Butterfly wings: Colour patterns and now gene expression patterns

The particular fascination of butterfly wings for developmental biologists (and others) lies in their spectacular array of colour patterns. The evolutionary and developmental relationships between these patterns have been analysed and we know something of the cell interactions involved in their formation⁽¹⁾. Now butterfly homologues of Drosophila wing-patterning genes have been identified, and their expression patterns offer the first clues to the molecular mechanisms which specify wing colour patterns⁽²⁾.     

Genetic structure of Quechua-speakers of the Central Andes and geographic patterns of gene frequencies in South Amerindian populations

A sample of 141 Quechua-speaking individuals of the population of Tayacaja, in the Peruvian Central Andes, was typed for the following 16 genetic systems: ABO, Rh, MNSs, P, Duffy, AcP1, EsD, GLOI, PGM1, AK, 6-PGD, Hp, Gc, Pi, C3, and Bf. The genetic structure of the population was analyzed in relation to the allele frequencies available for other South Amerindian populations, using a combination of multivariate and multivariable techniques. Spatial autocorrelation analysis was performed independently for 13 alleles to identify patterns of gene flow in South America as a whole and in more specific geographic regions. We found a longitudinal cline for the AcP1*a and EsD*1 alleles which we interpreted as the result of an ancient longitudinal expansion of a putative ancestral population of modern Amerindians. Monmonnier's algorithm, used to identify areas of sharp genetic discontinuity, suggested a clear east-west differentiation of native South American populations, which was confirmed by analysis of the distribution of genetic distances. We suggest that this pattern of genetic structures is the consequence of the independent peopling of western and eastern South America or to low levels of gene flow between these regions, related to different environmental and demographic histories.     

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.     

Comparison of erythrocyte markers gene frequencies in different populations

A comparison of erythrocyte markers (ABO, Rh system) gene frequencies was done by bar code diagrams in populations of variable ethnic origin. The results from missions for the development in Far East Asia (China, Indochina, New Guinea) were compared to well known gene frequencies of the populations living in other regions: inhabitants of the islands of the Pacific ocean, Europeans of New Zealand and Western Europe (France), Europeans of North America, Ameridans of Peru and Bolivia, Somalians of Africa. Polymorphism was observed in immense country very peopled, monomorphism was found in small and isolated region but polymorphism existed in tribes living in very isolated islands.     

Estimates of gene frequencies in two heterotic maize populations

Summary The present study was undertaken to obtain information on average gene frequency in two heterotic populations of maize (Zea mays L.), Mezcla Amarillo Selection (MAS) and J607. Sixty-four male plants were taken in each of the populations and each of these were crossed to a different set of eight plants, four of which belonged to the same population and four to the other population. This resulted in two groups of intra-population (within MAS and within J607) and two groups of inter-population (MAS X J607 and J607 X MAS) progenies. Each group consisted of 256 full-sib progenies on the pattern of the North Carolina Design I mating system. The male plants were selfed to produce 64 S₁ prgenies in each population. The materials were evaluated at two diverse locations, Ludhiana and Gurdaspur, for grain yield, ear length, ear girth, number of kernel rows, plant height, ear height and days to silk. An incomplete block design with two replications were used. The plot consisted of a 5 m long row. Ratios of estimated genetic components of variance and covariance were compared with corresponding theoretical ratios computed for a single locus for various gene frequencies and levels of dominance, and approximate ranges of the gene frequencies and their relative magnitude were worked out in the two populations. The average frequency of favourable genes for plant height was estimated as 0.6 in MAS and 0.8 in J607. For grain yield the average gene frequency was 0.8 to 0.9 in MAS and 0.7 to 0.8 in J607 whereas for ear height it was 0.5 to 0.7 in MAS and 0.4 to 0.6 in J607. The gene frequency in the two populations seemed to be similar for days to silk, ear length, ear girth and kernel rows.     

Diversity of some gene frequencies in European and Asian populations. VI. Geographic patterns of PGM and ACP

Genetic variation at the phosphoglucomutase-1 (PGM) and acid phosphatase (ACP) loci, in 160 and 120 European and Asian populations, respectively, is described by spatial autocorrelation statistics and directional variograms. Short-distance patterns of gene frequencies correspond to those predicted by models of isolation by distance, but long-range differentiation of populations is observed as well. A possible role of climatic selection in maintaining the PGM polymorphism is supported by the north-south orientation of the gradient for that locus, but not by biochemical evidence. By and large, the observed patterns of gene frequencies seem to reflect a combination of demographic processes, subdivision and isolation of local populations among them.     

