Rapid Concerted Evolution via Gene Conversion at the <Emphasis Type="BoldItalic">Drosophila hsp70</Emphasis> Genes

We analyzed nucleotide variation in the hsp70 genes of Drosophila melanogaster (five genes) and D. simulans (four genes) to characterize the homogenizing and diversifying roles of gene conversion in their evolution. Gene conversion within and between the 87A7 and 87C1 gene clusters homogenize the hsp70 coding regions; in both D. melanogaster and D. simulans, same-cluster paralogues are virtually identical, and large intercluster conversion tracts diminish 87A7/87C1 divergence. Same-cluster paralogues share many polymorphisms, consistent with frequent intracluster conversion. Shared polymorphism is highly biased toward silent variation; homogenizing conversion interacts with purifying selection. In contrast to the coding regions, some hsp70 flanking regions show conversion-mediated diversification. Strong reductions of nucleotide variability and linkage disequilibria among conversion-mediated sites in hsp70Ab and hsp70Bb alleles sampled from a single natural population are consistent with a selective sweep. Comparison of the D. melanogaster and D. simulans hsp70 genes reveals whole-family fixed differences, consistent with rapid propagation of novel mutations among duplicate genes. These results suggest that the homogenizing and diversifying roles of conversion interact to drive dynamic concerted evolution of the hsp70 genes. Received: 25 June 2001 / Accepted: 10 October 2001     

Worldwide allele frequencies of the human apolipoprotein E gene: Climate,local adaptations,and evolutionary history

The ?4 allele of the apolipoprotein E (APOE) gene is associated with increased cholesterol levels and heart disease. Population allele frequencies of APOE have previously been shown to vary, with ?4 frequencies generally increasing with latitude. We hypothesize that this trend resulted from natural selection protecting against low‐cholesterol levels. In high‐latitude cold environments and low‐latitude hot environments, metabolic rate is elevated, which could require higher cholesterol levels. To explore this hypothesis, we compiled APOE allele frequencies, latitude, temperature, and elevation from populations around the world. ?4 allele frequencies show a curvilinear relationship with absolute latitude, with lowest frequencies found in the mid‐latitudes where temperatures generally require less expenditure on cooling/thermogenesis. Controlling for population structure in a subset of populations did not appreciably change this pattern of association, consistent with selection pressures that vary by latitude shaping ?4 allele frequencies. Temperature records also predict APOE frequency in a curvilinear fashion, with lowest ?4 frequencies at moderate temperatures. The model fit between historical temperatures and ?4 is less than between latitude and ?4, but strengthened after correcting for estimated temperature differences during the Paleolithic. Contrary to our hypothesis, we find that elevation did not improve predictive power, and an integrated measure of the cholesterol effect of multiple APOE alleles was less related to latitude than was ?4 alone. Our results lend mixed support for a link between past temperature and human APOE allele distribution and point to the need to develop better models of past climate in future analyses. Am J Phys Anthropol 143:13–20, 2010. © 2010 Wiley‐Liss, Inc.     

Hsp70 duplication in the Drosophila melanogaster species group: how and when did two become five?

To determine how the modern copy number (5) of hsp70 genes in Drosophila melanogaster evolved, we localized the duplication events that created the genes in the phylogeny of the melanogaster group, examined D. melanogaster genomic sequence to investigate the mechanisms of duplication, and analyzed the hsp70 gene sequences of Drosophila orena and Drosophila mauritiana. The initial two-to-four hsp70 duplication occurred 10--15 MYA, according to fixed in situ hybridization to polytene chromosomes, before the origin and divergence of the melanogaster and five other species subgroups of the melanogaster group. Analysis of more than 30 kb of flanking sequence surrounding the hsp70 gene clusters suggested that this duplication was likely a retrotransposition. For the melanogaster subgroup, Southern hybridization and an hsp70 restriction map confirmed the conserved number (4) and arrangement of hsp70 genes in the seven species other than D. melanogaster. Drosophila melanogaster is unique; tandem duplication and gene conversion at the derived cluster yielded a fifth hsp70 gene. The four D. orena hsp70 genes are highly similar and concertedly evolving. In contrast, the D. mauritiana hsp70 genes are divergent, and many alleles are nonfunctional. The proliferation, concerted evolution, and maintenance of functionality in the D. melanogaster hsp70 genes is consistent with the action of natural selection in this species.     

