Inversion and allozyme polymorphism show contrasting patterns of microgeographical population structure in a natural population of Drosophila buzzatii from Argentina

Second chromosome inversions and genotypic frequencies at seven allozyme loci were determined in a natural population of the cactophilic species Drosophila buzzatii that uses as breeding sites the necrotic cladodes of the prickly pear Opuntia quimilo and the rotting stems of cardón, Trichocereus terschekii. Different processes govern the evolutionary fate of inversion and allozyme polymorphisms. A pattern of heterotic balance for inversions seems to be acting uniformly in each breeding site and could depend on different regimes of density‐dependent selection within cactus hosts. Patterns of variation of allozymes revealed significant heterogeneity in allele frequencies for Esterase‐1 (Est‐1) among O. quimilo rots and Aldehyde oxidase (Aldox) and Xanthine dehydrogenase (Xdh) among T. terschekii substrates and showed gene‐cactus effects only for Esterase‐2 (Est‐2). Consistent and significant excesses of homozygotes were detected at both the within‐rot and in the total population levels that could be accounted for by diversifying selection among individual breeding sites.     

Inversions fail to account for allozyme clines

Allozyme and inversion data from natural populations of Drosophila melanogaster from the eastern United States were analyzed to determine whether the clines at allozyme loci are due to nonrandom associations with common cosmopolitan inversions. All inversions show strong clines. Clines were large and significant for half of the eight allozyme loci. An analysis of the contribution of inversions to clines of allozyme genes revealed three outcomes: the inversion cline (1) enhanced the allozyme cline, but was only partly responsible, (2) reduced the allozyme cline, and (3) had no effect. The allozyme clines were mainly determined by the pattern of allele frequencies within the chromosomal arrangements. Consequently, it was concluded that allozyme clines would exist in the absence of inversion clines.     

Inference of chromosomal inversion dynamics from Pool‐Seq data in natural and laboratory populations of Drosophila melanogaster

Sequencing of pools of individuals (Pool‐Seq) represents a reliable and cost‐effective approach for estimating genome‐wide SNP and transposable element insertion frequencies. However, Pool‐Seq does not provide direct information on haplotypes so that, for example, obtaining inversion frequencies has not been possible until now. Here, we have developed a new set of diagnostic marker SNPs for seven cosmopolitan inversions in Drosophila melanogaster that can be used to infer inversion frequencies from Pool‐Seq data. We applied our novel marker set to Pool‐Seq data from an experimental evolution study and from North American and Australian latitudinal clines. In the experimental evolution data, we find evidence that positive selection has driven the frequencies of In(3R)C and In(3R)Mo to increase over time. In the clinal data, we confirm the existence of frequency clines for In(2L)t, In(3L)P and In(3R)Payne in both North America and Australia and detect a previously unknown latitudinal cline for In(3R)Mo in North America. The inversion markers developed here provide a versatile and robust tool for characterizing inversion frequencies and their dynamics in Pool‐Seq data from diverse D. melanogaster populations.     

Geographic pattern of allozyme and inversion polymorphism on chromosome O of Drosophila subobscura and its evolutionary origin

The chromosome O of Drosophila subobscura was studied with respect to genetic variability at three enzyme loci (Odh, Me, and Lap-4) and with respect to inversion polymorphism. Population samples were taken from seven localities along a north-south gradient from Sweden and Scotland to Tunisia.The chromosomal analysis revealed clinal frequency changes for gene arrangements from north to south. With the enzyme loci Odh and Me allele frequencies are similar throughout the distribution range. Both loci are located outside the common inversion complex O₃₊₄. On the other hand, frequency changes parallel to those of the gene arrangements were observed for the alleles of the Lap-locus. Nonrandom associations between Lap-alleles and the superimposed gene arrangements O_ST, O₃₊₄, O₃₊₄₊₈, and O₃₊₄₊₂₃ were found. These gene arrangements differ from each other with respect to allele frequencies at the Lap-locus but for a given gene arrangement the relative frequencies of Lap-alleles remain relatively constant along the north-south gradient. Thus allele frequencies at the Lap-locus can be predicted from inversion frequencies.These observations can be interpreted in such a way that the pattern of allozyme variation within gene arrangements is due to founder effects caused by the unique origin of inversions. The gene blocks in the different inversions seem to represent more or less separated gene pools. In polymorphic populations the coexistence of genetically differentiated inversions presumably gives rise to heterotic interaction.     

