GENETIC DIVERSITY AND POPULATION STRUCTURE IN CAMELLIA JAPONICA L. (THEACEAE)

Camellia japonica is a widespread and morphologically diverse tree native to parts of Japan and adjacent islands. Starch gel electrophoresis was used to score allelic variation at 20 loci in seeds collected from 60 populations distributed throughout the species range. In comparison with other plant species, the level of genetic diversity within C. japonica populations is very high: 66.2% of loci were polymorphic on average per population, with a mean number of 2.16 alleles per locus; the mean observed and panmictic heterozygosities were 0.230 and 0.265, respectively. Genotypic proportions at most loci in most populations fit Hardy-Weinberg expectations. However, small heterozygote deficiencies were commonly observed (mean population fixation index = 0.129). It is suggested that the most likely cause of the observed deficiencies is population subdivision into genetically divergent subpopulations. The overall level of population differentiation is greater than is typically observed in out-breeders: The mean genetic distance and identity (Nei's D and I) between pairs of populations were 0.073 and 0.930, respectively, and Wright's Fst was 0.144. Differences among populations appeared to be manifested as variation in gene frequencies at many loci rather than variation in allelic composition per se. However, the patterns of variation were not random. Reciprocal clinal variation of gene frequencies was observed for allele pairs at six loci. In addition, principal components analysis revealed that populations tended to genetically cluster into four regions representing the geographic areas Kyushu, Shikoku, western Honshu, and eastern Honshu. There was a significant relationship between genetic and geographic distance (r = 0.61; P < 0.01). Analysis of variance on allozyme frequencies showed that there was approximately four times as much differentiation among populations within regions, as among regions. It is likely that the observed patterns of population relationships result from the balance between genetic drift in small subpopulations and gene flow between them.     

Allozyme diversity and geographic variation in the widespread coastal sedge, Carex arenaria

Abstract. Allozyme electrophoresis was used to investigate the structure of genetic variation in the rhizomatous coastal sedge, Carex arenaria, throughout its European range — from the SW Iberian peninsula to the Baltic region. Material was sampled from 77 sites in five geographic regions. Nine of the 13 investigated loci were polymorphic in the total material and there were interregional differences in the number of polymorphic loci per site and the percentage of variable sites. In the Scandinavia/Baltic region only 61% of the sites contained at least one locus with more than one allele, whereas all the British and SW Iberian sites were variable. There was a general tendency for the regional frequencies of the less common alleles at individual loci to decline from SW to NE. The mean (over loci and sites) within‐site gene diversity (H _site) was 0.064 (in calculations based on the number of observed multilocus allozyme genotypes within each sampling site). Although there was considerable variation between geographically adjacent sites, within‐site diversity showed a general decrease from SW to NE in Europe. There were significant differences in within‐region gene diversity (H_reg) for the four most variable loci between the five regions. H_reg generally decreased from SW to NE Europe and most loci showed the highest diversity in the SW Iberian peninsula and the Bay of Biscay regions. The mean (over loci) gene diversity in the total material (H_tot) was 0.070 and the levels of diversity in Carex arenaria are substantially lower than is usual in rhizomatous sedges. The within‐site, between‐site and between‐regional components of the total diversity were 92.4%, 2.5% and 5.1%, respectively. The low levels of overall gene diversity in C. arenaria and the successive decrease in diversity from SW to NE are interpreted in terms of the species’ history of postglacial spread into northern Europe. Despite the overall northwards decrease in diversity, the widespread occurrence of less common alleles and the lack of regional deviations from Hardy–Weinberg genotype frequency expectations suggest that C. arenaria is not predominantly self‐fertilized.     

Genetic structure and gene flow in a metapopulation of an endangered plant species,Silene tatarica

We investigated the distribution of genetic variation within and between seven subpopulations in a riparian population of Silene tatarica in northern Finland by using amplified fragment length polymorphism (AFLP) markers. A Bayesian approach-based clustering program indicated that the marker data contained not only one panmictic population, but consisted of seven clusters, and that each original sample site seems to consist of a distinct subpopulation. A coalescent-based simulation approach shows recurrent gene flow between subpopulations. Relative high FST values indicated a clear subpopulation differentiation. However, amova analysis and UPGMA-dendrogram did not suggest any hierarchical regional structuring among the subpopulations. There was no correlation between geographical and genetic distances among the subpopulations, nor any correlation between the subpopulation census size and amount of genetic variation. Estimates of gene flow suggested a low level of gene flow between the subpopulations, and the assignment tests proposed a few long-distance bidirectional dispersal events between the subpopulations. No apparent difference was found in within-subpopulation genetic diversity among upper, middle and lower regions along the river. Relative high amounts of linkage disequilibrium at subpopulation level indicated recent population bottlenecks or admixture, and at metapopulation levels a high subpopulation turnover rate. The overall pattern of genetic variation within and between subpopulations also suggested a 'classical' metapopulation structure of the species suggested by the ecological surveys.     