DNA sequence variation and latitudinal associations in hsp23, hsp26 and hsp27 from natural populations of Drosophila melanogaster

Heat shock genes are considered to be likely candidate genes for environmental stress resistance. Nucleotide variation in the coding sequence of the small heat shock genes (hsps) hsp26 and hsp27 from Drosophila melanogaster was studied in flies originating from the Netherlands and eastern Australia. The hsp26 gene was polymorphic for an insertion/deletion of three extra amino acids and two nonsynonymous changes in all populations. The hsp27 gene exhibited two nonsynonymous changes and three synonymous mutations. The hsp26 polymorphism showed a latitudinal cline along the east coast of Australia. This pattern was not confounded by the fact that the shsps are located in the inversion In(3 L)P which also shows a latitudinal cline in eastern Australia. A similar latitudinal cline was found for the previously described variation in hsp23, while frequencies of hsp27 alleles did not change with latitude. These findings suggest that variation at two of the shsps or closely linked loci are under selection in natural populations of D. melanogaster.     

S-element insertions are associated with the evolution of the Hsp70 genes in Drosophila melanogaster

The "selfish DNA" theory postulates that transposable elements (TEs) are intragenomic parasites, and that natural selection against deleterious effects associated with their presence is the main force preventing their genomic spread in natural populations. In agreement with this model, TEs in Drosophila melanogaster populations are usually found at low frequencies in most genomic locations. Only a few cases of fixation of TE insertions have been reported, usually in regions of low recombination, where selection is expected to be less effective. Here, we report a population genetics study on the apparent fixation of an S-element in a highly recombining region in two natural populations of D. melanogaster. Three similar fragments of an S-element are inserted into the 5' regions of three members of a heat shock gene family, Hsp70 (Hsp70Aa and Hsp70Ab in polytene chromosome band 87A, and Hsp70Bb in 87C). A PCR-based analysis suggests that the insertions are fixed or at high frequencies in the entire species. A population survey of the levels of nucleotide sequence variation at the insertion site in 87C in two natural populations of D. melanogaster provided evidence for reduced levels of variation in the region, normal levels of recombination, and selection, reflected in a significant departure from neutrality of the variant frequency spectrum. This was particularly strong for the S-element inverted repeats (IRs) and suggests that these are of functional significance for the host.     

Physiological stress and the maintenance of adaptive genetic variation in a livebearing fish

The importance of genetic variation in evolution is well established. Yet, the mechanisms by which genetic variation—particularly variation in traits under selection—is maintained in natural populations has long been an evolutionary puzzle. Understanding individual variables driving selection and their functional mechanisms is increasingly important in the context of global change and its potential consequences for biodiversity. Here we examined intra-population performance among allelic variants of a pleiotropic locus in response to thermal stress in the variable platyfish, Xiphophorus variatus. The wild-type tailspot allele exhibited significantly lower heat tolerance than all three pattern alleles found in the population, conforming to predictions based on previously observed correlations between temperature and pattern frequencies in the wild. Furthermore, differences between tailspot pattern frequencies in adults and juveniles were broadly consistent with this trend. Thus, it appears that physiological stress and reduced performance of the wild-type allele at higher relative temperatures is a mechanism balancing its frequency in natural populations. Temperature variation and not dissolved oxygen alone, as previously reported, is likely a important abiotic variable contributing to the maintenance of adaptive polymorphism. Furthermore, our findings underscore the potential implications of rising temperatures and physiological stress for levels of genetic variation in natural populations.     

Evolution of a length polymorphism in the human PER3 gene, a component of the circadian system

Period homologue 3 (PER3) is a component of the mammalian circa-dian system, although its precise role is unknown. A biallelic variable number tandem repeat (VNTR) polymorphism exists in human PER3, consisting of 4 or 5 repeats of a 54-bp sequence in a region encoding a putative phosphorylation domain. This polymorphism has previously been reported to associate with diurnal preference ("morningness" and "eveningness") and delayed sleep-phase syndrome. We have investigated the global allele frequencies of this variant in ethnically distinct indigenous populations. All populations were polymorphic, with the shorter (4-repeat) allele ranging in frequency from 0.19 (Papua New Guinea) to 0.89 (Mongolia). To investigate if allele frequency has been influenced by natural selection, the authors 1) tested for a correlation with latitude and mean annual insolation (incident sunlight energy), using classical markers to correct for historical population differentiation; and they 2) compared allele-frequency difference between European American, African American, and East Asian populations, as measured using F(ST), to an empirical null distribution of F(ST)values based on a genome-wide dataset of single nucleotide polymorphisms (SNPs) of presumed neutral loci that were previously typed by The SNP Consortium. The variation in allele frequencies between indigenous populations did not show a pattern that would indicate selective pressure on PER3resulting from day-length variation or mean annual insolation, and the allele-frequency difference between European Americans, African Americans, and East Asians was not an outlier when compared to the distribution for presumed neutral SNPs. We therefore find no evidence for differential or balancing selection in the contemporary pattern of global PER3allele frequencies.     

