Extent Of Polymorphism Research Articles

Molecular techniques in the assessment of genetic relationships between populations of Consolida (Ranunculaceae)

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. The genus Consolida (DC.) Gray (Ranuculaceae) belongs to tribe Delphinieae. It comprises approximately 52 species, including the members of the genus Aconitella Spach. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Consolida genetic diversity. Therefore, we collected and analyzed 19 species from 12 provinces of regions. Overall, one hundred and twenty-seven plant specimens were collected. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and principal component analysis (PCA) divided Consolida species into two groups. All primers produced polymorphic amplicons though the extent of polymorphism varied with each primer. The primer OPA-06 was found to be most powerful and efficient as it generated a total of 24 bands of which 24 were polymorphic. The Mantel test showed correlation (r = 0.34, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Consolida species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Consolida species. Our aims were 1) to assess genetic diversity among Consolida species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa.

Persistence of multiple patterns and intraspecific polymorphism in multi-species M\xfcllerian communities of net-winged beetles

BackgroundIn contrast to traditional models of purifying selection and a single aposematic signal in Müllerian complexes, some communities of unprofitable prey contain members with multiple aposematic patterns. Processes responsible for diversity in aposematic signaling are poorly understood and large multi-species communities are seldom considered.ResultsWe analyzed the phylogeny and aposematic patterns of closely related Eniclases net-winged beetles in New Guinea using mtDNA and nextRAD data. We suggest three clades of closely related and incompletely reproductively isolated lineages, detail the extent of polymorphism among Eniclases, and categorize their low-contrast aposematic patterns. The warning signal of Eniclases consists of body shape and color, with ambiguous color perception under some circumstances, i.e., when resting on the undersides of leaves. Field observations suggest that perception of the aposematic signal is affected by beetle behavior and environmental conditions. Local communities containing Eniclases consisted of 7–85 metriorrhynchine species assigned to 3–10 colour patterns.ConclusionAs a result, we suggest that under certain light conditions the aposematic colour signal is less apparent than the body shape in net-winged beetle communities. We document variable environmental factors in our study area and highly diverse multi-species communities of other net-winged beetles. Which implies dynamically changing community structure in space and time. Variable environmental conditions and diverse community composition are suggested to be favorable for the persistence of multiple aposematic patterns, imperfect mimics, and intraspecific polymorphism. Further research should identify the relative effect of these factors on purifying selection and the alleles which are responsible for phenotypic differences.

Evolutionary Determinants of Morphological Polymorphism in Colonial Animals.

Colonial animals commonly exhibit morphologically polymorphic modular units that are phenotypically distinct and specialize in specific functional tasks. But how and why these polymorphic modules have evolved is poorly understood. Across colonial invertebrates, there is wide variation in the degree of polymorphism, from none in colonial ascidians to extreme polymorphism in siphonophores, such as the Portuguese man-of-war. Bryozoa are a phylum of exclusively colonial invertebrates that uniquely exhibit almost the entire range of polymorphism, from monomorphic species to others that rival siphonophores in their polymorphic complexity. Previous approaches to understanding the evolution of polymorphism have been based on analyses of (1) the functional role of polymorphs or (2) presumed evolutionary costs and benefits based on evolutionary theory that postulates polymorphism should be evolutionarily sustainable only in more stable environments because polymorphism commonly leads to the loss of feeding and sexual competence. Here we use bryozoans from opposite shores of the Isthmus of Panama to revisit the environmental hypothesis by comparison of faunas from distinct oceanographic provinces that differ greatly in environmental variability, and we then examine the correlations between the extent of polymorphism in relation to patterns of ecological succession and variation in life histories. We find no support for the environmental hypothesis. Distributions of the incidence of polymorphism in the oceanographically unstable Eastern Pacific are indistinguishable from those in the more stable Caribbean. In contrast, the temporal position of species in a successional sequence is collinear with the degree of polymorphism because species with fewer types of polymorphs are competitively replaced by species with higher numbers of polymorphs on the same substrata. Competitively dominant species also exhibit patterns of growth that increase their competitive ability. The association between degrees of polymorphism and variations in life histories is fundamental to understanding of the macroevolution of polymorphism.