Gametic disequilibrium in populations of reindeer Chukchi and Asian Eskimos

Ten local populations of Reindeer Chukchi and four local populations of Asiatic Eskimos were surveyed for variation of nine polymorphic loci (MN, Ss, Cc, Ee, Duffy, AcP, PGM1, Hp, G3M). Pairwise linkage disequilibria were estimated from multilocus genotype frequencies using the Hill's method. Large amounts of linkage disequilibrium were found for the two pairs of linked genes MNSs and CcEe. The same pattern of non-random association between unlinked loci PGM1 and AcP was found in all subpopulations of both tribes that is induced by natural selection.     

High allozyme diversity and unidirectional linear migration patterns within a population of tetraploid Isoetes sinensis, a rare and endangered pteridophyte

Isoetes sinensis (Isoetaceae), an aquatic quillwort which occurs only in two fragmented sites of China as an allotetraploid, is critically endangered. Genetic variation among eight subpopulations of I. sinensis was examined in the Xin’an River (119°14′–15′E, 29°28′N) by using allozyme polymorphism. Eighteen loci of 10 enzyme systems were examined and used for the analysis of population genetic parameters. As expected for allotetraploids, fixed heterozygosity was found at four loci. A high level of genetic diversity was observed in the population, with mean number of alleles per loci of 1.8, and mean percentage of polymorphic loci of 55.6%, which were much higher than the average values in fern species. The genetic variation within each subpopulation was not positively correlated with its size, which may be explained by high gene flow (Nm = 2.57), clonal reproduction and fixed heterozygosity of allopolyploid. The I. sinensis population contained high clonal diversity (PD = 0.39, D = 0.95), indicating the successful seedling recruitment of the population. Significant positive relationship was detected between clonal diversity and the size of subpopulation. Partitioning the genetic diversity indicated that 91.1% of the genetic variation was within subpopulations and only 8.9% existed among subpopulations. The migration pattern of I. sinensis along the Xin’an River is best explained by a source–sink model, but with unidirectional gene flow among subpopulations underlined by hydrochoric force. The results were then discussed in relation to both in situ and ex situ conservation efforts of the population.     

Patterns of genetic diversity in population complexes of pacific chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis> Walbaum,from Asia and America,inferred from allozyme polymorphism data

Based on the data of Russian and foreign researchers, a database, consisting of 100 allozyme-coding loci examined in 288 chum salmon populations from Asia and Northern America, was constructed. Using G-test, genetic heterogeneity of Asian population samples of chum salmon was evaluated. Correlations between the frequencies of major alleles and geographic latitude of the mouths of native rivers were estimated. Using the methods of Nei and Cavalli-Sforza and Edwards, for different local chum salmon stock groups the genetic distances at the number of polymorphic enzyme loci were determined. Analysis of these distances made it possible to evaluate the patterns of genetic diversity in regional population groups from the Russian Far East, Japan, and North America. The proportions of genetic variation at each hierarchical level, identified in accordance with the geographical positions of the populations, were estimated through partitioning of variation in Asian populations into within and between-population components. It was demonstrated that intraspecific genetic structure of chum salmon corresponded geographic subdivision into regional population groups.     

Genetic distance and gene diversity among linguistically different tribes of Mexican Indians.

Using gene frequency data for 14 genetic loci, genetic distances between 13 tribes of Mexican Indians belonging to 12 language groups were determined and a dendrogram was constructed. The genetic distance between tribes is correlated more with geographic proximity than with language affinity. The gene diversity (heterozygosity) of the total population was decomposed into the three components, i.e., the gene diversity between three main linguistic groups, the gene diversity between tribes within the main linguistic groups and the gene diversity within tribes. About 95% of the total gene diversity exists within tribes, the intergroup and intertribe components being only about 5%.     