Identification of a candidate adaptive polymorphism for Drosophila life history by parallel independent clines on two continents

Life history traits are critical components of fitness and frequently reflect adaptive responses to environmental pressures. However, few genes that contribute to natural life history variation have been identified. Insulin signalling mediates the determination of life history traits in many organisms, and single gene manipulation in Drosophila melanogaster suggests that individual genes in the pathway have the potential to produce major effects on these quantitative traits. We evaluated allelic variation at two insulin signalling genes, the Insulin‐like Receptor (InR) and its substrate, chico, in natural populations of D. melanogaster. We found different patterns of variation: InR shows evidence of positive selection and clines in allele frequency across latitude; chico exhibits neutral patterns of evolution. The clinal patterns at InR are replicated between North America and Australia, showing striking similarity in the distribution of specific alleles and the rate at which allele frequencies change across latitude. Moreover, we identified a polymorphism at InR that appears to be functionally significant and consistent with hypothetical patterns of selection across geography. This polymorphism provides new characterization of genic regions of functionality within InR, and is likely a component in a suite of genes and traits that respond adaptively to climatic variation.     

Genetic drift within a protected polymorphism: enigmatic variation in color-morph frequencies in the candy-stripe spider, Enoplognatha ovata

The candy-stripe spider, Enoplognatha ovata, exhibits a striking color polymorphism comprising three morphs. A number of lines of evidence strongly suggest that this polymorphism is maintained by natural selection: its presence in a sister species, E. latimana; the physical nature of the variation; the virtual lack of monomorphic populations; the highly consistent rank-order of morphs within populations; and the presence of large-scale clines associated with climatic variables. However, the absence of selection is equally strongly suggested by very local surveys of morph frequencies over space and time, perturbation experiments, and a variance in morph frequency between populations that is virtually independent of spatial scale. In addition, local spatial patterns in one study site (Nidderdale, Yorkshire, England) have been explained in terms of intermittent drift over half a century ago, a hypothesis supported here by the distributions of four other genetic markers (two allozyme and two visible polymorphisms). A heuristic model is suggested that reconciles these apparently contradictory messages regarding the importance of drift and selection in this system. It is proposed that when allele frequencies of the color morph redimita lie between approximately 0.05 and 0.3, the deltaq on q plot is very shallow, so that within this region, where the majority of populations lie, selection is weak and drift is the major force determining local morph frequencies. However, outside this range of frequencies, powerful selection acts to protect the polymorphism. This model may apply to polymorphisms in other species and explain why evidence of selection in natural populations is often elusive.     

THE INTENSITY OF SELECTION ACTING ON THE COUCH POTATO GENE—SPATIAL–TEMPORAL VARIATION IN A DIAPAUSE CLINE

Cosmopolitan populations of Drosophila melanogaster have co‐opted a form of reproductive diapause to overwinter in northern populations. Polymorphism in the couch potato gene has been implicated in genetic variation for this diapause trait. Using a collection of 20 populations from Florida to Canada and 11 collections from 3 years in a Pennsylvania orchard, we estimated the allele frequencies for 15 single nucleotide polymorphisms (SNPs) in the couch potato gene. These include the specific polymorphism associated with diapause inducability. We find that the SNP polymorphism, 48034(A/T), is correlated with latitude and its frequencies are predicted by the incidence of diapause trait. We find that the clinal patterns for cpo SNPs sampled in 1997 are similar to the same SNPs sampled in 2009–2010. SNPs that show apparent associations with cpo expression are also clinal with the low‐expression allele increasing in frequency, as would be predicted from functional knockout studies of cpo. Finally, we see a significant pattern where the frequency of the diapause‐causing allele drops in frequency during the summer season, consistent with the drop in the incidence of the diapause trait. The selection required to drive this response is large, roughly 24% to 59% per generation depending on the degree of dominance.     

