Isolation by distance, linguistic similarity, and the genetic structure on Bougainville Island

Previous research has revealed extensive genetic variation among villages on Bougainville, in the Solomon Islands. Using previously published gene frequency data for seven loci, the role of isolation by distance in structuring genetic variation on Bougainville was reanalyzed. Newer methods of kinship estimation show that earlier estimates of the isolation by distance parameters were low. The fit of the model is highly significant (R2 = 0.409; P less than 0.001), and the parameter estimates indicate high isolation: a = 0.0538, b = 0.1978, L = -0.0057. Several methods of residual analysis were applied in order to determine factors affecting the fit of the model. Linguistic similarity has a significant effect on genetic variation once the effects of geographic distance are taken into account. Population-specific deviations from the expected model may be explained, in part, in terms of population history. Compared to other human populations, Bougainville Island shows an even greater among-group variation than has been suggested previously.     

An attempt at the historical reconstruction of the genetic demographic structure of the Moscow population at the turn of the 20th century]

The genetic demographic structure of the Moscow population at the turn of the 20th century was studied based on the data from parish books and census records. The main sources of population gene pool replenishment were analyzed, and migration coefficients and the main parameters of the model of isolation by distance were estimated. Data on so-called quasigenetic markers (ethnicity and birthplace) were used to reveal intrapopulation heterogeneity, which facilitates the adaptation of migrants to a new ethnic and cultural environment. The spatial subdivision was analyzed with the use of GST statistics. Muscovites exhibited a considerable positive assortative mating with respect to birthplace. The results of this study provide the necessary historical perspective for predicting the current genetic demographic trends in the Moscow population. It was shown that the co-efficients of marriage migration were almost the same (0.7 < m < 0.8) in the late 19th and mid-20th centuries; however, these values were two times greater than in the late 20th century. This decrease in marriage migration was accompanied by a threefold increase in the radius of centripetal migration and a threefold decrease in the level of isolation by distance. It was determined that the increase in the ethnic and genetic diversity of the Moscow population in the 20th century had started in the 1860s.     

Dynamics of the genetic demographic structure of the Kursk province population: migration processes

Marriage records from parish books of the second half of the 19th century and marriage records of 1967-1970 and 1993-1995 obtained from registry offices were used to analyze the dynamics of genetically significant parameters of migration and marriage structure with respect to spouses' birthplaces in populations of different hierarchical levels in the Kursk oblast. It was found that, among the persons contracting marriage (both males and females), the proportions of those who were born in the same population and those who were born in any population of the Kursk oblast decreased by about one third and one fifth, respectively, for the 130-year period. In rural and small urban populations, the coefficients of marriage migration in the 19th century were an order of magnitude lower than in the 20th century. The immigration to urban populations was maximum in the late 1960s (m = 0.745 in small towns and m = 0.680 in Kursk), and that to rural populations, in the 1990s (m = 0.344). In both urban and rural populations, the mean distance between the spouses' birthplaces has increased by several times for the period studied. The endogamy level has decreased approximately twofold: from 0.797 to 0.380 in Kursk, from 0.897 to 0.419 in small towns, and from 0.958 to 0.440 in rural districts. The marriage assortativeness with respect to birthplace was maximum in the late 19th century (K = 0.393-0.491) and minimum in the 1960s (K = 0.155-0.246). The increase in genetic diversity of the urban population of the Kursk oblast due to migration has been slowing down since the late 20th century, whereas the outbreeding level is still increasing in rural populations.     

The marriage migration characteristics of the Rostov oblast population

Marriage records have been used to study the marriage migration structure of five raions of the Rostov oblast. The mean ethnic marriage assortativeness in the Russian and Ukrainian rural populations are 1.16 and 1.6, respectively. The endogamy index of the urban population varies from 0.19 to 0.34; and that of the rural population, from 0.21 to 0.54. Malecot's isolation by distance parameters have been calculated. Genetic landscapes have been constructed.     

