Correlations between Isonymy Parameters

Several parameters of genetic and anthropological interest are commonly estimated in the analysis of the surnames' distribution in human populations. Among these parameters, the most important for population structure is unbiased Isonymy, equivalent to 4 times the value of F_st, the random component of inbreeding in a group. Fisher's α estimates the wealth of surnames in a group, and Karlin-McGregorv is considered proportional to migration rates. Recently, other parameters like Entropy and Redundance of the surname's distribution were introduced in the analysis and estimated. In the present work, the parameters obtained through isonymy analysis of 759,500 telephone users in 379 Communes of Sicily are correlated with variables such as sample size, population size and density, and number of surnames in the Commune. In Sicily, the parameters or their logarithm are Gammadistributed. It is observed that the number of surnames is strongly correlated with most parameters or with their logarithm, and that it is in turn strongly correlated with sample size.     

Isonymy and isolation by distance in Italy

The isonymy structure of Italy was studied using the surname distribution of 5,043,580 private telephone users selected from a 1996 commercial CD-ROM that contains all 24 million users in the country. The users were distributed in 123 towns selected on a geographic basis. The 123 towns were either on the main communication roads of the country or at the ends of such roads. The shortest distance between nearest neighbor towns was 5.3 km (Carrara and Massa), and the largest distance was 1,136 km (Aosta and Castrignano del Capo). The number of different surnames found in the whole analysis was 215,623. Lasker's distance, the negative value of the logarithm of random isonymy between localities, was linearly and significantly correlated with the logarithm of geographic distance, with r = 0.63 +/- 0.008. A dendrogram was built from the matrix of isonymy distances, using UPGMA. It separates the Italian towns into 5 main clusters: 1 in the southern portion of the country, a second cluster toward the center, and 3 in the northern area of Italy. Within each cluster small subclusters with specific geographic distributions could be related to regional borders. Comparisons with the results of a previous analysis of Switzerland and Germany's structures are given. From the present analysis isolation by distance emerges clearly, although it is less strong than in Switzerland and stronger than in Germany. The random component of inbreeding estimated from isonymy indicates that the southern area of Italy is on average more inbred than the northern area. In fact, the heterogeneity is greater in the northern area, particularly in the plain of the Po River, than anywhere else in Italy.     

Isonymy and isolation by distance in the Netherlands

The isonymy structure of the Netherlands was studied using the surname distribution of 2.4 million private telephone users selected from a 1996 commercial CD-ROM containing the names of 6.3 million users in the country. The users were distributed in 226 towns selected on a geographic basis to form an approximately regular grid throughout the Netherlands. Names of telephone users in each town were downloaded from the CD-ROM, with private users being selected for inclusion in the analysis. The shortest linear distance between several nearest neighboring towns was less than 2 km (e.g., Kampen and Ijsselmuiden, Krommen and Zaandijk, Hendrikdo and Papendrecht) and the longest distance was 326 km (Delfzijl and Oostburg ZL). The number of different surnames revealed by the analysis was 126,485. Lasker's distance, the negative value of the logarithm of isonymy between localities, was found to be significantly correlated with linear geographic distance, with r = 0.47 +/- 0.006. A dendrogram built using the matrix of isonymy distances, using the nearest neighbor-joining method, separates the Dutch towns into several clusters, most of them correlated with traditional Dutch regions. Comparisons with the results of previous analyses of the structure of other European countries are given. From the present analysis, isolation by distance emerges clearly, and it is relevant, although much weaker than in Switzerland, Austria, Italy, and Germany. The random component of inbreeding estimated from isonymy indicates a considerable degree of homogeneity in the Netherlands.     

Isonymy, consanguinity and repeated pairs of surnames in Aromun populations

The Aromuns represent a small and almost unknown people that live scattered over the Balkan Peninsula. Due to their language, that is very similar to classical Latin, they are in a special position. The Aromuns settled only in more recent times. Until now they lived as shepherds, as caravan guides and merchants and lead a semi-nomadic life. We are currently carrying out studies to determine the genetic structure of this population. To facilitate the interpretation of these data, we are also trying to obtain other important parameters that pertain to migration processes and the genealogical structure of this populations. The data arise from three areas in Albania, the Republic of Macedonia and Romania. The inbreeding coefficient and the proportion of repeated pairs of surnames was calculated through the use of genealogies and the isonymy method. The difference between these three populations are due primarily to confounding by selection of mates and family composition.     

