Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus

With the aim of understanding the mechanism of maintenance of protein polymorphism, we have studied the properties of allele frequency distribution and the number of alleles per locus, using gene-frequency data from a wide range of organisms (mammals, birds, reptiles, amphibians, Drosophila and non-Drosophila invertebrates) in which 20 or more loci with at least 100 genes were sampled. The observed distribution of allele frequencies was U-shaped in all of the 138 populations (mostly species or subspecies) examined and generally agreed with the theoretical distribution expected under the mutation-drift hypothesis, though there was a significant excess of rare alleles (gene frequency, 0 ~ 0.05) in about a quarter of the populations. The agreement between the mutation-drift theory and observed data was quite satisfactory for the numbers of polymorphic (gene frequency, 0.05 ~ 0.95) and monomorphic (0.95 ~ 1.0) alleles.—The observed pattern of allele-frequency distribution was incompatible with the prediction from the overdominance hypothesis. The observed correlations of the numbers of rare alleles, polymorphic alleles and monomorphic alleles with heterozygosity were of the order of magnitude that was expected under the mutation-drift hypothesis. Our results did not support the view that intracistronic recombination is an important source of genetic variation. The total number of alleles per locus was positively correlated with molecular weight in most of the species examined, and the magnitude of the correlation was consistent with the theoretical prediction from mutation-drift hypothesis. The correlation between molecular weight and the number of alleles was generally higher than the correlation between molecular weight and heterozygosity, as expected.     

Statistical Studies on Protein Polymorphism in Natural Populations I. Distribution of Single Locus Heterozygosity

Surveying the literature, the frequency distribution of single-locus heterozygosity among protein loci was examined in 95 vertebrate and 34 invertebrate species with the aim of testing the validity of the mutation-drift hypothesis. This distribution did not differ significantly from that expected under the mutation-drift hypothesis for any of the species examined when tested by the Kolmogorov-Smirnov goodness-of-fit statistic. The agreement between the observed interlocus variance of heterozygosity and its theoretical expectation was also satisfactory. There was an indication that variation in the mutation rate among loci inflates the interlocus variance of heterozygosity. The variance of heterozygosity for a homologous locus among different species was also studied. This variance generally agreed with the theoretical value very well, though in some groups of Drosophila species there was a significant discrepancy. The observed relationship between average heterozygosity and the proportion of polymorphic loci was in good agreement with the theoretical relationship. It was concluded that, with respect to the pattern of distribution of heterozygosity, the majority of data on protein polymorphisms are consistent with the mutation-drift hypothesis. After examining alternative possible explanations involving selection, it was concluded that the present data cannot be explained adequately without considering a large effect of random genetic drift, whether there is selection or not.     

Contrasting microsatellite variation between subalpine and western larch, two closely related species with different distribution patterns

Subalpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.) represent two closely related species with contrasting abundance and distribution patterns in Western North America. Genetic diversity at seven informative microsatellite loci was determined for 19 populations of subalpine larch and nine populations of western larch. Contrasting genetic diversity and patterns of population differentiation were observed between the two species. The overall within-population genetic diversity parameters were lower in subalpine larch (A = 3.2; A(P) = 3.6; H(E) = 0.418) than in western larch (A(P) = 5.51; H(E) = 0.580), a pattern that is likely related to historical or demographic factors. No evidence of interspecific hybridization was observed. Significantly more population differentiation (theta = 0.15; R(ST) = 0.07), consistent with more restricted gene flow, was observed for subalpine larch as compared to western larch (theta = 0.05; R(ST) = 0.04). Under the assumption of an infinite allele mutation model, 12 of the 19 subalpine larch populations showed signs of deviation from the mutation-drift equilibrium, which suggests Holocene population bottlenecks and fluctuations in effective population size for this species. None of the western larch populations deviated significantly from the mutation-drift equilibrium. For both species, Mantel's test revealed a significant positive relationship between geographical and genetic distances indicative of isolation by distance. A similar geographical structure was detected in both species, suggesting at least two genetically distinct glacial populations in each species. The various implications for gene conservation are discussed.     

