Genetic Diversity and Population Structure of Dioscorea tokoro Makino, a Dioecious Climber

Abstract Dioscorea tokoro Makino is a herbaceous climber species widespread in East Asia. Genetic structure of a natural population of D. tokoro was examined employing starch gel electrophoresis of allozymes. Genotypes of seven loci were studied for 1,128 individuals. Twenty-six populations located mainly in the Kinki district of Japan were subgrouped into four large clusters by the geographical distribution of alleles. The D. tokoro population was revealed to contain greater total genetic diversity ( H_T =0.282) and higher intrapopulational genetic diversity ( H_S =0.258) than other outcrossing species for which data are available. On the other hand, interpopulational differentiation ( G_ST =0.096) was smaller than in other outcrossers. For the heterozygosity deficiency observed ( F_IT =0.125), population subdivision ( F_ST =0.096) and inbreeding within the population ( F_IS =0.067) were revealed to contribute to the same extent. From these F -statistics, the migration rate among subpopulations and the rate of between-relative matings were estimated. Overall results on the genetic structure of the D. tokoro population indicated a high gene flow among its subpopulations, and this may be the consequence of its life form as a climber and its habitat in a disturbed environment. During the study, the geographical cline of Pgi allele frequencies was observed. This finding was supposed to be the result of the selection imposed on Pgi by the temperature differences between localities.     

Historical Selection, Amino Acid Polymorphism and Lineage-Specific Divergence at the G6pd Locus in Drosophila Melanogaster and D. Simulans

The nucleotide diversity across 1705 bp of the G6pd gene is studied in 50 Drosophila melanogaster and 12 D. simulans lines. Our earlier report contrasted intraspecific polymorphism and interspecific differences at silent and replacement sites in these species. This report expands the number of European and African lines and examines the pattern of polymorphism with respect to the common A/B allozymes. In D. melanogaster the silent nucleotide diversity varies 2.8-fold across localities. The B allele sequences are two- to fourfold more variable than the derived A allele, and differences between allozymes are twice as among B alleles. There is strong linkage disequilibrium across the G6pd region. In both species the level of silent polymorphism increases from the 5' to 3' ends, while there is no comparable pattern in level of silent site divergence or fixation. The neutral model is not rejected in either species. Using D. yakuba as an outgroup, the D. melanogaster lineage shows a twofold greater rate of silent fixation, but less than half the rate of amino acid replacement. Lineage-specific differences in mutation fixation are inconsistent with neutral expectations and suggest the interaction of species-specific population size differences with both weakly advantageous and deleterious selection.     

Molecular evolution of two linked genes, Est-6 and Sod, in Drosophila melanogaster.

We have obtained 15 sequences of Est-6 from a natural population of Drosophila melanogaster to test whether linkage disequilibrium exists between Est-6 and the closely linked Sod, and whether natural selection may be involved. An early experiment with allozymes had shown linkage disequilibrium between these two loci, while none was detected between other gene pairs. The Sod sequences for the same 15 haplotypes were obtained previously. The two genes exhibit similar levels of nucleotide polymorphism, but the patterns are different. In Est-6, there are nine amino acid replacement polymorphisms, one of which accounts for the S-F allozyme polymorphism. In Sod, there is only one replacement polymorphism, which corresponds to the S-F allozyme polymorphism. The transversion/transition ratio is more than five times larger in Sod than in Est-6. At the nucleotide level, the S and F alleles of Est-6 make up two allele families that are quite different from each other, while there is relatively little variation within each of them. There are also two families of alleles in Sod, one consisting of a subset of F alleles, and the other consisting of another subset of F alleles, designed F(A), plus all the S alleles. The Sod F(A) and S alleles are completely or nearly identical in nucleotide sequence, except for the replacement mutation that accounts for the allozyme difference. The two allele families have independent evolutionary histories in the two genes. There are traces of statistically significant linkage disequilibrium between the two genes that, we suggest, may have arisen as a consequence of selection favoring one particular sequence at each locus.     

