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H Innan

Publications and source records attributed to H Innan.

14 recordsLinked to original sources
PubMed2001

Species and recombination effects on DNA variability in the tomato genus.

Population genetics theory predicts that strong selection for rare, beneficial mutations or against frequent, deleterious mutations reduces polymorphism at linked neutral (or weakly selected) sites. The reduction of genetic variation is expected to be more severe when recombination rates are lower. In outbreeding species, low recombination rates are usually confined to certain chromosomal regions, such as centromeres and telomeres. In contrast, in predominantly selfing species, the rarity of double heterozygotes leads to a reduced effective recombination rate in the whole genome. We investigated the effects of restricted recombination on DNA polymorphism in these two cases, analyzing five Lycopersicon species with contrasting mating systems: L. chilense, L. hirsutum, L. peruvianum, L. chmielewskii, and L. pimpinellifolium, of which only the first three species have self-incompatibility alleles. In each species, we determined DNA sequence variation of five single-copy genes located in chromosomal regions with either high or low recombination rate. We found that the mating system has a highly significant effect on the level of polymorphism, whereas recombination has only a weak influence. The effect of recombination on levels of polymorphism in Lycopersicon is much weaker than in other well-studied species, including Drosophila. To explain these observations, we discuss a number of hypotheses, invoking selection, recombination, and demographic factors associated with the mating system. We also provide evidence that L. peruvianum, showing a level of polymorphism (almost 3%) that is comparable to the level of divergence in the whole genus, is the ancestral species from which the other species of the genus Lycopersicon have originated relatively recently.

DNA↗
PubMed2001

Selection intensity against deleterious mutations in RNA secondary structures and rate of compensatory nucleotide substitutions.

A two-locus model of reversible mutations with compensatory fitness interactions is presented; single mutations are assumed to be deleterious but neutral in appropriate combinations. The expectation of the time of compensatory nucleotide substitutions is calculated analytically for the case of tight linkage between sites. It is shown that selection increases the substitution time dramatically when selection intensity Ns > 1, where N is the diploid population size and s the selection coefficient. Computer simulations demonstrate that recombination increases the substitution time, but the effect of recombination is small when selection is weak. The amount of linkage disequilibrium generated in the process of compensatory substitution is also investigated. It is shown that significant linkage disequilibrium is expected to be rare in natural populations. The model is applied to the mRNA secondary structure of the bicoid 3' untranslated region of Drosophila. It is concluded that average selection intensity Ns against single deleterious mutations is not likely to be much larger than 1.

3' Untranslated Regions↗
PubMed1999

A method for estimating nucleotide diversity from AFLP data.

A method for estimating the nucleotide diversity from AFLP data is developed by using the relationship between the number of nucleotide changes and the proportion of shared bands. The estimation equation is based on the assumption that GC-content is 0.5. Computer simulations, however, show that this method gives a reasonably accurate estimate even when GC-content deviates from 0.5, as long as the number of nucleotide changes per site (nucleotide diversity) is small. As an example, the nucleotide diversity of the wild yam, Dioscorea tokoro, was estimated. The estimated nucleotide diversity is 0.0055, which is larger than estimations from nucleotide sequence data for Adh and Pgi.

DNA Fingerprinting↗
PubMed1999

DNA variation in the wild plant Arabidopsis thaliana revealed by amplified fragment length polymorphism analysis.

To investigate the level and pattern of DNA variation of Arabidopsis thaliana at the entire genome level, AFLP analysis was conducted for 38 ecotypes distributed throughout the world. Ten pairs of selective primers were used to detect a total of 472 bands, of which 374 (79. 2%) were polymorphic. The frequency distribution of polymorphic bands was skewed toward an excess of singleton variation. On the basis of AFLP variation, nucleotide diversity for the entire genome was estimated to be 0.0106, which was within the range reported previously for specific nuclear genes. The frequency distribution of pairwise distance was bimodal because of an ecotype (Fl-3) with a large number of unique bands. Linkage disequilibrium between polymorphic AFLPs was tested. The proportion of significant linkage disequilibria was close to random expectation after neglecting the ecotype Fl-3. This result indicates that the effect of recombination could not be ignored in this selfing species. A neighbor-joining tree was constructed on the basis of the AFLP variation. This tree has a star-like topology and shows no clear association between ecotype and geographic origin, suggesting a recent spread of this plant species and limited migration between its habitats.

Arabidopsis↗
PubMed1998

The amount and pattern of DNA polymorphism under the neutral mutation hypothesis.

The amount and pattern of DNA polymorphism can give useful information on the maintenance mechanism of genetic variation at the DNA level. In this note we have shown the amount and pattern of DNA polymorphism expected under the neutral theory. The amount of DNA polymorphism can be estimated from the average number of nucleotide differences per site, the proportion of segregating sites, and so on. We have shown how to estimate theta from these quantities, where theta = 4Nv, N is the effective population size and v is the mutation rate per site per generation. We have also shown the expectations of the nucleotide variation within and between allelic classes.

Base Sequence↗
PubMed1997

Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana.

