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PubMed2004

Population genetic structure in European populations of Spiranthes romanzoffiana set in the context of other genetic studies on orchids.

Spiranthes romanzoffiana Cham. is restricted in Europe to the British Isles, where it is recognised as a conservation priority species due to frequent extirpation of populations along with no evidence of seed set; vegetative reproduction has been invoked as the sole means of perpetuation and dispersal. To investigate the reproductive ecology of this species, 17 populations have been sampled for chloroplast microsatellites and amplified fragment length polymorphisms (AFLPs). These markers revealed a previously unsuspected genetic-geographic split in the species, which correlates with differences in patterns of within-population variation. Northern populations were fixed for one chloroplast haplotype but showed high levels of AFLP genotypic diversity consistent with sexual reproduction (proportion of genotypes distinguishable, PD = 0.98). More southerly populations showed fixed differences from the northern populations in their chloroplast haplotype and for 10 AFLP markers. They harboured only 12 unique multilocus genotypes among 113 individuals from six populations (PD = 0.11). These genotypes differed mostly by single bands, and none by more than 4/138 loci, with identical multilocus genotypes occurring in widely separated populations. This uniformity in southern populations is consistent with agamospermous or autogamous reproduction, and/or an extreme population bottleneck. Finally, the observed patterns of population differentiation in S. romanzoffiana are compared with other studies of orchids, revealing a wide range of values that belie recent contrasting published generalisations that claim that orchids show either higher, or lower, levels of population differentiation than other plant families.

Chloroplasts↗
PubMed2005

HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research.

BACKGROUND: Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distributed in differently organised databases and web sites not well integrated among them. Moreover it is not generally possible for the user to submit and contemporarily analyse its own data comparing them with the content of a given database, both for population genetics and mitochondrial disease data. RESULTS: HmtDB is a well-integrated web-based human mitochondrial bioinformatic resource aimed at supporting population genetics and mitochondrial disease studies, thanks to a new approach based on site-specific nucleotide and aminoacid variability estimation. HmtDB consists of a database of Human Mitochondrial Genomes, annotated with population data, and a set of bioinformatic tools, able to produce site-specific variability data and to automatically characterize newly sequenced human mitochondrial genomes. A query system for the retrieval of genomes and a web submission tool for the annotation of new genomes have been designed and will soon be implemented. The first release contains 1255 fully annotated human mitochondrial genomes. Nucleotide site-specific variability data and multialigned genomes can be downloaded. Intra-human and inter-species aminoacid variability data estimated on the 13 coding for proteins genes of the 1255 human genomes and 60 mammalian species are also available. HmtDB is freely available, upon registration, at http://www.hmdb.uniba.it. CONCLUSION: The HmtDB project will contribute towards completing and/or refining haplogroup classification and revealing the real pathogenic potential of mitochondrial mutations, on the basis of variability estimation.

Computational Biology↗
PubMed1999

[Geography of genetic processes in the population: genetic migration in Northern Eurasia (Central Asia region)].

Based on the data of the census of 1970, a map of the rates of gene migrations in the rural population of Central Asia and Kazakhstan was drawn. The corrected average value for 35 populations of oblasts (administrative regions) and autonomous republics was m = 0.0606 +/- 0.0102. The estimate obtained from the mapped data was 0.0799 +/- 0.0014, which is 1.2-fold higher than similar values for Europe. The relationship between the rate of gene migration m, the genetically effective population size Ne, and the density of elementary populations in the studied area Pp was analyzed by means of correlation and regression analyses. The following relationship was obtained: m = A/Ne + BPp, where A > 0 and B < 0. This was accounted for by the fact that the migration flow is mainly directed to the less densely populated rural areas. Given that the region was chosen somewhat artificially, studying gene migrations in Central Asia and Kazakhstan as separate historical, geographic, and genetic subregions of northern Eurasia might be a better approach.

Asia↗
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↗
PubMed2006

[Population genetic variation and structure analysis on five populations of mirror carp Cyprinus carpio L. using microsatellites].