Molecular Evolution of a Pervasive Natural Amino-Acid Substitution in Drosophila cryptochrome

Genetic variations in circadian clock genes may serve as molecular adaptations, allowing populations to adapt to local environments. Here, we carried out a survey of genetic variation in Drosophila cryptochrome (cry), the fly’s dedicated circadian photoreceptor. An initial screen of 10 European cry alleles revealed substantial variation, including seven non-synonymous changes. The SNP frequency spectra and the excessive linkage disequilibrium in this locus suggested that this variation is maintained by natural selection. We focused on a non-conservative SNP involving a leucine - histidine replacement (L232H) and found that this polymorphism is common, with both alleles at intermediate frequencies across 27 populations surveyed in Europe, irrespective of latitude. Remarkably, we were able to reproduce this natural observation in the laboratory using replicate population cages where the minor allele frequency was initially set to 10%. Within 20 generations, the two allelic variants converged to approximately equal frequencies. Further experiments using congenic strains, showed that this SNP has a phenotypic impact, with variants showing significantly different eclosion profiles. At the long term, these phase differences in eclosion may contribute to genetic differentiation among individuals, and shape the evolution of wild populations.     

Population distribution of the methionine allele at the PRNP codon 129 polymorphism in Europe and the Middle East

Methionine homozygosity at codon 129 of the prion protein gene is a risk factor for Creutzfeldt-Jakob disease. Knowledge of M129V polymorphism in normal populations may contribute to a better understanding of prion diseases. M129V polymorphism was studied in 2201 normal subjects, originating from 15 populations from Europe and the Middle East. Mean heterozygosity in these populations is 38.9%, and there is some significant geographic heterogeneity between them. A comparison of M129 allele frequencies in these 15 populations to those already published for 8 European countries plus Turkey shows significant correlations with both latitude (r = -0.77) and longitude (r = 0.69). The geographic map of methionine allele frequencies indicates an east-west gradient of decreasing methionine allele values from the Middle East to Western Europe.     

Studies of esterase 6 in Drosophila melanogaster XII. Evidence for temperature selection of Est 6 and Adh alleles

Changes in allele frequencies at the esterase 6 (Est 6) and alcohol dehydrogenase (Adh) enzyme loci of Drosophila melanogaster and simulans are examined in natural populations and artificial populations maintained at two temperatures. Results from cage populations at 18 °C and 25 °C provide evidence for temperature selection at both loci. Seasonal population samples show no significant change in gene frequencies for either locus, a reasonable outcome given the small selection coefficients found in cage populations. The temperature effect for the Adh locus appears to be direct: natural selection of the fast allele in cool environs and of the slow allele in warm environs. The temperature effect for Est 6 is weaker and complicated by sex differences and deviations from Hardy-Weinberg expectation. This evidence and different Est 6 frequencies found for melanogaster and simulans, in conjunction with evidence of the male reproductive function of this enzyme, suggest that Est 6 polymorphisms are maintained in natural populations by a complex form of sexual selection.     

Association of hsp70-2 and hsp-hom gene polymorphisms with risk of acute high-altitude illness in a Chinese population

High-altitude illness (HAI) is a potentially fatal condition involving genetic and environmental components. Accumulated experimental evidence suggests that heat shock proteins (Hsps), especially HSP70, can protect cells and organs against different types of damage. We investigated whether genetic variation in constitutive and inducible hsp70 genes could be associated with risk of HAI. The association between polymorphisms of the HSP70 family genes and risk of HAI was determined in 56 patients with HAI and in 100 matched controls by genotyping for the polymorphisms +190 G/C, +1267 A/G, 2437 G/C in the hsp70-1, hsp70-2, and hsp70-hom genes by using polymerase chain reaction-restriction fragment length polymorphism. The data showed that there was no statistically significant difference in the genotype and allele distributions of hsp70-1, in hsp70-2 allele and hsp70-2 A/A and A/B genotypes, and in allele distribution of hsp70-hom among patients with HAI and controls (chi2 test, P > 0.05). However, there was a significantly higher frequency of hsp70-2 B/B and hsp70-hom A/A and B/B genotypes and a significantly lower frequency of the hsp70-hom A/B genotype in the HAI patients compared with the controls (P < 0.05 for all). The risk associated with the hsp70-2 B/B and hsp70-hom A/A, A/B, and B/B genotypes were 4.017 (95% CI = 1.496-10.781; P = 0.004), 2.434 (95% CI = 1.184-5.003; P = 0.012), 0.299 (95% CI = 0.148-0.602, P = 0.001), and 5.880 (95% CI =1.145-30.196, P = 0.026), respectively. Our results suggest that individuals with hsp70-2 B/B and hsp70-hom A/B and B/B genotypes may be more susceptible to HAI, whereas those with hsp70-hom A/B genotype may be tolerant to HAI. Further studies in individuals of different age and sex are warranted to elucidate the underlying mechanisms of this association and the possible functions of different genotypes of hsp70-2 and hsp70-hom under hypoxic stress.     

