In general, the results are quite encouraging about the usefulness of sparse data designs to estimate population dose response.

Computer Simulation↗
PubMed1985

Social selection in human populations: sufficient conditions for protection of deleterious alleles in a subdivided population.

Population dynamics of wild type (A1) and the deleterious genes (A2) under social selection have been studied by considering a subdivided population where the i-th subpopulation consists of Ni individuals with relative size ci (= Ni/sigma i Ni, i = 1,2, ..., n). A social selection model is constructed by assuming that the fitness of an individual is determined by its own as well as the parental phenotypes and that the number of migrants (M) from the ith subpopulation is divided equally into other subpopulations including the ith subpopulation itself. It has been shown that the gene frequency change depends on the loss of fitness of an individual due to the trait (gamma), an affected parent in the ith subpopulation (beta i), the probability that the heterozygote develops the trait (h), and the migration rates mi (= M/Ni). For 0 less than h less than or equal to 1, a sufficient condition for protection of the deleterious allele from extinction also depends on all of these parameters. However, when mi much less than 1 for all i, the condition is beta i less than gamma/(1 - gamma) for some i, whereas when mi much greater than h[gamma + beta i(1 - gamma)] for all i it is given by sigma i ci beta i less than -gamma/(1 - gamma). When h = 0, that condition is given by sigma ici beta i less than - gamma/(1 - gamma). Analyses also show that, when the deleterious alleles in a population are rare, the relative fitnesses of A1A1, A1A2, and A2A2 are given approximately by 1, 1-hS, and 1 - S, respectively, where S is the harmonic mean of Si = gamma + beta i(1 - gamma). Thus, under mutation-selection balance, the equilibrium frequency of deleterious alleles in the entire population is given by alpha/hS for 0 less than h less than or equal to 1 and square root alpha/S for h = 0, where alpha is the irreversible mutation rate from A1 to A2 in each generation. Population dynamics of rare deleterious genes under social selection can readily be studied by considering a finite population size.

Alleles↗
PubMed1994

Population dynamics of DNA fingerprint patterns within and between populations.

DNA fingerprint is a pattern of a variable number of bands (DNA fragments) with different sizes on a Southern gel for each individual, generated by one or many VNTR loci. Genetic divergence between individuals within and between populations can be studied in terms of number of shared bands between individuals. Using a population genetic model we show that the expectations of measures of genetic distance between populations based on band sharing data from DNA fingerprint patterns are functions of composite parameters M = 4Nv, and time of divergence (t) between populations, where N is the effective size of the populations, and v, the mutation rate. The expected genetic distance remains linear with time of divergence at least up to N generations as long as the average heterozygosity at the DNA fingerprint loci remains at or below 90%. Neither incomplete knowledge of the allele frequencies at each locus, nor the unknown number of loci underlying DNA fingerprint pattern, compromise these evolutionary dynamics of DNA fingerprint patterns. Applications of this theory to data on three human populations, and review of literature indicate that co-migration of alleles, and the presence of syntenic loci underlying the fingerprint pattern have little impact of the reliability of evolutionary conclusions from DNA fingerprint studies.

DNA Fingerprinting↗
PubMed1988

Microfilaria density distribution in the human population and its infectivity index for the mosquito population.

A new method of computing the infectivity index of microfilariae (mf) for the mosquito population is proposed using the estimated mf density distribution in the human population. the observed density distribution is considered a compound of the Poisson and the gamma distributions. The former distribution describes the probability of a specimen containing a specified number of mf and the latter describes the density distribution of mf in the host population. The mf infectivity index is the probability that a blood meal will include at least 1 mf, conditional on the population-density distribution of mf as specified by the gamma distribution. Actual data indicate that this population-density-based infectivity index can be considerably different from the conventional index based on the survey-density distribution. The level of the carrier rate of mf in a survey is greatly influenced, apart from the sample variation, by the average volume of blood taken from each person. The rate computed on the estimated population-density distribution of mf is convertible to any base amount of blood.

