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PubMed1982

Population genetics in the State of Nuevo Leon, Mexico. V. Frequencies of ABO, Rh (D), MN blood groups and other genetic traits.

During the last years we have been studying the phenotype and gene frequencies of blood groups and other genetic traits in order to learn the genetic composition of the human population in the State of Nuevo Leon. We tried to assess the influence of the different ancestral contributions in the degree of genetic diversity within the state, and also to evaluate the frequencies of some genetic traits in groups of persons suffering from various diseases. It has been found that for most traits the frequencies are intermediate to those reported for Mexican native and Spanish populations. It appears that the populations that recently immigrated to the State are the ones that have received more genetic influence from the Mexican natives, and those that have lived in the state since the last century are the ones that have received more genetic contribution from the Spanish.

ABO Blood-Group System↗

PubMed2006

[The population genetic structure analysis via microsatellite loci in new Silkies laying breeds].

Twenty microsatellite markers selected from the chicken GENBANK were analyzed for polymorphism in two new Silkies laying breeds. Allele frequencies were tested by the auto scan on ABI 3100-Avant Genetic Analyzer. The results suggested that the optimization test of multiplex PCR was successful and 18 pairs of microsatellite DNA markers were polymorphic. The average number of alleles detected by a pair of primers was 7.444. The average value of PIC was 0.669. The average observation population heterzygosity of the 18 markers was 0.3962, and the average expected population heterzygosity of the 18 markers was 0.7301. The number of bands tested on the auto scan was higher than that based on band presence or absence on gel, thus it was more suitable for genetic population analysis.

Animals↗

PubMed2005

A multilocus population genetic survey of the greater sage-grouse across their range.

The distribution and abundance of the greater sage-grouse (Centrocercus urophasianus) have declined dramatically, and as a result the species has become the focus of conservation efforts. We conducted a range-wide genetic survey of the species which included 46 populations and over 1000 individuals using both mitochondrial sequence data and data from seven nuclear microsatellites. Nested clade and structure analyses revealed that, in general, the greater sage-grouse populations follow an isolation-by-distance model of restricted gene flow. This suggests that movements of the greater sage-grouse are typically among neighbouring populations and not across the species, range. This may have important implications if management is considering translocations as they should involve neighbouring rather than distant populations to preserve any effects of local adaptation. We identified two populations in Washington with low levels of genetic variation that reflect severe habitat loss and dramatic population decline. Managers of these populations may consider augmentation from geographically close populations. One population (Lyon/Mono) on the southwestern edge of the species' range appears to have been isolated from all other greater sage-grouse populations. This population is sufficiently genetically distinct that it warrants protection and management as a separate unit. The genetic data presented here, in conjunction with large-scale demographic and habitat data, will provide an integrated approach to conservation efforts for the greater sage-grouse.

Animals↗

PubMed1990

A population genetic model of selection that maintains specific trinucleotides at a specific location.

Periodic appearances of specific trinucleotides along the DNA sequence have been reported in the chicken core DNA, and the phenomenon has been suggested to be related to the supercoiling of DNA around nucleosomes. A population genetic model is constructed in which selection is operating to maintain specific trinucleotides at a specific location on the DNA sequence. Assuming low mutation rates, equilibrium probabilities of the appearances of respective trinucleotides were computed. Vague patterns appeared if the product of the effective size and the selection coefficient was 0.1-2.0. The genetic load and substitution rates in the equilibrium state were also computed. When the model was applied to the chicken DNA data, the product of the effective size and the selection coefficient was estimated to be 0.1-0.2. With this intensity of selection, the substitution rate was hardly different from that in the case without selection. However, the genetic load became fairly large. Considering the large number of times that DNA coils about nucleosomes, the number of trinucleotide sites must be very large, and thus the total load might be too large. Epistasis among these sites to reduce the total load is suggested to exist if selection is responsible for this periodic pattern observed in the chicken core DNA.

Alleles↗

PubMed1979

Population genetics of multigene family with special reference to decrease of genetic correlation with distance between gene members on a chromosome.