FERTILITY SELECTION ON A DISCRETE FLORAL POLYMORPHISM IN CLARKIA (ONAGRACEAE)

This study investigated fertility selection on a flower petal pigmentation polymorphism in Clarkia gracilis ssp. sonomensis. Natural populations are typically composed of nearly 100% spotted-petal plants, although rare populations contain a majority of unspotted plants. I compared fitness values for the two morphs using a simple fertility model to estimate selection for experimental arrays of plants placed into existing populations of different phenotypic frequencies. Both male and female reproductive success were estimated as well as the pattern of mating among phenotypes. Although the separate fitness components varied from no differences to a strong advantage for spotted plants, for every situation the selection calculations predicted an increase in the frequency of the spotted allele. Pollinator behavior and postpollination mechanisms may be responsible for the fitness differences. The apparent inability of the unspotted allele to spread though most natural populations is consistent with its selective disadvantage in this study.     

Is there really natural selection affecting the l frequencies (long hair) in the Brazilian cat populations?

The scientific literature on cat genetics contains a presumed typical example of natural selection affecting l frequencies (long hair) in 16 Brazilian cat populations. It has been observed that the hotter and more tropical the climate in Brazil, the lower the values of l frequencies in the cat populations. Nevertheless, this study of some new cat populations in Latin America showed that all of them, independent of the climate, had high or very high l frequencies. l postulate that an alternative migrational-historical hypothesis exists that explains the correlation between the l frequencies and climate characteristics (which are correlated with the latitude) without using natural selection explanations concerning the appearance of the l allele in Brazil.     

Near Fixation of 374l Allele Frequencies of the Skin Pigmentation Gene SLC45A2 in Africa

The L374F polymorphism of the SLC45A2 gene, encoding the membrane-associated transporter protein that plays an important role in melanin synthesis, has been suggested to be associated with skin color in human populations. In this study, the detailed distribution of the 374f and 374l alleles has been investigated in 2,581 unrelated subjects from 36 North, East, West, and Central African populations. We found once more the highly significant (p < 0.001) correlation coefficient (r = 0.957) cline of 374f frequencies with degrees of latitude in European and North African populations. Almost all the African populations located below 16° of latitude are fixed for the 374l allele. Peul, Toucouleur, and Soninké populations have 374l allele frequencies of 0.06, 0.03, and 0.03, respectively.     

The effects of heat shock and acclimation temperature on hsp70 and hsp30 mRNA expression in rainbow trout: in vivo and in vitro comparisons

Heat shock (25° C) of 10° C-acclimated rainbow trout Oncorhynchus mykiss led to increases in heat shock protein 70 (hsp70) mRNA in blood, brain, heart, liver, red and white muscle, with levels in blood being amongst the highest. Hsp30 mRNA also increased with heat shock in all tissues with the exception of blood. When rainbow trout blood was heat shocked in vitro , both hsp70 and hsp30 mRNA increased significantly. In addition, these in vitro experiments demonstrated that blood from fish acclimated to 17° C water had a lower hsp70 mRNA heat shock induction temperature than did 5° C acclimated fish (20 v. 25° C). The hsp30 mRNA induction temperature (25° C), however, was unaffected by thermal acclimation. While increases in hsp70 mRNA levels in blood may serve as an early indicator of temperature stress in fish, tissue type, thermal history and the particular family of hsp must be considered when evaluating stress by these molecular means.     

A General Model of Negative Frequency Dependent Selection Explains Global Patterns of Human ABO Polymorphism

The ABO locus in humans is characterized by elevated heterozygosity and very similar allele frequencies among populations scattered across the globe. Using knowledge of ABO protein function, we generated a simple model of asymmetric negative frequency dependent selection and genetic drift to explain the maintenance of ABO polymorphism and its loss in human populations. In our models, regardless of the strength of selection, models with large effective population sizes result in ABO allele frequencies that closely match those observed in most continental populations. Populations must be moderately small to fall out of equilibrium and lose either the A or B allele (N_e ≤ 50) and much smaller (N_e ≤ 25) for the complete loss of diversity, which nearly always involved the fixation of the O allele. A pattern of low heterozygosity at the ABO locus where loss of polymorphism occurs in our model is consistent with small populations, such as Native American populations. This study provides a general evolutionary model to explain the observed global patterns of polymorphism at the ABO locus and the pattern of allele loss in small populations. Moreover, these results inform the range of population sizes associated with the recent human colonization of the Americas.