Statistics of natural populations. III. Sequential sampling plans for the estimation of gene frequencies

In previous work several models have been developed for genetic surveys of natural populations. Parents of unknown genotype are collected from a natural population, polymorphic at a single genetic locus. From each of these N cryptic parents a number of offspring are identified for their genotype. Our problem is to select an efficient offspring sampling plan for estimating the frequency of an allele in the cryptic adult population based on the N family profiles of juvenile genotypes. A criterion called the information per unit cost of observation is introduced to evaluate sequential sampling plans, in which the number of offspring per family examined is random. Some simple, practical schemes for stopping the sampling of offspring from a collected parent are introduced; one example is stopping when: (i) the offspring are definitive about the parental genotype(s) for the first time; (ii) a fixed number of one genotype only is seen; or (iii) a fixed maximum feasible number of offspring have been genotyped. This sampling scheme is recommended. For each sampling scheme, the best linear unbiased estimator and the sequential maximum likelihood estimator of the allele frequency are characterized. From the moments of these estimators, it is then possible to tabulate efficient sequential sampling plans, which are better (in the sense of information per unit cost), just as simple, and less costly than corresponding fixed sampling plans in use.     

Mitochondrial DNA haplotype frequencies in natural and experimental populations of Drosophila subobscura.

The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Esporles (Majorca, Balearic Islands, Spain). This population, like other European ones, is characterized by the presence of two very common (>96%) mitochondrial haplotypes (called I and II) and rare and endemic haplotypes that appear at very low frequencies. There is no statistical evidence of positive Darwinian selection acting on the mitochondrial DNA variants according to Tajima''s neutrality test. Two experimental populations, with one replicate each, were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. Both populations were started with the two most frequent mitochondrial haplotypes, but at different initial frequencies. After 13 to 16 generations, haplotype II reached fixation in three cages and its frequency was 0.89 by generation 25 in the fourth cage. Random drift can be rejected as the force responsible for the observed changes in haplotype frequencies. There is not only statistical evidence of a linear trend favoring a mtDNA (haploid) fitness effect, but also of a significant nonlinear deviation that could be due to a nuclear component.     

Principal component analysis of gene frequencies of Chinese populations

Principal components (PCs) were calculated based on gene frequencies of 130 alleles at 38 loci in Chinese populations, and geographic PC maps were constructed. The first PC map of the Han shows the genetic difference between Southern and Northern Mongoloids, while the second PC indicates the gene flow between Caucasoid and Mongoloids. The first PC map of the Chinese ethnic minorities is similar to that of the second PC map of the Han, while their second PC map is similar to the first PC map of the Han. When calculating PC with the gene frequency data from both the Han and ethnic minorities, the first and second PC maps most resemble those of the ethnic minorities alone. The third and fourth PC maps of Chinese populations may reflect historical events that allowed the expansion of the populations in the highly civilized regions. A clear-cut boundary between Southern and Northern Mongoloids in the synthetic map of the Chinese populations was observed in the zone of the Yangtze River. We suggest that the ancestors of Southern and Northern Mongoloids had already separated before reaching Asia. The ancestors of the Southern Mongoloids may result from the initial expansion from Africa or the Middle East, via the south coast of Asia, toward Southeast Asia, and ultimately South China. Upon reaching the Yangtze River, they might even have crossed the river to occupy the nearby regions for a period of time. The ancestors of the Northern Mongoloids probably expanded from Africa via the Northern Pamirs, first went eastward, then towards the south to reach the Yangtze River. The expansion of the Northern Mongoloids toward the south of the Yangtze River happened only in the last 2 or 3 thousand years.     

Principal component analysis of gene frequencies of Chinese populations

Principal components (PCs) were calculated based on gene frequencies of 130 alleles at 38 loci in Chinese populations, and geographic PC maps were constructed. The first PC map of the Han shows the genetic difference between Southern and Northern Mongoloids, while the second PC indicates the gene flow between Caucasoid and Mongoloids. The first PC map of the Chinese ethnic minorities is similar to that of the second PC map of the Han, while their second PC map is similar to the first PC map of the Han. When calculating PC with the gene frequency data from both the Han and ethnic minorities, the first and second PC maps most resemble those of the ethnic minorities alone. The third and fourth PC maps of Chinese populations may reflect historical events that allowed the expansion of the populations in the highly civilized regions. A clear-cut boundary between Southern and Northern Mongoloids in the synthetic map of the Chinese populations was observed in the zone of the Yangtze River. We suggest that the a     

Genetic variation in natural populations: patterns and theory.

Allozymic variation in natural populations of plants, animals, and humans based on studies published prior to early 1976 and involving 243 species, in which 14 or more loci were tested, is herein reviewed. Explanatory models are compared and contrasted in view of the evidence to see which theories best explain genetic variation in natural populations. The analysis suggests that the amounts of genetic polymorphism and heterozygosity vary nonrandomly between loci, populations, species, habitats, and life zones, and are correlated with ecological heterogeneity. Natural selection, in some form, may often be the major determinant of genetic population structure and differentiation. Yet precise critical experiments must be designed to test possible alternative hypotheses, to establish direct cause-effect relationships between ecological and genetic profiles, and to assay the contribution of single and multilocus structures to fitness.     