Latitudinal clines in<Emphasis Type="Italic">Drosophila melanogaster</Emphasis>: Body size,allozyme frequencies,inversion frequencies,and the insulin-signalling pathway

Many latitudinal clines exist inDrosophila melanogaster: in adult body size, in allele frequency at allozyme loci, and in frequencies of common cosmopolitan inversions. The question is raised whether these latitudinal clines are causally related. This review aims to connect data from two very different fields of study, evolutionary biology and cell biology, in explaining such natural genetic variation inD. melanogaster body size and development time. It is argued that adult body size clines, inversion frequency clines, and clines in allele frequency at loci involved in glycolysis and glycogen storage are part of the same adaptive strategy. Selection pressure is expected to differ at opposite ends of the clines. At high latitudes, selection onD. melanogaster would favour high larval growth rate at low temperatures, and resource storage in adults to survive winter. At low latitudes selection would favour lower larval critical size to survive crowding, and increased male activity leading to high male reproductive success. Studies of the insulin-signalling pathway inD. melanogaster point to the involvement of this pathway in metabolism and adult body size. The genes involved in the insulin-signalling pathway are associated with common cosmopolitan inversions that show latitudinal clines. Each chromosome region connected with a large common cosmopolitan inversion possesses a gene of the insulin transmembrane complex, a gene of the intermediate pathway and a gene of the TOR branch. The hypothesis is presented that temperateD. melanogaster populations have a higher frequency of a ’thrifty’ genotype corresponding to high insulin level or high signal level, while tropical populations possess a more ’spendthrift’ genotype corresponding to low insulin or low signal level.     

Latitudinal clines for nucleotide polymorphisms in the Esterase 6 gene of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Previous studies have found non-neutral patterns of nucleotide polymorphism in the promoter and coding regions of Est6 in D. melanogaster. Coding region polymorphism peaks around two closely linked replacement differences associated with the EST6-F/EST6-S allozyme polymorphism. The promoter contains two common, highly diverged haplotype groups, P1 and P7, that differentially affect Est6 expression. Allozyme studies have also revealed latitudinal clines in EST6-F and EST6-S frequencies that recur across continents. Here we analyse nucleotide polymorphisms across the promoter and the region of peak coding sequence polymorphism in 10 Australian populations along a 25° latitudinal gradient in order to examine the basis for the allozyme clines. As with the earlier studies, we find an excess of intermediate to high frequency variants in both the P1/P7 region and around the two EST6-F/EST6-S replacements in some populations. The two EST6-F/EST6-S replacement polymorphisms show latitudinal clines whereas the P1 and P7 groups of promoter haplotypes do not. However the strongest clines are for three co-segregating silent site polymorphisms in a 4 bp stretch at the 3′ end of the sequenced region. Monte Carlo simulations show that the clines for those three sites can explain all others in the data but none of the others can explain those three. Thus the allozyme clines may not reflect selection on either the P1/P7 polymorphism or the two replacements previously associated with the EST6-F/EST-S difference.     

Contrasting patterns of phenotypic variation linked to chromosomal inversions in native and colonizing populations of Drosophila subobscura

In fewer than two decades after invading the Americas, the fly Drosophila subobscura evolved latitudinal clines for chromosomal inversion frequencies and wing size that are parallel to the long‐standing ones in native Palearctic populations. By sharp contrast, wing shape clines also evolved in the New World, but the relationship with latitude was opposite to that in the Old World. Previous work has suggested that wing trait differences among individuals are partially due to the association between chromosomal inversions and particular alleles which influence the trait under consideration. Furthermore, it is well documented that a few number of effective individuals founded the New World populations, which might have modified the biometrical effect of inversions on quantitative traits. Here we evaluate the relative contribution of chromosomal inversion clines in shaping the parallel clines in wing size and contrasting clines in wing shape in native and colonizing populations of the species. Our results reveal that inversion‐size and inversion‐shape associations in native and colonizing (South America) populations are generally different, probably due to the bottleneck effect. Contingent, unpredictable evolution was suggested as an explanation for the different details involved in the otherwise parallel wing size clines between Old and New World populations of D. subobscura. We challenge this assertion and conclude that contrasting wing shape clines came out as a correlated response of inversion clines that might have been predicted considering the genetic background of colonizers.     

