Genetic structure of the human population in the Po delta

The genetic structure of the population of Ferrara Province in the Po delta in Italy was investigated using chi 2 analysis, kinship analysis, analysis of correspondences, and geographical mapping of principal components of gene frequencies. chi 2 Analysis tests for Hardy-Weinberg equilibrium and for heterogeneity of gene and phenotype frequencies; kinship analysis tests for association between indicators of genetic and geographic proximity; analysis of correspondences relates localities and genetic systems in an eigenvectorial space; and geographic mapping displays the principal components of gene frequencies in the real space. In 1,364 adults in 26 residential units, seven presumably neutral isoenzyme systems were typed; ACP1 ESD, GLO I, GPT, PGD, PGM1 and PGP. It was found that average kinship for these neutral systems is correlated with geographic distance in this small area, but not as strongly as kinship for beta-thalassemia. A north-south gradient was observed for ESD. Analysis of correspondences indicated GPT, PGM1, and GLO I as the systems contributing most to differentiation within the province. The maps obtained from principal components of gene frequencies were consistent with the migrational history of the area.     

Is the flavin-deficient red blood cell common in Maremma, Italy, an important defense against malaria in this area?

There is a high prevalence of a familial flavin-deficient red blood cell in Ferrara province in the Po delta in northern Italy, believed to have been selected for by malaria which was endemic from the 12th century. In the present study, activities of FAD-dependent red-cell glutathione reductase (EGR) in the Grosseto area of Maremma on the west coast of Italy where malaria was endemic from 300 B.C. are compared both with activities in the Ferrara area and with activities where there was no history of endemic malaria--in the Florence area and in London in people of Anglo-Saxon origin. EGR activities were similar in Grosseto and Ferrara and were significantly lower than in Florence and London. As previously found in Ferrara, low EGR activity in Grosseto was shown to be unrelated to low dietary riboflavin intake. These findings in Grosseto, suggesting selection by malaria, are particularly interesting because, unlike the situation in Ferrara and most other malarial areas, the prevalence of thalassemia and glucose-6-phosphate dehydrogenase deficiency is very low, and they do not appear to have been selected for in Maremma. It is possible that a flavin-deficient red cell, known to inhibit growth of the malaria parasite, was an important protecting factor in the population of this area over the centuries.     

Population genetics in the province of Ferrara. I. Genetic distances and geographic distances.

The ABO and Rh systems of the population in 26 residential units in the province of Ferrara were studied to detect the effect of genetic drift on the differentiation of gene frequencies. Results obtained from principal components analysis and dendrograms were similar. A significant correlation between genetic and geographic distance was found. It was therefore hypothesized that in the area of Ferrara children born to parents originating from different communes were heterozygous at more loci than children born to parents originating from the same commune. It was also thought that it may be possible to use geographic distance between birthplaces of parents as an indicator of hybridity in their children.     

Genetic structures in the population of Veneto.

The genetic structures of the population residing in the provinces of Venice and Rovigo in the Veneto region at the north of the Po delta in Italy was studied in 1,210 individuals residing in 18 sampling areas, using the phenotype and gene frequencies of 7 red cell enzymes: acid phosphatase (ACP1), esterase D (ESD), glyoxalase I (GLOI), glutamic-pyruvic transaminase (GPT), 6-phosphogluconate dehydrogenase (6-PGD), phosphoglucomutase 1 (PGM1), and phosphoglycollate phosphatase (PGP). For the analysis of the distributions of phenotype and gene frequencies, standardized variance and kinship profiles were used. It was found that the genetic differentiation within each province is low, and that only two systems, GPT and PGP, are significantly different between the two provinces. The samples studied seem to belong to a mainly homogeneous population.     

First Report of Fusarium proliferatum Causing Rot of Stored Garlic Bulbs (Allium sativum L.) in Italy

During 2011, Fusarium rot of stored garlic was detected on bulbs of ‘Aglio Bianco’ (white garlic) in Piacenza, Ferrara and Rovigo districts. Bulbs, harvested in July, were asymptomatic. During conservation in the drying sheds, approximately thirty percent of bulbs appeared emptied and softened. Fusarium proliferatum was consistently recovered from infected bulbs. The morphological identification was confirmed by Translation Elongation Factor 1‐alpha gene sequencing. Koch postulates were checked through pathogenicity tests. The disease has already been reported in Serbia, Germany, Spain, United States, China and India, but to our knowledge, this is the first report of F. proliferatum garlic bulb rot in Italy.     