In this paper, population genetic variability and genetic structure of five populations of an important cultivation species, mirror carp (Cyprinus carpio L.) were analyzed using 30 microsatellite loci. The observed (Ho) and expected (He) heterozygosity values, polymorphic information content (PIC) and number of effective alleles (Ae) were all determined. The genetic similarity coefficient and Nei's standard genetic distance were computed based on the allele frequencies. The Hardy-Weinberg equilibrium was checked by chi2 test. Genetic differentiation and hierarchical partition of genetic diversity were evaluated by FST and Nm. A dendrogram was constructed based on UPGMA methods using PHYLIP software package supported by a bootstrap value of 91.0%. Totally 7,083 fragments were procured. Their lengths were from 102 bp to 446 bp. For each locus, 1-16 alleles were amplified, adding up to 356 alleles in all the 5 populations. We found the genetic variability level was relatively high in all five populations, as shown by Ae = 1.07-2.30, He= 0.70-0.78 and PIC=0.69-0.75, respectively. The genetic similarity coefficients were all above 0.52, indicating their close genetic relationships. The UPGMA phylogenetic tree showed mirror carps sampled from Donggang, Fengcheng and Liaozhong were clustered into one group and the other two populations, both collected from Songpu, were grouped together. There were obvious relations between genetic distances and geographical distributions of the five populations. No fragments were amplified from some loci of EST-SSRs, which may suggest the loss of these loci in mirror carp genome or sequence divergence at the primer binding sites. These null alleles may result from selection because functional genes are under more selection pressure than non-encoding loci. Overall, population genetic variation is high for each of the five mirror carp, and the differentiations are also significant among populations.

Alleles↗
PubMed1977

[Medico-genetic study of the population of the Samarkand region. II. Population-genetic description of 4 kishlaks of the Urgut district].

This report is a second one in a series of works devoted to the medico-genetical screening of Uzbekistan populations. The paper comprises the results of the analysis of the populational structure of one of the village councils (soviets) of the Urgut District of the Samarkand Region. The main parameters of the population studied were as follows: total number 1529 persons, the average number of inhabitants of one village--328. The proportion of the inhabitants studied--56%, the average number of persons per family--5.22; the average period between subsequent generations--30-35 years, the gametic index--0.8, the inbreeding coefficient inferred from pedigrees--0.018899--0.00781, Fst = 0.03577, the average genetic distanse according to Edwards--0.0231-0.0671. The distribution of Mendelian markers (ABO, Rh, Hp and Ptc) was studied. The observed ratio between a high degree of inbreeding and a relatively low extent of isolation of populations permits to explain satisfactorily the distribution and frequencies of hereditary pathology in the Urgut District of the Samarkand Region pointed out in the previous report.

Adolescent↗
PubMed2000

Low among-population genetic differentiation in Chinese bisexual Artemia populations.

We studied the population genetic structure of nine bisexual Artemia sinica populations from the provinces of Inner Mongolia, Shanxi and Qinghai in China, using variation at nine allozyme loci (cellulose acetate electrophoresis). There is a clear-cut tendency for an increase in genetic variation, as measured by heterozygosity, with increasing habitat size. Although we observe a positive relationship between genetic differentiation and geographical distance, overall FST values are low: populations separated by approximately 1000 km show average FST values of 0.05-0.1, whereas populations separated by 100 km show no genetic differentiation at all.

Alleles↗
PubMed2005

Population genetic structure of two columnar cacti with a patchy distribution in eastern Brazil.

The genetic variability and population genetic structure of six populations of Praecereus euchlorus and Pilosocereus machrisii were investigated. The genetic variability in single populations of Pilosocereus vilaboensis, Pilosocereus aureispinus, and Facheiroa squamosa was also examined. All of these cacti species have a patchy geographic distribution in which they are restricted to small areas of xeric habitats in eastern Brazil. An analysis of genetic structure was used to gain insights into the historical mechanisms responsible for the patchy distribution of P. euchlorus and P. machrisii. High genetic variability was found at the populational level in all species (P=58.9-92.8%, A(p)=2.34-3.33, H(e)=0.266-0.401), and did not support our expectations of low variability based on the small population size. Substantial inbreeding was detected within populations (F(IS)=0.370-0.623). In agreement with their insular distribution patterns, P. euchlorus and P. machrisii had a high genetic differentiation (F(ST)=0.484 and F(ST)=0.281, respectively), with no evidence of isolation by distance. Accordingly, estimates of gene flow (N(m)) calculated from F(ST) and private alleles were below the level of N(m)=1 in P. machrisii and P. euchlorus. These results favored historical fragmentation as the mechanism responsible for the patchy distribution of these two species. The genetic distance between P. machrisii and P. vilaboensis was not compatible with their taxonomic distinction, indicating a possible local speciation event in this genus, or the occurrence of introgression events.