Trade-offs between male and female reproduction associated with allozyme variation in phosphoglucoisomerase in an annual plant (Clarkia unguiculata: Onagraceae)

The genotype of an individual for allozymes such as phosphoglucoisomerase (Pgi) is often not neutral with regard to fitness. Studies of several taxa have found consistent fitness differences among Pgi genotypes expressing different allozymes. We conducted a greenhouse experiment with Clarkia unguiculata to determine whether allelic variation at the Pgi-C1 locus may affect components of male and female function. We found significant differences in siring success between pollen donors homozygous for different Pgi alleles. When a mixture of pollen was applied to stigmas under conditions of gametophytic competition (more pollen deposited on stigmas than there are ovules available to fertilize), donors homozygous for the C allele of Pgi sired more seeds per fruit than B-allele donors. Differences between genotypes with respect to female fertility per fruit contrasted with the male advantage associated with the C allele. Recipients homozygous for the C allele produced fruits with more aborted seeds and fewer viable seeds than recipients homozygous for the B allele. These results suggest that allelic variation at a single locus may have opposing effects on male and female reproductive success in C. unguiculata, and that trade-offs between the two types of reproductive success could contribute to the maintenance of variation at the Pgi-C1 locus.     

Evolutionary History of the Sex-Peptide (Acp70a) Gene Region in Drosophila Melanogaster

In Drosophila the products of the seminal fluid stimulate oviposition and suppress remating in the female. Of all the accessory gland peptides (Acp's) involved in these two responses, the sex-peptide (coded by the Acp70A gene) is among the best characterized at the functional level. A 1.2-kb fragment encompassing the Acp70A gene of nine lines from a natural population of D. melanogaster and one allele of D. sechellia was sequenced to study the forces shaping nucleotide variation within and between species. The coding region of D. simulans and D. mauritiana was also sequenced. A Ser to Ala replacement polymorphism at the last position of the signal peptide was detected in D. melanogaster. The Ser and Ala alleles are at intermediate frequencies. The level of nucleotide variation is lower for the derived Ala allele, which is compatible with a recent origin and an increase in frequency due to positive selection. Variation at the 5' flanking region is structured in two major highly differentiated haplotypes, whose distribution does not conform to neutral expectations. Selective and/or historical factors could contribute to the observed overall patterning of nucleotide variation at the Acp70A region.     

Nucleotide variation at the hypervariable esterase 6 isozyme locus of Drosophila simulans

Esterase 6 (Est-6/EST6) is polymorphic in both Drosophila melanogaster and D. simulans for two common allozyme forms, as well as for several other less common variants. Parallel latitudinal clines in the frequencies of the common EST6-F and EST6-S allozymes in these species have previously been interpreted in terms of a shared amino acid polymorphism that distinguishes the two variants and is subject to selection. Here we compare the sequences of four D. simulans Est-6 isolates and show that overall estimates of nucleotide heterozygosity in both coding and 5' flanking regions are more than threefold higher than those obtained previously for this gene in D. melanogaster. Nevertheless, the ratio of replacement to exon silent-site polymorphism in D. simulans is less than the ratio of replacement to silent divergence between D. simulans and D. melanogaster, which could be the result of increased efficiency of selection against replacement polymorphisms in D. simulans or to divergent selection between the two species. We also find that the amino acid polymorphisms separating EST6- F and EST6-S in D. simulans are not the same as those that separate these allozymes in D. melanogaster, implying that the shared clines do not reflect shared molecular targets for selection. All comparisons within and between the two species reveal a remarkable paucity of variation in a stretch of nearly 400 bp immediately 5' of the gene, indicative of strong selective constraint to retain essential aspects of Est-6 promoter function.      

Molecular population genetics of ref(2)P, a locus which confers viral resistance in Drosophila

The ref(2)P locus (2-54.2) is polymorphic for two allelic forms in natural populations of Drosophila melanogaster, ref(2)Po and ref(2)Pp. The latter allele confers resistance to the rhabdovirus sigma infecting wild populations. Previous work, based on a small sample of prescreened restrictive (resistant) and permissive (susceptible) alleles, identified a large number of amino acid replacement changes (7) relative to synonymous changes (1). Such protein variability could be the result of variation-enhancing selection. To further test the selection hypothesis, we have examined the DNA sequences of ten randomly chosen lines of D. melanogaster and one line of D. simulans. Nine of the ten lines are permissive; D. simulans does not harbor the virus. The melanogaster alleles contain 4 synonymous changes, 19 noncoding changes, and 13 amino acid replacement changes, indicating a relatively high level of polymorphism. Three sequenced restrictive alleles have nearly identical sequences, indicating that they are relatively young. Compared to the permissive alleles, they share only a complex deletion at codon 34, CAG-AAT to GGA, which our analysis indicates to be the site conferring the restrictive phenotype. Patterns of polymorphism and divergence differ from neutral predictions by several criteria for the amino terminal region, which contains the complex deletion (codons 1-91), but not the remainder of the protein (codons 92-599). We find a higher rate of evolution on the D. melanogaster lineage than on the D. simulans lineage. The relatively large amount of both replacement and silent polymorphism in the permissive alleles and the lack of divergence between permissive and restrictive alleles suggests that the sigma virus and ref(2)P may be engaged in an evolutionary race in which new restrictive alleles are continually arising but are relatively short-lived.      