Major Histocompatibility Complex (MHC) class II sequence polymorphism in long-finned pilot whale (Globicephala melas) from the North Atlantic

Determining how intra-specific genetic diversity is apportioned among natural populations is essential for detecting local adaptation and identifying populations with inherently low levels of extant diversity which may become a conservation concern. Sequence polymorphism at two adaptive loci (MHC DRA and DQB) was investigated in long-finned pilot whales (Globicephala melas) from four regions in the North Atlantic and compared with previous data from New Zealand (South Pacific). Three alleles were resolved at each locus, with trans-species allele sharing and higher levels of non-synonymous to synonymous substitution, especially in the DQB locus. Overall nucleotide diversities of 0.49?±?0.38% and 4.60?±?2.39% were identified for the DRA and DQB loci, respectively, which are relatively low for MHC loci in the North Atlantic, but comparable to levels previously described in New Zealand (South Pacific). There were significant differences in allele frequencies within the North Atlantic and between the North Atlantic and New Zealand. Patterns of diversity and divergence are consistent with the long-term effects of balancing selection operating on the MHC loci, potentially mediated through the effects of host-parasite coevolution. Differences in allele frequency may reflect variation in pathogen communities, coupled with the effects of differential drift and gene flow.     

Nonmetric tooth crown traits in the Ami tribe, Taiwan aborigines: comparisons with other east Asian populations.

The frequencies of occurrence of 17 tooth crown traits in the living Ami tribe, which inhabits the east coast of Taiwan, were investigated and compared with other East Asian populations based on Turner's (1987) Mongoloid dental variation theory. Principal coordinate analysis based on Smith's mean measure of divergence using frequencies of the 17 traits suggests that the Ami tribe together with the Yami tribe and the Bunun tribe is included in the sinodont group typical of the Chinese mainland and northeast Asia. In light of these results and the estimated distribution of sinodonty and sundadonty in the past and the present, we speculate that the gene flow from Chinese mainlanders to native sundadonts, who seem to have migrated northward to Taiwan, contributed significantly to the formation of the living Taiwan aboriginal groups, sinodonts. Among the aboriginal tribes of Taiwan, the Ami have characteristics intermediate between those of the Yami and the Bunun. The relative positions of these tribes in East Asian populations suggests that the extent of sinodontification and of genetic isolation is one of the causes of the intertribal variation.     

Among-locus variation in Fst: fish, allozymes and the Lewontin-Krakauer test revisited.

Variation among loci in the distribution of allele frequencies among subpopulations is well known; how to tell when the variation exceeds that expected when all loci are subject to uniform evolutionary processes is not well known. If locus-specific effects are important, the ability to detect those effects should vary with the level of gene flow. Populations with low gene flow should exhibit greater variation among loci in Fst than populations with high gene flow, because gene flow acts to homogenize allele frequencies among subpopulations. Here I use Lewontin and Krakauer's k statistic to describe the variance among allozyme loci in 102 published data sets from fishes. As originally proposed, k > 2 was considered evidence that the variation in Fst among loci is greater than expected from neutral evolution. Although that interpretation is invalid, large differences in k in different populations suggest that locus-specific forces may be important in shaping genetic diversity. In these data, k is not greater for populations with expected low levels of gene flow than for populations with expected high levels of gene flow. There is thus no evidence that locus-specific forces are of general importance in shaping the distribution of allele frequencies at enzyme loci among populations of fishes.     

GENETIC VARIABILITY OF GELIDIUM CANARIENSIS (RHODOPHYTA) DETERMINED BY ISOZYME ELECTROPHORESIS1

The populations of Gelidium canariensis (Grunow) Seoane-Camba from the Canary Islands were analyzed for genetic variability by isozyme electrophoresis in 1989 and 1990. Each population was divided into sporophytic and gametophytic subpopulations. Twenty-three to 27 putative alleles corresponding to 22 gene loci were analyzed. Sev-enteen loci were monomorphic in all six subpopulations, and five were polymorphic in at least one subpopulation. Significant deviations from Hardy-Weinberg equilibrium were found. The amount of genetic variability (percentage of polymorphic loci, mean number of alleles per locus, and average gene diversity) of haploid subpopulations was lower than that of diploid subpopulations. No correlation between genetic distance and geographical distance was found. Low genetic differentiation between sporophytic and gametophytic subpopulations of the same locality was obsewed in two populations. The low genetic diversity and genetic differentiation suggest that the genetic structure of the populations of G. canariensis from the Canary Islands is due to a combination of founder effects and the predominance of asexual reproduction. Initial differences in gene frequencies may have persisted because of insufficient time to reach a higher level of differentiation.     