A mathematical method is developed which enables us to treat exactly the process of coincidental evolution under mutation, unequal intrachromosomal crossing-over as well as ordinary crossing-over between homologous chromosomes in a finite population of the effective size N. It makes use of finite difference equations involving two quantities denoted by fi and phi i, in which fi is the identity coefficient of two gene members that are i steps apart on the same chromosome and phi i is that of two members i steps apart on two homologous chromosomes. When the number of genes (n) per family is large, the finite difference equations can be approximately by ordinary second-order differential equations which can then be solved analytically. Results obtained by the present method are compared with the corresponding results previously obtained by one of us (T.O.) using conventional diffusion models of gene frequency changes in population genetics. It is shown that the previous results obtained by T.O. regarding second-order statistics are essentially valid, and they give good approximations particularly when N beta is small, where beta is the rate of ordinary interchromosomal crossing-over within the multigene family.

Base Sequence↗

PubMed2005

Local genetic population structure in an endangered plant species, Silene tatarica (Caryophyllaceae).

Genetic substructuring in plant populations may evolve as a consequence of sampling events that occur when the population is founded or regenerated, or if gene dispersal by pollen and seeds is restricted within a population. Silene tatarica is an endangered, perennial plant species growing along periodically disturbed riverbanks in northern Finland. We investigated the mechanism behind the microspatial genetic structure of S. tatarica in four subpopulations using amplified fragment length polymorphism markers. Spatial autocorrelation revealed clear spatial genetic structure in each subpopulation, even though the pattern diminished in older subpopulations. Parentage analysis in an isolated island subpopulation indicated a very low level of selfing and avoidance of breeding between close relatives. The mean estimated pollen dispersal distance (24.10 m; SD = 10.5) was significantly longer and the mean seed dispersal distance (9.07 m; SD = 9.23) was considerably shorter than the mean distance between the individuals (19.20 m; SD = 13.80). The estimated indirect and direct estimates of neighbourhood sizes in this subpopulation were very similar, 32.1 and 37.6, respectively. Our results suggested that the local spatial genetic structure in S. tatarica was attributed merely to the isolation-by-distance process rather than founder effect, and despite free pollen movement across population, restricted seed dispersal maintains local genetic structure in this species.

DNA, Plant↗

PubMed1991

Genetic population structure of Italy. II. Physical and cultural barriers to gene flow.

Three approaches were employed to evaluate the relative importance of geographic and linguistic factors in maintaining genetic differentiation of Italian populations as shown by blood groups and erythrocyte and serum markers. Genetic distances are closer to linguistic than to geographic distances. Gene-frequency change across 12 linguistic boundaries is significantly more rapid than at random locations. The zones of sharp genetic variation correspond to physical barriers to gene flow and to boundaries between dialect families, which overlap widely. However, two linguistically differentiated populations appear genetically differentiated despite the absence of physical obstacles to gene flow around them. The Po River is associated with abrupt genetic change only in the area where it corresponds to a dialect boundary. At most loci the genetic population structure seems affected by linguistic rather than geographic factors; exceptions are the systems that were subject to malarial selection in geographically close but linguistically heterogeneous localities. Gene flow appears to homogenize gene frequencies within regions corresponding to dialect families but not between them, leading to the patchy distributions of allele frequencies that were detected in an earlier study.

Alleles↗

PubMedDate not supplied

[Population genetics of the D1S80 system in a Central Poland region].

Population data concerning the D1S80 system based on the analysis of 775 persons from Central Poland region was presented. Accordance with the Hardy and Weinberg equilibrium (HWE) was proved using two different statistical approaches. The parameters for the appropriateness of this marker for investigations in the analysed population was also assessed: heterozygosity--0.79, PIC--0.77, PD--0.93, PE--0.62, PI--12.8 and frequency of mutation events--0.27%.

Alleles↗

PubMedDate not supplied

[Characterization of intra-population genetic polymorphism of the Colorado potato beetle using ISSR-markers and phenotypes].

The level of genetic diversity was estimated in a local population of Colorado potato beetle using ISSR-markers and specific pronotum patterns. In contrast to the unchanged level of diversity in ISSR, Shannon's diversity index calculated on the base of pronotum pattern variants was decreasing during summer testifying adaptivity of that sign. The results also show the difference in the level of genetic diversity of females comparing to males.

