Genetic and cultural transmission in Sicily as revealed by names and surnames

The study of names as cultural characters and of surnames, which behave like genetic markers, is useful for comparing cultural and genetic transmission. Genetic transmission has a unique vertical component, which also can be present in the transmission of cultural traits associated with a horizontal (or epidemic) component resulting from local customs or fashion. Our aims in this study are to infer genetic patterns in Sicily from surnames and names and to evaluate and compare the consequences of vertical versus horizontal transmission of cultural markers. Names and surnames of 88,383 consanguineous spouses collected in 16 dioceses of Sicily were analyzed by multivariate analysis to reveal and compare the geographic clusters obtained from both sets of data. As a result, both data sets indicate a major separation between the eastern and the western region of Sicily. Also, distance matrices obtained from names are highly correlated with those from surnames. But names seem to form fewer and larger geographic clusters, whereas surnames are more greatly subdivided into smaller clusters. The most common male names present a different pattern from surnames. Vertical transmission is the cause of the similarity of the main geographic patterns of names and surnames and their correspondence with findings from geography of genes, and horizontal cultural transmission explains the major differences. Furthermore, the genetic and cultural affinities can be correlated with the historical background of Sicily.     

RARE ALLELES AS INDICATORS OF GENE FLOW

A. method for estimating the average level of gene flow in a subdivided population, as measured by the average number of migrants exchanged between local populations, Nm, is presented. The results from a computer simulation model show that the logarithm of Nm is approximately linearly related to the logarithm of the average frequency of private alleles, p?(1), in a sample of alleles from the population. It is shown that this result is relatively insensitive to changes in parameters of the model other than Nm and the number of individuals sampled per population. The dependence of the value of p?(1) on the numbers of individuals sampled provides a rough way to correct for differences in sample size. This method was applied to data from 16 species, showing that estimated values of Nm range from much greater than 1 to less than 0.1. These results confirm the qualitative analysis of Slatkin (1981). This method was also applied to subsamples from a population to show how to measure the extent of isolation of local populations.     

Estimation,variance and optimal sampling of gene diversity II. Diploid locus

Nei's analysis of diversity at a diploid locus is extended to a population subdivided into a large number of subpopulations. The diversities and the heterozygotes frequency are defined with respect to the total population and unbiasedly estimated in a two-stage random cluster sampling. The fixation indices F _IS, F _IT andF _ST are derived, then inter- and intra-population variances of the estimated parameters are studied. We show that there is a unique sample size per population which yields the best accuracy in estimatingF _ST and F _IS, respectively, at a given locus. These results are illustrated with an analysis of DNA diversity in a forest tree and compared to those obtained under the Hardy-Weinberg assumption.     

Interpopulation relationship by isonymy: application to ethnosocial groups and illegitimacy

The application of the isonymic method to establish interpopulation relationships is made difficult by such factors as: (1) a small population size; (2) the subdivision of the population into ethnosocial groups; and (3) the existence of individuals born extramaritally. The present study analyzes the validity of the isonymy method in populations where such difficulties exist. Lasker's R(ij) relationship coefficients were calculated in base to marital records from six Pocho parishes (Argentina) for the period 1766 to 1840. Three endogamous ethnosocial groups were considered-Spanish, American Indians, "Mestizos"--and a fourth group combining mates of the three previous groups. For each ethnosocial category, and taking into account paternal surnames, maternal surnames (both for legitimate and illegitimate mates), and whole surnames merged, R(i) interparish relationship matrices were obtained. All these matrices were correlated by means of the Mantel test. Maternal surnames of illegitimate mates show a similar pattern to the maternal surnames of legitimate mates and to all surnames of each category. Groups with larger sample size in every parish intercorrelate regardless of ethnosocial category. Results suggest the convenience of maximizing the sample size and using maternal surnames in populations with high illegitimacy.     

