Estimation of the Stationary Gene Migration Rate: A Cartographic Approach

A method of geographic mapping of the stationary (limiting) gene migration rate has been developed. The method is based on approximation of the empirical distribution of gene frequencies by a theoretical steady-state distribution. The maximum likelihood method and the ² minimization method are used to obtain consistent estimations of the gene migration rate as a parameter of the steady-state distribution. The new method makes it possible to determine the geographical distribution of the ratio between the properties of the population migration structure described by the stepping-stone and island models and to construct a geographical map of ² values. This map approximately reflects the distribution of natural selection pressure on the gene pool if genetic processes are quasisteady.     

Geography of the stationary gene migration rate among the population of Northern Eurasia

Approximation of the empirical distribution of gene frequencies by a theoretical steady-state distribution was used to obtain a geographical distribution of the limiting gene migration rates in the northern Eurasian population. The rate averaged over the map was m = 0.0432 +/- 0.0003. A geographical map of chi 2 values, which reflect the local nonstationarity character of genetic processes and intensity of selection on the distribution of gene frequencies, is presented. Over 90.1% of northern Eurasia, the chi 2 values satisfy the goodness-of-fit test at a significance level of alpha = 0.1. The geographical distribution that characterizes the ratio between the stepping-stone and island properties of the population migration structure has been obtained. Combined analysis of the spatial characteristics of population migration structure demonstrated that the Pacific coast of Eurasia has played a special role in population genetic processes. This is most likely related to populating the Far East by humans in the remote past and, probably, their more recent expansion to North America through Beringia. The Caucasian region is shown to be extremely stable in terms of the stationarity of migration processes, which agrees with the general view on traditional Caucasian isolates.     

The Geography of the Stationary Gene Migration Rate in the Human Population of Northern Eurasia

Approximation of the empirical distribution of gene frequencies by a theoretical steady-state distribution was used to obtain a geographical distribution of the limiting gene migration rates in the Northern Eurasian population. The rate averaged over the map was = 0.0432 ± 0.0003. A geographical map of ²values, which reflect the local nonstationarity character of genetic processes and intensity of selection on the distribution of gene frequencies, is presented. Over 90.1% of Northern Eurasia, the ²values satisfy the goodness-of-fit test at a significance level of = 0.1. The geographical distribution that characterizes the ratio between the stepping-stone and island properties of the population migration structure has been obtained. Combined analysis of the spatial characteristics of population migration structure demonstrated that the Pacific coast of Eurasia has played a special role in population genetic processes. This is most likely related to populating the Far East by humans in the remote past and, probably, their more recent expansion to North America through Beringia. The Caucasian region is shown to be extremely stable in terms of the stationarity of migration processes, which agrees with the general view on traditional Caucasian isolates.     

Clines with Variable Migration

The consequences of a discontinuity in the migration rate and of a geographical barrier in the habitat are studied in a diffusion model of migration and selection. The treatment is restricted to a single diallelic locus in a monoecious population in the absence of mutation and random drift. It is supposed further that migration is independent of genotype, the population density remains constant and uniform, and Hardy-Weinberg proportions obtain locally. It is shown that a discontinuity in the migration rate leads to a jump in the slope of the gene frequency, but not in the gene frequency itself, while a localized geographical barrier has precisely the opposite effect. These features of the gene frequency behavior are quantitatively related to the migration rate. The influence of the above inhomogeneities in migration on the maintenance of an allele in an environmental pocket is examined. The extent to which the critical condition for polymorphism is made less stringent by decreased migration outside the pocket and by a geographical barrier between the pocket and the rest of the habitat is evaluated.     

Migration between continents: geographical structure and long-distance gene flow in Porpidia flavicunda (lichen-forming Ascomycota)

Historical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long-distance dispersal. Porpidia flavicunda is a lichen-forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA-sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Québec, Baffin Island, Western Greenland and Northern Scandinavia. DNA-sequence data sets of three nuclear gene fragments (LSU, RPB2 and beta-tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long-distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance.     

Identification and mapping of chi115 gene and DNA markers linked to it in pea (Pisum sativum L.)