Genetic diversity and population structure of sickleweed (Falcaria vulgaris; Apiaceae) in the upper Midwest USA

Sickleweed (Falcaria vulgaris), an introduced species native to Europe and Asia, grows as an aggressive weed in some areas of the upper Midwest in the United States. We are reporting genetic diversity and population structure of sickleweed populations using microsatellite markers and nuclear and chloroplast DNA sequences. Populations showed high genetic differentiation but did not show significant geographic structure, suggesting random establishment of different genotypes at different sites was likely due to human mediated multiple introductions. Three genetic clusters revealed by microsatellite data and presence of six chlorotypes supported our hypothesis of multiple introductions. Chloroplast DNA sequence data revealed six chlorotypes nested into two main lineages suggesting at least two introductions of sickleweed in the upper Midwest. Some individuals exhibited more than two alleles at several microsatellite loci suggesting occurrence of polyploidy, which could be a post-introduction development to mitigate the inbreeding effects. High genetic variation in the introduced range attributable to multiple introductions and polyploidy may be inducing the evolution of invasiveness in sickleweed. Results of this study provide valuable insights into the evolution of sickleweed and baseline data for designing proper management practices for controlling sickleweed in the United States.     

Alternative approaches to population structure

There are three approaches to DNA identification: tectonic, halieutic and icarian, of which the tectonic is sensible, the halieutic impractical, and the icarian idiotic. The rationale and consequences of these approaches are detailed.Editor's commentsThe author captures the harsh tone that has often characterized the debate over the use of DNA for human identification. It should be mentioned that D.L. Hartl, E.S. Lander and R.C. Lewontin were invited to respond. The positions of these three authors are contained in their papers, listed in the Bibliography. Readers should note, in particular, Budowle and Lander (1994).     

Gene-history correlation and population structure

Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the correlation of gene histories in established demographic models for genetic evolution and show how to extend the analysis to more realistic (but more complicated) models of demographic structure. We identify two contributions to the correlation of gene histories in divergent populations: linkage disequilibrium, and differences in the demographic history of individuals in the sample. These two factors contribute to correlations at different length scales: the former at small, and the latter at large scales. We show that recent mixing events in divergent populations limit the range of correlations and compare our findings to empirical results on the correlation of gene histories in the human genome.     

The population structure of south-central Bougainville

The technique of population structure analysis is described and then applied to blood polymorphic, anthropometric, and demographic data collected from residents of south-central Bougainville Island, Territory of New Guinea. The results from these various analyses are relatively consistent, and support the idea that this theoretical model can be applied successfully to real sets of biological data and that valid conclusions concerning the breeding structure of human populations can be reached. A comparison of breeding structures from various parts of the world reveals how sharply subdivided the breeding structure in Melanesia is, and how relatively rapidly the coefficient of kinship declines over distance in that area.     

Genetic structure of the Udmurt population

Integrated study of the genetic structure of the Udmurt population with respect to different genetic systems has been performed. Data on the genes of genetic diseases, abiotic parameters analyzed by population statistic methods, and DNA polymorphism are summarized. The populations of six raions (districts) of Udmurt Republic (the Mozhga, Malaya Purga, Sharkan, Debesy, Igra, and Glazov raions) have been studied. The total population studied was 267 655 people (an urban population of 150 119 people and a rural population of 117 536 people), including 155 346 Udmurts. The population structure has been studied in six districts on the basis of the vital statistics, Crow’s indices, Malecot’s isolation by distance parameters, ethnically assortative marriage parameters, endogamy indices, inbreeding-endogamy (ie) indices, and frequencies of the genotype and allele frequencies of four DNA markers (17 alleles). The prevalences of hereditary diseases have been calculated for different population groups: urban and rural populations, Udmurts and other ethnic groups. These groups, especially the urban and rural populations, substantially differed from one another in the prevalences of autosomal dominant (AD) and autosomal recessive (AR) diseases. The correlation between the prevalence of AD and AR diseases and the ie index is positive and significant. The spectrum of hereditary diseases detected in six districts of Udmurtia comprises 149 diseases (80, 57, and 12 AD, AR, and X-linked diseases, respectively). Accumulation of individual diseases in districts of Udmurtia and accumulation of diseases in Udmurtia as compared to regions studied earlier has been found. Cluster analysis of the frequencies of genes of AD and AR diseases and DNA markers has determined the gene geographic position of Udmurts.     

