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At least 163 records · Page 9Linked to original sources
PubMed1998

Population genetic diversity in relation to microsatellite heterogeneity.

Nine populations (Germans, Turks, Moroccans, Ovambos, Ugandans, Chinese, Japanese, Papuans, and Australian Aborigines) were investigated using six microsatellite systems (HumCD4, Hum F13B, HumFES/FPS, HumTH01, HumVWA, and D21S11), so-called STRs (short tandem repeats). Allele frequency data and sequencing results were used to compare the population genetic diversity among these populations. The genetic differences varied depending on the STR applied. According to the systems investigated, we defined three categories of STR microvariation: LOMs (low microvariation systems), INMs (intermediate microvariation systems), and HIMs (high microvariation systems). LOMs (STRs: CD4, FES, F13B, TH01) are characterised by a number of repeats between 5-15 and a stable repeat sequence. INMs and HIMs each showed an increasing number of repeats and additional sequence variation in the repeat motifs. The rate of new mutations was associated with the extent of microvariation. The reconstruction of phylogenetic trees led to a clustering in an early split of the African populations followed by further branching of the Asian/Melanesian and the Caucasian groups.

Africa↗
PubMed1999

The evolutionary biology and population genetics underlying fungal strain typing.

Strain typing of medically important fungi and fungal population genetics have been stimulated by new methods of tapping DNA variation. The aim of this contribution is to show how awareness of fungal population genetics can increase the utility of strain typing to better serve the interests of medical mycology. Knowing two basic features of fungal population biology, the mode of reproduction and genetic differentiation or isolation, can give medical mycologists information about the intraspecific groups that are worth identifying and the number and type of markers that would be needed to do so. The same evolutionary information can be just as valuable for the selection of fungi for development and testing of pharmaceuticals or vaccines. The many methods of analyzing DNA variation are evaluated in light of the need for polymorphic loci that are well characterized, simple, independent, and stable. Traditional population genetic and new phylogenetic methods for analyzing mode of reproduction, genetic differentiation, and isolation are reviewed. Strain typing and population genetic reports are examined for six medically important species: Coccidioides immitis, Histoplasma capsulatum, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and A. flavus. Research opportunities in the areas of genomics, correlation of clinical variation with genetic variation, amount of recombination, and standardization of approach are suggested.

Biological Evolution↗
PubMed2006

Nemo: an evolutionary and population genetics programming framework.

UNLABELLED: Nemo is an individual-based, genetically explicit and stochastic population computer program for the simulation of population genetics and life-history trait evolution in a metapopulation context. It comes as both a C++ programming framework and an executable program file. Its object-oriented programming design gives it the flexibility and extensibility needed to implement a large variety of forward-time evolutionary models. It provides developers with abstract models allowing them to implement their own life-history traits and life-cycle events. Nemo offers a large panel of population models, from the Island model to lattice models with demographic or environmental stochasticity and a variety of already implemented traits (deleterious mutations, neutral markers and more), life-cycle events (mating, dispersal, aging, selection, etc.) and output operators for saving data and statistics. It runs on all major computer platforms including parallel computing environments. AVAILABILITY: The source code, binaries and documentation are available under the GNU General Public License at http://nemo2.sourceforge.net.

Biological Evolution↗
PubMed1995

Effect of non-random sampling on the estimation of parameters in population genetics.

The amount and pattern of genetic variation in a population can be estimated from genes or DNA sequences sampled from the population. Although random sampling is assumed in almost all cases, we often do not know whether sampling is random or not. Using a simple non-random sampling model, the effects of non-random sampling on the estimation of parameters in population genetics were investigated. This non-random sampling model assumes that n genes are randomly sampled with replacement from m genes which were randomly sampled from a large random mating population, and various degrees of non-randomness can be generated by changing the value of m. The results obtained show that the effect of non-random sampling on the number of alleles and the number of segregating sites is substantially large whereas the effect of non-random sampling on heterozygosity and the average number of nucleotide differences is negligibly small unless non-randomness is extremely large. The effects of non-random sampling on the tests of neutrality were also investigated, and the results obtained indicate that the effect of non-random sampling is stronger on Fu and Li's tests than on Tajima's test.

Alleles↗
PubMed2006

Population genetic structure of Arabidopsis lyrata in Europe.

Population genetic theory predicts that the self-incompatible and perennial herb, Arabidopsis lyrata, will have a genetic structure that differs from the self-fertilizing, annual Arabidopsis thaliana. We quantified the genetic structure for eight populations of A. lyrata ssp. petraea in historically nonglaciated regions of central Europe. Analysis of 20 microsatellite loci for 344 individuals demonstrated that, in accordance with predictions, diploid populations had high genome-wide heterozygosity (H(O) = 0.48; H(E) = 0.52), high within-population diversity (83% of total) compatible with mutation-drift equilibrium, and moderate differentiation among populations (F(ST) = 0.17). Within a single population, the vast majority of genetic variability (92%) was found at the smallest spatial scale (< 3 m). Although there was no evidence of biparental inbreeding or clonal propagation at this scale (F(IS) = 0.003), significant fine-scale spatial autocorrelation indicated localized gene flow presumably due to gravity dispersed seeds (Sp = 0.018). Limited gene flow between isolated population clusters (regions) separated by hundreds of kilometres has given rise to an isolation by distance pattern of diversification, with low, but significant, differentiation among regions (F(ST) = 0.05). The maintenance of geographically widespread polymorphisms and uniformly high diversity throughout central Europe is consistent with periglacial survival of A. lyrata ssp. petraea north of the Alps in steppe-tundra habitats during the last glacial maximum. As expected of northern and previously glaciated localities, A. lyrata in Iceland was genetically less diverse and highly differentiated from central Europe (H(E) = 0.37; F(ST) = 0.27).