Temporal dynamics and variation of multilocus ISSR-PCR DNA markers in the Uman' population of Drosophila melanogaster over two decades (1984-2004)

The temporal dynamics of genomic variation in the Uman' (Ukraine) population of Drosophila melanogaster over the period 1984-2004 was studied using multilocus ISSR markers. Considerable polymorphism of the genomic DNA fragments corresponding to ISSR markers was found in the D. melanogaster population studied: the values of average heterozygosity varied from 0.085 to 0.127 depending on the year. Significant differences in the frequencies of dominant alleles between the samples of different years were recorded for 12 of the 30 DNA fractions detected. These changes are nondirectional and random. The pattern of detected variation suggests the determining influence of gene drift and migration process on the variation of noncoding DNA sequences in the Uman' population of D. melanogaster.     

Temporal dynamics and variation of multilocus ISSR-PCR DNA markers in the Uman’ population of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> over two decades (1984–2004)

The temporal dynamics of genomic variation in the Uman’ (Ukraine) population of Drosophila melanogaster over the period 1984–2004 was studied using multilocus ISSR markers. Considerable polymorphism of the genomic DNA fragments corresponding to ISSR markers was found in the D. melanogaster population studied: the values of average heterozygosity varied from 0.085 to 0.127 depending on the year. Significant differences in the frequencies of dominant alleles between the samples of different years were recorded for 12 of the 30 DNA fractions detected. These changes are nondirectional and random. The pattern of detected variation suggests the determining influence of gene drift and migration process on the variation of noncoding DNA sequences in the Uman’ population of D. melanogaster.     

Diversifying selection underlies the origin of allozyme polymorphism at the phosphoglucose isomerase locus in Tigriopus californicus

The marine copepod Tigriopus californicus lives in intertidal rock pools along the Pacific coast, where it exhibits strong, temporally stable population genetic structure. Previous allozyme surveys have found high frequency private alleles among neighboring subpopulations, indicating that there is limited genetic exchange between populations. Here we evaluate the factors responsible for the diversification and maintenance of alleles at the phosphoglucose isomerase (Pgi) locus by evaluating patterns of nucleotide variation underlying previously identified allozyme polymorphism. Copepods were sampled from eleven sites throughout California and Baja California, revealing deep genetic structure among populations as well as genetic variability within populations. Evidence of recombination is limited to the sample from Pescadero and there is no support for linkage disequilibrium across the Pgi locus. Neutrality tests and codon-based models of substitution suggest the action of natural selection due to elevated non-synonymous substitutions at a small number of sites in Pgi. Two sites are identified as the charge-changing residues underlying allozyme polymorphisms in T. californicus. A reanalysis of allozyme variation at several focal populations, spanning a period of 26 years and over 200 generations, shows that Pgi alleles are maintained without notable frequency changes. Our data suggest that diversifying selection accounted for the origin of Pgi allozymes, while McDonald-Kreitman tests and the temporal stability of private allozyme alleles suggests that balancing selection may be involved in the maintenance of amino acid polymorphisms within populations.     

Differential selective pressures on the merozoite surface protein 2 locus of Plasmodium falciparum in a low endemic area

195 Plasmodium falciparum merozoite surface protein-2 alleles collected in Tak Province, Thailand, in 1996 and 2006 revealed extremely limited sequence polymorphism except in the variable (V) region, which defines the two allelic families 3D7 and FC27. This pattern is most easily explained by repeated inter-allelic gene conversion events homogenizing alleles outside the V region. Comparison of synonymous and nonsynonymous differences in V regions within allelic families supported the hypothesis that amino acid sequence polymorphism in this region is selectively favored. The pattern of sequence differentiation supported the hypothesis that repeats in the V region have evolved by concerted evolution in the 3D7 family but not in the FC27 family. In the FC27 family two alleles of relatively high frequency were the most common V-region alleles in both 1996 and 2006, while 3D7 alleles constituted a significantly greater proportion of the sequences collected in 2006 (56.1%) than of those collected in 1996 (28.9%). These changes in the frequencies of 3D7 alleles may reflect increased intensity of selection on the P. falciparum population in Thailand as a result of effective control measures that have sharply reduced the incidence of malaria infection.     