Migration as a factor in natural selection

Migration is defined as the movement of genes from one locality or population to another. If certain genotypes tend to migrate more than others we have migrational selection. Evidence for migrational selection is discussed. A distinction is made between the dispersion of individuals from a point giving a leptokurtic distribution of migration distances, and large scale movements of individuals from one population to another.Models for large scale unidirectional migrations where genotypes vary in viability before and after migration are cosidered. These lead to different equilibrium points before and after migration.Models for reciprocal migration between two populations are discussed. It is shown that the gene frequencies of the two populations may diverge under the influence of varying migration rates and varying viabilities of the genotypes. Furthermore, more than one stable equilibrium point may be possible for a given set of viabilities. Equilibria are shown to be possible for viabilities not implying simple overdominance. In migratory birds, where there are two annual migrations between two localities, migrational selection may lead to differing gene frequencies in the two localities.The need for data on migration in different organisms is stressed. It is suggested that man is especially suitable for migration studies.     

Geographic Variation in Genetic Dominance of the Color Morphs of the Red-Backed Salamander, PLETHODON CINEREUS

Female parent-offspring phenotypic data on color morph frequencies in the red-backed salamander, Plethodon cinereus, were obtained from two Virginia localities (164 broods from Greene County and 97 broods from Giles County). The color morph data indicate that the striped morph is genetically dominant in Giles County and recessive in Greene County. It is suggested that epistatic interaction of two or more loci is responsible for the difference between the localities.     

Isozyme genotype-environment relationships in natural populations of the harvester ant,Pogonomyrmex barbatus,from Texas

Three different allelic isozyme systems (two esterases, ESH and ESR, and a malic dehydrogenase, MDH) were analyzed in population samples of a species of ant, Pogonomyrmex barbatus, from Texas. Allelic frequencies were determined for several collection localities, and a number of significant differences were found. Principal component analysis was used to compare the patterns of variability of the allelic frequencies with environmental factors. Significant correlation was particularly evident with respect to weather and the pattern of variability in both esterases, and it is therefore suspected that natural selection is important in determining the allele frequency patterns. Observed and expected genotypic proportions were found in good agreement, generally, but in some localities homozygotes appeared in significantly greater numbers than expected. Heterotic selective maintenance was thus not indicated. Correlation found between patterns of variability in the enzyme systems themselves was consistent with the hypothesis that all three enzyme systems were affected by the environmental factors.Supported in part by USPHS Research Grants No. GM 15769, GM 11609, and GM 11546 and Texas A & I University Faculty Research Grant No. 449-N-68. The field work and laboratory analyses in this investigation were done while the senior author was at the University of Texas, and the data were analyzed at North Carolina State University. The computing was supported by Grant FR-00011 of the National Institutes of Health. Paper number 2784 of the Journal Series of the North Carolina Agricultural Experiment Station, Raleigh, North Carolina.     

Spatial patterns of human gene frequencies in Europe

The aims of this study of spatial patterns of human gene frequencies in Europe are twofold. One is to present new methodology developed for the analysis of such data. The other is to report on the diversity of spatial patterns observed in Europe and their interpretation as evidence of population processes. Spatial variation in 59 allele and haplotype frequencies (26 genetic systems) for polymorphisms in blood antigens, enzymes, and proteins is analyzed for an aggregate of 3,384 localities, using homogeneity tests, one-dimensional and directional spatial correlograms, and SYMAP interpolated surfaces. The data matrices are reduced to reveal the principal patterns by clustering techniques. The findings of this study can be summarized as follows: 1) There is significant heterogeneity in allele frequencies among the localities for all but one genetic system. 2) There are significant spatial patterns for most allele frequencies. 3) There is a substantial minority of clinal patterns in these populations. Clinal trends are found more frequently in HLA alleles than for other variables. North-south and northwest-southwest gradients predominate. 4) There is a strong decline in overall genetic similarity with geographic distance for most variables. 5) There are few, if any, appreciable correlations in pairs of allele frequencies over the continent, and there is little interesting correlation structure in the resulting correlation matrix. 6) Few spatial correlograms are markedly similar to each other, yet they form well-defined clusters. Spatial variation patterns, therefore, differ among allele frequencies. Patterns of human gene frequencies in modern Europe are diverse and complex. No single model suffices for interpretation of the observed genetic structure. Some clinal patterns reported here support the Neolithic demic-expansion hypothesis, others suggest latitudinal selection. Most of the clinal patterns are in HLA alleles, but there is also evidence from ABO for east-west migration diffusion. The majority of patterns are patchy, consistent with hypotheses of isolation by distance or of settlement of genetically differing, subsequently expanding ethnic groups. While undoubtedly there has been an ongoing stochastic process of differentiation consistent with the isolation-by-distance model, this has not obscured the directional patterns caused by migration (demic diffusion), and has perhaps only reinforced the contribution from settlement of ethnic units to patterns of genetic variation. However, the impact of the latter is most difficult to discern and requires further methodological developments.     