Genetic structure of the Utah Mormons: isonymy analysis

Isonymy analysis is reported for a sample of 188,895 marriages extracted from the Utah Genealogical Database. Inbreeding rates estimated by isonymy are low, ranging from 0.005 for the earliest marriage cohort (1800-1809) to 0.0008 in the most recent cohort (1950-1959). The inbreeding values decrease considerably through time, but they are consistently higher than inbreeding values estimated from pedigrees. Several explanations are offered for this, including polyphyletism of surnames and the presence of Scandinavian patronyms in this population. Random isonymy between subdivisions is also compared with random kinship estimated from migration matrices. In terms of within-subdivision kinship, the two approaches yield similar results. However, the results are quite dissimilar for between-subdivision kinship. This reflects the recent and nonrandom settlement of Utah by different ethnic groups with different surname distributions. In later time periods, the correlations between the two types of kinship estimates increase, showing that migration patterns (which are strongly determined by geographic distance) exert an increasing influence on the distribution of surnames. Logistic regression is performed on a subset of marriages (n = 88,202), using isonymous vs. nonisonymous marriage as the dependent variable. The independent variables are year of marriage, geographic distance between husband's and wife's birthplaces, endogamous vs. exogamous marriage, and population sizes of husband's and wife's birthplaces. Year of marriage and geographic distance are shown to be significant independent predictors of isonymous marriage.     

Frequency distributions from birth,death, and creation processes

The time-dependent frequency distribution of groups of individuals versus group size was investigated within a continuum approximation, assuming a simplified individual growth, death and creation model. The analogy of the system to a physical fluid exhibiting both convection and diffusion was exploited in obtaining various solutions to the distribution equation. A general solution was approximated through the application of a Green's function. More specific exact solutions were also found to be useful. The solutions were continually checked against the continuum approximation through extensive simulation of the discrete system. Over limited ranges of group size, the frequency distributions were shown to closely exhibit a power-law dependence on group size, as found in many realizations of this type of system, ranging from colonies of mutated bacteria to the distribution of surnames in a given population. As an example, the modeled distributions were successfully fit to the distribution of surnames in several countries by adjusting the parameters specifying growth, death and creation rates.     

Estimation,variance and optimal sampling of gene diversity

An extension of Nei's analysis of diversity in a subdivided population is proposed for a haploid locus. The differentiation G _STbecomes a natural extension of Wright's F _STand generalizes Weir and Cockerham's parameter of co-ancestry by relaxing the assumption of identical correlation for all the alleles. Inter- and intrapopulation variances of the estimated diversities and differentiation are derived. Finally, the optimal sampling strategy for measuring G _STwhen a fixed number of individuals can be analysed is considered. It is shown that, at a given locus, there is a unique sample size per population which yields the smallest variance of G _ST,regardless of the number of populations studied. These theoretical developments are illustrated with an analysis of chloroplast DNA diversity in a forest tree. The results emphasize the necessity of sampling many populations, rather than many individuals per population, for an accurate measurement of the subdivision of gene diversity at a single locus.     

A measure of species diversity related to the lognormal distribution of individuals among species

An investigation has been made of the relation between species diversity and the lognormal distribution of individuals among species, using phytoplankton samples from the Indian Ocean. The area under the truncated lognormal curve representing a sample gives the total number of species, S, while the logarithmic standard deviation, σ, gives a measure of the scatter of distribution of individuals among species, the other factor affecting diversity. Using a method described by Hald, truncated lognormal curves were fitted to the phytoplankton data and estimates obtained for the mean, ξ, the logarithmic standard deviation, σ, the number of species in the modal octave, N_o, and the number of species in the population universe, N. Since one is interested in a sample only in so far as it reflects the properties of the population from whence it came, estimated population parameters were used to define measures of diversity by which means it was hoped to obtain a diversity index independent of sample size, i.e., a diversity value related more to the population than to the sample.     