Animals↗
PubMed2026

Differences in structural color and population genetic structure of Western and Central Palearctic Polyommatus icarus populations.

The blue structural coloration of male Polyommatus icarus butterflies functions as a sexual signaling trait and exhibits remarkable spectral stability within populations despite being generated by highly complex photonic nanoarchitectures. The correlation of the blue sexual signaling color and population genetic variation of the butterflies was investigated across the Western and Central Palearctic regions. Dorsal wing reflectance spectra was measured for 95 male specimens and compared with the population genetic structure revealed in 99 specimens by 18 recently developed microsatellites. Reflectance measurements indicated a clear separation between the European and Central Asian populations, consistent with our previous findings, while the intermediate populations near the Ural Mountains exhibited distinct European spectral characteristics. In contrast, genetic variation showed limited structuring and correlated primarily with geographic distance, as indicated by a significant isolation-by-distance pattern. Thus, although both reflectance and genetic variations are geographically structured, spectral properties are only weakly correlated with genetic differentiation. Populations near the Ural Mountains exhibited genetic ancestry linked to Central Palearctic groups, while displaying distinct Western Palearctic coloration, suggesting that the focal species' sexual signaling is strongly influenced by local factors. These findings suggest that sexual signaling coloration may evolve at least partially independently of the neutral genetic background, offering additional insight into evolutionary divergence across broad geographic scales.

Animals↗
PubMed2001

High within-population mitochondrial DNA variation due to microvicariance and population mixing in the land snail Euhadra quaesita (Pulmonata: Bradybaenidae).

A high level of geographical variation at an exceptionally fine scale was detected in the mitochondrial 16S ribosomal RNA genes of a land snail species Euhadra quaesita from the Kanto region of Japan. In total, 50 haplotypes were detected from 27 populations, with most sample sites possessing private alleles. In some individual populations the different haplotypes do not fall as a monophyletic group, so that some of the haplotypes are phylogenetically distant, differing from each other by > 10%. In contrast, phylogenetically similar haplotypes were found in separate sites at long distances from their main distribution. Together, these findings strongly suggest that contraction and expansion of populations has occurred repeatedly in the past. The subsequent expansion of populations and migration from different areas may have mixed distant populations. This repetition of isolation and mixing has resulted in an exceptionally fine scale of geographical variation, and the accumulation of high genetic diversity within and between populations of this species.

Alleles↗
PubMedDate not supplied

Distributions of HLA-DRB1/DQB1 alleles and haplotypes in the north-eastern Thai population: indicative of a distinct Thai population with Chinese admixtures in the central Thais.

The phenotype and gene frequencies of HLA class II alleles were studied in the North-eastern Thai population. Blood samples were collected from 100 unrelated healthy North-eastern Thais. The HLA-DRB1 and DQB1 genes were typed using the polymerase chain reaction--sequence specific primer (PCR-SSP) and polymerase chain reaction--sequence specific oligonucleotide probe (PCR-SSO) techniques. Twenty-six HLA-DRB1 and 11 DQB1 alleles were found in this population. DRB1*1202, 1502, 0405 and DQB1*0502/0504, 0301/0304 alleles were commonly found. Linkage disequilibrium analysis suggested the existence of 13 DR-DQ haplotypes. The DRB1*1502-DQB1*0501 haplotype was the most common. The DRB1*1106-DQB1*0301/0304 haplotype was found only in North-eastern Thais and not in other Thai populations. Comparative analysis of the HLA-DR/DQ alleles revealed differences in the distributions of these alleles amongst different ethnic groups. Interestingly, the distributions of HLA class II alleles in Central Thai, North-eastern Thai and Southern Chinese populations are similar. However, it appears that the distribution in the Central Thais is a mixture of those in Southern Chinese and North-eastern Thais, suggesting the existence of Thai-Chinese admixtures in the Central Thai population. This study provides basic information for further studies of the MHC in anthropology, organ transplantation and disease susceptibility in the North-eastern Thai population.