Single Nucleotide Polymorphism within the LDLR gene and responsiveness of cynomolgus macaque (Macaca fascicularis) to atherogenic diet

Taher A, Solihin DD, Sulistiyani, Sajuthi D, Astuti DA. 2016. Single Nucleotide Polymorphism within the LDLR gene and responsiveness of cynomolgus macaque (Macaca fascicularis) to atherogenic diet. Biodiversitas 17: 430-434. Genetic variation within low density lipoprotein receptor (LDLR) gene has been associated with normal variation of plasma lipid profiles and risks of coronary heart diseases (CHD) in human. Although cynomolgus macaque (Macaca fascicularis) is one of non-human primates commonly used as models in atherosclerosis research, little is known about the extent of polymorphism within the LDLR gene and its consequences on responsiveness to atherogenic diet. In this study, two regions of LDLR gene, namely exon 6 and intron 5, were sequenced in a sample of 22 male cynomolgus macaques which had differences in responsiveness to atherogenic diet. The objective of the study was to identify single nucleotide polymorphism (SNP) within the LDLR gene and to evaluate the kinds of haplotypes in relation to the responsiveness of the cynomolgus macaque to atherogenic diet. Sequence analysis revealed that there were two SNPs at exon 6, i.e. IVS5-6C > G and 825C > G, which were distributed in 3 haplotypes, and five SNPs at intron 5, i.e. g.IVS5+99T > C, g.IVS5+173G > T, g.IVS5+327A > G, g.IVS5−96C > T, and g.IVS5−6C > G, which were distributed in 6 haplotypes. It was found that haplotype II (GC) at 6 base pairs prior to the exon 6 and haplotype III (CGGTG) within the intron 5 were associated with hyporesponsiveness to atherogenic diet. The results showed that potential SNP existed within the exon 6 and intron 5 can be used as genetic markers for selecting hypo- from hyperresponders.
 Keywords: Hyporesponsiveness, LDLR gene, Macaca fascicularis, SNP

Identification of QTLs on chromosome 1B for grain quality traits in bread wheat (Triticum aestivum L.)

The present study was designed considering the importance of grain quality traits, genetic diversity and marker-trait association analysis in wheat. A significant amount of genetic diversity was found for various seed traits though the genotypes included in the study were found structured. The extent of polymorphism was high with a range of 2-13 alleles and average of 6.5 alleles per locus. Population structure was detected with 30 unlinked SSRs that divided the population of 92 genotypes in three sub-populations. Extensive LD extent was found on chromosome 1B with 42 SSRs specific for 1B chromosome. Marker-trait associations were determined using mixed linear model, where, population structure and kinship calculated on the basis of unlinked markers were covariated with 1B specific markers and traits data. Eight QTLs for five traits including protein, gluten contents, test weight bread and chapati making quality. Protein content, test weight, bread quality and Glu-B1 were found significantly associated with primers WMC419 (32 cM); WMC128 (30 cM), WMC419 (32 cM); WMC818 (17 cM) and WMC416 (44 cM), respectively.

A limit to the divergent allele advantage model supported by variable pathogen recognition across HLA-DRB1 allele lineages.

Genetic diversity in human leukocyte antigen (HLA) molecules is thought to have arisen from the co‐evolution between host and pathogen and maintained by balancing selection. Heterozygote advantage is a common proposed scenario for maintaining high levels of diversity in HLA genes, and extending from this, the divergent allele advantage (DAA) model suggests that individuals with more divergent HLA alleles bind and recognize a wider array of antigens. While the DAA model seems biologically suitable for driving HLA diversity, there is likely an upper threshold to the amount of sequence divergence. We used peptide‐binding and pathogen‐recognition capacity of DRB1 alleles as a model to further explore the DAA model; within the DRB1 locus, we examined binding predictions based on two distinct phylogenetic groups (denoted group A and B) previously identified based on non‐peptide‐binding region (PBR) nucleotide sequences. Predictions in this study support that group A allele and group B allele lineages have contrasting binding/recognition capacity, with only the latter supporting the DAA model. Furthermore, computer simulations revealed an inconsistency in the DAA model alone with observed extent of polymorphisms, supporting that the DAA model could only work effectively in combination with other mechanisms. Overall, we support that the mechanisms driving HLA diversity are non‐exclusive. By investigating the relationships among HLA alleles, and pathogens recognized, we can provide further insights into the mechanisms on how humans have adapted to infectious diseases over time.

Group 1 Allergen Genes in Two Species of House Dust Mites, Dermatophagoides farinae and D. pteronyssinus (Acari: Pyroglyphidae): Direct Sequencing, Characterization and Polymorphism.