Surnames in Bolivia: A study of the population of Bolivia through isonymy

In Bolivia, the Hispanic dual surname system is used. To describe the isonymic structure of Bolivia, the surname distribution of 12,139,448 persons registered in the 2006 census data was studied in 9 districts and 112 provinces of the nation, for a total of 23,244,064 surnames. The number of different surnames found was 174,922. Matrices of isonymic distances between the administrative units (districts and provinces) were constructed and tested for correlation with geographic distance. In the 112 provinces, isonymic distances were correlated with geographic distance (r = 0.545 ± 0.011 for Euclidean, 0.501 ± 0.012 for Nei's, and 0.556 ± 0.010 for Lasker's distance). The multiple regression of the surname effective number (α), equivalent to the allele effective number in a genetic system, was nonsignificant on latitude and longitude; however, it was highly significant and negative on altitude (r = ?0.72). Because the Andes extend from north to south in west‐central Bolivia, random inbreeding was lowest in the eastern districts, and highest in mountainous western Bolivia. Average α for the provinces was 122 ± 2; for the districts, it was 216 ± 29, and for the whole of Bolivia it was 213. The geographical distribution of α in the provinces is compatible with the settlement of subsequent groups of migrants moving from east and north toward the center and south of Bolivia. The relative frequency of indigenous surnames is correlated positively with altitude. This suggests that the country was populated by recent low‐density demic diffusion over a low‐density indigenous population. This may have been a common phenomenon in the immigration to tropical South America. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.     

EFFECTIVE POPULATION SIZE IN A CONTINUOUSLY DISTRIBUTED POPULATION

An individual-based simulation model was created to examine genetic variability, time until fixation and spatial genetic structure in a continuously distributed population. Previous mathematical models for continuously distributed populations have the difficulty that the assumption of independent reproduction and independent dispersal of offspring cause clumped spatial distribution and thus violate an assumption of random spatial distribution. In this study, this problem is avoided by considering the dispersal behavior of offspring. The simulation results showed that the inbreeding effective population size estimated by the rate of decrease of heterozygosity during the first 15 generations corresponds to the neighborhood size calculated by the standard deviation of the dispersal distance (σ_T). This inbreeding effective population size does not greatly change with the area of simulation when the densities and σ_T are the same. However, the inbreeding effective population size estimated by heterozygosity using the first 500 generations is larger than the neighborhood size calculated by the dispersal distance and increases with the area of simulation with the same densities. The variance effective population size, estimated by time until fixation of alleles, increases with dispersal distance (σ_T) and with the area of simulation given the same densities. The inbreeding effective population size and variance effective population size were smaller than the actual population size unless σ_T is sufficiently large (2 σ_T > approximate L/2, where L is a side of the simulation square).     

Isonymic relationships in ethno-social categories (Argentinian colonial period) including illegitimate reproduction

Surnames provide a useful method to study the structure of human populations for which biological data are not available. The isonymic method has had multiple applications, but difficulties emerge when dealing with groups where extramarital reproduction is common and the sample size is small, and even more so when only paternal surnames are taken into account.Therefore, it could be of interest to retain female surnames, including those of unmarried mothers. This study was carried out using all birth records froman Argentinian population in the colonial period, which was characterized by the presence of different ethno-social groups (Spanish, Indian and 'Mestizo'or mixed Spanish-Indian) and various reproductive patterns regarding legitimacy. Coefficient of relationship by isonymy (Ri) kinship matrices between geographical populations were obtained, and the results derived from sets of surnames (paternal, maternal of legitimate and illegitimate children,and all surnames in the registers) compared. The results show similar surname distribution regardless of the set of surnames and group considered.Kinship Ri matrices using paternal surnames, maternal surnames of legitimate children, maternal surnames of illegitimate children, and the set of whole surnames showed the same relationships among populations, indicating a similar pattern for Spanish, Indian and Mixed ethno-social groups. Mantel test correlation between all pairs of matrices was significant in all different ethno-social groups. The results suggest that in populations with high illegitimacy, such as that studied here, it is possible to include maternal surnames, even corresponding to single mothers, in order to consider total reproduction and therefore maximize sample size.     