Animals↗

PubMed2004

Molecular population genetic analysis differentiates two virulence mechanisms of the fungal avirulence gene NIP1.

Deletion or alteration of an avirulence gene are two mechanisms that allow pathogens to escape recognition mediated by the corresponding resistance gene in the host. We studied these two mechanisms for the NIP1 avirulence gene in field populations of the fungal barley pathogen Rhynchosporium secalis. The product of the avirulence gene, NIP1, causes leaf necrosis and elicits a defense response on plants with the Rrs1 resistance gene. A high NIP1 deletion frequency (45%) was found among 614 isolates from different geographic populations on four continents. NIP1 was also sequenced for 196 isolates, to identify DNA polymorphisms and corresponding NIP1 types. Positive diversifying selection was found to act on NIP1. A total of 14 NIP1 types were found, 11 of which had not been described previously. The virulence of the NIP1 types was tested on Rrs1 and rrs1 barley lines. Isolates carrying three of these types were virulent on the Rrs1 cultivar. One type each was found in California, Western Europe, and Jordan. Additionally, a field experiment with one pair of near-isogenic lines was conducted to study the selection pressure imposed by Rrs1 on field populations of R. secalis. Deletion of NIP1 was the only mechanism used to infect the Rrs1 cultivar in the field experiment. In this first comprehensive study on the population genetics of a fungal avirulence gene, virulence to Rrs1 in R. secalis was commonly achieved through deletion of the NIP1 avirulence gene but rarely also through point mutations in NIP1.

Amino Acid Sequence↗

PubMed2004

[Multiple nonlinear statistical method of population genetic structure based on the allelic polymorphism data].

The distribution and structure of the allelic polymorphism data are analyzed and it is pointed out that the distribution of allelic polymorphism data reveals the characteristic of closed data (also named as compositional data or data of constant sum). It is interpreted that the correlation structure of the allelic polymorphism data contains null correlations introduced by "closure" and the statistical distribution of the data is not normal because of its constant row sum, which resulted in great difficulties in analyzing the data with traditional multiple linear statistical methods such as principal component analysis, factor analysis, cluster analysis and canonical correlation analysis. Based on the theory of compositional data analysis proposed by Aitchison in 1982, a multiple nonlinear statistical method originating from the "logratios" approach to the statistical analysis of compositional data is put forward in this paper. As an example, the "logratios" method was used to analyze the genetic structure of TH01 polymorphic loci in Chinese population and the results were compared with those of multiple linear methods such as component principal. It is concluded that the "logratios" multiple nonlinear principle component analysis is a better method with the virtue of sensitivity and specificity for analyzing the genetic structure of population from the data of allelic polymorphism.

Alleles↗

PubMed2003

Haplotype analysis in population genetics and association studies.

Several studies of haplotype structures in the human genome in various populations have been published recently. Such knowledge may provide valuable information on human evolutionary history and lead to the development of more efficient strategies to identify genetic variants that increase susceptibility to human diseases. In this review, we summarize the current understanding of haplotype structure, diversity, and distribution in the human genome, with a focus on statistical issues in using haplotypes for studies of population genetics and evolutionary history, as well as to identify genetic variants underlying complex human traits.

Evolution, Molecular↗

PubMed2001

Population genetic structure of variable drug response.

Geographic patterns of genetic variation, including variation at drug metabolizing enzyme (DME) loci and drug targets, indicate that geographic structuring of inter-individual variation in drug response may occur frequently. This raises two questions: how to represent human population genetic structure in the evaluation of drug safety and efficacy, and how to relate this structure to drug response. We address these by (i) inferring the genetic structure present in a heterogeneous sample and (ii) comparing the distribution of DME variants across the inferred genetic clusters of individuals. We find that commonly used ethnic labels are both insufficient and inaccurate representations of the inferred genetic clusters, and that drug-metabolizing profiles, defined by the distribution of DME variants, differ significantly among the clusters. We note, however, that the complexity of human demographic history means that there is no obvious natural clustering scheme, nor an obvious appropriate degree of resolution. Our comparison of drug-metabolizing profiles across the inferred clusters establishes a framework for assessing the appropriate level of resolution in relating genetic structure to drug response.

