Two complementary perspectives on inter-individual genetic distance

This paper examines population structure through the prism of pairwise genetic distances. Two complementary perspectives, framed as two simple questions, are explored: Q1: What is the probability that a random pair of individuals from the same local population is more genetically dissimilar than a random pair from two distinct populations? Q2: On average, how genetically different are two individuals from the same local population, in comparison with two individuals chosen from any two distinct populations? Models are developed to provide quantitative answers for the two questions, given allele frequencies across any number of markers from two diploid populations. The probability from Q1 is shown to drop to zero with increasing number of genetic markers even for very closely-related populations and rare alleles. The average genetic dissimilarity of two individuals from distinct populations diverges from the average dissimilarity of two individuals from the same population by a percentage dependent on estimates of population differentiation. This perspective also suggests a measure of population distance based on the intuitive notion of pairwise genetic distance, along with a simple method of estimation. Results from recent empirical research on inter-individual genetic distance in human populations are analyzed in the context of the theoretical framework.     

Genetic identity between populations when mutation rates vary within and across loci

A formula is derived for the probability that two genes taken at random from the same locus in two populations isolated at time t ago are of the same allelic type. The model assumed is a neutral one where there are possibly different mutation rates between different alleles. Inequalities are derived for this probability. A particular result is that for a fixed overall mutation rate, the probability is least for the infinite alleles model. Inequalities and approximations are found for Nei's genetic identity at one locus when mutation rates vary, and also for the identity across loci when the overall mutation rates per locus vary. Genetic identity at the molecular level is considered and a probability generating function found for the number of segregating sites between two randomly chosen gametes from two divergent populations, under various models.     

A population genetic study in the Ochamchir region, Abkhazia, SSR

The reported longevity of residents of the Soviet Socialist Republic of the Caucasus has focused considerable attention on this population. However, little is known of the genetic composition of this population. With this in mind, several village populations of the Ochamchir Region, Abkhazia, SSR, were typed for 37 discrete genetic blood groups, erythrocyte and plasma protein loci. Gene and haplotype frequencies calculated for the polymorphic markers were determined and the results used in an analysis of intervillage heterogeneity and genetic distance analysis comparing the Abkhazians to European and Asian reference populations. The Abkhazians are approximately equal distance from European and West Asian populations in a genetic sense, and this is consistent with their geographical location. In addition to the usual genetic polymorphisms, rare electrophoretic variants were encountered at the lactate dehydrogenase A and phosphohexose isomerase loci. These results suggest that the population of the Ochamchir Region is relatively homogeneous and not distinctly different from its geographical neighbors.     

The genetic structure of populations of Chuckotka Peninsula Eskimos and Chuckchi based on study of 13 loci of serum and erythrocyte proteins and enzymes

The Eskimos and Chuckchi of the Chuckotka Peninsula were studied at 13 loci of serum and erythrocyte proteins and enzymes by electrophoresis. Six loci-including albumin, transferrin, carbonic anhydrase I and II, monoamine oxidase, and superoxide dismutase-were monomorphic in the studied populations. The mean frequencies of alleles in nine polymorphic loci of Chuckotka Eskimos and Chuckchi, Eskimos of Alaska, Canada, and Greenland, some Mongoloid populations of Siberia, American Indians, and Lapps of circumpolar areas of Western Europe were obtained. The genetic distances between these populations were calculated. The Eskimos of Chuckotka were closest to the Alaskan Eskimos. The relative heterozygosity of Chuckotka Eskimos was calculated and was the highest in Chuckchi. The average heterozygosity in Eskimo populations increased in the following order, from least to greatest: Chuckotka Eskimos, St. Lawrence Island Eskimos, Alaskan Eskimos, Greenland Eskimos, and Canadian Eskimos. The average heterozygosity of the Chuckchi was similar to that of Western Hemisphere Eskimos.     

Comparative population structure of three snook species (Teleostei: Centropomidae) from the eastern central Pacific

Three snook species, Centropomus viridis, Centropomus medius, and Centropomus robalito, from the eastern central Pacific, representing three of the four proposed phyletic lineages in the genus, were analyzed for genetic variability by means of allozyme and RAPD to evaluate the divergence between populations at different levels of dispersal ability and to evaluate the importance of barriers to dispersal in the population subdivision and genetic diversity. Levels of genetic diversity among species estimated by allozymes were similar and consistent with the observed levels of differentiation in marine fish species. Mean heterozygosity ranged from 0.089 for C. viridis to 0.10 for C. robalito. Genetic diversity for the snook species studied was slightly higher than the mean estimation reported in allozymes for 106 marine fish (0.055) and for anadromous fish species (0.043 to 0.057). Multilocus allele frequency homogeneity tests and population-subdivision estimates for both allozyme and RAPD markers revealed the existence of population structure in C. viridis and C. medius, in coincidence with geographic separation of samples, whereas no divergence was detected in C. robalito. This finding may be attributed to the greater population size of C. robalito, which originated by a recent population range expansion, and hence the potential for dispersal is mediated by larval drift. Fluctuations in population size and population range expansion are used to explain discrepancies between levels of genetic diversity and population structure in the studied species. Supplementary material to this paper is available in electronic format at     

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.     