Variation in repeat number at 20 microsatellite loci of Arabidopsis thaliana was studied in a worldwide sample of 42 ecotypes to investigate the pattern and level of polymorphism in repetitive sequences in natural plant populations. There is a substantial amount of variation at microsatellite loci despite the selfing nature of this plant species. The average gene diversity was 0.794 and the average number of alleles per locus was 10.6. The distribution of alleles was centered around the mean of repeat number at most loci, but could not be regarded as normal. There was a significantly positive correlation between the number of repeats and the amount of variation. For most loci, the observed number of alleles was between the expected values of the infinite allele and stepwise mutation models. The two models were rejected by the sign test. Linkage disequilibrium was detected in 12.1% of the pairwise comparisons between loci. In phylogenetic tree, there was no association between ecotype and geographic origin. This result is consistent with the recent expansion of A. thaliana throughout the world.

Alleles↗
PubMed1997

The amounts of nucleotide variation within and between allelic classes and the reconstruction of the common ancestral sequence in a population.

The amounts of nucleotide variation within and between allelic classes were studied. The expectation and variance of the number of segregating sites and the expectation of the average number of pairwise differences among a sample of DNA sequences were obtained by using the theory of gene genealogy with no recombination. When the ancestral allelic class is unknown, it was found that the amount of variation within an allelic class increases with its frequency in the sample, while the amount of variation between two allelic classes is the largest when the two allelic classes exist equally. On the other hand, if we know the ancestral allelic class, as the frequency of the mutant allelic class increases, the amounts of variation within the mutant allelic class and between two allelic classes increase and the amount of variation within the ancestral allelic class decreases. As an example, we analyzed the polymorphism in the ND5 gene of Drosophila melanogaster and constructed the common ancestral sequence with high confidence, suggesting that the pattern of polymorphism within species gives useful information to know the ancestral sequence of the species.

Alleles↗
PubMed1997

Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana.

To investigate DNA variation in natural plant populations, a 1.8-kb region of the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As in the Adh region, dimorphism was detected throughout the investigated ChiA region, suggesting the possibility that dimorphic DNA variation exists in the entire nuclear genome of A. thaliana. The ChiA region was divided into two blocks by an intragenic recombination between two parental sequence types, which diverged 7.4 MYA under the assumption that nucleotide mutation rate per site per year is mu = 10(-9). Nucleotide diversity in the entire ChiA region was 0.0104. Tajima's test was significantly negative for both nucleotide and indel variations, which was manifested as an excess of unique polymorphisms. However, the level and pattern of polymorphism in the ChiA region were inconsistent with simple theoretical explanations. The HKA test detected no difference in the levels of intra- and interspecific variations between the ChiA and Adh regions. In the ChiA coding region, no difference in the patterns of synonymous and replacement variation was found in intra- and interspecific comparisons by the MK test. Although it was difficult to determine the exact genetic mechanism acting on the ChA locus, these results suggested that the ChA locus region was under the same genetic mechanism before and after the establishment of A. thaliana as a species.

Alcohol Dehydrogenase↗
PubMed1996

Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana.

Nucleotide variation in the Adh region of the wild plant Arabidopsis thaliana was analyzed in 17 ecotypes sampled worldwide to investigate DNA polymorphism in natural plant populations. The investigated 2.4-kb Adh region was divided into four blocks by intragenic recombinations between two parental sequence types that diverged 6.3 million years (Myr) ago, if the nucleotide mutation rate mu = 10(-9) is assumed. Within each block, dimorphism of segregating variations was observed with intermediate frequencies, which caused a substantial amount of nucleotide variation in A. thaliana at the species level. The first recombination introduced the divergent variation that resulted in dimorphism in this plant species approximately 3.3 Myr ago, and three subsequent intragenic combinations have occurred sporadically in approximately 1.1-Myr intervals. It was shown that there was only a limited number (six) of sequence types in this species and that no clear association was observed between sequence type and geographic origin. Taken together, these results suggest that A. thaliana has spread over the world only recently. It can be concluded that recombination played an important role in the evolutionary history of A. thaliana, especially through the generation of DNA polymorphism in the natural populations of this plant species.

Alcohol Dehydrogenase↗
PubMed1995

DNA fingerprinting study on the intraspecific variation and the origin of Prunus yedoensis (Someiyoshino).

In order to investigate the intraspecific variation of Prunus yedoensis (Someiyoshino) and interspecific relationship among P. yedoensis, P. lannesiana (Oshimazakura) and P. pendula (Edohigan), DNA fingerprinting study was conducted by using two different kinds of probes, M13 repeat sequence and (GACA)4 synthetic oligonucleotide. In this study, 68 plants of P. yedoensis grown in 46 prefectures in Japan were investigated. All the P. yedoensis individuals investigated showed the completely same banding pattern, indicating their clonal origin from a single plant. On the other hand, each of P. lannesiana and P. pendula individuals investigated showed a unique banding pattern, suggesting a considerable amount of genetic variation in these two species. About 90% of bands in DNA fingerprints of P. yedoensis were detected in either P. lannesiana or P. pendula. This result supports the hypothesis that P. yedoensis is an interspecific hybrid between P. lannesiana and P. pendula. From those results, it is concluded that P. yedoensis was produced only once through hybridization between P. lannesiana and P. pendula, and that this particular hybrid plant has been spread vegetatively all over Japan.

Base Sequence↗