Symbolic trephinations and population structure

The sample examined consists of 19 skulls with symbolic trephinations and 86 skulls without trepanations dated from the X century. Skulls were all excavated in the Great Hungarian Plain in the Carpathian Basin, which was occupied by the Hungarian conquerors at the end of the IX century. The variations of 12 cranial dimensions of the trephined skulls were investigated and compared to the skulls without trepanations after performing a discriminant analysis. The classification results evince that the variability of non-trephined skulls shows a more homogeneous and a more characteristic picture of their own group than the trephined samples, which corresponds to the notion, formed by archaeological evidence and written historical sources, of a both ethnically and socially differing population of the Hungarian conquerors. According to historical research, a part of the population was of Finno-Ugric origin, while the military leading layer of society can be brought into connection with Turkic ethnic groups. All the same, individuals dug up with rich grave furniture and supposed to belong to this upper stratum of society are primarily characterized by the custom of symbolic trephination, and, as our results demonstrate, craniologically they seem to be more heterogeneous.     

Size-frequency and population structure of brachiopods

The living terebratulids, Terabratulina unguicula, Terebratalia transversa, Laqueus vancouverensis, and the rhynchonelid Hemithiris psittacea were studied in the San Juan Islands, Washington, U.S.A. Those results and a review of a the literature lead to the conclusion that most brachiopod populations experience episodic recruitment at intervals which may be irregular. The occurrence of juveniles attached to adults, brooding, and bi- or multimodal size-frequency distributions demonstrate that, contrary to a previously suggested hypothesis, adult brachiopods do not generally exclude juveniles from the same area. The commony observed rarity of small individuals is regarded as a product of local recruitment failure due to patchy distribution of larvae; it does not justify the assumption that brachiopods are unaffected by high post-larval juvenile mortality. However, the frequent rarity of small individuals confirms that this cannot be used as a criterion of transport in assemblages of fossil brachiopods.     

Genetic structure of the Udmurt population

Integrated study of the genetic structure of the Udmurt population with respect to different genetic systems has been performed. Data on the genes of genetic diseases, abiotic parameters analyzed by population statistic methods, and DNA polymorphism are summarized. The populations of six raions (districts) of Udmurt Republic (the Mozhga, Malaya Purga, Sharkan, Debesy, Igra, and Glazov raions) have been studied. The total population studied was 267,655 people (an urban population of 150,119 people and a rural population of 117,536 people), including 155,346 Udmurts. The population structure has been studied in six districts on the basis of the vital statistics, Crow's indices, Malecot's isolation by distance parameters, ethnically assortative marriage parameters, endogamy indices, inbreeding-endogamy (ie) indices, and frequencies of the genotype and allele frequencies of four DNA markers (17 alleles). The prevalences of hereditary diseases have been calculated for different population groups: urban and rural populations, Udmurts and other ethnic groups. These groups, especially the urban and rural populations, substantially differed from one another in the prevalences of autosomal dominant (AR) and autosomal recessive (AR) diseases. The correlation between the prevalence of AD and AR diseases and the ie index is positive and significant. The spectrum of hereditary diseases detected in six districts of Udmurtia comprises 149 diseases (80, 57, and 12 AD, AR, and X-linked diseases, respectively). Accumulation of individual diseases in districts of Udmurtia and accumulation of diseases in Udmurtia as compared to regions studied earlier has been found. Cluster analysis of the frequencies of genes of AD and AR diseases and DNA markers has determined the gene geographic position of Udmurts.     

Origins and population genetics of weedy red rice in the USA

Weedy red rice (Oryza sativa spontonea) is a persistent and problematic weed of rice culture worldwide. A major hypothesis for the mechanism of production of this weed in South and Southeast Asia is hybridization between cultivated rice (Oryza sativa) and wild rice (Oryza rufipogon). However, weedy red rice can often be found outside the range of O. rufipogon leaving questions on the origin and process behind weedy rice infestations. In the USA, weedy red rice was first documented as early as 1846 and has continued to affect rice production areas. In this study, we attempt to identify the origin and population structure of weedy red rice sampled from the USA using both DNA sequence data from a neutral nuclear locus as well as microsatellite genotype data. Results suggest that two major accessions of weedy rice exist, strawhull and blackhull, and these forms may both hybridize with the cultivated rice of the USA, O. sativa japonica. Using population assignment of multilocus genotype signatures with principal component analysis and structure, an Asian origin is supported for US weedy rice. Additionally, hybridization between strawhull and blackhull varieties was inferred and may present the opportunity for the production of new weedy forms in the future.     