Dynamics of the Genetic Demographic Structure of the Kursk Oblast Population: Migration Processes

Marriage records from parish books of the second half of the 19th century and marriage records of 1967–1970 and 1993–1995 obtained from registry offices were used to analyze the dynamics of genetically significant parameters of migration and marriage structure with respect to spouses' birthplaces in populations of different hierarchical levels in the Kursk oblast. It was found that, among the persons contracting marriage (both males and females), the proportions of those who were born in the same population and those who were born in any population of the Kursk oblast decreased by about one third and one fifth, respectively, for the 130-year period. In rural and small urban populations, the coefficients of marriage migration in the 19th century were an order of magnitude lower than in the 20th century. The immigration to urban populations was maximum in the late 1960s (m = 0.745 in small towns and m = 0.680 in Kursk), and that to rural populations, in the 1990s (m = 0.344). In both urban and rural populations, the mean distance between the spouses" birthplaces has increased by several times for the period studied. The endogamy level has decreased approximately twofold: from 0.797 to 0.380 in Kursk, from 0.897 to 0.419 in small towns, and from 0.958 to 0.440 in rural districts. The marriage assortativeness with respect to birthplace was maximum in the late 19th century (K = 0.393–0.491) and minimum in the 1960s (K= 0.155–0.246). The increase in genetic diversity of the urban population of the Kursk oblast due to migration has been slowing down since the late 20th century, whereas the outbreeding level is still increasing in rural populations.     

Genetic structure of the Saguenay, 1852-1911: evidence from migration and isonymy matrices

The Saguenay is a region in northeastern Québec populated in the second half of the 19th century through migration from other parts of Québec. The present-day population of nearly 300,000 is the result of both immigration and high rates of intrinsic growth. This population has been of interest to geneticists because of the high incidence of certain hereditary diseases, notably spastic ataxia, tyrosinemia, agenesis of the corpus callosum, vitamin D-dependent rickets, and myotonic dystrophy. Parent-offspring migration and isonymy matrices were used to estimate random kinship using the Malécot model for six 10-year time periods from 1852-1911. Comparisons between two estimates of kinship--one from parent-offspring migration matrices (phi) and the other from isonymy (R)--and geographic distance were made using both product-moment and Mantel correlation. Comparisons of within- and between-subdivision kinship were made using nonparametric and Mantel correlation. Within-subdivision kinship from the phi matrix was also compared with kinship estimated from marriage dispensations for endogamous marriages. The estimates of random kinship from the parent-offspring matrices showed a good fit with geography. However, isonymy did not correlate well with geographic distance; and phi and R showed no correlation until the last two time periods, and the diagonal of phi did not correlate with the marriage dispensations. Examination of scatterplots of phi vs. R suggests that nonrandom migration during the process of settlement formation is responsible for the lack of correlation. While movement across space seems to be highly dependent on distance, nonrandom selection of migrants means that between-subdivision estimates of kinship based on migration are not congruent with those obtained by other methods. On the whole, genetic differentiation seems to have been low due to the high levels of movement between subdivisions and immigration. The weak dependence of genetic structure on geographic distances in the present population is demonstrated by mapping the geographic distribution of cases of three recessively inherited diseases.     

Epidemiology of monogenic hereditary diseases in Rostov oblast: Population dynamic factors determining the differentiation of the load of hereditary diseases in eight districts

A genetic epidemiological study has been carried out in eight raions (districts) of Rostov oblast (region) of Russia: Tsimlyansk, Volgodonskoi, Tselina, Egorlykskaya, Millerovo, Tarasovskaya, Rodionovo-Nesvetaiskaya, and Matveevo-Kurgan raions. The population structure (the parameters of the isolation by distance model, ethnic assortative marriage, random inbreeding (F _ST), endogamy index, and ie) and the genetic demographic characteristics of the regional population (vital statistics, Crow’s index, and its components) have been analyzed. The total sample size was 320 925 subjects (including 114 106 and 206 816 urban and rural residents, respectively). The load of the main types of Mendelian diseases (autosomal dominant (AD), autosomal recessive (AR), and X-linked diseases) has been calculated for the total sample from eight districts and separately for the urban and rural populations. Substantial differences between individual districts in the AD and AR genetic loads have been found, especially upon separation into urban and rural samples. The results of correlation analysis suggest that migration and genetic drift are the main factors of genetic differentiation of populations with respect to the prevalence of hereditary diseases.     