The gene pool of the Belgorod oblast population: I. Differentiation of all district populations based on anthroponymic data

The gene pool of the entire population of all the 21 raions (districts) of the Belgorod oblast (region) has been studied using anthroponymic data. Considerable geographic variations of the number of surnames and the degree of population subdivision (0.00003 < f _r ^* < 0.00125) in the 21 districts have been demonstrated. Districts with low population subdivision levels are mainly located in the central and southwestern raions of the Belgorod oblast, contain an urbanized area (city), and border on Ukraine (they are characterized by a considerable Ukrainian immigration). Urbanization significantly affects the population structure of the Belgorod oblast. In urbanized districts, rural populations lack the relationships between the population size, number of surnames, and population subdivision level (f _r).     

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.     

Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detection

Identifying local adaptation is crucial in conservation biology to define ecotypes and establish management guidelines. Local adaptation is often inferred from the detection of loci showing a high differentiation between populations, the so‐called F_ST outliers. Methods of detection of loci under selection are reputed to be robust in most spatial population models. However, using simulations we showed that F_ST outlier tests provided a high rate of false‐positives (up to 60%) in fractal environments such as river networks. Surprisingly, the number of sampled demes was correlated with parameters of population genetic structure, such as the variance of F_STs, and hence strongly influenced the rate of outliers. This unappreciated property of river networks therefore needs to be accounted for in genetic studies on adaptation and conservation of river organisms.     

Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods,sample size and population structure

The distribution of fitness effects (DFE) of new mutations has been of interest to evolutionary biologists since the concept of mutations arose. Modern population genomic data enable us to quantify the DFE empirically, but few studies have examined how data processing, sample size and cryptic population structure might affect the accuracy of DFE inference. We used simulated and empirical data (from Arabidopsis lyrata) to show the effects of missing data filtering, sample size, number of single nucleotide polymorphisms (SNPs) and population structure on the accuracy and variance of DFE estimates. Our analyses focus on three filtering methods—downsampling, imputation and subsampling—with sample sizes of 4–100 individuals. We show that (1) the choice of missing-data treatment directly affects the estimated DFE, with downsampling performing better than imputation and subsampling; (2) the estimated DFE is less reliable in small samples (<8 individuals), and becomes unpredictable with too few SNPs (<5000, the sum of 0- and 4-fold SNPs); and (3) population structure may skew the inferred DFE towards more strongly deleterious mutations. We suggest that future studies should consider downsampling for small data sets, and use samples larger than 4 (ideally larger than 8) individuals, with more than 5000 SNPs in order to improve the robustness of DFE inference and enable comparative analyses.     

Portuguese migration to the Canary Islands: an analysis based on surnames

As a part of a wider analysis of population and genetic exchange between Spain and Portugal, the long-term pattern of Portuguese immigration to the Canary Islands was studied by means of the frequency of Portuguese surnames. A database of 1,995,833 individuals was obtained from the Spanish National Statistics Institute (2006). Among the 826 most frequent surnames to appear, 79 surnames of Portuguese origin were selected. The distribution of these surnames by municipalities and islands, the Fisher index of diversity, and the Lasker inter-population relationship coefficients R(ij) were considered. These coefficients were inter-correlated and correlated with other variables that could have influenced the distribution of surnames. From the observed distribution of the frequency of surnames, a non-random migration pattern conditioned by economic factors was found. The greatest diversity of surnames existed in cane cultivating areas after the first arrival of Portuguese immigrants. A later dispersion of surnames among islands was correlated with the inter-island geographic distances. In some islands the arrival of new immigrants continued due to their strategic location within the Canary archipelago. The Canary Islands reveal a high frequency and diversity of Portuguese surnames. The results also prove a heterogeneous distribution of these surnames throughout the archipelago. In contrast to the Portuguese archipelagos, some Canary localities have received immigrants continuously because of their economic importance in sugar cane cultivation and strategic geographic location on the maritime routes to Africa and America.     