Allozyme polymorphisms within and among open-pollinated and adapted exotic populations of maize

Summary Twelve U.S. Corn Belt open-pollinated and five adapted exotic populations of maize (Zea mays L.) were assayed for allozyme (allele) variation at 13 enzyme marker loci. Extensive allozyme variability was observed in all populations studied. No locus was monomorphic over all populations. Each of the lociIdh2, Got1, Mdh2, Pgd1, andPgd2 expressed two allozymes over all populations,Adh1, Acp1, Prx1, andEst1 each had three allozymes present,Est4, Glu1, andEnp1 had five allozymes, andAcp4 had six allozymes present. Significant deviations of genotypic frequencies were detected from Hardy-Weinberg equilibrium frequencies and 94% of average Fixation Index values indicated heterozygote deficiencies, which suggested that nonrandom mating and/or natural selection favoring homozygotes were possible factors affecting the maintenance or loss of genetic variability marked by these enzyme loci. Genetic distance and cluster analyses indicated that the observed genetic variability at the 13 enzyme loci was closely related to Dent and Flint types of maize.     

Analysis of inbreeding in a colonizing population of Drosophila subobscura

An analysis of the effects of inbreeding on the genetic structure of a colonizing population of Drosophila subobscura has been carried out. Species of Drosophila, particularly D. subobscura, may have lethal alleles associated with chromosomal inversions and our aim was to assess the extent to which the genome is balanced in this way. The frequencies of chromosomal inversions were compared between a large population and a set of 72 lines that were maintained by brother-sister mating for 10 generations. Fisher's matrix method was used to calculate the expected homozygosity in these inbred lines for 5 allozyme loci (Aph, Hk-1, Lap, Odh, and Pept-1) used as markers of large chromosomal segments. Furthermore, the expected rates of fixation corresponding to these allozyme loci were also calculated. The results show that the amount of homozygosis observed did not differ significantly from expectations (with the corresponding loss of lines as a consequence of the reduction in viability). However, two deviations from strict neutrality were observed: there was a heterozygote excess at the Lap locus, and the frequency of the O ₅ inversion (always associated with a lethal gene in colonizing populations) was higher than expected.     

Chromosome inversion polymorphisms in Drosophila melanogaster II. Geographic clines and climatic associations in Australasia,North America and Asia

The four paracentric autosomal chromosome inversions In(2L)t, In(2R)NS, In(3L)P and In(3R)R are commonly polymorphic in natural populations of D. melanogaster in Australasia, North America and Asia, with latitudinal clines in the frequencies of each inversion in each region. In each region inversion frequency decreases with increasing distance from the equator, although the precise relationship between frequency and latitude varies between inversions and, for In(2L)t and In(2R)NS, among regions. Each inversion also shows a longitudinal cline in at least one region but none show such a cline in all three. Although no inversion's frequency is associated with the same climatic variable in all three regions, inversion frequencies are generally positively related to annual maximum temperature and, more particularly, minimum temperature and minimum rainfall. The directions of the latitudinal clines and the climatic associations are consonant with evidence from D. melanogaster that inversion frequencies decline in winter. They are also consonant with evidence from some other Drosophila species that inversion heterozygosities are lower at the geographic margins than at the centre of the species' ranges.     

Dissecting adaptive clinal variation: markers, inversions and size/stress associations in Drosophila melanogaster from a central field population

Many organisms show latitudinal variation for quantitative traits that is assumed to be due to climatic adaptation. These clines provide an opportunity to study the genetics of the adaptive process both at the phenotypic and the underlying molecular levels. Yet researchers rarely try to link variation in quantitative traits to their underlying molecular genetic basis. We describe a novel approach for exploring the genetic basis for clinal variation in size and stress traits in Drosophila melanogaster. We look for associations between genetic markers and traits that exhibit clinal patterns on the east coast of Australia using a single, geographically central population. There are strong associations between markers found within In(3R)Payne and variation in size, suggesting that this inversion explains much of the clinal variation in this trait. We also find that development time is associated with the Adh allozyme locus, cold resistance is negatively associated with the In(3L)Payne inversion and a genetic marker for Hsp70, a heat‐shock protein, is associated with heat resistance. Finally we discuss the importance of inversions in clinal variation for quantitative traits and for identifying quantitative trait loci.     

Mating system and multilocus associations in a natural population of Pseudotsuga menziesii (Mirb.) Franco