Qualitative Traits Variation in Sorghum (<Emphasis Type="Italic">Sorghum Bicolor</Emphasis> (L.) Moench) Germplasm from,Eastern Highlands of Ethiopia

Forty-five sorghum germplasm growing in the Eastern Highlands of Ethiopia were evaluated for 10 qualitative traits. Phenotypic frequencies between the accessions from each of the nine Aanaas and Alemaya University, grouped in 10 localities were tabulated. Phenotypic diversity index, H′, was analysed and the result indicated the between localities component of diversity to be relatively smaller than the variation in H′ among characters within localities. The value of H′ for all sample germplasm ranged from 0.36 to 0.95 with a mean of 0.71. The results showed that there is a wide morpho-agronomical diversity among the sample germplasm studied. This information can be used for the conservation of these germplasm resources and future improvement work of the sorghum crop.     

Variation in mating propensity and fertility in isofemale strains of Drosophila ananassae

Mating propensity and fertility were studied in five laboratory strains of Drosophila ananassae which were established from single females collected from different geographical localities. The results show statistically significant variation among different isofemale lines with respect to mating propensity and fertility. The strains showing greater sexual activity produce more progeny. Thus, there is a positive correlation between mating activity and fertility in D. ananassae. The comparison of mating frequencies of strains and their hybrids reveals the existence of heterosis and reciprocal effects. The data suggest that the males are more subject to intrasexual selection.     

Spatial population genetic structure of a bacterial parasite in close coevolution with its host

Knowledge of a species’ population genetic structure can provide insight into fundamental ecological and evolutionary processes including gene flow, genetic drift and adaptive evolution. Such inference is of particular importance for parasites, as an understanding of their population structure can illuminate epidemiological and coevolutionary dynamics. Here, we describe the population genetic structure of the bacterium Pasteuria ramosa, a parasite that infects planktonic crustaceans of the genus Daphnia. This system has become a model for investigations of host–parasite interactions and represents an example of coevolution via negative frequency‐dependent selection (aka “Red Queen” dynamics). To sample P. ramosa, we experimentally infected a panel of Daphnia hosts with natural spore banks from the sediments of 25 ponds throughout much of the species range in Europe and western Asia. Using 12 polymorphic variable number tandem repeat loci (VNTR loci), we identified substantial genetic diversity, both within and among localities, that was structured geographically among ponds. Genetic diversity was also structured among host genotypes within ponds, although this pattern varied by locality, with P. ramosa at some localities partitioned into distinct host‐specific lineages, and other localities where recombination had shuffled genetic variation among different infection phenotypes. Across the sample range, there was a pattern of isolation by distance, and principal components analysis coupled with Procrustes rotation identified congruence between patterns of genetic variation and geography. Our findings support the hypothesis that Pasteuria is an endemic parasite coevolving closely with its host. These results provide important context for previous studies of this model system and inform hypotheses for future research.     