Alleles↗
PubMedDate not supplied

[A population genetics analysis of the structure of hybrid populations of Rana esculenta L. complex (Amphibia, Ranidae)].

Population-genetic analysis conducted in hybrid populations of Rana esculenta complex from neighbourhood of Kiev has shown a high portion of recombinant frogs within Rana esculenta specimens and limitation of gene flows from one species to the other. The mechanisms of limitations are connected with assortative crossings within R. ridibunda and R. lessonae and low viability of frogs with a recombined genotype.

Animals↗
PubMed2002

Population genetic structure of Tomicus piniperda L. (Curculionidae: Scolytinae) on different pine species and validation of T. destruens (Woll.).

Genetic diversity and population structure of Tomicus piniperda was assessed using mitochondrial sequences on 16 populations sampled on 6 pine species in France. Amplifications of Internal transcribed space 1 (ITS1) were also performed. Our goals were to determine the taxonomic status of the Mediterranean ecotype T. piniperda destruens, and to test for host plant or geographical isolation effect on population genetic structure. We showed that T. piniperda clusters in two mtDNA haplotypic groups. Clade A corresponds to insects sampled in continental France on Pinus sylvestris, P. pinaster and P. uncinata, whereas clade B gathers the individuals sampled in Corsica on P. pinaster and P. radiata and in continental France on P. pinea and P. halepensis. Insects belonging to clade A and clade B also consistently differ in the length of ITS1. Individuals belonging to both clades were found once in sympatry on P. pinaster. Genetic distances between clades are similar to those measured between distinct species of Tomicus. We concluded that clade B actually corresponds to the destruens ecotype and forms a good species, T. destruens. Analyses of molecular variance ( amova ) were conducted separately on T. destruens and T. piniperda to test for an effect of either geographical isolation or host species. Interestingly, the effect of host plant was significant for T. piniperda only, while the effect of geographical isolation was not. Pine species therefore seems to act as a significant barrier to gene flow, even if host race formation is not observed. These results still need to be confirmed by nuclear markers.

Animals↗
PubMed1999

Determining the source of individuals: multilocus genotyping in nonequilibrium population genetics.

Recently founded populations represent an enormous challenge for genetic analysis: new populations are often genetically impoverished, making it hard to find sufficiently variable markers, and what little variation is present tends to be ancestral, rendering phylogenetic methods inappropriate. Recently, novel genetic markers and new statistical analyses have made multilocus genotyping an invaluable tool in the fledgling field of nonequilibrium population genetics. Such advances are not of mere academic interest but address questions of great economic, medical and conservation significance.

Journal Article↗
PubMed1997

[Molecular genetics of myotonic dystrophy--population genetics of the CTG repeat expansion of the MTPK gene].

The CTG repeat number in the 3'-untranslated region of the myotonin protein kinase (MTPK) gene varies between 5 and 37 in normal individuals, whereas myotonic dystrophy (DM) patients have expansions from 50 to 3000 copies. However little is known about the molecular mechanisms or the genetic control of the expansion of triplet repeats. To explain the dynamic mutation mechanism and high prevalence in the population, slippage theory, multistep model and meiotic drive hypothesis have been proposed. Recent studies have shown that repeat expansion may affect neighboring genes (59 gene and DMAHP gene), or exert its effect at the RNA level by modulating the binding of (CUG)n-RNA binding proteins which are required for the maturation, stability and translation of specific mRNAs.

Genetics, Population↗
PubMed1984

Population bottlenecks and nonequilibrium models in population genetics. I. Allele numbers when populations evolve from zero variability.