On a Martingale Approach for the Estimation of the Parameters of a Bivariate Carrier Borne Epidemic Model in Presence of a Linear Relationship Between Carriers and Suspectibles

The present investigation is to waive the restriction of PICARD (1980) viz. x₀ + y₀ = n (the size of the population) for the obvious reason that the size of the susceptible population exposed to risk will depend on the growth rate of carriers and to evolve a simple methodology for the estimation of parameters of Downton's bivariate model. A lienar relationship of X_t on Y_t enabled to predict the size of the susceptible population exposed to the risk by a given number of carriers at any time. The same linear equation, when incorporated in Downton's bivariate model has generated the marginal process of Y_t. Using several Martingales constructed on the basis of the above marginal process, the minimum number of carriers that can bring out an epidemic and various parameters of Downton's model have been estimated.     

Evolution in populations of Swedish sand lizards: genetic differentiation and loss of variability revealed by multilocus DNA fingerprinting

The Swedish sand lizard (Lacerta agilis) is a relict species from the period of warmth following the last glacial episode and has a fragmented distribution in central Sweden and a more continuous distribution in the southern part of the country. We used this model system of colonization–extinction for a study of genetic variability within and among Swedish populations from different parts of the distribution range using multilocus DNA fingerprinting. The results from the Swedish populations are then contrasted with those from a large Hungarian population in the centre of the species geographical distribution range, which is likely to closely resemble the ancestral founding population of Sweden. Swedish populations have a low level of genetic variability compared with the Hungarian reference population, which showed a genetic variability within the range described for outbred populations. Within the Swedish populations, the average bandsharing was 0.61, the mean heterozygosity 0.45 and the estimated number of alleles 2.7. The figures for the Hungarian population were a bandsharing of 0.19, a heterozygosity of 0.89 and an estimated number of alleles of 9.8. A population bottleneck, common to all Swedish sand lizards, is indicated by less than 20% of the alleles in the Hungarian population being retained in the Swedish populations, and higher bandsharing similarity between different Swedish populations (0.33) as opposed to the Hungarian population (0.19). The limited variability found in Swedish sand lizards is strongly subdivided between populations, with an average F_ST of 0.32, indicating a very limited gene flow between the isolated populations, as well as between populations in the region where the sand lizard has a more or less continuous distribution (F_ST = 0.41).     

Population structure of São Miguel Island, Azores: a surname study

The knowledge of a population structure may constitute a powerful tool for mapping genes underlying susceptibility to Mendelian and complex diseases. To obtain a better understanding of the population structure of S?o Miguel Island (Azorean Archipelago, Portugal), we carried out a surname survey using the surnames listed in the most recent telephone book (2001). We identified 1315 different surnames in a total of 27,621 subscribers. The frequency of the different surnames was used to calculate the following parameters: isonymy (I), random component of inbreeding (FST), genetic diversity according to Fisher (alpha), migration rate according to Karlin-McGregor (v) and Nei's genetic distance. Eleven localities were selected, according to population size and geographic distribution, for analysis using the above parameters. Our results show that 51% of Salga's population and 52% of Sete Cidades's population are represented by six and eight surnames, respectively. These figures demonstrate the effective isolation of these two small places, which are located at opposite ends of S?o Miguel Island. Salga, Achada, and Sete Cidades present the lowest values of Fisher's alpha, indicating less genetic diversity. In contrast, the capital, Ponta Delgada, presents the highest value of alpha (78.13), indicating more genetic diversity. Our data indicate that the clustering of the localities corresponds to the geographic features of the island, where localities close together tend to share similar surnames. In conclusion, the population of S?o Miguel is relatively homogeneous and may constitute an ideal model for genetic mapping studies.