Arabidopsis↗
PubMed1991

Convergence of one-dimensional diffusion processes to a jump process related to population genetics.

A conjecture on the convergence of diffusion models in population genetics to a simple Markov chain model is proved. The notion of bi-generalized diffusion processes and their limit theorems are used systematically to prove the conjecture. Three limits; strong selection-weak mutation limit, moderate selection-weak mutation limit, weak selection-weak mutation limit are considered for typical diffusion models in population genetics.

Genetics, Population↗
PubMed2005

simuPOP: a forward-time population genetics simulation environment.

SUMMARY: simuPOP is a forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease. At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios. AVAILABILITY: simuPOP is freely available at http://simupop.sourceforge.net, distributed under GPL license.

Algorithms↗
PubMed1995

Use of DNA fingerprinting for human population genetic studies.

DNA fingerprinting techniques have been used in population genetic studies on many different kinds of organisms. Here, we present new applications for multilocus DNA fingerprint probes in population studies and demonstrate the applicability of DNA fingerprinting to human population genetics, using M13 phage DNA as a probe. The new approach, which is based on a factor method of numerical coding of nonquantitative data (factor correspondence analysis-FCA), shows good agreement between population position, as indicated by the three principal factors, and ethnogenetic proximity.

Azerbaijan↗
PubMed2004

Current and historical patterns of drainage connectivity in eastern Australia inferred from population genetic structuring in a widespread freshwater fish Pseudomugil signifer (Pseudomugilidae).

Dispersal can play an important role in the genetic structuring of natural populations. In this regard, freshwater fishes often exhibit extensive population genetic subdivision and are ideal subjects for investigating current and historical patterns of connection and dissociation between drainages. We set out to generate a comprehensive molecular phylogeny for a widespread freshwater fish from eastern Australia, the Pacific blue-eye Pseudomugil signifer. Although movement via flood events may be important in the southern end of the species' range, genetic structuring revealed the importance of historical drainage connections and dissociations in mediating or disrupting dispersal. A dominant feature of our phylogeny is a split between northern and southern populations, which appears to be congruent with a biogeographical barrier recently implicated as important for the connectivity of freshwater organisms in eastern Australia. The extent of the split also has taxonomic implications consistent with suggestions that the Pacific blue-eye may represent more than a single species.

Animals↗
PubMed2001

Toward a new synthesis: population genetics and evolutionary developmental biology.

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.

Adaptation, Biological↗
PubMed1989

Human population genetic studies of five hypervariable DNA loci.

Population genetic studies were performed using DNA probes that recognize five hypervariable loci (D2S44, D14S1, D14S13, D17S79, and DXYS14) in the human genome. DNA from approximately 900 unrelated individuals, subdivided into three ethnic groups (American blacks, Caucasians, and Hispanics) were digested with PstI and were successively hybridized to each DNA probe. The number of distinct DNA fragments identified for each of these regions varies from 30 to more than 80. An allele frequency distribution was determined for each locus and each ethnic group. The results show significant differences, between ethnic groups, in the pattern of distribution as well as in the relative frequency of the most common alleles of D2S44, D14S1, and D14S13 but only small differences in others (i.e., D17S79 and DXYS14). The results presented show that the analysis of these loci can have useful applications in population genetics as well as in identity tests.

Alleles↗
PubMed1987

[A complex medico-genetic study of West Siberian populations. I. Formulation of a problem. Goals and objectives of the study. Population genetic characteristics of Northern Khanty].

Purposes and tasks of the complex medical and genetic study of West-Siberian inhabitants were formulated. Demographic parameters for the North Khanty inhabitants, such as size, dynamics of the tertiary sex ratio, marriage structure and migration processes were presented. Mating and intrapopulation migration patterns are determined by spatial subdivision, because of the vast territory and the traditional way of life, and by isolation by distance. Index of the isolocal endogamy equals to 0.364. The portion of mixed marriages is 22.7% and that of the gametic contribution of immigrants - 7.3%. Inbreeding coefficient by isonymy is 0.00097. Effective population size of the five subpopulations studied as a whole is 25% of their total number.

Consanguinity↗
PubMed1979

[Correlation of heredity and environmental factors in the etiology of Vilyui encephalomyelitis. II. A population genetic study in districts of Vilyui encephalomyelitis distribution].

Population-genetic investigation was carried out in the regions endemic for Viljuisk encephalomyelitis (VE). The following indices were estimated: the relationship coefficient, the inbreeding coefficient, the intensity of migration, genetic structure of the population. The aim of the investigation was to explain causes of intrapopulational and, in some cases, of intragenus accumulation of the VE patients. No evidence of isolation or increased inbreeding were found in highly affected populations. The genetic structure of a group of VE patients tested for 9 polymorphic systems did not reveal any deviation from the control group. Several VE cases in healthy populations occured in some years after the immigration of a VE patient. These data confirm the hypothesis that VE is transmitted from a VE patient to healthy persons. Among these persons fall ill those who have a hereditary determined increased sensitivity to VE which results in intrapopulation and intragenus accumulation of VE cases.

Adult↗