Chlorophyll mutant Chi115 was induced by ethylmethane sulfonate (EMS) treatment of seeds of genotype Torsdag in Moscow State University and is characterized by lighter plant color. The monogenic nature of the mutant was determined by analyzing the F2 population from a cross between two P. sativum genotypes, WL1238 and Chi115. To establish a local map around the chi115 gene, the RAPD and ISSR techniques were used with 45 RAPD and 10 ISSR primers in combination with bulked segregant analysis (BSA). Linkage of 12 RAPDs and 2 ISSRs to the chi115 locus was observed in analysis of F2 single plants. Two RAPD markers that were closely associated with the chi115 gene were converted into the sequence characterized amplified region (SCAR) markers. By lowering the LOD score to 2, the linkage group containing the chi115 gene could be linked to the b gene (color of the flower) on linkage group III. Nevertheless, to prove the result obtained, three CAPS markers Sodmt, TubA1, and Rb were chosen on linkage group III. The results of linkage analysis showed that these CAPS markers were located within the linkage group including the chi115 gene.     

Geography of genetic processes in populations: gene migrations in Siberia and Far East

A map of gene migration rate m in the indigenous population of Siberia and the Russian Far East was constructed on the basis of data obtained from questionnaires of 1960 to 1990. The mean gene migration rate weighted with respect to the region area and averaged over 3951 grid nodes was m = 0.0083. Weighting with respect to population density yielded a significantly lower rate (m = 0.0053), which reflected a more intense gene exchange in less populous regions of traditional nomadism. The association between gene migration rate m and genetically effective population size Ne was analyzed. The parameter Nem, which characterizes the interpopulation gene diversity, was used to identify regions where this parameter is autoregulated and those where the autoregulatory mechanisms were disrupted. A tree of ethnolinguistic types was constructed. Its analysis did not reveal any association between migration structure and linguistic characteristics, suggesting that the spreading of cultural elements is not necessarily associated with migration. The tree was also used to construct a map of ethnos-forming migration; its major element reflected migration from the Baikal and Altai regions to the ethnic region of modern Yakuts.     

豆科锦鸡儿属(Caragana Fabr.)植物地理分布与分化研究

豆科锦鸡儿属约80种,可以明确地分为6组14系。编绘了79个种的分布图,在此基础上,描述了每个种的分布范围和生存生境,以系和组为单位探讨了锦鸡儿属植物各类群的分布规律,并进一步研究了种类形成和演化过程。Sect. Caragana为东亚--蒙古高原分布型,其Ser. Caraganae的种类在东亚地区随纬度的变化呈现出明显的地理替代分布规律, Ser. Microphyllae在蒙古高原地区随经度的干旱梯度变化呈现出清晰的种类替代关系,本组各系间也有明显的地理替代分布现象。Sect. Prunosa为东亚--中亚间断分布型。Sect. Longispina为喜马拉雅分布型。Sect. Tragacan thoides为环青藏高原--北极高山分布型。Sect. Frutescentes广泛分布于亚洲干旱地区。Sect. Chamlagu为东亚分布型。本属种类可分为6个分布型,分布型之间的关系揭示了亚洲干旱区植物区系形成的渊源和联系。Sect. Caragana为本属的原始类群,起源于东亚,曾广泛分布于亚洲大陆,随青藏高原的隆起,原始类群就地分化形成不同的类群,在此基础上迁移分化适应,形成了现代多样的分布格局,中亚为本属的分化中心。     

An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks

MOTIVATION: Probabilistic Boolean networks (PBNs) have been proposed to model genetic regulatory interactions. The steady-state probability distribution of a PBN gives important information about the captured genetic network. The computation of the steady-state probability distribution usually includes construction of the transition probability matrix and computation of the steady-state probability distribution. The size of the transition probability matrix is 2(n)-by-2(n) where n is the number of genes in the genetic network. Therefore, the computational costs of these two steps are very expensive and it is essential to develop a fast approximation method. RESULTS: In this article, we propose an approximation method for computing the steady-state probability distribution of a PBN based on neglecting some Boolean networks (BNs) with very small probabilities during the construction of the transition probability matrix. An error analysis of this approximation method is given and theoretical result on the distribution of BNs in a PBN with at most two Boolean functions for one gene is also presented. These give a foundation and support for the approximation method. Numerical experiments based on a genetic network are given to demonstrate the efficiency of the proposed method.     

