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PubMed1999

Spatial and temporal population genetic structure of the butterfly aglais urticae L. (Lepidoptera, nymphalidae)

The genetic diversity and the temporal and spatial genetic population structure of the butterfly Aglais urticae, a highly mobile species, were studied by allozyme electrophoresis. High levels of allozyme diversity were found. Most of the total genetic diversity occurred at the within-population scale rather than at the between-population scale. This variation could not be accounted for by Wright's model of 'isolation by distance'. No significant temporal variation was observed for those populations that were sampled in different years. A process combining high movement rate between neighbouring patches, long-distance migration and rare extinction/recolonization is suggested to explain the observed genetic structure. This hypothesis is favoured over an island model of population structure because migration in A. urticae is uniform neither with distance nor with time.

Journal Article↗
PubMed2005

The "Kriging" model of spatial genetic structure in human population genetics.

This paper presents the application of Kriging technique in the field of human population genetics for quantifying the spatial genetic heterogeneity of HLA-A locus in the area of China,and for mapping its spatial genetic structure using the measurement of synthetic genetic structure (SPC) and the principal components (PC). Both principles of the method and the basic equations are given. The Kriging model has several advantages over other interpolation and smoothing methods. Firstly, it relies on the structure of the spatial genetic semivariogram model, which can be used to quantify the spatial genetic heterogeneity of the locus (loci) before mapping its spatial genetic structure. Secondly, it is virtually unbiased in the interpolation situation,where the location to be estimated is surrounded by data on all sides and is influenced within the range of these data. Thirdly, it allows of estimative error of interpolation, which can be used to appraise the predicting effect for the spatial estimation,and the error maps can be used to decide where to introduce new sampling population genetic data. However, the "Kriging" model also has some disadvantages. Firstly,when the theoretical spatial genetic semivariogram can not be fitted by any models, the "Kriging" model can not be set up. Secondly, if the Kriging model was built by a poor spatial genetic semivariogram,the Kriging estimation standard deviation is remarkably high in the whole area, hence the Kriging model can not be suitable to estimating the distribution of spatial genetic structure. In these situations,the interpolation algorithm, whose assumption is spatial random rather than spatial autocorrelation,such as the Cavalli-Sforza method in Genography, inverse distance-weighted methods, splines, should be used to estimate or map the distribution of spatial genetic structure.

Genetics, Population↗
PubMed1999

Host-parasite population genetics: a cross-sectional comparison of Bulinus globosus and Schistosoma haematobium.

The genetic population structures of the freshwater snail Bulinus globosus and its trematode parasite Schistosoma haematobium from 8 river sites in the Zimbabwean highveld were compared using randomly amplified DNA (RAPD) markers. There was significant variability between snail populations collected at different sites, but schistosome populations only showed differentiation at a wider geographical scale (between 2 non-connected river systems). For snails, genetic distance was better correlated with proximity along rivers than absolute geographical separation. In contrast, schistosome genetic distance was better correlated with absolute geographical separation than proximity along rivers. These results are consistent with different dispersal mechanisms for snails and schistosomes and the implications for host-parasite coevolution are discussed.

Animals↗
PubMed2006

Perfect simulation from nonneutral population genetic models: variable population size and population subdivision.

We show how the idea of monotone coupling from the past can produce simple algorithms for simulating samples at a nonneutral locus under a range of demographic models. We specifically consider a biallelic locus and either a general variable population size mode or a general migration model for population subdivision. We investigate the effect of demography on the efficacy of selection and the effect of selection on genetic divergence between populations.

Algorithms↗
PubMed2000

Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L.).

We have used eight pairs of simple sequence repeat (SSR) primers to analyse the genetic diversity in 130 individuals of coconut (Cocos nucifera L.) comprising 75 tall individuals and 55 dwarf individuals, representing 94 different coconut ecotypes throughout the world. A total of 51 alleles were detected, with an average of 6.4 alleles per locus. Fifty alleles were detected in tall coconuts (talls; mean alleles/locus 6.3) compared with only 26 (mean/locus 3.3) in dwarfs, and the average diversity value in talls (0.589) was also significantly higher than that in dwarfs (0.348). Using the eight SSRs we were able to uniquely discriminate 116 of the 130 individuals. A phenetic tree based on DAD (absolute distance) values clustered individuals into five groups, each mainly composed of either talls or dwarfs. These results provide evidence in support of previous hypotheses concerning the dissemination of coconut, as well as important new information for conservation and breeding purposes.