长江野鲤(Cyprinus carpio)及两种养殖鲤群体遗传多样性评估

为了给鲤鱼遗传资源保护及利用提供较为准确的基础数据,利用10对微卫星标记分析了黄河鲤(Huanghe Cyprinus carpio,人工养殖群体)、长江野鲤(Changjiang wild Cyprinus carpio,安徽段)、安徽养殖鲤(Anhui cultured Cyprinus carpio,宿州市)群体遗传多样性。遗传多样性分析实验表明:3个群体均具有较高的遗传水平,且长江野鲤群体遗传多样性高于黄河鲤、安徽养殖鲤;卡方检验表明:3个群体在较大程度上受到人类活动及生态环境变化的影响,30个位点中76.67%的位点显著偏离Hardy-Weinberg平衡。遗传距离、遗传相似度、非加权组平均法(unweighted pair-group method with arithmetic means,UPGMA)聚类树及贝叶斯聚类分析均显示,长江野鲤与安徽养殖鲤亲缘关系较近,研究情况与实际生产中养殖户从长江里获得鲤鱼亲本用于繁殖苗种的现象相符。突变-漂移平衡分析显示,在TPM模式下,Wilcoxon符号秩次检验中黄河鲤群体显著偏离突变-漂移平衡,需进一步扩大选育群体。总体来说,黄河鲤、长江野鲤、安徽养殖鲤群体遗传多样性均较高,具有进一步的选育空间。     

Patterns of Post-Glacial Genetic Differentiation in Marginal Populations of a Marine Microalga

This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS) sequences and Amplified Fragment Length Polymorphism (AFLP) of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F _ST) between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms.     

Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations

The effect of a mutation on fitness may differ between populations depending on environmental and genetic context, but little is known about the factors that underlie such differences. To quantify genome-wide correlations in mutation fitness effects, we developed a novel concept called a joint distribution of fitness effects (DFE) between populations. We then proposed a new statistic w to measure the DFE correlation between populations. Using simulation, we showed that inferring the DFE correlation from the joint allele frequency spectrum is statistically precise and robust. Using population genomic data, we inferred DFE correlations of populations in humans, Drosophila melanogaster, and wild tomatoes. In these species, we found that the overall correlation of the joint DFE was inversely related to genetic differentiation. In humans and D. melanogaster, deleterious mutations had a lower DFE correlation than tolerated mutations, indicating a complex joint DFE. Altogether, the DFE correlation can be reliably inferred, and it offers extensive insight into the genetics of population divergence.     

大鳞副泥鳅5个野生群体的遗传多样性分析

利用微卫星分子标记分析了天津地区于桥水库、大黄堡湿地、七里海湿地、团泊水库和潮白新河5个野生大鳞副泥鳅群体的遗传多样性。5个群体在12个微卫星位点共检测到98个等位基因,平均等位基因数为8.500;有效等位基因数为2.713;平均观测杂合度为0.526;平均期望杂合度为0.544。5个群体间的遗传分化指数介于0.021~0.106之间,平均遗传分化指数为0.059,属中低水平的遗传分化。AMOVA分析结果显示,在总的变异中,94.1%的遗传变异来自群体内,5.90%的遗传变异来自于群体间。根据Nei’s遗传距离所绘制的系统树显示,于桥水库、团泊水库、七里海湿地和大黄堡湿地4个群体的遗传距离相对较小聚为一支,潮白新河群体单独为一支。遗传瓶颈效应分析表明,该5个群体近期未经受遗传瓶颈效应,处于突变-漂移平衡。总体来看,天津地区5个野生大鳞副泥鳅群体的遗传多样性较高,可作为品种选育的基础群体。     

Genetic Variation in Natural Populations of Five Drosophila Species and the Hypothesis of the Selective Neutrality of Protein Polymorphisms