Inferring the evolutionary history of divergence despite gene flow in a lizard species,Scincella lateralis (Scincidae), composed of cryptic lineages

Although recent radiations are fruitful for studying the process of speciation, they are difficult to characterize and require the use of multiple loci and analytical methods that account for processes such as gene flow and genetic drift. Using multilocus sequence data, we combine hierarchical cluster analysis, coalescent species tree inference, and isolation‐with‐migration analysis to investigate evolutionary relationships among cryptic lineages of North American ground skinks. We also estimate the extent that gene flow has accompanied or followed diversification, and also attempt to account for and minimize the influence of gene flow when reconstructing relationships. The data best support seven largely parapatric populations that are broadly concordant with mitochondrial (mt)DNA phylogeography throughout most of the species range, although they fail to fully represent extensive mtDNA divergence along the Gulf Coast. Relationships within and among three broad geographical groups are well supported, despite evidence of gene flow among them. Rejection of an allopatric divergence model partially depends on the inclusion of samples from near parapatric boundaries in the analyses, suggesting that allopatric divergence followed by recent migration may best explain migration rate estimates. Accounting for geographical variation in patterns of gene flow can improve estimates of migration–divergence parameters and minimize the influence of contemporary gene flow on phylogenetic inference. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Predictive models and spatial variations of vital capacity in healthy people from 6 to 84 years old in China based on geographical factors

The aim of this study was to provide a scientific basic for a unified standard of the reference value of vital capacity (VC) of healthy subjects from 6 and 84 years old in China. The normal reference value of VC was correlated to seven geographical factors, including altitude (X ₁), annual duration of sunshine (X ₂), annual mean air temperature (X ₃), annual mean relative humidity (X ₄), annual precipitation amount (X ₅), annual air temperature range (X ₆) and annual mean wind speed (X ₇). Predictive models were established by five different linear and nonlinear methods. The best models were selected by t-test. The geographical distribution map of VC in different age groups can be interpolated by Kriging’s method using ArcGIS software. It was found that the correlation of VC and geographical factors in China was quite significant, especially for both males and females aged from 6 to 45. The best models were built for different age groups. The geographical distribution map shows the spatial variations of VC in China precisely. The VC of healthy subjects can be simulated by the best model or acquired from the geographical distribution map provided the geographical factors for that city or county of China are known.     

A coalescence approach to gene conversion

In this paper we develop a coalescent model with intralocus gene conversion. Such models are of increasing importance in the analysis of intralocus variability and linkage disequilibrium. We derive the distribution of the waiting time until a gene conversion event occurs in a sample in terms of the distribution of the length of the transferred segment, zeta. We do not assume any specific form of the distribution of zeta. Further, given that a gene conversion event occurs we find the distribution of (sigma, tau), the end points of the transferred segment and derive results on correlations between local trees in positions chi(1) and chi(2). Among other results we show that the correlation between the branch lengths of two local trees in the coalescent with gene conversion (and no recombination) decreases toward a nonzero constant when the distance between chi(1) and chi(2) increases. Finally, we show that a model including both recombination and gene conversion might account for the lack of intralocus associations found in, e.g., Drosophila melanogaster.     

Identification and Mapping of chi115 Gene and DNA Markers Linked to It in Pea (Pisum sativum L.)

Chlorophyll mutant Chi115 was induced by ethylmethane sulfonate (EMS) treatment of seeds of genotype Torsdag in Moscow State University and is characterized by lighter plant color. The monogenic nature of the mutant was determined by analyzing the F₂ population from a cross between two P. sativum genotypes, WL1238 and Chi115. To establish a local map around the chi115gene, the RAPD and ISSR techniques were used with 45 RAPD and 10 ISSR primers in combination with bulked segregant analysis (BSA). Linkage of 12 RAPDs and 2 ISSRs to the chi115locus was observed in analysis of F₂ single plants. Two RAPD markers that were closely associated with the chi115 gene were converted into the sequence characterized amplified region (SCAR) markers. By lowering the LOD score to 2, the linkage group containing the chi115 gene could be linked to the b gene (color of the flower) on linkage group III. Nevertheless, to prove the result obtained, three CAPS markers Sodmt, TubA1, and Rb were chosen on linkage group III. The results of linkage analysis showed that these CAPS markers were located within the linkage group including thechi115gene.     

