Isolation by distance and correlation analysis of distance measures in the study of population structure: example from the Island of Hvar

Assessment of the population structure on the island of Hvar is based on the analysis of Malécot's isolation by distance model. We have tested the fit of the model by regression analysis of different measures of similarity (genetic kinship) and distance [Hamming's HSM distance for linguistic data; Mahalanobis's D2 distances for anthropometric head and body dimensions, radiogrammetric dimensions of metacarpal bones, physiological (cardiorespiratory) traits, and quantitative dermatoglyphic properties of the digitopalmar complex; and Edwards's E2 for frequencies of erythrocyte antigens]. Good fit of the model for linguistic and anthropometric data, which was demonstrated in previous studies on other eastern Adriatic populations, is confirmed. We compared parameters of the model with those already published for various populations in the eastern Adriatic and other parts of the world. We also evaluated the pattern of correlations between different measures of geographic, biological, and sociocultural distances through principal components analysis and interpreted the results within the context of microevolutionary theory and the population's ethnohistorical background.     

Isolation by distance in Middle Dalmatia-Yugoslavia

Parameters of Malécot's isolation-by-distance model are estimated for biological (anthropometric head and body dimensions, morphometric dimensions of metacarpal bones, quantitative and qualitative dermatoglyphic traits, and physiological/cardiorespiratory/variables) and linguistic distances and migrational kinship on the island of Korcula and the Peljesac peninsula in Middle Dalmatia, Croatia, Yugoslavia. Resulting parameters and the fit of the model are compared, for both regions, as well as with results of similar analysis in other parts of the world. The fit of the model is highly significant for migrational kinship and linguistic distances and less so for biological traits. Differences between these two populations, which live under basically similar ecological conditions, are explained by variation in biological and sociocultural history.     

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.     

Sets of complementary phenotypic relationships across five isolated populations: Traces of expression of different gene complexes?

The aim of this study is to search for certain repeating phenotypic patterns, i.e. sets of complementary relationships across five isolated populations, which may represent the traces of expression of different genes or gene complexes. The study was conducted among isolates of five island populations of eastern Adriatic, Croatia, and the data were collected between 1979 and 1990. Selected phenotypic characteristics included measures of biological distances (e.g. anthropometrical body and head distances, physiological, dermatoglyphic and radiogrammetric bone distances), while other examined traits included sociocultural (linguistic), bio-cultural (migrational kinship) and genetic distances. The sample consisted of 6,286 examinees from 43 villages of five isolate populations. Correlations between distance matrices based on examined traits were analyzed in each of five populations using Mantel's test of matrix correspondence, and factor analysis (rotated principal component) was then performed over obtained correlation matrices. The results showed that there were several consistent and significant correlations between some analyzed traits across all of the studied isolate populations, which might indicate their regulation by the shared gene complexes or genome regions. The analyses identified three main clusters of correlations in all five isolate populations: the first one containing anthropometric measures (body and head measures and physiological properties in both sexes), the second one containing geographic distance-related traits (migrational kinship, linguistic and genetic distances), and the third one containing dermatoglyphic properties and radiogrammetric bone measures in both sexes. The higher order varimax rotation over the matrix of factor correlations revealed that the primary source of variation within all five analyzed populations was not sex-related, but rather variable-specific.     

Isolation by distance on the Island of Korcula: correlation analysis of distance measures

Within the framework of holistic anthropological investigations of the rural populations on the Island of Korcula, various measures of biological distances between eight villages were estimated (Mahalanobis' D2 for anthropometric, physiological, and dermatoglyphic traits); socio-cultural similarities and distances were determined (kinship coefficient estimated from migrational data and Hemming similarity measure estimated from linguistic data). A matrix of Spearman's rank correlation coefficients among these measures demonstrated a pattern of interdependencies, which we analysed further by principal components analysis. The first component reflects the cumulative effect of different processes acting on the initial gene distribution over a long period of time; the second component represents initial population structure; and the third component reflects recent migration influences.     

Alternative bioassays of kinship between loci.