Spatial characteristics of marriage migration in the Belgorod population

Data from marriage records of the city of Belgorod for 1960, 1985, and 1995 have been used to calculate parameters characterizing migration in the Belgorod population. The marriage migration coefficients (m) in these years were 0.83, 0.68, and 0.58, respectively, and the endogamy indices were 0.05, 0.13, and 0.22, respectively. The marriage convergence (K) with respect to birthplace in the same years were 0.15, 0.13, and 0.14, respectively. In the period studied, spatial parameters reflecting the genetic efficiency of migration increased. The mean migration distance also increased; it was 430, 667, and 926 km in 1960, 1985, and 1995, respectively. The migration distances for men and women in the same years were 477, 725, and 986 km and 383, 609, and 866 km, respectively. The radius of the Belgorod population in terms of Malecot's isolation by distance model increased in the period studied (55, 81, and 95 km in 1960, 1985, and 1995, respectively). The parameter b in that period decreased (0.00110, 0.00074, and 0.00062, respectively), which indicates a decrease in the inbred component. The increase in marital distance (590, 796, and 891 km in 1960, 1985, and 1995, respectively) indicates a steady increase in the outbred component of the population.     

Evolutionary and statistical properties of three genetic distances

Many genetic distances have been developed to summarize allele frequency differences between populations. I review the evolutionary and statistical properties of three popular genetic distances: DS, DA, and theta;, using computer simulation of two simple evolutionary histories: an isolation model of population divergence and an equilibrium migration model. The effect of effective population size, mutation rate, and mutation mechanism upon the parametric value between pairs of populations in these models explored, and the unique properties of each distance are described. The effect of these evolutionary parameters on study design is also investigated and similar results are found for each genetic distance in each model of evolution: large sample sizes are warranted when populations are relatively genetically similar; and loci with more alleles produce better estimates of genetic distance.     

Distribution, endogamy, and isolation of Malas of Chittoor district, Andhra Pradesh, India

This study investigates the distribution of Malas, a scheduled caste population of Andhra Pradesh, their isolates in different eco-cultural zones, and their endogamy and isolation by marriage district. The Malas, formerly "untouchables," occupy the lowest status in the Hindu hierarchy. The sample consists of 10% of Malas from 10% of the villages in 2 taluks of Chitoor district of Andhra Pradesh. 6 Mala populations--Tangala, Maladasari, Pakanati, Rampala, Murikinati, and Bommanati--live in the area. These populations show a regionality in their distribution, with very little overlapping even when 2 populations inhabit the same village. Of 885 marriages in the 6 endogamous populations, all but 3 have been contracted between individuals belonging to the same Mala group. The 3 exogamous marriages took place between Mala men and women from another caste. Such small exceptions to the general rule do not mean that the Mala populations are not breeding isolates; these 6 populations satisfy Wright's island model. The high incidence of matings between closely related populations also contributes to their genetic and breeding isolation. Consanguineous marriages range from 26.76 to 38.75%. The distance between the birth place of spouses in miles, called marriage distance, shows a range from 7.72 to 15.71 miles. Lower values mean higher population densities. Groups within each population are isolated by distance and form small overlapping Mendelian populations, approaching a stepping stone model with continuous variation of genetic traits between adjacent groups of people.     