Cocos↗
PubMed1981

[Population genetics of the population in the European north of the RSFSR. V. An evaluation of the virtual size of the population by computer simulation of marriage and migration processes].

The paper deals with the effect of assortative matings on some parameters of population structure. To solve this problem, two rural populations near Archangelsk (river Peosa region) were used. Some genetic and demographic characteristics of these populations were described in previous publications. A comparison between random matches through a random number generator and true marriages was made by computer estimation of the spouses kinship coefficients. Significant avoidance of first and second cousins marriages in real populations was discovered. As a consequence of this avoidance of consanguinity, the effective breeding size of villages is increased twofold. Similar results were obtained by estimation os isonymy.

Computers↗
PubMed1979

[Population genetics of the population of the northern European RSFSR. III. Demographic and genetic characteristics of two rural communities of the Pinezhskii District of the Arkhangel'sk Region].

The paper deals with the distribution of genetic markers (systems ABO, Rh, Hp, PTC) and a number of phenotyping traits (folding of arms, hand clasping, tongue rolling, right- and left-handedness, the type of ear lobe, the types of dermatoglyphics patterns) in the inhabitants of 5 villages in the Pinezhsky district of the Arkhangelsky region of the RSFSR. The data presented in this work were obtained in the course of examination of over 900 persons. Among the systems analysed there was a statistically significant deviation from Hardy-Weinberg's equlibrium. It took place in two the least villages. In one case--for ABO blood groups, in another--for Hp system. There are an interesting fact of the excess of heterozygotes 2-1 and some excess of the group 0. Statistically significant differences between villages were shown for four genetic systems. Data on migrations, distribution of gene frequencies and estimated genetic and phenotype distances between villages of the same village community and between two communities suggest, that each village community can be considered as separate subdivided population. Considering the uniformity of the environmental pressure in the region examined, the heterogeneity of the population studied is apparently associated with a random genetic drift.

Blood Group Antigens↗
PubMed1979

[Population genetics of the population of the European north of the RSFSR. IV. The level of blood relationship in 5 villages of Pinega District, Archangel Province].

Computer program "RODAN-1" is used for inbreeding coefficient estimation. The population studied consists of two communities of 5 villages. 385 marriages were computed. The coefficient of inbreeding is 0.00145 for pedigree for rural Russian population (the Arkhangelsk region). The inverse dependence between a village size and corresponding data of inbreeding coefficient is suggested. An attempt was undertaken to estimate the genealogical information value for each pedigree and average information value for a village.

Arctic Regions↗
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

Multiple hybrid origins, genetic diversity and population genetic structure of two endemic Sorbus taxa on the Isle of Arran, Scotland.

Understanding the processes that have given rise to polyploid hybrid taxa is central to our understanding of plant evolution. In this study, we use an array of genetic markers in a population analysis to elucidate the hybrid origins of the Arran whitebeams Sorbus arranensis and S. pseudofennica, two woody plant taxa endemic to the Isle of Arran, Scotland. It has been proposed that S. arranensis was derived by hybridization between S. aucuparia and S. rupicola, and that subsequent hybridization between S. arranensis and S. aucuparia gave rise to S. pseudofennica. Analyses of species-specific isozyme, nuclear intron and chloroplast DNA markers confirm the proposed origin of S. arranensis, and indicate that S. aucuparia was the female parent in the hybridization. Analysis of microsatellite markers suggests that there have been at least three origins of S. arranensis on Arran. Microsatellite markers also support the proposed hypothesis for the origin of S. pseudofennica, and indicate at least five hybrid origins of this taxon. In total, three multilocus genotypes of S. arranensis and eight of S. pseudofennica were detected on Arran and multilocus genotypic diversity levels Hg were 0.09 and 0.63, respectively. Genetic differentiation (thetaST) values based on multilocus genotypes are substantial (0.344 and 0.470 for S. arranensis and S. pseudofennica, respectively) implying limited seed flow among populations. These results indicate that the endemic Sorbus taxa on Arran are the products of multiple and ongoing evolutionary events. This information must be incorporated into management policies for their future conservation.

Conservation of Natural Resources↗
PubMed2001

Plague dynamics and population genetics of the desert locust: can turnover during recession maintain population genetic structure?