Estimating genetic drift and effective population size from temporal shifts in dominant gene marker frequencies

Measurement of temporal change in allele frequencies represents an indirect method for estimating the genetically effective size of populations. When allele frequencies are estimated for gene markers that display dominant gene expression, such as, e.g. random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers, the estimates can be seriously biased. We quantify bias for previous allele frequency estimators and present a new expression that is generally less biased and provides a more precise assessment of temporal allele frequency change. We further develop an estimator for effective population size that is appropriate when dealing with dominant gene markers. Comparison with estimates based on codominantly expressed genes, such as allozymes or microsatellites, indicates that about twice as many loci or sampled individuals are required when using dominant markers to achieve the same precision.     

Breed differences in allele frequency of the dopamine receptor D4 gene in dogs.

We previously reported that the dog dopamine receptor D4 (DRD4) gene is polymorphic as observed in humans, and four alleles were identified based on the number and/or order of the 12 and 39 bp sequences located in the homologous region of human DRD4. To assess the diversity of the DRD4 gene in dogs we examined the allelic variations in four breeds (beagle, golden retriever, Shetland sheepdog, and shiba) employing the polymerase chain reaction (PCR). As a result, we found three novel alleles and determined the DNA sequences of these alleles. The beagle shared four alleles, including 396, 435, 447a, and 447b, with the 435 (52.6%) and 447a (39.5%) alleles being common. The golden retriever had the 435 and 447a alleles, and the 435 allele was frequent (73.3%). In the Shetland sheepdog, the 435, 447a, and 498 alleles were observed, of which the 447a allele was most frequent (82.5%). The shiba had five alleles-447a, 447b, 486, 498, and 549-and the 447b allele was most common (55.4%). These findings suggest that the allele frequency varied among the four dog breeds, and analysis of the DRD4 polymorphism may therefore be useful for elucidating the relationships among dog breeds.     

Short tandem repeat polymorphism of the D2S1242 locus in a Japanese population

Allele frequencies and sequence characteristics of the D2S1242 short tandem repeat (STR) locus were studied in a Japanese population sample. A total of 10 D2S1242 alleles and 34 genotypes were identified in 273 unrelated Japanese individuals. The five most common alleles detected had frequencies of over 10%. No deviations from Hardy-Weinberg equilibrium were found when the expected allele values were compared with the observed values. Sequence analysis of each allele showed a tetranucleotide polymorphism. Alleles 9 to 14 had different sequence structures than alleles 15 to 19. Allele 18 had a different sequence in the Japanese sample compared to an Austrian sample. The power of discrimination was 0.95. The present results demonstrate that the D2S1242 STR locus is a useful genetic marker in the Japanese population.     

两个国内小型猪品种GH基因部分序列的多态性分析

目的对西藏小型猪和广西巴马小型猪生长激素基因（GH基因）部分序列的多态性进行分析。方法采用内切酶ApaI和Hin6I对西藏小型猪（108头）和广西巴马小型猪（132头）GH基因-119 bp～＋486 bp之间的区域进行PCR-RFLPs分析。结果 （1）从ApaI酶切产生的结果来看,ApaI酶切产生A（449 bp＋101 bp＋55bp）,B（316 bp＋133 bp＋101 bp＋55 bp）两种等位基因。等位基因A的频率高于等位基因B,等位基因A为优势基因。AA基因型频率高于AB和BB基因型频率;（2）从Hin6I酶切产生的结果来看,Hin6I酶切产生G1（605bp）、G2（498 bp＋107 bp）、G3（449 bp＋156 bp）、G4（449 bp＋107 bp＋49 bp）四种等位基因。等位基因G4的频率高于等位基因G1、G2、G3。等位基因G1频率很低。基因型G2G3、G2G4、G3G4、G4G4的频率较高。（3）由酶切产生的基因和基因型多态性,发现西藏小型猪与广西巴马小型猪在该基因部分序列差异不显著（P〉0.05）。结论国内的优质实验用小型猪,如西藏小型猪和广西巴马小型猪等位基因A频率均较高。     