濒危植物独花兰的形态变异及其适应意义

采用ANOVA和UPGMA等方法对濒危植物独花兰(Changnieniaamoena)分布于庐山、新宁和神农架3个地点的12个自然居群的形态变异进行了研究,探讨其形态多样性水平和地理变异式样及其可能的适应机制。结果表明,庐山居群13个性状的平均观测值均高于新宁和神农架居群。在物种水平上各个性状存在较丰富的变异,变异系数(CV值)为0.02–0.30。尽管同一性状在不同居群中的变异程度较大,但总体而言,花部器官的变异性比营养器官低。单因素方差分析显示3个地区间多个形态性状存在极显著差异(P<0.01);UPGMA聚类分析也表明这3个地区分别形成明显不同的分支。值得注意的是,神农架地区龙门河和关门山两个地点间存在明显的形态分化,而这种形态分化是以传粉者为媒介自然选择的结果。相关性分析显示,营养器官之间、花部器官之间,以及营养器官与花部器官之间均存在较高的相关性。上述结果对进一步了解独花兰的适应机制以及制定科学的保护策略提供了有益的资料。     

Nested cladistic analysis, phylogeography and speciation in the Timarcha goettingensis complex (Coleoptera, chrysomelidae)

The Timarcha goettingensis complex is a monophyletic assemblage of closely related leaf beetles (Chrysomelidae), distributed from the north half of the Iberian Peninsula to Central Europe. Oligophagy, mountainous habitat and apterism are factors which are assumed to promote speciation in these beetles. We have used cytochrome oxidase subunit II mitochondrial DNA genealogies obtained from 31 sampling localities and a nested geographical distance analysis to assess the population structure and demographic factors explaining the geographical distributions of the mtDNA haplotypes in the T. goettingensis complex. The results show that there is a significant association between genetic structuring and geography. Inferences about the historical population processes in the species complex are discussed, being in general in accordance with contiguous range expansions and past fragmentations. The use of the cohesion species concept approach suggests the existence of several systematic ranks among the different T. goettingensis populations, which is in part supported by ecological traits such as trophic selection and altitudinal distribution.     

Immunoglobulin allotypes of Kenyan olive baboons: Troop frequencies,linkage disequilibria,and comparisons with other studies

Sera from a total of 564 olive baboons collected at six different localities in west central Kenya were examined for the presence of cross-reactive immunoglobulin allotypes with reagents used for human sera. Serum samples were tested for Km (1 and 3), Glm (1–3 and 17), andG3m (5, 6, 10, 11, 13–16, 21, 24, and 26). Polymorphism was found for Glm (1 and 17) and G3m (10, 13, and 15). These findings on antigen presence, absence, and polymorphism show broad similarities to, along with some differences from, previous studies of baboons. Our data support the view that there are variations in allotype frequencies between troops at single localities, as well as differences among geographically separated areas. Linkage disequilibria for Gm allotypes differ in strength and direction among the various local Kenya olive baboon populations.     

The Genetic Structure of a Tribal Population, the Yanomama Indians. Xv. Patterns Inferred by Autocorrelation Analysis

Fifteen allele frequencies have previously been determined for 50 villages of the Yanomama, an Amerindian tribe from southern Venezuela and northern Brazil. These frequencies were subjected to spatial autocorrelation analysis to investigate their population structure. There are significant spatial patterns for most allele frequencies. Clinical patterns, investigated by one-dimensional and directional spatial correlograms, were relatively few in number and were moderate in strength. Overall, however, there is a marked decline in genetic similarity with geographic distance. The results are compatible with a hierarchic population structure superimposed on the geography, and generated by a stochastic fission-fusion model of village propagation, followed by localized gene flow. Strong temporal autocorrelations of allele frequencies based on linguistic-historical distances representing time since divergence were also found. There appears to be a stronger relation between geography and linguistic-historical hierarchic subdivisions than between either feature and genetic distances. These findings confirm by different approaches the results of earlier analyses concerning the important roles of both stochastic and social factors in determining village allele frequencies and the occurrence within this tribe of some allele frequency clines most likely due to the operation of chance historical processes.     

Isozyme Frequency Patterns in DROSOPHILA PAVANI Associated with Geographical and Seasonal Variables

Fourteen population samples of Drosophila pavani were obtained from a number of localities in Chile. The populations sampled were dispersed over 7 degrees of latitude and 1800 meters of elevation, and were drawn at three different times. Sixteen electrophoretic loci were assayed for each population; eight of the loci were analyzed statistically for geographic variation; the other eight were essentially monomorphic. For all eight variable loci, variation in allelic frequencies among populations was highly significant. In all cases, a significant portion of the variation among populations was associated with variation in gross environmental variables (latitude, elevation, month of collection). The implications of the evidence were discussed, and the authors concluded that there was suggestive evidence for selection.     