Group 1 allergens of Dermatophagoides farinae (Der f 1) and D. pteronyssinus (Der p 1) dominate overall allergic responses in house dust mite allergy patients. The need for accurate identification and characterization of representative variants of group 1 allergens in any given geographic locality has been emphasized for development of appropriate allergen extracts. Regional amino acid sequence polymorphism has been described but the extent of this polymorphism is not well understood. Such data are completely absent for the USA and many other countries. Most previous studies used cDNA libraries generated by reverse transcriptase (RT-PCR) and/or primers amplifying shorter fragments of this gene. Using novel species-specific primers and direct PCR, we document group 1 allergen gene sequence polymorphism in populations of D. farinae and D. pteronyssinus from the USA and Pakistan. We report two novel introns (nt pos 87 and 291) in both species, and the absence of intron 3 in Der p 1. Thirteen silent and one novel non-synonymous mutation (Tryptophan W197 to Arginine R197) were detected in D. farinae. The potential medical significance of the latter mutation is discussed. Two haplotypes of the Der f 1 gene were identified, haplotype 1 (63%) was more frequent than haplotype 2 (18%). Polymorphism in Der f 1 displayed geographical localization, since both haplotypes were present in mite populations from Pakistan whereas haplotype 1 was observed only in the USA. In Der p 1, a silent mutation at nt (aa) position 1011(149) and four non-synonymous mutations at positions 589(50), 935(124), 971(136), 1268(215) were observed. These mutations were reported from many other geographic regions, suggesting that polymorphism in the Der p 1 gene is panmictic. The extent of polymorphism in both genes is substantially lower than that reported previously (0.10–0.16% vs 0.31–0.49%), indicating the need for careful evaluation of potential polymerase errors in studies utilizing RT-PCR.

ITS polymorphisms shed light on hybrid evolution in apomictic plants: a case study on the Ranunculus auricomus complex.

The reconstruction of reticulate evolutionary histories in plants is still a major methodological challenge. Sequences of the ITS nrDNA are a popular marker to analyze hybrid relationships, but variation of this multicopy spacer region is affected by concerted evolution, high intraindividual polymorphism, and shifts in mode of reproduction. The relevance of changes in secondary structure is still under dispute. We aim to shed light on the extent of polymorphism within and between sexual species and their putative natural as well as synthetic hybrid derivatives in the Ranunculus auricomus complex to test morphology-based hypotheses of hybrid origin and parentage of taxa. We employed direct sequencing of ITS nrDNA from 68 individuals representing three sexuals, their synthetic hybrids and one sympatric natural apomict, as well as cloning of ITS copies in four representative individuals, RNA secondary structure analysis, and landmark geometric morphometric analysis on leaves. Phylogenetic network analyses indicate additivity of parental ITS variants in both synthetic and natural hybrids. The triploid synthetic hybrids are genetically much closer to their maternal progenitors, probably due to ploidy dosage effects, although exhibiting a paternal-like leaf morphology. The natural hybrids are genetically and morphologically closer to the putative paternal progenitor species. Secondary structures of ITS1-5.8S-ITS2 were rather conserved in all taxa. The observed similarities in ITS polymorphisms suggest that the natural apomict R. variabilis is an ancient hybrid of the diploid sexual species R. notabilis and the sexual species R. cassubicifolius. The additivity pattern shared by R. variabilis and the synthetic hybrids supports an evolutionary and biogeographical scenario that R. variabilis originated from ancient hybridization. Concerted evolution of ITS copies in R. variabilis is incomplete, probably due to a shift to asexual reproduction. Under the condition of comprehensive inter- and intraspecific sampling, ITS polymorphisms are powerful for elucidating reticulate evolutionary histories.

Characterising the phenotypic diversity of Papilio dardanus wing patterns using an extensive museum collection.

The history of 20th Century evolutionary biology can be followed through the study of mimetic butterflies. From the initial findings of discontinuous polymorphism through the debates regarding the evolution of mimicry and the step-size of evolutionary change, to the studies on supergene evolution and molecular characterisation of butterfly genomes, mimetic butterflies have been at the heart of evolutionary thought for over 100 years. During this time, few species have received as much attention and in-depth study as Papilio dardanus. To assist all aspects of mimicry research, we present a complete data-derived overview of the extent of polymorphism within this species. Using historical samples permanently held by the NHM London, we document the extent of phenotypic variation and characterise the diversity present in each of the subspecies and how it varies across Africa. We also demonstrate an association between “imperfect” mimetic forms and the transitional race formed in the area where Eastern and Western African populations meet around Lake Victoria. We present a novel portal for access to this collection, www.mimeticbutterflies.org, allowing remote access to this unique repository. It is hoped that this online resource can act as a nucleus for the sharing and dissemination of other collections databases and imagery connected with mimetic butterflies.