Craniometric variation,genetic theory,and modern human origins

Recent controversies surrounding models of modern human origins have focused on among-group variation, particularly the reconstruction of phylogenetic trees from mitochondrial DNA (mtDNA) and, the dating of population divergence. Problems in tree estimation have been seen as weakening the case for a replacement model and favoring a multiregional evolution model. There has been less discussion of patterns of within-group variation, although the mtDNA evidence has consistently shown the greatest diversity within African populations. Problems of interpretation abound given the numerous factors that can influence within-group variation, including the possibility of earlier divergence, differences in population size, patterns of population expansion, and variation in migration rates. We present a model of within-group phenotypic variation and apply it to a large set of craniometric data representing major Old World geographic regions (57 measurements for 1,159 cases in four regions: Europe, Sub-Saharan Africa, Australasia, and the Far East). The model predicts a linear relationship between variation within populations (the average within-group variance) and variation between populations (the genetic distance of populations to pooled phenotypic means). On a global level this relationship should hold if the long-term effective population sizes of each region are correctly specified. Other potential effects on withingroup variation are accounted for by the model. Comparison of observed and expected variances under the assumption of equal effective sizes for four regions indicates significantly greater within-group variation in Africa and significantly less within-group variation in Europe. These results suggest that the long-term effective population size was greatest in Africa. Closer examination of the model suggests that the long-term African effective size was roughly three times that of any other geographic region. Using these estimates of relative population size, we present a method for analyzing ancient population structure, which provides estimates of ancient migration. This method allows us to reconstruct migration history between geographic regions after adjustment for the effect of genetic drift on interpopulational distances. Our results show a clear isolation of Africa from other regions. We then present a method that allows direct estimation of the ancient migration matrix, thus providing us with information on the actual extent of interregional migration. These methods also provide estimates of time frames necessary to reach genetic equilibrium. The ultimate goal is extracting as much information from present-day patterns of human variation relevannt to issues of human origins. Our results are in agreement with mismatch distribution analysis of mtDNA, and they support a “weak Garden o Eden” model. In this model, modern-day variation can be explained by divergence from an initial source (perhaps Africa) into a number o small isolated populations, followed by later population expansion throughout our species. The major populationn expansions of Homo sapiens during and after the late Pleistocene have had the effect of “freezing” ancient patterns of population structure. While this is not the only possible scenario, we do note the close agreement with ecent analyses of mtDNA mismatch distibutions. © 1994 Wiley-Liss, Inc.     

The Marriage Migration Characteristics of the Rostov Oblast Population

Marriage records have been used to study the marriage migration structure of five raions of the Rostov oblast. The mean ethnic marriage assortativeness in the Russian and Ukrainian rural populations are 1.16 and 1.6, respectively. The endogamy index of the urban population varies from 0.19 to 0.34; and that of the rural population, from 0.21 to 0.54. Malecot’s isolation by distance parameters have been calculated. Genetic landscapes have been constructed.__________Translated from Genetika, Vol. 41, No. 7, 2005, pp. 981–985.Original Russian Text Copyright © 2005 by Kriventsova, El’chinova, Amelina, Zinchenko.     

Spatial Characteristics of Marriage Migration in the Belgorod Population

Data from marriage records of the city of Belgorod for 1960, 1985, and 1995 have been used to calculate parameters characterizing migration in the Belgorod population. The marriage migration coefficients (m) in these years were 0.83, 0.68, and 0.58, respectively, and the endogamy indices were 0.05, 0.13, and 0.22, respectively. The marriage convergence (K) with respect to birthplace in the same years were 0.15, 0.13, and 0.14, respectively. In the period studied, spatial parameters reflecting the genetic efficiency of migration increased. The mean migration distance also increased; it was 430, 667, and 926 km in 1960, 1985, and 1995, respectively. The migration distances for men and women in the same years were 477, 725, and 986 km and 383, 609, and 866 km, respectively. The radius of the Belgorod population in terms of Malecot’s isolation by distance model increased in the period studied (55, 81, and 95 km in 1960, 1985, and 1995, respectively). The parameter b in that period decreased (0.00110, 0.00074, and 0.00062, respectively), which indicates a decrease in the inbred component. The increase in marital distance (590, 796, and 891 km in 1960, 1985, and 1995, respectively) indicates a steady increase in the outbred component of the population.__________Translated from Genetika, Vol. 41, No. 5, 2005, pp. 686–696.Original Russian Text Copyright © 2005 by Atramentova, Filiptsova.     