The desert locust (Schistocerca gregaria) undergoes crowding-induced phase transformation from solitary form to gregarious form. The transformations involves changes in behaviour, colour, development, morphometry, fecundity and endocrine physiology. Recession populations of the desert locust exist primarily in the solitary phase as small populations in patchy environments and are prone to extinction because of climatic events. Significant genetic differentiation among recession populations along the Red Sea coast of Eritrea was previously reported. It was hypothesized that despite the mixing effect of recurrent swarms, metapopulation dynamics could have produced genetic divergence among these highly scattered recession populations. A Monte Carlo simulation of the population dynamics of the desert locust in a metapopulation setting, with a realistic range of parameter values clearly demonstrated that this is possible. Population growth was represented by a discrete-time logistic equation. The duration of recessions and swarms was sampled from normal distributions whose means and standard deviations were varied based on reported estimates. An average recession duration of 10 +/- 3 generations and swarm periods half as long but almost twice as variable produced a partitioning of the total genetic variance most similar to that in the empirical study. In conventional metapopulation analysis, whether turnover leads to increased or reduced divergence is dependent on the number of colonists relative to the number of recurrent migrants, and on whether the colonists arise from a single patch or many patches. In the case of locusts, the stochastic boom and bust cycle is the overriding factor. Divergence between patches during recession due to founder effect and recurrent drift is balanced by the high rate of mixing during plagues.

Alleles↗
PubMed1994

Population genetics of filamentous fungi.

Population genetics aims to understand causes and consequences of the genetic structure of populations, i.e. distributions of genetic variants in space and time. Among the most important determinants of the genetic population structure is the genetic system itself, which is the collection of processes and mechanisms responsible for the transmission of genetic information. Filamentous fungi offer excellent opportunities for studying the effects of the genetic system on genetic population structure. Apart from their advantage as laboratory organisms, they exhibit a wide variety of genetic systems. In particular, their inherent capacity for anastomosis provides unique possibilities for investigating rates and consequences of horizontal gene transfer. Furthermore, the temporary confinement of the products of meiosis in a common structure (the ascus) enables the study of competitive and antagonistic interactions between the meiotic products. An intriguing example of the latter is the phenomenon of 'spore killing', resulting in distorted meiotic segregation. This paper concentrates on population level research of the occurrence of vegetative incompatibility in Aspergillus and Neurospora species and to what extent this will inhibit horizontal transmission of genetic information, and on spore killing in Podospora anserina.

Biological Evolution↗
PubMed2003

Mitochondrial DNA sequence-based population genetic structure of the firefly, Pyrocoelia rufa (Coleoptera: Lampyridae).

The genetic divergence, population genetic structure, and possible speciation of the Korean firefly, Pyrocoelia rufa, were investigated on the midsouthern Korean mainland, coastal islets, a remote offshore island, Jedu-do, and Tsushima Island in Japan. Analysis of DNA sequences from the mitochondrial COI protein-coding gene revealed 20 mtDNA-sequence-based haplotypes with a maximum divergence of 5.5%. Phylogenetic analyses using PAUP, PHYLIP, and networks subdivided the P. rufa into two clades (termed clade A and B) and the minimum nucleotide divergence between them was 3.7%. Clade A occurred throughout the Korean mainland and the coastal islets and Tsushima Island in Japan, whereas clade B was exclusively found on Jeju-do Island. In the analysis of the population genetic structure, clade B formed an independent phylogeographic group, but clade A was further subdivided into three groups: two covering western and eastern parts of the Korean peninsula, respectively, and the other occupying one eastern coastal islet and Japanese Tsushima Island. Considering both phylogeny and population structure of P. rufa, the Jeju-do Island population is obviously differentiated from other P. rufa populations, but the Tsushima Island population was a subset of the Korean coastal islet, Geoje. We interpreted the isolation of the Jeju-do population and the grouping of Tsushima Island with Korean coastal islets in terms of Late Pleistocene-Holocene events. The eastern-western subdivision on the Korean mainland was interpreted partially by the presence of a large major mountain range, which bisects the midpart of the Korean peninsula into western and eastern parts.

Animals↗
PubMed2005

WinPop 2.5: software for representing population genetics phenomena.