Analysis of chromosomal polymorphism in barley (Hordeum vulgare L. ssp. vulgare) and between H. vulgare and H. chilense using three-color fluorescence in situ hybridization (FISH)

The aim of the present work was to study chromosomal polymorphism within cultivated barley (Hordeum vulgare ssp. vulgare) using three-color fluorescence in situ hybridization (FISH). The physical distribution of the most frequently used, highly repetitive DNA sequences (GAA)7 specific for pericentromeric heterochromatic regions, the ribosomal DNA clone pTa71, specific for the 45S rDNA, and the barley-specific telomere-associated sequence HvT01, was investigated to reveal genetic diversity in metaphase spreads of ten barley genotypes with diverse geographical origin, growth habit and row number. A wild relative of barley, Hordeum chilense was also studied in order to compare the polymorphism between and within Hordeum species. Significant differences in the hybridization patterns of all three DNA probes could be detected between the two related species, but only probes pTa71 and HvT01 showed variation in the intensity and/or position of hybridization sites among genotypes of H. vulgare ssp. vulgare. The extent of polymorphism was less than that earlier reported for molecular markers and was restricted to the long chromosome arms, with differences between the chromosomes. 1H and 3H proved to be the most variable chromosomes and 4H and 6H the most conserved.

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

BackgroundSinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains.ResultsWith sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.ConclusionsIn conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.

Two Theileria parva CD8 T Cell Antigen Genes Are More Variable in Buffalo than Cattle Parasites, but Differ in Pattern of Sequence Diversity

Background Theileria parva causes an acute fatal disease in cattle, but infections are asymptomatic in the African buffalo (Syncerus caffer). Cattle can be immunized against the parasite by infection and treatment, but immunity is partially strain specific. Available data indicate that CD8+ T lymphocyte responses mediate protection and, recently, several parasite antigens recognised by CD8+ T cells have been identified. This study set out to determine the nature and extent of polymorphism in two of these antigens, Tp1 and Tp2, which contain defined CD8+ T-cell epitopes, and to analyse the sequences for evidence of selection.Methodology/Principal FindingsPartial sequencing of the Tp1 gene and the full-length Tp2 gene from 82 T. parva isolates revealed extensive polymorphism in both antigens, including the epitope-containing regions. Single nucleotide polymorphisms were detected at 51 positions (∼12%) in Tp1 and in 320 positions (∼61%) in Tp2. Together with two short indels in Tp1, these resulted in 30 and 42 protein variants of Tp1 and Tp2, respectively. Although evidence of positive selection was found for multiple amino acid residues, there was no preferential involvement of T cell epitope residues. Overall, the extent of diversity was much greater in T. parva isolates originating from buffalo than in isolates known to be transmissible among cattle.Conclusions/SignificanceThe results indicate that T. parva parasites maintained in cattle represent a subset of the overall T. parva population, which has become adapted for tick transmission between cattle. The absence of obvious enrichment for positively selected amino acid residues within defined epitopes indicates either that diversity is not predominantly driven by selection exerted by host T cells, or that such selection is not detectable by the methods employed due to unidentified epitopes elsewhere in the antigens. Further functional studies are required to address this latter point.

Single nucleotide polymorphism in the genes of mce1 and mce4 operons of Mycobacterium tuberculosis: analysis of clinical isolates and standard reference strains