Analysis of F ST outliers at allozyme loci in Pacific salmon: implications for natural selection

Natural selection has been invoked to explain the observed geographic distribution of allozyme allele frequencies for a number of teleost species. The effects of selection on allozyme loci in three species of Pacific salmon were tested. A simulation-based approach to estimate the null distribution of population differentiation (F _ST) and test for F _ST outliers was used. This approach showed that a majority of allozyme loci conform to neutral expectations predicted by the simulation model, with relatively few F _ST outliers found. No consistent F _ST outlier loci were found across species. Analysis of population sub-groups based on geography and genetic identity reduced the number of outlier loci for some species, indicating that large geographic groups may include genetically divergent populations and/or that there is geographic heterogeneity in selection pressure upon allozyme loci. Two outlier allozyme loci found in this analysis, lactate dehydrogenase-B and malic enzyme, have been shown to be influenced by selection in other teleost species. This approach is also useful in identifying allozyme loci (or other genetic markers) that meet assumptions for population genetic study.     

ECOLOGICAL GENETICS OF A MOSAIC HYBRID ZONE: MITOCHONDRIAL,NUCLEAR, AND REPRODUCTIVE DIFFERENTIATION OF CRICKETS BY SOIL TYPE

We investigated the effects that habitat variation has on the structure and dynamics of a hybrid zone between two closely related crickets in Connecticut. A collecting protocol was developed in which crickets were sampled from characteristic habitats on either side of the hybrid zone and from two distinct habitat types within the zone. Presumptive pure Gryllus pennsylvanicus were sampled from fields in northwestern Connecticut and represent “inland” populations. “Pure” Gryllus firmus were sampled from beaches along the coast and represent the “coastal” populations. Crickets from within the hybrid zone were sampled from two different soil types: the “loam” populations from loamy soils and the “sand” populations from sandy soils. Moreover, an attempt was made to identify closely adjacent sand and loam localities to determine the scale of habitat variation and its possible effects on hybrid-zone structure. In general, there was little variation in morphological traits or in allozyme and mtDNA genotype frequencies among localities from within each of the four habitat types. Between each of the closely situated sand and loam localities within the hybrid zone, however, there were very significant differences in each of these sets of markers. In addition, crickets from hybrid-zone populations were tested for reproductive isolation. The asymmetric outcome of hybrid crosses that exists across the zone (Harrison, 1983) also exists on a finer ecological scale within the zone. Thus, this hybrid zone is a mosaic of strikingly differentiated populations. The dynamics of hybrid zones with mosaic structures are discussed in contrast to the traditional clinal models. The data are also discussed in light of the semipermeable nature of species boundaries. The extent to which a species boundary is permeable varies not only from one genetic marker to the next, but also with the ecological and geographic context of species interaction.     

Reproductive diapause and life-history clines in North American populations of Drosophila melanogaster

Latitudinal clines are widespread in Drosophila melanogaster, and many have been interpreted as adaptive responses to climatic variation. However, the selective mechanisms generating many such patterns remain unresolved, and there is relatively little information regarding how basic life-history components such as fecundity, life span and mortality rates vary across environmental gradients. Here, it is shown that four life-history traits vary predictably with geographic origin of populations sampled along the latitudinal gradient in the eastern United States. Although such patterns are indicative of selection, they cannot distinguish between the direct action of selection on the traits in question or indirect selection by means of underlying genetic correlations. When independent suites of traits covary with geography, it is therefore critical to separate the widespread effects of population source from variation specifically for the traits under investigation. One trait that is associated with variation in life histories and also varies with latitude is the propensity to express reproductive diapause; diapause expression has been hypothesized as a mechanism by which D. melanogaster adults overwinter, and as such may be subject to strong selection in temperate habitats. In this study, recently derived isofemale lines were used to assess the relative contributions of population source and diapause genotype in generating the observed variance for life histories. It is shown that although life span, fecundity and mortality rates varied predictably with geography, diapause genotype explained the majority of the variance for these traits in the sampled populations. Both heat and cold shock resistance were also observed to vary predictably with latitude for the sampled populations. Cold shock tolerance varied between diapause genotypes and the magnitude of this difference varied with geography, whereas heat shock tolerance was affected solely by geographic origin of the populations. These data suggest that a subset of life-history parameters is significantly influenced by the genetic variance for diapause expression in natural populations, and that the observed variance for longevity and fecundity profiles may reflect indirect action of selection on diapause and other correlated traits.