We have studied genetic variation at 30-32 loci coding for enzymes in natural populations of five species of Drosophila. The average proportion of heterozygous loci per individual is 17.7 +/- 0.4%. The average proportion of polymorphic loci per population is 69.2 +/- 2.6% or 49.8 +/- 2.2%, depending on what criterion of polymorphism is used. The following generalizations are advanced: (1) The amount of genetic polymorphism varies considerably from locus to locus. (2) At a given locus, populations of the same species are very similar in the amount and pattern of genetic variation. (3) However, at some loci large differences sometimes occur between local populations of the same species. (4) The amount of variation at a given locus is approximately the same in all five species. (5) When different species are compared, the pattern of the variation is either essentially identical or totally different at a majority of loci. We have tested the hypothesis that protein polymorphisms are selectively neutral by examining four predictions derived from the hypothesis. Our results are at variance with every one of the predictions. We have measured the amount of genetic differentiation, D, between taxa of various degrees of evolutionary divergence. The average value of D is 0.033 for local populations, 0.228 for subspecies, 0.226 for semispecies, 0.538 for sibling species, and 1.214 for morphologically distinguishable species. Our results indicate that a substantial degree of genetic differentiation (22.8 allelic substitutions for every 100 loci) occurs between allopatric populations that have diverged to the point where they might become different species if they were to become sympatric. However, very little additional genetic change is required for the development of complete reproductive isolation. After the speciation process is completed, species continue to diverge genetically from each other.     

Genetic Structure of Earthworm Populations at a Regional Scale: Inferences from Mitochondrial and Microsatellite Molecular Markers in Aporrectodea icterica (Savigny 1826)

Despite the fundamental role that soil invertebrates (e.g. earthworms) play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci) and mitochondrial markers (COI). Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations.     

Flies across the water: genetic differentiation and reproductive isolation in allopatric desert Drosophila

Between sister species of Drosophila, both pre- and postzygotic reproductive isolation commonly appear by the time a Nei's genetic distance of 0.5 is observed. The degree of genetic differentiation present when allopatric populations of the same Drosophila species exhibit incipient reproductive isolation has not been systematically investigated. Here we compare the relationship between genetic differentiation and pre- and postzygotic isolation among allopatric populations of three cactophilic desert Drosophila: D. mettleri, D. nigrospiracula, and D. mojavensis. The range of all three is interrupted by the Gulf of California, while two species, D. mettleri and D. mojavensis, have additional allopatric populations residing on distant Santa Catalina Island, off the coast of southern California. Significant population structure exists within all three species, but only for allopatric populations of D. mojavensis is significant isolation at the prezygotic level observed. The genetic distances for the relevant populations of D. mojavensis were in the range of 0.12, similar to that for D. mettleri whose greatest D = 0.11 was unassociated with any form of isolation. These observations suggest further investigations of Drosophila populations with genetic distances in this range be undertaken to identify any potential patterns in the relationship between degree of genetic differentiation and the appearance of pre- and/or postzygotic isolation.     

A Study of Linkage Disequilibrium in British Populations of DROSOPHILA SUBOBSCURA

Data have been obtained concerning the genetic content of samples of O chromosomes from three British populations, and J chromosomes from one population, of Drosophila subobscura. Some improvements to the genetic map of the O and J chromosomes have been made. Allele frequencies at the loci studied do not show much geographical variation, except where associations with geographically varying gene arrangements distort the picture. Striking nonrandom associations between alleles at three enzyme loci and closely linked O chromosome gene arrangements are present. Some historical explanation for these associations cannot at present be ruled out, but it is clear that a very high degree of genetic differentiation must exist between different gene arrangements in this species. There is no convincing direct evidence for linkage disequilibrium between pairs of enzyme loci, although there is a significant association between close linkage and a high value of the linkage disequilibrium measure. This suggests that there may be disequilibria between closely linked enzyme loci that are too small to be individually detectable. These results are in broad agreement with those reported by workers on other Drosophila species. At present there appears to be no evidence to support the concept that selection is sufficiently strong at individual enzyme loci to produce a high degree of nonrandom associations. (Franklin and Lewontin 1970).     