Contrasting patterns of variation in MHC loci in the Alpine newt

Major histocompatibility complex (MHC) genes are essential in pathogen recognition and triggering an adaptive immune response. Although they are the most polymorphic genes in vertebrates, very little information on MHC variation and patterns of evolution are available for amphibians, a group known to be declining rapidly worldwide. As infectious diseases are invoked in the declines, information on MHC variation should contribute to devising appropriate conservation strategies. In this study, we examined MHC variation in 149 Alpine newts ( Mesotriton alpestris ) from three allopatric population groups in Poland at the northeastern margin of the distribution of this species. The genetic distinctiveness of the population groups has previously been shown by studies of skin graft rejection, allozymes and microsatellites. Two putative expressed MHC II loci with contrasting levels of variation and clear evidence of gene conversion/recombination between them were detected. The Meal-DAB locus is highly polymorphic (37 alleles), and shows evidence of historical positive selection for amino acid replacements and substantial geographical differentiation in allelic richness. On the contrary, the Meal-DBB locus exhibits low polymorphism (three alleles differing by up to two synonymous substitutions) and a uniform distribution of three alleles among geographical regions. The uniform frequencies of the presumptively neutral Meal-DBB alleles may be explained by linkage to Meal-DAB . We found differences in allelic richness in Meal-DAB between regions, consistent with the hypothesis that genetic drift prevails with increasing distance from glacial refugia. Pseudogene loci appear to have evolved neutrally. The level of DAB variation correlated with variation in microsatellite loci, implying that selection and drift interplayed to produce the pattern of MHC variation observed in marginal populations of the Alpine newt.     

Identification of novel single nucleotide polymorphisms in the DGAT1 gene of buffaloes by PCR-SSCP

Diacylglycerol O-acyltransferase 1 (DGAT1) is a microsomal enzyme that catalyzes the final step of triglyceride synthesis. The DGAT1 gene is a strong functional candidate for determining milk fat content in cattle. In this work, we used PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing to examine polymorphism in the region spanning exon 7 to exon 9 of the DGAT1 gene in Murrah and Pandharpuri buffaloes. Three alleles (A, B and C) and four novel single-nucleotide polymorphisms were identified in the buffalo DGAT1 gene. The frequencies of the alleles differed between the two buffalo breeds, with allele C being present in Murrah but not in Pandharpuri buffalo. The allele variation detected in this work may influence DGAT1 expression and function. The results described here could be useful in examining the association between the DGAT1 gene and milk traits in buffalo.     

DNA polymorphism in the Mongolian population. Restriction fragment length polymorphism analysis of mitochondrial DNA]

Restriction enzyme fragment patterns in the D loop and deletion-insertion polymorphism in the V noncoding region of human mitochondrial DNA (mt DNA) were analysed in Mongolian population using the polymerase chain reaction. Polymorphisms were detected and mt DNAs classified into 40 types using seven enzymes--AvaII, BamHI, CfrI131, KpnI, EcoRV, HaeIII RsaI and Asian specific deletion and insertion. The allele frequencies of the polymorphisms and gene diversity were determined. The data obtained for Mongolian population and the literature data were comparatively studied.     

秦川牛和中国荷斯坦牛POU1F1基因多态性研究

采用PCR-RFLP技术研究了秦川牛(QQ)和中国荷斯坦牛(HC)共计218头个体POU1F1基因的多态性。结果表明: 秦川牛及中国荷斯坦牛群体POU1F1-HinfⅠ基因座的451 bp 的PCR产物经限制性酶HinfⅠ消化后表现多态, 其等位基因A/B频率分别为0.232/0.768、0.132/0.868; 两个群体AA、AB和BB 3种基因型的频率分别为0.030/0.403/0.567、0.007/0.251/0.742。在该基因座秦川牛群体处于Hardy-Weinberg平衡状态, 中国荷斯坦牛群体处于不平衡状态。它们在该基因座的杂合度、有效等位基因数、Shannon信息熵、多态信息含量分别为0.356/1.553/0.541/0.292、0.229/1.297/0.390/0.203; 秦川牛群体的位点杂合度、有效等位基因数、Shannon信息熵、多态信息含量均大于中国荷斯坦牛群体。