Methods for estimating gene frequencies and detecting selection in bacterial populations

Recent breakthroughs in molecular technology, most significantly the polymerase chain reaction (PCR) and in situ hybridization, have allowed the detection of genetic variation in bacterial communities without prior cultivation. These methods often produce data in the form of the presence or absence of alleles or genotypes, however, rather than counts of alleles. Using relative allele frequencies from presence-absence data as estimates of population allele frequencies tends to underestimate the frequencies of common alleles and overestimate those of rare ones, potentially biasing the results of a test of neutrality in favor of balancing selection. In this study, a maximum-likelihood estimator (MLE) of bacterial allele frequencies designed for use with presence-absence data is derived using an explicit stochastic model of the host infection (or bacterial sampling) process. The performance of the MLE is evaluated using computer simulation and a method is presented for evaluating the fit of estimated allele frequencies to the neutral infinite alleles model (IAM). The methods are applied to estimate allele frequencies at two outer surface protein loci (ospA and ospC) of the Lyme disease spirochete, Borrelia burgdorferi, infecting local populations of deer ticks (Ixodes scapularis) and to test the fit to a neutral IAM.     

Estimating levels of gene flow in natural populations

The results from a simulation model of selection, mutation and genetic drift in a geographically subdivided population are presented. The infinite-alleles mutation model of Kimura and Crow (1964) is asumed, and both advantageous and deleterious mutations are considered. It is shown that the average frequency of an allele conditioned on the number of local populations it appears in-the conditional average frequency-is approximately independent of both the selection intensity and mutation rates assumed, but depends strongly on the overall level of gene flow. This result justifies the use of the conditional average frequency to obtain a rough estimate of the level of gene flow in a subdivided population. Data from 16 species are presented and discussed. There are large differences in the conditional average frequencies of different species, although there is some consistency within taxa. Some species apparently have high levels of gene flow and others, particularly salamanders, have low levels. Alternative explanations for the patterns found in the data are considered.     

Correlation of gene frequencies between neutral linked genes in finite populations

The mean squared correlation (r²) of gene frequencies between two selectively neutral loci in segregating populations is obtained using an approximation based on expanding the formula for r² in terms up to eighth moments. The moments are evaluated for all populations, whether segregating or not, but when combined with the probability of segregation, quite accurate results are obtained. Formulae for the moments and an approximation for the probability of segregation are given for populations of large size (N) and small recombination fraction (c). The method is extended to evaluate the variance of r². The coefficient of variation of r² exceeds unity for a wide range of Nc values.     

Contrasting patterns of natural variation in global Drosophila melanogaster populations

Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey using neutral microsatellites and mitochondrial sequence variation jointly. Thirty-five populations originating from five continents were compared. In agreement with previous microsatellite studies, sub-Saharan African populations were the most variable ones. Consistent with previous reports of a single 'out of Africa' habitat expansion, we found that non-African populations contained a subset of the African alleles. The pattern of variation detected for the mitochondrial sequences differed substantially. The most divergent haplotypes were detected in the Mediterranean region while Africa harboured most haplotypes, which were all closely related. In the light of the well-established African origin of D. melanogaster, our results cast severe doubts about the suitability of mtDNA for biogeographic inference in this model organism.     

Variation in tissue-specific gene expression among natural populations

Background

Variation in gene expression is extensive among tissues, individuals, strains, populations and species. The interactions among these sources of variation are relevant for physiological studies such as disease or toxic stress; for example, it is common for pathologies such as cancer, heart failure and metabolic disease to be associated with changes in tissue-specific gene expression or changes in metabolic gene expression. But how conserved these differences are among outbred individuals and among populations has not been well documented. To address this we examined the expression of a selected suite of 192 metabolic genes in brain, heart and liver in three populations of the teleost fish Fundulus heteroclitus using a highly replicated experimental design.

Results

Half of the genes (48%) were differentially expressed among individuals within a population-tissue group and 76% were differentially expressed among tissues. Differences among tissues reflected well established tissue-specific metabolic requirements, suggesting that these measures of gene expression accurately reflect changes in proteins and their phenotypic effects. Remarkably, only a small subset (31%) of tissue-specific differences was consistent in all three populations.

Conclusions

These data indicate that many tissue-specific differences in gene expression are unique to one population and thus are unlikely to contribute to fundamental differences between tissue types. We suggest that those subsets of treatment-specific gene expression patterns that are conserved between taxa are most likely to be functionally related to the physiological state in question.