Genetic Structure of Different Populations of Walking Catfish (Clarias batrachus L.) in Bangladesh

Information on genetic variation is essential for conservation and stock improvement programs. Seven dinucleotide microsatellite loci were analyzed to reveal genetic variability in three wild populations (Kella beel, Hakaluki haor, and Shobornokhali beel) and one hatchery population of the freshwater walking catfish, Clarias batrachus, in Bangladesh. Upon PCR amplification, the alleles were separated on polyacrylamide gel using a sequencing gel electrophoresis system and visualized by the silver-staining method. The loci were polymorphic (P95) in all the populations. Differences were observed in number and frequency of alleles as well as heterozygosity in the studied populations. Current gene diversity (He) was higher than expected under mutation-drift equilibrium, significantly in the Hakaluki haor and Shobornokhali beel populations, indicating a recent genetic bottleneck. Population differentiation (FST) values were significant (P<0.05) in all the population pairs. A relatively high level of gene flow and a low level of FST values were found between wild population pairs compared to hatchery-wild pairs. The unweighted pair group method with averages dendrogram based on genetic distance resulted in two major clusters: the hatchery population was alone in one cluster whereas the three wild populations made another cluster. The results reflect some degree of genetic variability in C. batrachus populations indicating potentialities for improving this species through a selective breeding program. The results revealed a recent bottleneck in some wild populations of C. batrachus. Protection of habitat may help increase the population size and lower the risk of vulnerability of the species in the future.     

Heritability of Two Morphological Characters within and among Natural Populations of Drosophila melanogaster

Heritabilities of wing length and abdominal bristle number, as well as genetic correlations between these characters, were determined within and among populations of Drosophila melanogaster in nature. Substantial "natural" heritabilities were found when wild-caught flies from one population were compared to their laboratory-reared offspring. Natural heritabilities of bristle number approximated those derived from laboratory-raised parents and offspring, but wing length heritability was significantly lower in nature than in the laboratory. Among-population heritabilities, estimated by regressing population means of wild-caught flies against those of their laboratory-reared descendants, were close to 0.5. The genetic differentiation of populations was clinal with latitude, and was accompanied by significant geographic differences in the norms of reaction to temperature. These clines are similar to those reported on other continents and in other Drosophila species, and are almost certainly caused by natural selection. Genetic regressions between the characters reveal that the cline in bristle number may be a correlated response to geographic selection on wing length, but not vice versa. Our results indicate that there is a sizable genetic component to phenotypic variation within and among populations of D. melanogaster in nature.     

Polymorphism and Locus-Specific Effects on Polymorphism at Microsatellite Loci in Natural Drosophila Melanogaster Populations

We have studied the natural variation at microsatellite loci in two African and five non-African populations of Drosophila melanogaster. Ten dinucleotide simple sequence loci were cloned from chromosomally mapped P1 clones and typed for single individuals from isofemale lines of the respective populations. We find that the African populations harbor the largest degree of diversity, while the non-African populations show a lower diversity. This supports previous results that D. melanogaster originated in Africa and spread across the rest of the world in historic times. Using genetic distance measures, we find also a distinct population subdivision between the non-African populations. Most interestingly, we find for some loci in some populations a strongly reduced variability, which cannot be explained by bottleneck effects. Employing a conservative test based on the variance in repeat number, we find that at least one locus in one population deviates significantly from the expectations of mutation-drift equilibrium. We suggest that this may be due to a recent selective sweep in this chromosomal region that may have been caused by a linked locus that was involved in local adaptation of the population.     