In this study four asymptotically equivalent estimates of kinship are derived, in the general case and for kinship between multiallelic loci. Two estimates based on chi 2 agree closely, with the Shannon estimate giving the smaller variance. The PAH, GH, GM, and HBB systems conform to a recombinational model with an evolutionary size of approximately 4,000 and a ratio of recombination to physical distance of approximately 1.4 X 10(-5) morgans/kb, as predicted on the basis of the genetic and physical lengths of the human genome. The INS and D11S12 systems have a much more rapid decline of kinship with physical distance, suggesting overlapping RFLPs (unrecognized allelism), recombinational hot spots, or selection. Sources of error in predicting kinship over small distances are discussed.     

Genetic and socio-cultural differentiation in the aborigines of Arnhem Land, Australia

Four tribes of Arnhem Land were surveyed for dermatoglyphics; based on pattern intensity indices, total ridge-counts, and a distance statistic combining the two, it was shown that the tribes can be arranged into western (Tiwi, Gunwinggu) and eastern (“Murngin” and Andilyaugwa) groups. This substantiates observations made on Arnhem Land by linguists and social anthropologists. From a survey of allele frequency traits of blood factors and P.T.C. tasting, distance statistics were computed between the four tribes. These confirmed the relative isolation of the extreme Arnhem Land tribes. Distance statistics were also computed between the four tribes and two Central Australian tribes, the Aranda and Wailbri. The Aranda and “Murngin” were relatively close together agreeing with theories that the Aranda are derived from a not too remote southwards migration from north Arnhem Land, as supported by linguistic data. Correlations between the biological, geographical and linguistic distances were positive, and generally agreed with the expectation that socio-cultural and linguistic barriers are important in regulating gene flow between populations. This study emphasizes the need to consider biological distances in association with ecological and socio-cultural factors.     

Genetic structure and heterozygosity in the kuru region,Eastern Highlands of New Guinea

Genetic structure of 20 of the 37 linguistic groups in the Eastern Highlands of New Guinea including the kuru region is analyzed using information on blood groups and serum protein polymorphisms. The average individual is heterozygous at 28.6% of loci and the average number of alleles per locus is 1.234. Coefficients of kinship for linguistic groups range from 0.005 for the sweet potato cultivating North Fore to 0.075 for the isolated Pawaians whose dietary staple is sago and who depend more on hunting and gathering. As one selects linguistic groups with smaller and smaller population size and increasing isolation, one finds that kinship coefficients rise as much as tenfold, but there is no concomitant loss of heterozygosity or trend toward fixation of alleles. Genetic relationships established by genetic distance trees and by principal components analysis are comparable and are consistent with other anthropological observations.     

Haplotype kinship for three populations of the Goettingen minipig

To overcome limitations of diversity measures applied to livestock breeds marker based estimations of kinship within and between populations were proposed. This concept was extended from the single locus consideration to chromosomal segments of a given length in Morgan. Algorithms for the derivation of haplotype kinship were suggested and the behaviour of marker based haplotype kinship was investigated theoretically. In the present study the results of the first practical application of this concept are presented. Full sib pairs of three sub-populations of the Goettingen minipig were genotyped for six chromosome segments. After haplotype reconstruction the haplotypes were compared and mean haplotype kinships were estimated within and between populations. Based on haplotype kinships a distance measure is proposed which is approximatively linear with the number of generations since fission. The haplotype kinship distances, the respective standard errors and the pedigree-based expected values are presented and are shown to reflect the true population history better than distances based on single-locus kinships. However the marker estimated haplotype kinship reveals variable among segments. This leads to high standard errors of the respective distances. Possible reasons for this phenomenon are discussed and a pedigree-based approach to correct for identical haplotypes which are not identical by descent is proposed.     

Taxonomic congruence in Eskimoid populations.

The study compares distance relationships in Eskimoid populations based on metric and attribute data with linguistic relationships based on structural and lexicostatistical data. Taxonomic congruence and the non-specificity hypothesis are investigated by matrix correlations and by a clustering procedure. The matrix correlation approaches employed are the Pearson product-moment correlation coefficient and the Spearman rank-order correlation coefficient. An unweighted pair-group clustering procedure provides a visual comparison of biological and linguistic relationships. Data consist of 74 craniometric measurements and 28 cranial observations taken on 12 Eskimoid populations. Mahalanobis' D2 and Balakrishnan and Sanghvi's B2 were used to compute the metric and attribute distances, respectively. The results indicate that a strict adherence to the non-specificity hypothesis is untenable. Also, there is better concordance between the sexes for metric distances than for attribute distances, and the metric data are more concordant with linguistic relationships than are the attribute data.     