BackgroundThe presence of four mammalian cell entry (mce) operons in Mycobacterium tuberculosis suggests the essentiality of the functions of the genes in these operons. The differential expression of the four mce operons in different phases of in vitro growth and in infected animals reported earlier from our laboratory further justifies the apparent redundancy for these genes in the genome.Here we investigate the extent of polymorphism in eight genes in the mce1 and mce4 operons of M. tuberculosis from four standard reference strains (H37Rv, H37Ra, LVS (Low Virulent Strain) and BCG) and 112 clinical isolates varying in their drug susceptibility profile, analysed by direct sequencing and Sequenom MassARRAY platform.ResultsWe discovered 20 single nucleotide polymorphisms (SNPs) in the two operons. The comparative analysis of the genes of mce1 and mce4 operons revealed that yrbE1A [Rv0167] was most polymorphic in mce1 operon while yrbE4A [Rv3501c] and lprN [Rv3495c] had the highest number of SNPs in the mce4 operon. Of 20 SNPs, 12 were found to be nonsynonymous and were further analysed for their pathological relevance to M. tuberculosis using web servers PolyPhen and PMut, which predicted five deleterious nonsynonymous SNPs. A mutation from proline to serine at position 359 of the native Mce1A protein was most deleterious as predicted by both PolyPhen and PMut servers. Energy minimization of the structure of native Mce1A protein and mutated protein was performed using InsightII. The mutated Mce1A protein showed structural changes that could account for the effects of this mutation.ConclusionsOur results show that SNPs in the coding sequences of mce1 and mce4 operons in clinical isolates can be significantly high. Moreover, mce4 operon is significantly more polymorphic than mce1 operon (p < 0.001). However, the frequency of nonsynonymous substitutions is higher in mce1 operon and synonymous substitutions are more in mce4 operon. In silico modeling predict that nonsynonymous SNP at mce1A [Rv0169], a virulence gene could play a pivotal role in causing functional changes in M. tuberculosis that may reflect upon the biology of the bacteria.

RAPD based genetic stability analysis among micropropagated, synthetic seed derived and hardened plants of Bacopa monnieri (L.): a threatened Indian medicinal herb

Bacopa monnieri (L.), a highly endangered miracle medicinal herb with global interest, is one of the popular ancient Indian ayurvedic plants. With ever increasing demand for Bacopa based formulations in pharmaceutical industries, there is a need to preserve the stocks of the plant through biotechnological approaches. Randomly amplified polymorphic DNA (RAPD) fingerprinting approach was applied to analyze the genetic stability of 19 different B.monnieri plants randomly selected after micropropagation, regrowth from alginate encapsulated uninodal cuttings (before and after storage at 4°C) and hardening with the mother plant (wild type). 16 arbitrary decamer primers amplified a total of 334 reproducible distinct DNA fragments ranging from 180 to 1,500 bp, of which 262 (78.4%) were monomorphic and the rest (21.5%) were polymorphic with an average of 20.8 bands per primer. The extent of polymorphism was low to moderate. Primers OPAK 14, OPM 15 and OPD 13 generated 69, 46 and 42% polymorphic patterns. Primers OPA 04, OPU 13 and OPD 08 generated 100% monomorphic pattern. Similarity matrix based on Jaccard’s coefficient revealed that pair wise values between the wild type and its analyzed plants ranged from 0.00 to 0.92 and among the micropropagated, synthetic seed derived and hardened plants, the range of genetic distance is from 0.67 to 0.92. Unweighted pair group method with arithmetic averages cluster analysis resulted in one loose group of the wild type with three subgroups. The present study paves the way for the identification and maintenance of genetically uniform B. monnieri plants micropropagated in the lab, plants regrown from synthetic seeds and hardened in the field.

Sequence variation and selection of small RNAs in domesticated rice

BackgroundEndogenous non-coding small RNAs (21-24 nt) play an important role in post-transcriptional gene regulation in plants. Domestication selection is the most important evolutionary force in shaping crop genomes. The extent of polymorphism at small RNA loci in domesticated rice and whether small RNA loci are targets of domestication selection have not yet been determined.ResultsA polymorphism survey of 94 small RNA loci (88 MIRNAs, four TAS3 loci and two miRNA-like long hairpins) was conducted in domesticated rice, generating 2 Mb of sequence data. Many mutations (substitution or insertion/deletion) were observed at small RNA loci in domesticated rice, e.g. 12 mutation sites were observed in the mature miRNA sequences of 11 MIRNAs (12.5% of the investigated MIRNAs). Several small RNA loci showed significant signals for positive selection and/or potential domestication selection.ConclusionsSequence variation at miRNAs and other small RNAs is higher than expected in domesticated rice. Like protein-coding genes, non-coding small RNA loci could be targets of domestication selection and play an important role in rice domestication and improvement.

Allele polymorphism of microsatellite loci in pea Pisum sativum L. lines, varieties, and mutants

Interlinear polymorphism at 23 microsatellite loci was studied in 40 Pisum sativum lines, varieties, and mutants and proved to be high, 61.6% on average. Varieties bred for different end uses substantially differed in the extent of polymorphism and allele composition. Polymorphism of microsatellite loci was shown to be suitable for developing passports of industrial pea varieties.