Patterns of Genetic and Reproductive Traits Differentiation in Mainland vs. Corsican Populations of Bumblebees

Populations on islands often exhibit lower levels of genetic variation and ecomorphological divergence compared to their mainland relatives. While phenotypic differentiation in characters, such as size or shape among insular organisms, has been well studied, insular differentiation in quantitative reproductive traits involved in chemical communication has received very little attention to date. Here, we investigated the impact of insularity on two syntopic bumblebee species pairs: one including species that are phylogenetically related (Bombus terrestris and B. lucorum), and the other including species that interact ecologically (B. terrestris and its specific nest inquiline B. vestalis). For each bumblebee species, we characterized the patterns of variation and differentiation of insular (Corsican) vs. mainland (European) populations (i) with four genes (nuclear and mitochondrial, 3781 bp) and (ii) in the chemical composition of male marking secretions (MMS), a key trait for mate attraction in bumblebees, by gas chromatography-mass spectrometry (GC-MS). Our results provide evidence for genetic differentiation in Corsican bumblebees and show that, contrary to theoretical expectations, island populations of bumblebees exhibit levels of genetic variation similar to the mainland populations. Likewise, our comparative chemical analyses of MMS indicate that Corsican populations of bumblebees are significantly differentiated from the mainland yet they hold comparative levels of within-population MMS variability compared to the mainland. Therefore, insularity has led Corsican populations to diverge both genetically and chemically from their mainland relatives, presumably through genetic drift, but without a decrease of genetic diversity in island populations. We hypothesize that MMS divergence in Corsican bumblebees was driven by a persistent lack of gene flow with mainland populations and reinforced by the preference of Corsican females for sympatric (Corsican) MMS. The impoverished Corsican bumblebee fauna has not led to relaxation of stabilizing selection on MMS but to consistent differentiation chemical reproductive traits on the island.     

Genetic Variation within and Between Domesticated Chinook Salmon, Oncorhynchus tshawytscha, Strains and their Progenitor Populations

Domesticated chinook salmon strains in British Columbia (BC), Canada are believed to have originated primarily from populations of the Big Qualicum (BQ) River and Robertson Creek (RC) on Vancouver Island in the early 1980s. The number of parental fish that gave rise to the domesticated strains and their subsequent breeding history during approximately five ensuing generations of domestication were not documented. Genetic variation at 13 microsatellite loci was examined in samples from two domesticated strains and the two progenitor populations to determine the genetic relationships among them. The domesticated strains had lower allelic diversity and tended to have lower levels of expected heterozygosity than did the BQ and RC progenitor populations. Only three alleles over all 13 loci were detected in the domesticated strains that were not present in the BQ and RC samples, whereas the progenitor strains possessed over 25 (BQ) and 43 (RC) private alleles. Genetic distance and F_ST values also indicated a closer relationship of the domesticated strains with the BQ than the RC population. One domesticated strain had a significant excess of heterozygosity compared with that expected under conditions of mutation-drift equilibrium, indicative of a recent genetic bottleneck. Genetic differentiation between the domesticated strains was as great as that distinguishing them from the progenitor populations, indicating that the genetic base of domesticated chinook salmon could be increased by hybridization. The existence of genetically distinct domesticated strains of chinook salmon in coastal BC generates the need for an evaluation of potential genetic interactions between domesticated escapees and natural spawning populations.     

Genetic Differentiation between Geographically Distant Populations of DROSOPHILA MELANOGASTER

We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and south. These differences arise mainly from seven loci that show gene-frequency patterns suggestive of latitudinal clines in allele frequencies. The clinal variation is such that subtropical populations are more heterozygous than temperate populations. These results are discussed in relation to the selectionist and neutralist hypotheses of genetic variation in natural populations.     