Genetic data on Alghero population (Sardinia): Contrast between biological and cultural evidence

Data on 20 genetic polymorphisms (61 alleles) in the Algehero population on the northwestern coast of Sardinia are presented and discussed in relation to its linguistic peculiarity inside the island. Since the Aragonese (Spain) conquest of Sardinia in the 13th century, the Catalan language, the same as that spoken in Northeastern Spain and certain districts of Southern France, has been used in Alghero even until today. Analysis for heterogeneity of gene frequency distributions indicates that the genetic information obtained on Alghero is adequate to discriminate Sardinians from other neighbouring populations. Genetic variation between populations measured through genetic distances and principal-component analysis shows that the present-day population of Alghero is much closer genetically to Sardinians than to Catalonians. Our genetic results do not support any interpretation of the linguistic affinities between Alghero and Catalonia at present as indicative of biological kinship. © 1994 Wiley-Liss, Inc.     

Bioassay of kinship in Micronesia

Phenotype bioassay agrees with clan isonymy, anthropometrics, and migration in estimating the mean kinship within a Micronesian population, relative to large distances, as 0.05. Various calculations of occupancy for the Eastern Carolines from ethnohistory, kinship, and glottochronology average around 1,000 years. Estimates of isolation by distance are in agreement for different indicators of population structure. Problems of kinship bioassay are discussed.     

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.     

Genetic differentiation among Sardinian villages.

The present study reports an analysis of genetic differentiation among 14 Sardinian villages located mainly in the center of the island. Chi-square tests show significant genetic heterogeneity among villages, and analyses by F- and R- statistics indicate an essentially random pattern of differentiation for all alleles. Using the kinship methods of Morton, a matrix, R, with elements rij describing the correlations between the gene frequencies of villages i and j is obtained. Use of Malécot's formula relating the rij to the geographic distances between villages shows a rapid decline of kinship with increasing distance but reveals essentially no relationship for distances over 40 km. Rotation of a two-dimensional reduction of the kinship matrix to maximum congruence with the geographic distances indicates that about 25% of the genetic distances can be accounted for by the geographic location of the villages. Isolation due in part to cultural factors, genetic drift, and special local or regional patterns of villages associations appear to be involved in the pattern of genetic variation.     

Palmar pattern frequencies as indicators of relationships among Sardinian linguistic groups of males

Palmar pattern frequencies were used to calculate distance coefficients between Sardinian linguistic groups of males for the purpose of verifying, by means of correlation matrix analyses, whether or not the dermatoglyphic traits considered lead to a reliable identification of the biological relationships on the basis of the linguistic backgrounds of these groups. With Sanghvi's as the distance measure and by using palmar pattern frequencies in the Hy area, Th/I, II, III, and IV interdigital areas and all traits together for palms combined or separated were calculated dermatoglyphic distance measures. Mantel tests of matrix correspondence showed that, by using palmar pattern frequencies in the Th/I interdigital area (palms combined), in the II, III, and IV interdigital areas, or all traits together for palms combined and separated, statistical significance between dermatoglyphic and linguistic distances can be obtained, even when the effect of geography is removed; there is no statistically significant correspondence between geographic and dermatoglyphic distance matrices, even when the effect of language is removed. The results obtained in this study by means of the Mantel test procedure demonstrate that the dermatoglyphic traits analyzed, with the exception of palmar pattern frequencies in the Hy area and in the Th/I interdigital area for plams separated when these areas are used singly, can be considered as a good set of variables to use in finding biological relationships between Sardinian linguistic groups of males examined on the basis of their linguistic backgrounds.     

Genetic and linguistic coevolution in Northern Island Melanesia

Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may emphasize more ancient demographic events, including population splits associated with the early colonization of major world regions.     