Genetic distances and ordination: the land snail Helix aspersa in north Africa as a test case

We examined the efficiencies of ordination methods in the treatment of gene frequency data at intraspecific level, using metric and nonmetric distance measures (Nei's and Rogers' genetic distances, chi 2 distance). We assessed initial processes responsible for the geographical distribution of the Mediterranean land snail Helix aspersa. Seventeen enzyme loci from 30 North African snail populations were considered in the present analysis. Five combinations of distance/multivariate analysis were compared: correspondence analysis (CA), nonmetric multidimensional scaling (NMDS) on Nei's, Rogers', and chi 2 distances, and principal coordinates analysis on Rogers' distances. Configuration of the objects resulting from ordination was projected onto three-dimensional graphics with the minimum spanning tree or the relative neighborhood graph superimposed. Pre- and postordination or clustering distance matrices were compared by means of correlation methods. As expected, all combinations led to a clear west versus east pattern of variation. However, the intraregional relationships and degree of connectivity between pairs of operational taxonomic units were not necessarily constant from one method to another. Ordination methods when applied with Nei's and Rogers' distances provided the best fit, with original distances (r = 0.98) compared with UPGMA clustering (r approximately 0.75). The Nei/NMDS combination seems to be a good compromise (distortion index dt = 10%) between Rogers/NMDS, which produces a more confusing pattern of differentiation (dt = 24%), and chi 2/CA, which tends to distort large distances (dt = 31%). NMDS obviously provides a powerful method to summarize relationships between populations, when neither hierarchical structure nor phylogenetic inference are required. These findings led the discussion on the good performance of NMDS, the appropriate distances to be used, and the potential application of this method to other types of allelic data (such as microsatellite loci) or data on nucleotide sequences of genes.     

Paths and cycles in breakpoint graph of random multichromosomal genomes.

We study the probability distribution of the distance d = n + chi - kappa - psi between two genomes with n markers distributed on chi chromosomes and with breakpoint graphs containing kappa cycles and psi "good" paths, under the hypothesis of random gene order. We interpret the random order assumption in terms of a stochastic method for constructing the bicolored breakpoint graph. We show that the limiting expectation of E[d] = n - 1/2chi - 1/2 log n+chi/2chi. We also calculate the variance, the effect of different numbers of chromosomes in the two genomes, and the number of plasmids, or circular chromosomes, generated by the random breakpoint graph construction. A more realistic model allows intra- and interchromosomal operations to have different probabilities, and simulations show that for a fixed number of rearrangements, kappa and d depend on the relative proportions of the two kinds of operation.     

中国湿润半湿润地区啮类动物的分布格局

系统收集并整理了我国湿润半湿润地区啮类动物的地理分布资料,基于GIS技术,通过生境分析,确定了每个物种的分布范围,采用6470 km2的等面积栅格作为地理分布单元,系统研究我国湿润半湿润地区啮类动物地理分布规律.我国湿润半湿润地区有啮类动物156种,隶属于2目、12科、62属,占我国啮类动物总数的71.23%.地理单元的物种丰富度分析结果表明,云南西部到四川中部的横断山区、陕西秦岭和甘肃南部山地的啮类动物丰富度较高;河北省东南部、山东、河南、江苏、安徽的长江以北地区及长江三角洲、湖南和湖北的沿江地区以及四川盆地等地物种丰富度较低.地理单元有无物种分布的层次聚类分析结果表明,我国湿润半湿润地区分为三大区域:东部季风区的南北两区(以长江下游-秦岭一线分界),以及青藏高原的半湿润区.     