Spatial and geographic characteristics of marriage migration in the Lugansk population

Data from the Lugansk City Registry Office archives of 1960, 1985, 1990, and 2000 were used to calculate genetic demographic parameters characterizing marriage migration. The migration coefficients (m) in these years were 0.69, 0.54, 0.47, and 0.36; the endogamy indices were 12.1, 24.4, 30.5, and 43.2%, and the marriage contingency coefficients with respect to birthplace (K) were 0.12, 0.10, 0.11, and 0.13, respectively. The mean migration distance increased by a factor of 1.5 (from 599 to 870 km), and the mean parent-offspring distance decreased by a factor of 1.3 (from 415 to 317 km) during the period between 1960 and 2000. The mean marriage distance increased from 654 to 718 km between 1960 and 1985 and then decreased to 594 km by the year 2000. The proportion of "long-distance" migrations calculated using Malecot's model increased from 0.013 to 0.021 between 1960 and 1990 and decreased to 0.005 by 2000. The proportion of "short-distance" migrations was 0.77 in 1960 and 0.51 in 2000. The migration efficiency increased from 0.09 to 0.18 between 1960 and 1990 and decreased to 0.07 by 2000. In the years studied, the indices of isolation by distance (b) were 0.0005, 0.0004, 0.0005, and 0.0002, and the population "radii" were 90, 118, 119, and 168 km, respectively.     

R-matrix analysis and patterns of gene flow in India

An appraisal on the usefulness of R-matrix analysis and the model of Harpending and Ward (1982) to study the population structure of Indian populations is made in the light of prevalent marriage patterns, caste structure, and cultural specificity of the region. With the help of available data on the migration histories and geographical backgrounds of marine fishermen on the east coast of India, and through the historical analysis of marriage patterns, it is demonstrated that the routine inferences based on the regression plots of average heterozygosity versus genetic distance from the centroid may not generally be apt for the Indian situation. Increased heterozygosity among migrant fishermen seems to have resulted from mating patterns within this community rather than from external gene flow. In either case, the genetic implications are supposedly identical. Nevertheless, when making inferences regarding local population structure it is important to have detailed knowledge of mating patterns and the cultural context of the region under study.     

Admixture in a biologically African caste of black Americans

Social and historical factors account for much of the variation in European ancestry among different Black American populations, including that of McNary, Arizona. The Black population of McNary is socioculturally and geographically isolated. Admixture estimates based upon reflectometry and serological data suggest that this population has less than 5% European ancestry. Anthropometric and hemoglobin data also suggest that this population is more African in ancestry than other Black American populations. Admixture estimates for the population are complicated by several factors. Genetic drift has probably affected Black McNary; estimated effective population size (Ne) is 52.11 and the coefficient of breeding isolation is less than 50. Frequencies of the alleles B, O, and r support this hypothesis; they are quite atypical for a Black American group. Selective migration and occupational selection may also have influenced the current genetic composition of Black McNary. Over 80% of the Black residents of McNary were born in backwoods lumbering towns in the American South. Most Black families in McNary trace their economic reliance on lumbering back several generations. Historical sources and demographic data from Black McNary suggest that Southern Black millworking families formed an endogamous unit that produced this caste, which has a relatively small amount of European ancestry.     