Unwrapping the Laccaria genome

Unwrapping the <i>Laccaria</i> genome

Selective pressure on the merozoite surface protein-1 genes of Plasmodium vivax, P. knowlesi and P. cynomolgi

Background: The merozoite surface protein 1 (msp-1) of malarial parasites is a promising target for malaria vaccine development. Because antigenic polymorphism of this protein occurs in both Plasmodium falciparum and P. vivax, it is important to know the extent of sequence variation of this gene in nonhuman primate malarias that can infect humans. Objective: To determine the complete nucleotide sequences of the msp-1 genes of Plasmodium knowlesi (Pkmsp-1) and P. cynomolgi (Pcymsp-1) and their evolutionary history comparing with an orthologous gene of P. vivax (Pvmsp-1). Method: The msp-1 genes of P. knowlesi and P. cynomolgi were amplified by the polymerase chain reaction and their nucleotide sequences were determined directly from the amplified products. Sequences were aligned using the Clustal X program. The extent of polymorphism is expressed in terms of nucleotide diversity (π) and the average number of nucleotide substitutions per site between populations (Dxy) in pair-wise comparison. The ratio of nucleotide substitutions at synonymous and nonsynonymous sites was computed by the McDonald and Kreitman test to detect evidence of departure from neutrality. The phylogenetic tree was constructed by the neighbor-joining method using the maximum composite likelihood with 1,000 bootstrap iterations. Results: The deduced amino acid sequences of the msp-1 of P. knowlesi, P. cynomolgi and P. vivax exhibit sequence similarity, ranging from 56.2 to 60.8 %. Variable blocks detected in Pkmsp-1 and Pcymsp-1 are located in regions corresponding to variable blocks of Pvmsp-1. Sliding window plots of Dxy along the entire coding regions of the msp-1 genes gave similar profiles for each pair of comparison. Pvmsp-1 is more closely related to Pcymsp-1 than that of Pkmsp-1 based on a phylogenetic analysis. However, the Tajima’s relative rate test suggests that the merozoite surface protein 1 (msp-1) of each species has not evolved at the same rate. The McDonald-Kreitman test detects positive selection on regions equivalent to blocks 1 and 9 of Pvmsp-1. Conclusion: The msp-1 genes of P. knowlesi, P. cynomolgi and P. vivax exhibit a similar pattern of sequence variation. Regions equivalent to conserved blocks 1 and 9 of Pvmsp-1 have evolved under positive selective pressure, suggestive of functional importance probably as targets for host immune responses.

Molecular variation of the shuttle craft and Lim3 genes, controlling the development of the nervous system, in a natural Drosophila melanogaster population

Comparative polymorphism of the first exon and first intron of the shuttle craft (stc) and Lim3 genes and their putative regulatory 5'-flanking sequences was analyzed using 20 sequenced natural alleles. A comparison of the stc and Lim3 genes showed that the extent of polymorphism was similar in their introns and corresponded to the variation level characteristic of Drosophila melanogaster, while the putative regulatory region and first intron of the stc gene proved to be more variable than the corresponding regions of the Lim3 gene. Since the genes under study occurred on the same chromosomes isolated from one population and were close together in a region having a high recombination rate, the difference in the extent of polymorphism between the regulatory and coding regions was explained by individual characteristics of each gene. The results made it possible to assume that the extent of polymorphism of the coding gene regions is maintained by balancing selection.

The hitch-hiking effect of a favourable gene

SUMMARY When a selectively favourable gene substitution occurs in a population, changes in gene frequencies will occur at closely linked loci. In the case of a neutral polymorphism, average heterozygosity will be reduced to an extent which varies with distance from the substituted locus. The aggregate eifect of substitution on neutral polymorphism is estimated; in populations of total size 10 6 or more (and perhaps of 10 4 or more), this eifect will be more important than that of random fixation. This may explain why the extent of polymorphism in natural populations does not vary as much as one would expect from a consideration of the equilibrium between mutation and random fixation in populations of different sizes. For a selectively maintained polymorphism at a linked locus, this process will only be important in the long run if it leads to complete fixation. If the selective coefficients at the linked locus are small compared to those at the substituted locus, it is shown that the probability of complete fixation at the linked locus is approximately exp (— Nc), where c is the recombinant fraction and N the population size. It follows that in a large population a selective substitution can occur in a cistron without eliminating a selectively maintained polymorphism in the same cistron.