A biogeographic genetic approach for testing the role of reinforcement: the case of Drosophila pseudoobscura and D. persimilis

Abstract.— The role of reinforcement in speciation can be explained by two distinct models. In model I, two diverged populations hybridize and produce fertile hybrids that successfully backcross (hybridization with gene flow). In model II, two populations hybridize but succeeding backcrosses are unproductive (hybridization without gene flow). Using Drosophila persimilis and D. pseudoobscura , we have tested model I by comparing the extent of heterospecific introgression in sympatric versus allopatric populations. We show that certain expectations of this particular model of reinforcement, which is based on hybridization and gene flow between divergent populations after secondary contact, are not realized in these two species. The evidence consists of the similarity of genetic distances as well as proportions of unique/rare alleles between sympatric and allopatric heterospecific populations and a negative correlation between genetic distance and geographical distance between heterospecific populations, which suggests ecological differentiation. This approach in quantifying differential gene flow has important consequences to studies that compare sympatric and allopatric isolation using genetic distance. Following model I, one would expect a pattern of higher prezygotic isolation in sympatric species compared to allopatric species of the same genetic distance simply as a result of an underestimation of genetic distance due to introgression between sympatric populations. We suggest more parsimonious explanations such as reinforcement without genetic exchange (model II) and ecological differentiation, which require high levels of preexisting reproductive isolation between populations.     

Population genetic study of allozyme variation in natural populations of Drosophila antonietae (Insecta, Diptera)

Drosophila antonietae is an endemic South American cactophilic species found in relictual xerophytic vegetation, mostly associated with Cereus hildmaniannus cactus. Low differentiation among populations of this species has been detected using several markers. In this work, we performed an allozyme genetic variability analysis of 11 natural populations of D. antonietae and included a discussion about the possible influences of several evolutionary processes that might be acting to maintain the pattern observed. The genetic variability of 14 isoenzyme loci was analysed and showed a high genetic diversity (average observed heterozygosity = 0.319) and a moderate genetic differentiation among populations ( F statistics = 0.0723). A correlation between genetic and geographical and ecological distances was detected among pairs of populations and the regional equilibrium analysis was thus applied. This analysis resulted in Nm (number of migrants) of approximately 3.21, indicating that moderate levels of both gene flow and genetic drift occur in this species, with gene flow overlapping genetic drift. However, considering ecological features of drosophilids, we propose a hypothesis to explain the moderate differentiation encountered as a result of three different processes, or a combination of them: (1) gene flow; (2) a short period of differentiation, i.e. maintenance of ancestral polymorphism; and (3) action of natural selection. Moreover, if gene flow is present, the high genetic diversity compared with other cactophilic and non-cactophilic species could be due to differential selection in different populations followed by gene exchange among them. These factors are discussed in the light of D. antonietae 's historical and evolutionary association with the host cactus.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. III. Variations in Genetic Structure and Their Causes between Drosophila melanogaster and Its Sibling Species Drosophila simulans

The natural populations of Drosophila melanogaster and Drosophila simulans were compared for their genetic structure. A total of 114 gene-protein loci were studied in four mainland (from Europe and Africa) and an island (Seychelle) populations of D. simulans and the results were compared with those obtained on the same set of homologous loci in fifteen worldwide populations of D. melanogaster. The main results are as follows: (1) D. melanogaster shows a significantly higher proportion of loci polymorphic than D. simulans (52% vs. 39%, P<0.05), (2) both species have similar mean heterozygosity and mean number of alleles per locus, (3) the two species share some highly polymorphic loci but they do not share loci that show high geographic differentiation, and (4) D. simulans shows significantly less geographic differentiation than D. melanogaster. The differences in genetic differentiation between the two species are limited to loci located on the X and second chromosomes only; loci on the third chromosome show similar level of geographic differentiation in both species. These two species have previously been shown to differ in their pattern of variation for chromosomal polymorphisms, quantitative and physiological characters, two-dimensional electrophoretic (2DE) proteins, middle repetitive DNA and mitochondrial DNA. Variation in niche-widths and/or genetic "strategies" of adaptation appear to be the main causes of differences in the genetic structure of these two species.