Alleles↗
PubMedDate not supplied

HLA-DRB1 frequencies of the Comorian population and their genetic affinities with Sub-Saharan African and Indian Oceanian populations.

BACKGROUND: Ethnic-historic sources have considered the Comorian population to be the result of an amalgamation of African, Arabian and Southeast Asian groups. AIM: This study seeks to determine the genetic relationships and contributions from Sub-Saharan Africa and Indian Oceania and to reconstruct past migration events. SUBJECTS AND METHODS: The human leukocyte antigen (HLA) polymorphism of a Comorian population was described and analysed. RESULTS: Genetic distances and multidimensional scaling analyses showed complex patterns of genetic differentiation in the Indian Oceanian area as a result of continuous gene flow occurring within the past approximately 2500 years. Nevertheless, the Comorian genetic pool appears to be a mix of Bantu-speaking and Arab populations as testified to by admixture estimations of almost 50-60% and 27-33%, respectively. CONCLUSION: The Comorian population may represent the eastern limit of the recent and massive eastward Bantu expansion. In contrast to the population from Madagascar (Merina), only a restricted influence of Austronesian populations was found.

Africa South of the Sahara↗
PubMed1991

A comprehensive study of genic variation in natural populations of Drosophila melanogaster. IV. Mitochondrial DNA variation and the role of history vs. selection in the genetic structure of geographic populations.

Preliminary studies with restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in natural populations of Drosophila melanogaster revealed considerable variation in terms of nucleotide sequence and overall size. In this report we present data from more isofemale lines and more restriction enzymes, and explore the utility of the data in inferring a colonization history of this species. Size variation in the noncoding A + T-rich region is particularly plentiful, with size variants occurring in all restriction site haplotypes in all populations. We report here classes of small-scale mobility polymorphisms (apparent range of 20 bp) in specific restriction fragments in the coding region. The variation in one such fragment appears to be generated even more rapidly than in the noncoding region. On the basis of the distribution of restriction site haplotypes, the species range can be divided into three major regions along longitudinal lines: Euro-African populations are the most diverse and are taken to be oldest; Far East populations have a complex distribution of haplotypes; Western Hemisphere populations are the least diverse and are interpreted to be the youngest. The history inferred from mtDNA alone is remarkably similar to one based on several nuclear markers. The mtDNA haplotype distribution is also very different from that of allozymes in these same populations. We interpret this as further evidence that natural selection is still the most parsimonious explanation for the parallel latitudinal allozyme clines in this species.

Animals↗
PubMed2005

Genetic differentiation among populations of the salt marsh beetle Pogonus littoralis (Coleoptera: Carabidae): a comparison between Atlantic and Mediterranean populations.

Genetic differentiation was studied among populations of the salt marsh beetle Pogonus littoralis (Coleoptera: Carabidae), comparing Atlantic and Mediterranean populations over a large part of its range. The genetic structure of this highly mobile beetle was investigated by studying allozyme polymorphism at nine enzyme loci in 13 populations. Mediterranean P. littoralis were highly significantly differentiated from Atlantic populations. Moreover, more isolated Atlantic populations showed increased differentiation and decreased genetic diversity compared to less fragmented Mediterranean populations.

Animals↗
PubMed1996

Geographic variation in human mitochondrial DNA control region sequence: the population history of Turkey and its relationship to the European populations.