Chi-Square Distribution↗

PubMed2002

[Ancient DNA studies: from paleopathology to population genetics].

We discuss the relevance of ancient DNA studies for novel approaches to a variety of fields of scientific inquiry, including population and evolutionary genetics, prehistoric archaeology, paleopathology and history of human diseases. To exemplify the potential of ancient DNA research, we provide accounts of studies currently conducted at our laboratories in four different areas: 1) origins of the dog and phylogeny of prehistoric Italian canids; 2) paleogenetics of ancient Roma; 3) antiquity for variant alleles implicated in disease predisposition; 4) molecular investigation of pathologic lesions in Italian mummies of Renaissance age. The implications of the results obtained are briefly outlined.

DNA↗

PubMed2006

Bayesian clustering using hidden Markov random fields in spatial population genetics.

We introduce a new Bayesian clustering algorithm for studying population structure using individually geo-referenced multilocus data sets. The algorithm is based on the concept of hidden Markov random field, which models the spatial dependencies at the cluster membership level. We argue that (i) a Markov chain Monte Carlo procedure can implement the algorithm efficiently, (ii) it can detect significant geographical discontinuities in allele frequencies and regulate the number of clusters, (iii) it can check whether the clusters obtained without the use of spatial priors are robust to the hypothesis of discontinuous geographical variation in allele frequencies, and (iv) it can reduce the number of loci required to obtain accurate assignments. We illustrate and discuss the implementation issues with the Scandinavian brown bear and the human CEPH diversity panel data set.

Animals↗

PubMed2004

Population genetics of tumor suppressor genes.

Cancer emerges when a single cell receives multiple mutations. For example, the inactivation of both alleles of a tumor suppressor gene (TSG) can imply a net reproductive advantage of the cell and might lead to clonal expansion. In this paper, we calculate the probability as a function of time that a population of cells has generated at least one cell with two inactivated alleles of a TSG. Different kinetic laws hold for small and large populations. The inactivation of the first allele can either be neutral or lead to a selective advantage or disadvantage. The inactivation of the first and of the second allele can occur at equal or different rates. Our calculations provide insights into basic aspects of population genetics determining cancer initiation and progression.

Alleles↗

PubMed1985

[Population genetics of Dagestan highlanders].

Subdivision of some isolates and heterogenic populations in Daghestan is analysed by human gene and phen frequencies. Comparative population study of phenotypic variability of quantitative characters (anthropometric, neurodynamic and psychodynamic) is carried out. Common hierarchy of variability for all populations as well as an effect of inbreeding and panmixis on variability of the above-mentioned quantitative characters in different populations is demonstrated.

Altitude↗

PubMed2003

Evolution and population genetics of the H-ras minisatellite and cancer predisposition.

Case-control studies have implicated rare length H-ras minisatellite alleles in cancer risk. In Europeans, this locus has four common alleles, and a larger number of rare alleles; possession of a rare allele has been identified as a risk factor responsible for 5-10% of some cancers. This unusual model of predisposition has been controversial in case-control studies, but also makes characteristic predictions about the population genetics of the locus, which we examine in this study. Using minisatellite variant repeat ("MVR") mapping, and compound haplotypes composed of the minisatellite and surrounding substitutional polymorphisms, we have reconstructed the main steps in the evolution of this locus in human populations. MVR-calibrated measurements of allele length yield rare allele frequencies significantly higher than most previous studies, and show that most other analyses have not distinguished two common alleles of 84 and 85 repeat units. Alleles classified as "rare" in European populations predominate (70%) in the African sample studied. Small-pool PCR (SP-PCR) analysis on common alleles in sperm DNA gives an estimate for the germline minisatellite mutation rate of about 0.05% (95% confidence upper limit 0.15%). Overall, our results do not reflect a locus subject to frequent mutation and strong selection, and are difficult to reconcile with the proposed cancer predisposition. Restricted variation at this locus is most simply explained by low mutation rate, and although definitive case-control studies can only be performed using methods capable of reproducibly distinguishing rare and common alleles, our work suggests that most studies to date have not resolved alleles adequately.

Alleles↗