The curriculum for genetics courses is shifting from a classical to a more molecular genetics focus, increasing the importance of subjects such as population genetics. Population genetics is a computational and statistical field that requires a good understanding of the nature of stochastic events. It is a difficult field for biology students with a limited mathematical background and there is a need for visualisation tools to facilitate understanding by the use of practical examples. WinPop provides students and researchers with a visual tool to allow the simulation and representation of population genetics phenomena. WinPop is a user-friendly software meant for use in population genetics courses and basic research. WinPop 2.5 contains six different modules that represent and simulate population genetics models. Genotype and allele frequencies are calculated under the different models: panmixia, genetic drift, assortative matings, selection, gene flow and mutation. The program's interface presents information in Cartesian graphics and isosceles triangular coordinate systems, allowing the user to save graphical and textual data output from the simulations. WinPop is developed in Visual Basic 6.0 and uses Windows 95 and higher. WinPop 2.5 can be downloaded from http://www.genedrift.org/winpop.php.

Algorithms↗
PubMed2006

The population genetics of phenotypic deterioration in experimental populations of Bacillus subtilis.

Although many examples of trait loss exist in nature, the underlying population genetic mechanism responsible for the loss is usually unknown. Selective or neutral processes can result in the deterioration of a trait, and often one of these is inferred based on indirect evidence. Furthermore, selective pressures that are unique to particular environments and the effect these might have on the population genetic cause of trait loss are not well understood. Here we describe an experimental evolution system where two different environments were used for addressing the population genetic cause of trait loss throughout evolutionary time. We found that growth in minimal medium (i.e., prototrophy) was lost in all populations regardless of the experimental environment and that the pattern of trait loss in one environment was due to selection, whereas in the other environment the cause remains inconclusive.

Bacillus subtilis↗
PubMed2005

Population genetic study in two Transylvanian populations using forensically informative autosomal and Y-chromosomal STR markers.

Our study provides population genetic data on two population samples collected in a Hungarian speaking region of Transylvania, Romania. Allele frequency and profile databases were generated on 17 autosomal STR loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, VWA, FGA, TH01, TPOX, CSF1PO, Penta E and Penta D) as well as at the 12 European Y-STR extended haplotype loci (DYS19, DYS389-I/II, DYS390, DYS391, DYS392, DYS393, DYS385 loci, DYS437, DYS438 and DYS439). Data were compared to a Central Hungarian (Budapest region) population sample [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27] that was used as a reference group of the Hungarian population. Calculating the F(ST) indices and with the pairwise comparisons of interpopulation molecular variance (AMOVA) the two populations from Transylvania could be fit into the Hungarian population data showing less substructuring effects as compared to the previous findings in Hungary [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27; B. Egyed, S. Füredi, M. Angyal, I. Balogh, L. Kalmar, Z. Padar, Analysis of the population heterogeneity in Hungary using fifteen forensically informative STR markers, Forensic Sci. Int. 158 (2005) 244-249].

Chromosomes, Human, Y↗
PubMed2004

A nation's genes for a cure to cancer: evolving ethical, social and legal issues regarding population genetic databases.

The advent of the human genome sequence has focused research on understanding underlying genetic links to complex diseases such as cancer, asthma and heart disease. In the past few years, individual countries, such as Iceland, Estonia, Singapore and the United Kingdom, have created national databases of their citizens' DNA for comparative research. Most recently, an international consortium including Nigeria, Japan, China and the United States launched a $100 million project called the International HapMap to map the human genome according to haplotypes, blocks of DNA that contain genetic variation. Such population genetic databases present challenging ethical, social and legal issues, yet regulation of genetic information has developed sporadically, from region to region, without a consistent international standard. Without a clear understanding of the consequences of genetic research in terms of individual and community-wide discrimination and stigmatization, genetic databases raise concerns about the protection of genetic information. This Note provides a survey of the evolving landscape of population genetic databases as a legislative and public policy tool for national and international regulators. It compares different approaches to regulating the collection and use of population genetic databases in order to understand what areas of consensus are formulating a foundation for an international standard. As the first population genetics project that will span multiple countries for the collection of DNA, the International HapMap has the potential to become an influential standard for the protection of population genetic information. This Note highlights issues among the national databases and the HapMap project that raise ethical, social and legal concerns for the future and recommends further protections for both individual donors and community interests.

Access to Information↗