The hypervariable segment I of the control region of the mtDNA (positions 16024-16383) was amplified from hair roots by PCR and sequenced in 45 unrelated individuals from Anatolia (Asian Turkey). Forty different sequences were found, defined by 56 variable positions, of which only one involves a transversion. The neighbor-joining tree of Kimura's distance matrix for all sequences shows four main clusters. Cluster D was found to be the most statistically robust of the four, and all the sequences in it shared a mutation that is present only in European and West Asian populations. The variability in cluster D could have originated between 37,000 and 107,000 years ago. No branch is unexpectedly long, denoting the absence of sequences that diverged much before the others. The pairwise difference distribution is bell-shaped, in accordance with a population expansion occurring roughly 35,000 to 100,000 years ago. When compared to other Caucasoid populations through the pairwise difference distribution, there is a pattern from the Middle East (older expansion) to the various European populations, with Turkey in an intermediate position; when Turkish sequences are compared through a neighbor-joining tree on a genetic distance matrix of populations, this position is again evidenced. Although there is a very low level of genetic divergence among Caucasoid populations as shown by mtDNA control region sequences, a geographic pattern of genetic variation emerges, denoting a stepping-stone position of Turkey between the Middle East and Europe, which is in agreement with the hypothesis of a replacement of Neanderthals by modern humans, which could be related to the Upper Paleolithic cultural expansion.

Base Sequence↗
PubMed2025

Pervasive fitness trade-offs revealed by rapid adaptation to shifting population densities in large experimental populations of Drosophila melanogaster.

Trade-offs are an inherent feature of organismal biology that are expected play a fundamental role in the evolution of natural populations. Efforts to quantify trade-offs are largely confined to phenotypic measurements and the identification of negative genetic-correlations among fitness-relevant traits. Here, we use time-series genomic data collected during experimental evolution in large, genetically diverse populations of Drosophila melanogaster to directly measure the manifestation of trade-offs in response to fluctuating selection on ecological timescales. Specifically, we first conducted a lab-based selection experiment to quantify a genome-wide signal of antagonistic pleiotropy elicited in response to shifting population densities and associated with reproduction and stress tolerance selection. In doing so, we identified a putative role of two cosmopolitan inversions in these trade-offs. We then conducted an independent experiment to show that a simple manipulation of increasing population density under controlled lab-based conditions identified loci that are relevant to selection during population expansion and collapse in a complex, semi-natural setting. In concert, our results reveal how adaptation in complex, natural environments can be coarse-grained in such a manner to drive repeatable and predictable patterns of genomic variation, and further add credence to models positing a role of generic fitness trade-offs in the maintenance of variation in natural populations.

Drosophila melanogaster↗
PubMed2005

Genetic variation and population structure in remnant populations of black rhinoceros, Diceros bicornis, in Africa.

Black rhinoceros (Diceros bicornis) are one of the most endangered mammal species in Africa, with a population decline of more than 96% by the end of the last century. Habitat destruction and encroachment has resulted in fragmentation of the remaining populations. To assist in conservation management, baseline information is provided here on relative genetic diversity and population differentiation among the four remaining recognized subspecies. Using microsatellite data from nine loci and 121 black rhinoceros individuals, and comparing the results with those of other African species affected in similar ways, Diceros bicornis michaeli retained the most genetic diversity (heterozygosity 0.675) compared with Diceros bicornis minor (0.459) and Diceros bicornis bicornis (0.505), suggesting that the duration of the known bottlenecks in these populations has only had a limited impact on diversity. Comparable and moderate degrees of population differentiation were found between D. b. minor, D. b. bicornis and D. b. michaeli. Results from the single sample available of the most endangered subspecies, Diceros bicornis longipes, showed the least diversity of all individuals examined. This information should assist conservation management decisions, especially those affecting population viability assessments and selection of individuals for translocations, and will also facilitate subspecies identification for ex situ individuals of uncertain origin.

Africa, Eastern↗
PubMed2006

HLA-C molecular characterization of a Lebanese population and genetic structure of 39 populations from Europe to India-Pakistan.