Comparing the genetic diversity and structure of indigenous Korean and Chinese populations of Laodelphax striatellus Fallén using mitochondrial haplotypes

The small brown planthopper, Laodelphax striatellus Fallén, is a major migratory pest from China to Korea and transmits viral diseases of rice plants. In this study, we compared the genetic structures of overwintered indigenous Korean and Chinese populations. The eight Korean populations consisted of 33 haplotypes, and 16 of these were newly identified. The genetic diversity of the Korean population revealed high haplotype diversity (Hd) and low nucleotide diversity (π) of 0.86 ± 0.017 and 0.0024 ± 0.0001 on average, respectively. These values for the Chinese population were Hd = 0.92 ± 0.016 and π = 0.0026 ± 0.0002. Overall, genetic distances by pairwise F_ST were generally low, ranging from ? 0.022 to 0.089. Moreover, the Korean population revealed its ongoing population expansion by showing negative values in the neutrality test (Tajima's D = ? 1.4, Fu's Fs = ? 15.8) and a unimodal pattern in the mismatch distribution analysis. The genetic structures and population relationships were determined using 8 indigenous Korean and 30 Chinese populations by Bayesian approaches and population tree construction, respectively. The genetic structure was inferred as five (K = 5), and all indigenous Korean populations as well as 10 Chinese populations from the Shanghai city, Anhui, Henan, Jiangsu, Liaoning, Shandong, and Zhejiang provinces were grouped into ‘G3’. These results provide partial support for unidirectional gene flow by migratory Chinese populations into Korea. Further analysis conducted using specimens from China and Korea collected in similar periods is necessary to clarify the migration population's origin and its effect on the genetic structure of the indigenous populations.     

The genetic structure of a tribal population, the Yanomama indians. VII. Anthropometric differences among Yanomama villages

Anthropometric data on 12 variables in 19 villages of the Yanomama Indians demonstrate significant heterogeneity in physique among villages of this tribe. Mahalanobis' distances (D²) calculated from the data lead to the tentative conclusion of a general correspondence between anthropometric and geographic distances separating villages. The mean stature of the Yanomama is smaller than that of most other South American tribes which have been measured, and the Yanomama are genetically distinct from the other small Indians as shown by genetic distances based on allele frequencies for a variety of genetic markers. Since some subjects were measured more than once by the same and by different observers, it was possible to calculate approximate estimates of variance within and between observers. Univariate analysis indicates that face height and nose height are especially susceptible to systematic differences in technique between observers. The variances obtained in this field study compare favorably with those of some classical laboratory studies described in the literature. It was found that measurement error nevertheless probably makes a substantial contribution to anthropometric distance between villages. The median error variance as a fraction of that of Herskovits ('30) is 0.62 for the seven measurements in common with this study. The median value of the error variance for the 12 variables in this study is between 16% and 17% of the total variance.     

Risso’s dolphins (<Emphasis Type="Italic">Grampus griseus</Emphasis>) in UK waters are differentiated from a population in the Mediterranean Sea and genetically less diverse

The Risso’s dolphin (Grampus griseus) has a worldwide distribution, but little is known about their population genetic structure. Local coastal populations are never known to be abundant, and are sometimes under anthropogenic impact. Therefore the question of regional differentiation by genetic drift and overall diversity levels is of conservation interest. Here we present preliminary data that clearly indicate genetic differentiation and lower genetic diversity of a population sampled in UK waters (primarily from the Western Isles, Scotland) compared to a Mediterranean sample. Significant differentiation was found in comparison with a sample from the Mediterranean for both microsatellite DNA markers (F _ST = 0.0296) and mtDNA sequence data (F _ST = 0.260; ϕ _ST = 0.542). Allelic diversity was lower in the UK for nearly all loci.     

The genetic structure of finland.