A simple numerical method was developed for the mean number and average age of alleles in a population that was initiated with no genetic variation following a sudden population expansion. The methods are used to examine the question of whether allele numbers are elevated compared with values seen in equilibrium populations having equivalent gene diversity. Excess allele numbers in expanding populations were found to be the rule. This was true whether the population began with zero variation or with low levels of variation in either of two initial distributions (initially an equilibrium allele frequency distribution or initially with loci occurring in only two classes of variation). Although the increase of alleles may persist for only a short time, when compared with the time which is required for approach to final equilibrium, the increase may be long when measured in absolute generation numbers. The pattern of increase in very rare alleles (those present only once in a sample) and the persistence of the original allele were also investigated.

Alleles↗
PubMed2000

Genetic erosion in northern marginal population of the common wild rice Oryza rufipogon Griff. and its conservation, revealed by the change of population genetic structure.

In order to monitor genetic erosion within the northern marginal population of common wild rice Oryza rufipogon Griff. from Dongxiang, Jiangxi Province, China, allozyme diversity encoded by 22 loci was analyzed electrophoretically from all the existing subpopulations in 1980, 1985 and 1994. The sample collected from the nine large subpopulations in 1980 showed the highest levels of genetic diversity (A = 1.27, P = 18.20%, Ho = 0.042 and He = 0.049) and a slight deviation from Hardy-Weinberg expectation (F = 0.143), the sample from five moderate ones in 1985 displayed medium levels of genetic diversity (A = 1.14, P = 13.60%, Ho = 0.008 and He = 0.049) and a great deviation from Hardy-Weinberg expectation (F = 0.837), and the sample from two small ones in 1994 demonstrated the lowest levels of genetic diversity (A = 1.09, P = 9.10%, Ho = 0.000 and He = 0.043) and the largest deviation from Hardy-Weinberg expectation (F = 1.000). The results not only documented the genetic erosion stemmed from the extinction of the subpopulations, but also revealed the drastic change of the population genetic structure due to the reduction of the population. Finally, some conservation strategies for the population are proposed.

DNA, Plant↗
PubMed2005

Modeling population genetic data in autotetraploid species.

Allozyme and PCR-based molecular markers have been widely used to investigate genetic diversity and population genetic structure in autotetraploid species. However, an empirical but inaccurate approach was often used to infer marker genotype from the pattern and intensity of gel bands. Obviously, this introduces serious errors in prediction of the marker genotypes and severely biases the data analysis. This article developed a theoretical model to characterize genetic segregation of alleles at genetic marker loci in autotetraploid populations and a novel likelihood-based method to estimate the model parameters. The model properly accounts for segregation complexities due to multiple alleles and double reduction at autotetrasomic loci in natural populations, and the method takes appropriate account of incomplete marker phenotype information with respect to genotype due to multiple-dosage allele segregation at marker loci in tetraploids. The theoretical analyses were validated by making use of a computer simulation study and their utility is demonstrated by analyzing microsatellite marker data collected from two populations of sycamore maple (Acer pseudoplatanus L.), an economically important autotetraploid tree species. Numerical analyses based on simulation data indicate that the model parameters can be adequately estimated and double reduction is detected with good power using reasonable sample size.

Alleles↗
PubMed2002

[Maximum entropy principle and population genetic equilibrium].

A general mathematic model of population genetic equilibrium was constructed based on the maximum entropy principle. We proved that the maximum entropy probability distribution was equivalent to the Hardy-Weinberg equilibrium law. A population reached genetic equilibrium when the genotype entropy of the population reached the maximal possible value. In information theory, the entropy or the information content is used to measure the uncertainty of a system. In population genetics, we can use entropy to measure the uncertainty of the genotype of a population. The agreement of the maximum entropy principle and the hardy-Weinberg equilibrium law indicated that random crossing is an irreversible process, which increases the genotype entropy of the population, while inbreeding and selection decrease the genotype entropy of the population. In animal or plant breeding, we often use selection and/or inbreeding to decrease the entropy of a population, and use intercrossing to increase the entropy of the population. In this point of view, breeding is actually regulating the entropy of population. By applying the basic principle of informatics in population genetics, we revealed the biological significance of the genotype entropy and demonstrated that we can work over population genetic problems with the principles and methods of informatics and cybernetics.

Animals↗