Global analysis of regional differences in craniometric diversity and population substructure.

Estimates of genetic diversity in major geographic regions are frequently made by pooling all individuals into regional aggregates. This method can potentially bias results if there are differences in population substructure within regions, since increased variation among local populations could inflate regional diversity. A preferred method of estimating regional diversity is to compute the mean diversity within local populations. Both methods are applied to a global sample of craniometric data consisting of 57 measurements taken on 1734 crania from 18 local populations in six geographic regions: sub-Saharan Africa, Europe, East Asia, Australasia, Polynesia, and the Americas. Each region is represented by three local populations. Both methods for estimating regional diversity show sub-Saharan Africa to have the highest levels of phenotypic variation, consistent with many genetic studies. Polynesia and the Americas both show high levels of regional diversity when regional aggregates are used, but the lowest mean local population diversity. Regional estimates of F(ST) made using quantitative genetic methods show that both Polynesia and the Americas also have the highest levels of differentiation among local populations, which inflates regional diversity. Regional differences in F(ST) are directly related to the geographic dispersion of samples within each region; higher F(ST) values occur when the local populations are geographically dispersed. These results show that geographic sampling can affect results, and suggest caution in making inferences regarding regional diversity when population substructure is ignored.     

The genetic structure of a tribal population, the Yanomama Indians XI. Gene frequencies for 10 blood groups and the ABH-Le secretor traits in the Yanomama and their neighbors; the uniqueness of the tribe.

In this paper we present the results of blood group typings for a total of 33 villages distributed among five South American Indian tribes--Yanomama (21 villages), Makiritare (eight villages), Macushi (two villages), Piaroa (one village), and Wapishana (one village). These new results for the Yanomama and Makiritare tribes have been combined with those previously reported to allow a better appreciation of the distribution of allelic frequencies in the tribes. The relationship of the Yanomama to other South American Indian tribes is investigated using data on six polymorphic loci (Rh, MNS, Fy, Jk, Di, Hp). By use of four genetic measures (two of genetic relationship and two of genetic diversity), we demonstrate that the Yanomama are genetically unique among a sample of 20 South American tribes. In addition, the Yanomama show somewhat less genetic diversity for the six loci analyzed than the average South American tribe. Taken together, these results indicate a rather long period of isolation for the population antecedent to the Yanomama--perhaps since the time of entry of man into the South American continent. The pattern of genetic relationships and genetic diversity for the 20 tribes is consistent with the hypothesis that evolution in South America proceeded by a process of fission-fusion leading to isolation of subpopulations with subsequent genetic differentiation as a consequence of population isolation. The uniqueness of the Yanomama appears to stem entirely from such a process, there being no evidence of any selective differential for the loci analyzed.     

Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci

Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern, western and southern Africa. In the total sample, 43 haplotypes were identified and an overall nucleotide diversity of 2.0% was observed. High levels of polymorphism were also observed at the microsatellite loci both at the level of number of alleles and gene diversity. Nine to 14 alleles per locus across populations and 44 alleles in the total sample were found. The gene diversity ranged from 0.51 to 0.72 in the localities studied. An analysis of molecular variance showed significant genetic differentiation between populations within regions and also between regions. The extent of subdivision between populations at the mtDNA control region was approximately twice as high as shown by the microsatellite loci (mtDNA F(ST) = 0.59; microsatellite R(ST) = 0.31). We discuss our results in the light of Pleistocene refugia and attribute the observed pattern to population divergence in allopatry accompanied by a recent population admixture following a recent population expansion.     

Genetic Variation and Differentiation of Larix decidua Populations in Swiss Alps (in English)

Genetic diversity within and among six subpopulations of Larix decidua Mill. from two altitudinal transects of Swiss Alps was investigated using 6 enzyme systems coding for 8 loci. Globally, the mean proportion of polymorphic loci was 22.9%, the average number of alleles per locus was 1.3, and the mean expected heterozygosity was 0.095. Only 5.8% of the genetic variation resided among populations. The mean genetic distance was 0.006. Several significant differences of gene frequencies were found between different age classes. Positive values of the species mean fixation index observed in this study suggested a considerable deficit of heterozygotes in the populations of L. decidua of Swiss Alps. At one of the sites (Arpette), the highest subpopulation in elevation gave the lowest level of genetic diversity (as evidenced by the lowest proportion of polymorphic loci and the lowest mean expected heterozygosity) and the largest value of genetic distance when compared to other subpopulations. The genetic differences between the highest subpopulation and the other ones suggest that the founder effect may be an important factor influencing genetic differentiation of L. decidua populations at Arpette transect.     

Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation,energy homeostasis and immune defence‐related genes

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study, we used a dense SNP array to identify candidate loci potentially underlying fine‐scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at subdrainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis and immune defence. These included the large‐effect age‐at‐maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations and that is also a candidate for local selection over the global range of Atlantic salmon. This region colocalized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and covaries with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.     

瑞士阿尔卑斯山欧洲落叶松居群的遗传变异和分化

应用等位酶分析技术,沿两个海拔梯度在瑞士阿尔卑斯山研究了欧洲落叶松（Larix decidua Mill.)居群内和居群间的遗传多态性,结果表明,多态性位点的比例为22.9%,平均每个位点的等位基因数为1.3,平均期望杂合度为0.095,遗传变异的5.8%存在于居群之间,平均遗传距离为0.006。几个有统计意义的基因频率差别在不同树龄类被发现,正在繁育系数值表明在瑞士阿尔卑斯山欧洲落叶松居群有相当的杂合体缺乏,在阿尔拜特（Ar-pette),海拔最高的亚居群与其他亚居群相比较显示最低的遗传多态性（如显示最低的我态性位点比例和最低的平均期望杂合度）和最大的遗传距离值,在最高亚居群和其他亚居群间的遗传差别暗示奠基效应可能是影响这个定样场所欧洲落叶松居群遗传分化的主要因素。     

Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis)

Surveys of nucleotide diversity in the wild ancestor of maize, Zea mays ssp. parviglumis, have revealed genomewide departures from the standard neutral equilibrium (NE) model. Here we investigate the degree to which population structure may account for the excess of rare polymorphisms frequently observed in species-wide samples. On the basis of sequence data from five nuclear and two chloroplast loci, we found significant population genetic structure among seven subpopulations from two geographic regions. Comparisons of estimates of population genetic parameters from species-wide samples and subpopulation-specific samples showed that population genetic subdivision influenced observed patterns of nucleotide polymorphism. In particular, Tajima's D was significantly higher (closer to zero) in subpopulation-specific samples relative to species-wide samples, and therefore more closely corresponded to NE expectations. In spite of these overall patterns, the extent to which levels and patterns of polymorphism within subpopulations differed from species-wide samples and NE expectations depended strongly on the geographic region (Jalisco vs. Balsas) from which subpopulations were sampled. This may be due to the demographic history of subpopulations in those regions. Overall, these results suggest that explicitly accounting for population structure may be important for studies examining the genetic basis of ecologically and agronomically important traits as well as for identifying loci that have been the targets of selection.     

Geographic and altitudinal allozyme variation in sorghum (Sorghum bicolor (L.) Moench) landraces from Ethiopia and Eritrea

The amount and distribution of genetic variation was investigated in 48 sorghum landrace accessions, representing 13 regions of origin and three adaptation zones (lowland, intermediate and highland elevation) in Ethiopia and Eritrea. Assaying 11 enzymes systems, 23 putative loci were scored for a total of 27 alleles. Nineteen loci were monomorphic and fixed for the same allele, while the remaining 4 loci, each with 2 alleles, were polymorphic across the 48 accessions. The results show significant differences in allele frequencies among the accessions, regions of origin and the adaptation zones. However, all measures of genetic variation used show that the accessions maintained much lower levels of variation than the corresponding mean values for self-pollinating crop plants, confirming previous conclusions that sorghum is depauperated in allozymic variation. The total gene diversity was 0.25, which partitioned 59% within and 41% among accessions. The latter was largely due to variation among accessions within the adaptation zones (38%), while only 3% was due to variation among accessions between the adaptation zones. Similarly, most of the total gene diversity was found within the regions of origin (80%) and within the adaptation zones (97%). Both the dendrogram constructed from NEI's unbiased genetic distance and the plot of the first two principal components distinguished three groups of regions. The level of gene flow was low among accessions, regions of origin and among accessions within adaptation zones, but high among adaptation zones. The results are discussed with emphasis on genetic resources conservation and utilization.