Medical genetic study of the population of Turkmenia. VI. Intrapopulation variability from an analysis of marriage migrations and ABO and Hp marker systems

By the sampling procedure, the distribution of phenotypic and genotypic frequencies of ABO and Hp systems and the structure of intermarriage migration in Turkmen population was studied. The geographical subdivision of the Turkmen population coincided with its ethnic divergency. The main Turkmen tribes are highly isolated (the gametic index is 0.965 to 1.0) and the differences in gene frequencies between tribes are significant. The mean gene frequencies for the ABO system in the Turkmen population are: I0-0.5373, IA-0.2601, IB-0.2025, these being Hp1-0.284, Hp2-0.716 for the Hp system.     

Mitochondrial DNA evidence for high levels of gene flow among populations of a widely distributed anadromous lamprey Entosphenus tridentatus (Petromyzontidae)

Mitochondrial DNA variation among 1246 individuals of Pacific lamprey ( Entosphenus tridentatus ) from 81 populations spanning 2600 km from the Skeena River, British Columbia, to the Ventura River, California, was surveyed using five restriction enzymes. A total of 29 composite haplotypes was detected in two gene fragments (ND2 and ND5). The three most common haplotypes, occurring in 91% of all samples, were present at similar frequencies in all regions. Samples were divided into six biogeographic regions based on sample distribution and geographical landmarks to assess geographic genetic structure. Analysis of molecular variance indicated that 99% of the genetic variation was explained by variability within drainages. The lack of geographical population structure is likely related to a life-history pattern that includes a prolonged larval freshwater stage, migration to oceanic feeding and return to fresh water to spawn. The lack of strong natal homing apparently promotes gene flow among drainages and regions.     

Analysis of quantitative trait loci using hybrid pedigrees: quantitative traits of animals

A method is proposed for analysis of quantitative traits in animal hybrid pedigrees formed by crosses between outbred lines differing in allele frequencies of the genes controlling the trait studied. The method is based on the decomposition of trait variances into components and uses maximization of the likelihood function for estimating model parameters, which allows the estimation of additive and dominance effects of the gene involved in trait determination and its allele frequencies, as well as determination of the chromosomal position of this gene relative to genotyped markers. To test the linkage of this gene with markers, a statistic with the noncentral chi(2) distribution has been chosen. Analytical expressions for the power of this method have been derived. The method has been tested on small model hybrid pedigrees. Phenotypic values of the trait and information on marker genotypes for each individual in hybrid pedigrees are original data for the analysis of a quantitative trait.     

Mortality from cardiovascular disease among interregional migrants in England and Wales.

OBJECTIVE--To investigate the extent to which geographical variations in mortality from ischaemic heart disease and stroke in Britain are influenced by factors in early life or in adulthood. DESIGN--Longitudinal study of migrants. SUBJECTS--1% sample of residents in England and Wales born before October 1939 and enumerated at the 1971 census (the Office of Population Censuses and Surveys'' longitudinal study). MAIN OUTCOME MEASURE--18,221 deaths from ischaemic heart disease and 9899 deaths from stroke during 1971-88 were analysed by areas of residence in 1939 and 1971. These included 2928 deaths from ischaemic heart disease and 1608 deaths from stroke among individuals moving between 14 areas defined by the major conurbations and nine standard administrative regions of England and Wales. RESULTS--The southeast to northwest gradient in mortality from ischaemic heart disease was related significantly to both the 1939 area (chi 2 = 6.09, df = 1) and area in 1971 (chi 2 = 5.05, df = 1). Geographical variations in mortality from stroke were related significantly to the 1939 area (chi 2 = 4.09, df = 1) but the effect of area in 1971 was greater (chi 2 = 8.07, df = 1). The effect of 1971 area on mortality from stroke was largely due to a lower risk of death from stroke among individuals moving into Greater London compared with migrants to the rest of the South East region (chi 2 = 4.54, df = 1). CONCLUSIONS--Geographical variations in mortality from cardiovascular disease in Britain may be partly determined by genetic factors, environmental exposures, or lifestyle acquired early in life, but the risk of fatal ischaemic heart disease and stroke changes on migration between areas with differing mortality. The low risk of death from stroke associated with residence in Greater London is acquired by individuals who move there.