Summary Arrays of open-pollinated seeds were assayed for allozyme polymorphisms at ten loci (Aat2, Est1, G6pd, Idh, Mdh2, Mdh3, Pgm, Sod, 6Pgd1, 6Pgd2) to obtain estimates of the outcrossing rate and assess multilocus association in a natural population of coastal Douglas-fir, Pseudotsuga menziesii (Mirb.) Franco. The allele frequencies in the samples of adult trees and pollen-gamete pool were similar. Maximum-likelihood estimators of the outcrossing rate for individual loci and two multilocus models were derived using counting methods. The single-locus maximum likelihood estimates (MLEs) of the outcrossing rate were significantly heterogeneous; they varied over a more than two-fold range from 0.404 to 0.935, with an average MLE of 0.741. Both multilocus MLEs of the outcrossing rate were 0.887. The sample of trees was in random mating equilibrium when assessed on a pairwise-locus basis using Burrows' composite measure of gametic disequilibrium, with one exception (Mdh2 Sod) that was attributable to a rare gametic class. In the sample of pollen gametes, 5 of the 45 pairwise-locus associations were nominally significant at the 0.05 level: Idh Est1, Mdh2 Sod, Aat2 Est1, Aat2 Mdh3, and Est1 Mdh3. These apparent associations were attributable in most cases to the relative excess of uncommon or rare paternal gametes of discernibly outcrossed embryos. An additional two-locus association was identified for Mdh2 Pgm which was marginally significant for the major partition of the contingency table that excluded paternal gametes with the rare allele Mdh2 ² .     

THE ASSOCIATION BETWEEN THE POLYMORPHISMS AT THE Adh AND αGpdh LOCI AND THE In(2L)t INVERSION IN DROSOPHILA MELANOGASTER IN RELATION TO TEMPERATURE

Substantial allele-frequency changes were observed at the Adh and αGpdh loci in a seminatural population of Drosophila melanogaster kept in a tropical greenhouse during 1972–1985. Further analysis of the changes at the Adh and αGpdh loci showed that linkage disequilibrium between these loci occurred for a prolonged period due to the presence of In(2L)t, a long inversion on the left arm of the second chromosome. We observed increases in the frequencies of In(2L)t and of short inversions on the left arm of the second chromosome in subpopulations kept at 29.5°C or 33°C. These inversion-frequency increases were accompanied by an increase in Adh^s and a decrease in αGpdh^s frequency. In populations kept at 20°C and 25°C, inversion frequencies decreased, while αGpdh^s allele frequencies decreased at 25°C and increased at 20°C. At 33°C, egg-to-adult survival of individuals possessing In(2L)t, either in the homokaryotypic or the heterokaryotypic state, was higher than that of the other karyotypes of identical allozyme constitution (i.e., Adh^s αGpdh^F). Thus it seems that In(2L)t has a selective advantage at high temperature. We argue that the observed changes in allele frequencies at the Adh and αGpdh loci are, in part, due to genic selection and are not merely the result of selection acting on the chromosome rearrangements and hitchhiking of the allozymes. The results are discussed with respect to the latitudinal clines found for In(2L)t, Adh, and αGpdh.     

DEVELOPMENT OF THE HYBRID SWARM BETWEEN PECOS PUPFISH (CYPRINODONTIDAE: CYPRINODON PECOSENSIS) AND SHEEPSHEAD MINNOW (CYPRINODON VARIEGATUS): A PERSPECTIVE FROM ALLOZYMES AND mtDNA

A comparison of allozyme and mtDNA frequencies was used for insight into a situation in the Pecos River, Texas where contact between the endemic pupfish (Cyprinodon pecosensis) and an introduced congener (C. variegatus) has resulted in rapid, geographically extensive genetic introgression. Temporal changes in mean frequencies of diagnostic allozyme markers indicate that the clinal pattern of introduced genetic material (Echelle and Connor 1989) is slowly decreasing in amplitude. Significant rank concordance in diagnostic allele frequencies among sites and across sampling years indicates directional influences upon temporal allele frequency change. These observations are consistent with the theory of gene flow in neutral clines. Levels of introgression indicated by each of four allozyme loci and mtDNA were roughly equivalent. The early history of the hybrid swarm is explained by genetic swamping, possibly mediated by selection for C. variegatus or C. variegatus × C. pecosensis, at a time when the normally abundant endemic species had been catastrophically depleted. High frequencies of an introduced GPI-A allele in all samples of intergrades suggests that the introduced genome originated with a single founding event.     

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.     

Linkage Disequilibrium in Natural Populations of DROSOPHILA MELANOGASTER. Seasonal Variation

Linkage disequilibrium among ten polymorphic allozyme loci and polymorphic inversions on chromosomes 2 and 3 in a natural population of Drosophila melanogaster was examined early and late in the annual season. Similar to previous studies, little linkage disequilibrium was observed among allozymes. The two significant cases that were observed in the first sample behaved in a contradictory way. One declined much more rapidly than expected due simply to recombination; the other declined slowly as expected. There was little change in allozyme or inversion frequencies during the season.     

Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions

Chromosomal inversions are important structural changes that may facilitate divergent selection when they capture co‐adaptive loci in the face of gene flow. However, identifying selection targets within inversions can be challenging. The high degrees of differentiation between heterokaryotypes, as well as the differences in demographic histories of collinear regions compared with inverted ones, reduce the power of traditional outlier analyses for detecting selected loci. Here, we develop a new approach that uses discriminant functions informed from inversion‐specific expectations to classify loci that are under selection (or drift). Analysis of RAD sequencing data we collected in a classic dipteran species with polymorphic inversion clines—Anopheles gambiae, a malaria vector species from sub‐Saharan Africa—demonstrates the benefits of the approach compared with traditional outlier analyses. We focus specifically on two polymorphic inversions, the 2La and 2Rb arrangements that predominate in dry habitats and the 2L+^a and 2R+^b arrangements in wet habitats, which contrast with the minimal geographic structure of SNPs from collinear regions. With our approach, we identify two strongly selected regions within 2La associated with dry habitat. Moreover, we also show that the prevalence of selection is greater in the arrangement 2L+^a that is associated with wet habitat (unlike presumed importance of selective divergence associated with the shift of the mosquitoes into dry habitats). We discuss the implications of these results with respect to studies of rapid adaptation in these malaria vectors, and in particular, the insights our newly developed approach offers for identifying not only potential targets of selection, but also the population that has undergone adaptive change.     

Inversion Polymorphisms in Populations of Drosophila Melanogaster in the South-West Islands of Japan: Comparisons with the Mainland Populations

Natural populations of D. melanogaster newly collected from the South-West Islands of Japan were examined for the frequencies of inversions, and the results, together with previous data, were compared with those of the mainland populations. The four Common cosmopolitan inversions (2Lt, 2RNS, 3LP, 3RP) were detected from most of the populations with higher frequencies. The three Rare cosmopolitan inversions (3LM, 3RC, 3RMo), three Quasi cosmopolitan inversions (2LA, 3LY, 3RK) and two new Endemic inversions were also found but with lower frequencies. Some of the South-West Island populations still maintained higher levels of inversion polymorphisms compared to the mainland populations, while others lost the polymorphisms to various degrees. The South-West Island populations were characterized by the higher frequency of In(3L)P. The ratios of In(3L)P/In(3R)P in the South-West Islands are significantly higher than those of the mainland populations, suggesting that the In(3L)P is relatively adaptive in the South-West Islands.     

Limits of the distal inversion in the t complex of the house mouse: Evidence from linkage disequilibria

The suppression of crossing-over and the consequent linkage disequilibrium of genetic markers within the t complex of the house mouse is caused by two large and two short inversions. The inversions encompass a region that is some 15 centiMorgans (cM) long in the homologous wild-type chromosome. The limits of the proximal inversions are reasonably welldefined, those of the distal inversions much less so. We have recently obtained seven new DNA markers (D17Tu) which in wild-type chromosomes map into the region presumably involved in the distal inversions of the t chromosomes. To find out whether the corresponding loci do indeed reside within the inversions, we have determined their variability among 26 complete and 12 partial t haplotypes. In addition, we also tested the same collection of t haplotypes for their variability at five D17Leh, Hba-ps4, Pim-1, and Crya-1 loci. The results suggest that the distal end of the most distal inversion lies between the loci D17Leh467 and D17Tu26. The proximal end of the large distal inversion was mapped to the region between the D17Tu43 and Hba-ps4 loci, but this assignment is rather ambiguous. The loci Pim-1, Crya-1, and the H-2 complex, which have been mapped between the Hba-sp4 and Grr within the large distal inversion, behave as if they recombine from time to time with their wildtype homologs.     

Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements in Drosophila pseudoobscura

The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with >10 inversions with appreciable frequencies and wide geographic distributions. This study analyses the genomic sequences of 54 strains of Drosophila pseudoobscura that carry one of six different chromosomal arrangements to test whether (i) genetic drift, (ii) hitchhiking with an adaptive allele, (iii) direct effects of inversions to create gene disruptions caused by breakpoints, or (iv) indirect effects of inversions in limiting the formation of recombinant gametes are responsible for the establishment of new gene arrangements. We found that the inversion events do not disrupt the structure of protein coding genes at the breakpoints. Population genetic analyses of 2,669 protein coding genes identified 277 outlier loci harbouring elevated frequencies of arrangement‐specific derived alleles. Significant linkage disequilibrium occurs among distant loci interspersed between regions with low levels of association indicating that distant allelic combinations are held together despite shared polymorphism among arrangements. Outlier genes showing evidence of genetic differentiation between arrangements are enriched for sensory perception and detoxification genes. The data presented here support the indirect effect of inversion hypothesis where chromosomal inversions are favoured because they maintain linked associations among multilocus allelic combinations among different arrangements.