The Finnish gene pool derives primarily from a relatively homogeneous Finno-Ugric population established during the Iron Age (100 B.C.-800 A.D.) in the southwest and southeast of Finland. Gene flow from Sweden to the southwest coastal areas, dating from prehistoric times, as well as the patterns of settlement and migration throughout Finland during the past 1000 years, appear to have been the major biosocial factors underlying the genetic structure of the contemporary population. Analysis of genetic variation and covariation at nine polymorphic loci in a large random sample of rural Finns, partitioned into either 8 countries or 27 geographic districts, showed that all of the essential features of the genetic structure suggested by the archaeological and historical data could be distinguished. Procedures for obtaining inference on the genetic structure of such a population are reviewed, including coefficients of similarity and (genetic) distance among subpopulations, the relation between linear or planar geographic structure and genetic covariation, and the methods for describing allelic differentiation. Bias resulting from the inappropriate assumption of a simple phylogenetic model can be substantial, expecially for the analysis of isolation by distance; procedures for avoiding misleading inference on the genetic structure are demonstrated.     

Amplified fragment length polymorphism analysis of the population structure and genetic diversity of Phoebe zhennan (Lauraceae), a native species to China

Phoebe zhennan S. Lee et F. N. Wei (Lauraceae), is the main source of Gold Phoebe, a rare and extremely valuable wood in China. However it has undergone a dramatic decline. In this study, we used 12 amplified fragment length polymorphism primer combinations to assay 92 accessions, which were highly representative of the entire P. zhennan germplasm. It revealed that P. zhennan consisted of three genetic populations, named as SCZ (central Sichuan), CQH (eastern Sichuan, Chongqin, Hubei and Hunan) and YG (Yunnan and Guizhou), probably owing to natural selection caused by topography differences. The CQH population further diverged into two geographical sub-populations: CD-CQ (SCD and west region of Chongqin) and HB-HN (eastern side of Chongqin, Hubei and Hunan). The loci were moderately polymorphic (40.4%). The genetic distance between SCZ and YG was the highest, between CD-CQ and HB-HN the lowest. Pairwise fixation indices (Ф_PT) between any inferred populations were significant. This rare species exhibited low genetic diversity; therefore, the results provided significant data related to the conservation and management of P. zhennan. That is, with this genetic information, land managers are equipped with better tools allowing them to more effectively protect this species and its limited genetic diversity.     

Isozyme analysis of genetic variability and population structure of Lactuca L. germplasm

Isozymes were used to investigate the genetic variability, population structure, and relationships of Lactuca germplasm. The isozyme systems revealed 16 putative loci of a total of 31 alleles. Out of these 16 loci, 11 were polymorphic. The average values of expected heterozygosity (H_e), observed heterozygosity (H_o), mean number of alleles per locus (A) and effective number of alleles per locus (A_e) were 0.2227, 0.266, 1.3005 and 1.369, respectively. The average fixation indices were lower than zero for most of the accessions studied, indicating an excess of heterozygotes. Genetic differentiation among accessions (F_ST) exhibited that 51.3% of the isozyme variation was recorded among accessions, and 48.7% of the genetic variation resided within accessions. The average values of total heterozygosity (H_T) and intra-accessional genetic diversity (H_S) were 0.352 and 0.171, respectively. Moreover, the inter-accessional genetic diversity (D_ST) ranged from 0 to 0.424 with an average of 0.18. Cluster analysis revealed that L. sativa cultivars were distributed throughout different Lactuca species. Thereby, isozymes results confirms the hypothesis of the polyphyletic origin of L. sativa. This high level of genetic variation proved that isozymes are efficient for polymorphism analysis of Lactuca germplasm.     

塔里木裂腹鱼群体遗传结构及遗传多样性分析

塔里木裂腹鱼为塔里木河水系特有濒危裂腹鱼类。研究采集5个群体(多浪渠首、喀拉喀什河、木扎提河、塔什库尔干、玉龙喀什河)塔里木裂腹鱼,扩增线粒体控制区第一高变区,共获得长度456 bp序列95条。塔里木裂腹鱼单倍型多样度和核苷酸多样度分别为0.7118、0.0024。AMOVA分析显示,群体间遗传分化显著。FST值统计检验表明,除喀拉喀什河群体与玉龙喀什河群体之间差异不显著外,其他两两群体之间都是显著的。分子系统树和单倍型网络图分析表明,塔里木裂腹鱼单倍型间关系较近。中性检验和mismatch分析显示,塔里木裂腹鱼群体经历过近期群体扩张事件。根据核苷酸不配对分布τ值计算其群体扩张时间为20万年前。天山、昆仑山的运动以及第四纪冰期-间冰期的变化可能影响了塔里木裂腹鱼的群体历史动态。