Genetic distances,geographic distances and migration between four villages of a single region in Slovakia

Genetic microdifferentiation has been studied among four endogamous villages of the Bystrica Valley in the Kysuce region of northwest Slovakia, which arose from a single ancestral population about 15 generations ago. Genetic distances and sample kinship between the villages were estimated from the gene frequencies of seven serum-group and isozyme genetic markers. The genetic distance was found to correlate positively (though insignificantly) with the geographic distance, and negatively with the intensity of migration between villages; the sample kinship correlates negatively with geography as well as with the genetic distance. This pattern of genetic structure within the area indicates that the genetic variation among the villages is attributable to the genetic drift. Thus, drift has brought about a detectable differentiation in the area within a limited period of approximately 300 years, in spite of the fact that the villages were not completely genetically isolated from each other. The finding of a negative correlation between the sample kinship and geographic distance indicates that the recent breakdown of genetic isolates in Slovakia is likely to be accompanied with an overall increase of heterozygosity.     

A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito

Understanding past dispersal and breeding events can provide insight into ecology and evolution and can help inform strategies for conservation and the control of pest species. However, parent–offspring dispersal can be difficult to investigate in rare species and in small pest species such as mosquitoes. Here, we develop a methodology for estimating parent–offspring dispersal from the spatial distribution of close kin, using pairwise kinship estimates derived from genome‐wide single nucleotide polymorphisms (SNPs). SNPs were scored in 162 Aedes aegypti (yellow fever mosquito) collected from eight close‐set, high‐rise apartment buildings in an area of Malaysia with high dengue incidence. We used the SNPs to reconstruct kinship groups across three orders of kinship. We transformed the geographical distances between all kin pairs within each kinship category into axial standard deviations of these distances, then decomposed these into components representing past dispersal events. From these components, we isolated the axial standard deviation of parent–offspring dispersal and estimated neighbourhood area (91 m), median parent–offspring dispersal distance (38 m) and oviposition dispersal radius within a gonotrophic cycle (25 m). We also analysed genetic structure using distance‐based redundancy analysis and linear regression, finding isolation by distance both within and between buildings and estimating neighbourhood size at 268 individuals. These findings indicate the scale required to suppress local outbreaks of arboviral disease and to target releases of modified mosquitoes for mosquito and disease control. Our methodology is readily implementable for studies of other species, including pests and species of conservation significance. [Correction added on 09 October 2020, after first online publication: 129 m corrected to 91 m; 75 m to 38 m; 36 m to 25 m.]     

The Allelic Correlation Structure of Gainj- and Kalam-Speaking People. II. the Genetic Distance between Population Subdivisions

The patterning of allele frequency variability among 18 local groups of Gainj and Kalam speakers of highland Papua New Guinea is investigated using new genetic distance methods. The genetic distances proposed here are obtained by decomposing Sewall Wright's coefficient FST into a set of coefficients corresponding to all pairs of population subdivisions. Two statistical methods are given to estimate these quantities. One method provides estimates weighted by sample sizes, while the other method does not use sample size weighting. Both methods correct for the within-individual and between-individual-within-groups sums of squares. Genetic distances among the Gainj and Kalam subdivisions are analyzed with respect to demographic, geographic, and linguistic variables. We find that a demographic feature, group size, has the greatest demonstrable association with the patterning of genetic distances. The pattern of geographic distances among groups displays a weak congruence with the pattern of genetic distances, and the association of genetic and linguistic diversity is very low. An effect of differences in group size on genetic distances is not surprising, from basic theoretical considerations, but genetic distances have not often been analyzed with respect to these variables in the past. The lack of correspondence between genetic distances and linguistic and geographic differences is an unusual feature that distinguishes the Gainj and Kalam from most other tribal populations.     

Variation in dental occlusion and arches among Melanesians of Bougainville Island, Papua New Guinea. II. Clinical variation, geographic microdifferentiation and synthesis

Patterns of geographic microdifferentiation for dental occlusion and the size and shape of the dental arches are described for 14 villages on Bougainville Island, Papua New Guinea. Occlusal variables, such as overjet, overbite, molar relationships, crowding or spacing, and malalignment vary less among villages than do arch length and width. Arch length and width decrease in size from north to south. The pattern of biological distance among villages for occlusal variables and arch size correspond poorly to anthropometric, linguistic, geographic and migrational distances. The value of occlusal variables and arch size for discriminating among populations, the biological interpretation of multivariate data and the objectives of research on geographic microdifferentiation are discussed.