Genetic diversity,effective population size,and structure among black bear populations in the Lower Mississippi Alluvial Valley,USA

Multiple small populations of American black bears Ursus americanus, including the recently delisted Louisiana black bear subspecies U. a. luteolus, occupy a fragmented landscape in the Lower Mississippi Alluvial Valley, USA (LMAV). Populations include bears native to the LMAV, bears translocated from Minnesota during the 1960s, and recently reintroduced and colonizing populations sourced from within the LMAV. We estimated population structure, gene flow, and genetic parameters important to conservation of small populations using genotypes at 23 microsatellite markers for 265 bears from seven populations. We inferred five genetic clusters corresponding to the following populations: White River and western Mississippi, Tensas River and Three Rivers, Upper Atchafalaya, Lower Atchafalaya, and Minnesota. Upper Atchafalaya was suggested as the product of Minnesota-sourced translocations, but those populations have since diverged, likely because of a founder effect followed by genetic drift and isolation. An admixture zone recently developed in northeastern Louisiana and western Mississippi between migrants from White River and Tensas River, resulting in a Wahlund effect. However, gene flow among most populations has been limited and considerable genetic differentiation accumulated (global F_ST?=?0.22), particularly among the three Louisiana black bear populations that existed when federal listing occurred. Consistent with previous bottlenecks, founder effects, and persisting isolation, all LMAV bear populations had low genetic diversity (A_R?=?2.08–4.81; H_E?=?0.36–0.63) or small effective population size (N_E?=?3–49). Translocating bears among populations as part of a regional genetic restoration program may help improve genetic diversity and increase effective population sizes.     

Genetic structure in an expanding cervid population after population reduction

The Norwegian red deer population (Cervus elaphus) was from the mid eighteenth to the early twentieth century drastically reduced in size and distribution but has the last century expanded both demographically and spatially. We have investigated genetic variation, differentiation and admixture in this spatially expanding ungulate population, using 14 microsatellites. The present genetic structure is moderate to strong with an average F _ST = 0.08. Low M-ratios indicate loss of genetic variation in all localities and signals of a recent bottleneck was identified in 14 of 15 localities. Genetic distances between the localities indicate two main routes of dispersal during expansion, from the north–west and south–west, respectively. Bayesian assignment tests verify a break of the dataset in two, and demonstrate 99.9% probability for the existence of five sub-populations, which coincide well with five relict populations described by historic records. Computer simulations suggest that the observed genetic differentiation is recent rather than ancient, and that it may be explained by models of fragmentation or of founder events and subsequent merging rather than by models of recent bottlenecks in some particular demes within an ancient genetic structure.     

A population approach to vegetation structure

Abstract

A synthesis is presented of some research results on the structure and dynamics of populations with respect to the phytocoenosis structure. The first aspects to be considered are concerned with the dynamism, distribution and reproductive strategy of Anemone nemorosa: the vegetation structure either favors or inhibits the various reproductive strategies, thereby influencing the distribution pattern of the species. The second area of the present study is the demography and quantitative structure of Cytisus sessilifolius populations with respect to the problematic of secondary successions: the first results obtained open up interesting prospectives on the relationship between the vegetation dynamics and the frutescent populations structure.     

Habitat-dependent population regulation and community structure

Summary Density-dependence provides a causal link between processes acting at different levels of ecological organization. The linkage between density-dependent habitat use, population regulation and community organization is examined on the basis of qualitative and quantitative differences between habitats. These differences are expressed as characteristic shapes on isodars which are lines of equal fitness, and are plotted in density space as lines at every point of which the fitness of individuals in one habitat is equal to that of individuals in another. Isodars can be constructed for single species or modified to include the effects of interacting species. Isodars are easily analyzed by linear regression to differentiate between alternative modes of population regulation and to suggest patterns of community structure. Different isodars are causally related to different kinds of community structure, and suggest the existence of four new forms of community organization; equal, differential, switched and mixed preferences. A preliminary isodar analysis on a common rodent species demonstrates that population regulation depends upon habitat, and that mixed preferences probably organize the rodent community. Habitat-dependent population regulation has farreaching implications to studies of temporal and spatial scale, and to all ecological processes that are density-dependent.