Patrilocality and recent migrations have little impact on shaping patterns of genetic structure of the armenian population

In general, genetic distances between human populations (also within one ethnic group) are larger for the Y chromosome markers than for the mtDNA. It is usually explained by higher rate of female versus male migration due to the cultural practice of patrilocality, when women move to their husbands’ residence after marriage. Recently found a reversed picture for the genetic variation in some ethno-territorial groups confirm the strict role of cultural traditions in shaping patterns of populations’ genetic structure. To test the role of patrilocality for the genetic structure of the Armenian population, we compared the Y chromosome and the mtDNA haplotype variations among and between geographical groups identified according to paternal (maternal) grandparental place of birth, from one side, and the populations currently living in the same geographical areas, from the other side. The results demonstrate that the Armenian population is regionally more structured for the Y chromosome than for the mtDNA. Additionally, in spite of expressed directivity of migration processes (caused by the phenomenon of patrilocality as well), the patterns of genetic variations for the populations of the same geographic areas remain without any significant changes during the last three generations.     

GM haplotype diversity of 82 populations over the world suggests a centrifugal model of human migrations

This study investigates the GM genetic relationships of 82 human populations, among which 10 represent original data, within and among the main broad geographic areas of the world. Different approaches are used: multidimensional scaling analysis and test for isolation by distance, to assess the correlation between genetic variation and spatial distributions; analysis of variance, to investigate the genetic structure at different hierarchical levels of population subdivision; genetic similarity map (geographic map distorted by available genetic information), to identify regions of high and low genetic variation; and minimal spanning network, to point out possible migration routes across continental areas. The results show that the GM polymorphism is characterized by one of the highest amounts of genetic variation observed so far among populations of different continents (Fct=0.3915, P < 0.0001). GM diversity can be explained by a model of isolation by distance (IBD) at most continental levels, with a particularly significant fit to IBD for the Middle East and Europe. Five peripheral regions of the world (Europe, west and south sub-Saharan Africa, Southeast Asia, and America) exhibit a low level of genetic diversity both within and among populations. By contrast, East and North African, Southwest Asian, and Northeast Asian populations are highly diverse and interconnected genetically by large genetic distances. Therefore, the observed GM variation can be explained by a "centrifugal model" of modern humans peopling history, involving ancient dispersals across a large intercontinental area spanning from East Africa to Northeast Asia, followed by recent migrations in peripheral geographic regions.     

Medico-genetic study of the population of Kostroma Province. VI. The parameters of isolation by distance in the populations of the Bui and Shar'ya Districts of Kostroma Province

A model of isolation by distance proposed by Malécot and developed by Morton is applied to the data on marriage distances collected in two regions of Kostroma Province. There is good agreement between the estimates of local inbreeding when using the isonymy method and the model of isolation by distance. Interpopulation kinship approaches 0 at the distance 700 km. The mean coefficient of kinship for parents in the families with autosomal-recessive pathology is 20 times higher than mean coefficient of kinship in the population.     

Population structure analysis using polygenic traits: estimation of migration matrices

Many studies of subdivided populations have attempted to determine the underlying migration rates that generate observed patterns of genetic differentiation. Most previous analyses have yielded only qualitative inferences about migration. In this paper I present a new method for estimating the full migration matrix from information on polygenic trait variation. The method employs multivariate quantitative genetic theory to provide a matrix formulation of the expected covariance structure in multigenerational subdivided populations for which information is available at different points in the life cycle. I develop a restricted maximum likelihood technique (REML) to take account of this additional life-cycle information and to estimate both the migration matrix and the ratio of effective population size to census size. To make the problem computationally tractable, the migration matrix is modeled as a log-linear function of a few covariates, such as subdivision size and geographic distance. I apply the technique to data on dermatoglyphic ridge counts for 1015 individuals of the Jirel population of east Nepal, considering two different age cohorts. In the adult cohort (individuals over 21 years of age) I examine data by both birthplace and residence and for the subadult cohort (under 21 years of age), by birthplace. Results from the REML technique reveal that the best-fitting migration model is a finite island model with an estimated endemicity of 0.730 +/- 0.105 and an estimated ratio of effective size to census size of 0.287 +/- 0.095. Both estimates are reasonable given known demographic data. In addition, Fst values predicted by the migration model are concordant with REML estimates obtained directly from the dermatoglyphic variation.