Lebanon is located at a continental crossroad between Europe, Africa, and Asia. This region has been the center of wide-scale movements of populations as well as the theater of genetic and cultural trade off among neighboring populations. In this study, HLA-C alleles were characterized by a PCR-SSOP (sequence-specific oligonucleotide probes) hybridization protocol in a sample of 97 Lebanese. A total of 23 alleles were identified with four predominant, Cw*0401, Cw*0602, Cw*0701/06, and Cw*1203, accounting for almost 60% of HLA-C allele frequencies. We included the Lebanese data into a broad analysis of the HLA-C genetic structure of a large set of populations located in Europe, the Middle East, and the Indian subcontinent. Our results indicate that Lebanese exhibit an intermediate genetic profile among the populations from the Middle East, which constitute a rather homogeneous genetic group. In Europe, a high correlation coefficient is found between genetic and geographic distances. In this continent, we also identified a significant genetic frontier following a north-east to south-west axis. This frontier cuts through the Alps and the Pyrenees, thus separating the north-western European populations from those located in the eastern and Mediterranean areas. Finally, the populations from India - Pakistan are very heterogeneous, particularly the Dravidians. Their differentiation has probably been caused by rapid genetic drift under complex influences of cultural, linguistic, and/or religious barriers. Overall, the results show that the HLA-C genetic patterns of these three geographic regions, i.e., the Middle East, Europe, and India-Pakistan, have been shaped by very different genetic histories.

Alleles↗
PubMed2002

Population dynamics of active and total ciliate populations in arable soil amended with wheat.

Soil protozoa are characterized by their ability to produce cysts, which allows them to survive unfavorable conditions (e.g., desiccation) for extended periods. Under favorable conditions, they may rapidly excyst and begin feeding, but even under optimal conditions, a large proportion of the population may be encysted. The factors governing the dynamics of active and encysted cells in the soil are not well understood. Our objective was to determine the dynamics of active and encysted populations of ciliates during the decomposition of freshly added organic material. We monitored, in soil microcosms, the active and total populations of ciliates, their potential prey (bacteria and small protozoa), their potential competitors (amoebae, flagellates, and nematodes), and their potential predators (nematodes). We sampled with short time intervals (2 to 6 days) and generated a data set, suitable for mathematical modeling. Following the addition of fresh organic material, bacterial numbers increased more than 1,400-fold. There was a temporary increase in the number of active ciliates, followed by a rapid decline, although the size of the bacterial prey populations remained high. During this initial burst of ciliate growth, the population of cystic ciliates increased 100-fold. We suggest that internal population regulation is the major factor governing ciliate encystment and that the rate of encystment depends on ciliate density. This model provides a quantitative explanation of ciliatostasis and can explain why protozoan growth in soil is less than that in aquatic systems. Internally governed encystment may be an essential adaptation to an unpredictable environment in which individual protozoa cannot predict when the soil will dry out and will survive desiccation only if they have encysted in time.

Animals↗
PubMed2006

Using ancestry-informative markers to define populations and detect population stratification.

A serious problem with case-control studies is that population subdivision, recent admixture and sampling variance can lead to spurious associations between a phenotype and a marker locus, or indeed may mask true associations. This is also a concern in therapeutics since drug response may differ by ethnicity. Population stratification can occur if cases and controls have different frequencies of ethnic groups or in admixed populations, different fractions of ancestry, and when phenotypes of interest such as disease, drug response or drug metabolism, also differ between ethnic groups. Although most genetic variation is inter-individual, there is also significant inter-ethnic variation. The International HapMap Project has provided allele frequencies for approximately three million single nucleotide polymorphisms (SNPs) in Africans, Europeans and East Asians. SNP variation is greatest in Africans. Statistical methods for the detection and correction of population stratification, principally Structured Association and Genomic Control, have recently become freely available. These methods use marker loci spread throughout the genome that are unlinked to the candidate locus to estimate the ancestry of individuals within a sample, and to test for and adjust the ethnic matching of cases and controls. To date, few case-control association studies have incorporated testing for population stratification. This paper will focus on the debate about the quantity and methods for selection of highly informative marker loci required to characterize populations that vary in substructure or the degree of admixture, and will discuss how these theoretically desirable approaches can be effectively put into practice.

Case-Control Studies↗