According to the neo-Darwinian view of evolution evolution rate ν depends solely on the environment variation rate γ, whereas in the non-Darwinian view evolution rate is determined mainly by the mutation rate μ. We have studied two kinds of population genetics models which exhibit both types of evolution in different parametric regions: one is a dynamical model representing infinite population, and the other is a Markov process model representing a nearly monomorphic finite population. In the infinite population model, after proving general time-derivative and μ-derivative formulas for the population average of quantitative traits, we show that if the mutation rate is adaptively determined, μ must be larger than ν in the stationary state. Loads of evolution are obtained in both regions. A high evolution rate such as ν=1 per genome per generation is consistent with Haldane’s value of tolerable load if and only if the functional constraint is not large and selection is weak, independent of whether the evolution is neo-Darwinian or non-Drawinian. As the selection intensity increases, ν is shown to change discontinuously from nearly μ to γ at the transition point. In the finite population model, the transition of ν is not discontinuous, but is very steep. On the other hand, no steep change of polymorphism takes place at the transition point. The steepness of the transition in our model suggests that real molecular evolution can be devided into either neo-Darwinian or non-Darwinian, and that the intermediate type of evolution is rather rare.
To examine the nucleotide diversity at silent (synonymous+intron+untranslated) and non-silent (nonsynonymous) sites in chimpanzees and humans, genes at six nuclear loci from two chimpanzees were sequenced. The average silent diversity was 0.19%, which was significantly higher than that in humans (0.05%). This observation suggests a significantly larger effective population size and a higher extent of neutral polymorphism in chimpanzees than in humans. On the other hand, the non-silent nucleotide diversity is similar in both species, resulting in a larger fraction of neutral mutations at non-silent sites in humans than in chimpanzees. Other types of polymorphism data were collected from the literature or databases to examine whether or not they are consistent with the nuclear DNA sequence polymorphism observed here. The nucleotide diversity at both silent and non-silent sites in mitochondrial (mt) DNA genes was compatible with that of the nuclear genes. Microsatellite loci showed a similar high extent of heterozygosity in both species, perhaps due to the combined effect of a high mutation rate and a recent population expansion in humans. At protein loci, humans are more heterozygous than chimpanzees, and the estimated fraction of neutral alleles in humans (0.84) is much larger than that in chimpanzees (0.26). These data show that the neutral fraction in non-silent changes is relatively large in the human population. This difference may be due to a relaxation of the functional constraint against proteins in the human lineage. To evaluate this possibility, it will be necessary to examine nucleotide sequences in relation to the physiological or biochemical properties of proteins.
An insertion sequence was found in a Mu homologue in the genome of Arabidopsis thaliana. The insertion sequence had poly(A) at the 3' end, and promoter motifs (A- and B-boxes) recognized by RNA polymerase III. The sequence was flanked by direct repeats of a 15-bp sequence of the Mu homologue, which appears to be a target-site sequence duplicated upon insertion. These findings indicate that the insertion sequence is a retroposon SINE, and it was therefore named AtSN (A. thaliana SINE). Many members of the AtSN family were identified through a computer-aided homology search of databases and classified into two subfamilies, AtSN1 and AtSN2, having consensus sequences 159 and 149 bp in length, respectively. These had no homology to SINEs in other organisms. About half of AtSN members were truncated through loss of a region at either end of the element. Most of them were truncated at the 5' end, and had a duplication of the target-site sequence. This suggests that the ones with 5' truncation retroposed by the same mechanism as those without truncation. Members of the AtSN1 or AtSN2 subfamilies had many base substitutions when compared with the consensus sequence. All of the members examined were present in three different ecotypes of A. thaliana (Columbia, Landsberg erecta, and Wassilewskija). These findings suggest that AtSN members had proliferated before the A. thaliana ecotype strains diverged.
Cypripedium calceolus was found in 1980 in Rebun Island off the north coast of Hokkaido, Japan, but the origin of this plant has been a controversial issue. In this study, we have made a comparative study by chloroplast DNA sequencing analysis among C. calceolus which occurs in Rebun Island and populations of C. calceolus from western Europe, China and far eastern Russia (Nakhodka), and also as references, C. macranthos in Japan and other Cypripedium species in North America. A Cypripedium cf. “calceolus”, found recently in eastern Hokkaido, was also included in this analysis. The C. calceolus samples analyzed were categorized into three groups, i.e., those from Western Europe, from China and far eastern Russia, and from Rebun Island. The C. calceolus in Rebun Island was clearly different from the others in terms of DNA sequence and morphological features. The C. cf. calceolus from eastern Hokkaido and one sample from Nadhodka, Russia, were also classified into the same group as those from Rebun Island, although some differences in their morphological features were observed. It is concluded that the C. calceolus found in Rebun Island is not identical with those growing in Europe and China. In addition, it was found that it may be possible to classify C. macranthos into two groups, namely groups which include or do not include var. rebunense. An unidentified Cypripedium species found in Rebun Island falls into the same group as var. rebunense.
We screened a gene trap library of Arabidopsis thaliana and isolated a line in which a gene encoding a homologue of monofunctional aspartake kinase was trapped by the reporter gene. Aspartate kinase (AK) is a key enzyme in the biosynthsis of aspartate family amino acids such as lysine, threonine, isoleucine, and methionine. In plants, two types of AK are known: one is AK which is sensitive to feedback inhibition by threonine and carries both AK and homoserine dehydrogenase (HSD) activities. The other one is monofunctional, sensitive to lysine and synergistically S-adenosylmethionine, and has only AK activity. We concluded that the trapped gene encoded a monofunctional aspartate kinase and designated as AK-lys3, because it lacked the HSD domain and had an amino acid sequence highly similar to those of the monofunctional aspartate kinases of A. thaliana. AK-lys3 was highly expressed in xylem of leaves and hypocotyls and stele of roots. Significant expression of this gene was also observed in trichomes after bolting. Slight expression of AK-lys3 was detected in vascular bundles and mesophyll cells of cauline leaves, inflorescence stems, sepals, petals, and stigmas. These results indicated that this aspartate kinase gene was not expressed uniformly but in a spatially specific manner.
In order to confirm the results obtained in the previous 1-year-term (December 12, 1998, through December 10, 1999) scorings and analyses of spontaneous pink mutant events (PMEs) in the stamen hairs of Tradescantia clone BNL 4430 cultivated in a nutrient solution circulating (NSC) growth chamber, similar scorings and analyses were continued for another 52-week period from December 11, 1999, through Decomber 8, 2000. The environmental conditions were not changed, except for a minor modification in the method of supplying the nutrient solution used. During the scoring period, 732, 128 stamen hairs with an average cell number of 24.90 cells were observed, and 2, 368 PMEs were detected. The overall spontaneous somatic mutation frequency was 1.35±0.03 PMEs per 104 hair-cell divisions, which was significantly lower than the value of 1.56±0.03 determined in the previous 52-week period, and the frequencies were lower during April through September than in other months, the period showing lower frequencies lasting 1-month longer than in the previous year. The present results reconfirmed the occurrence of a clear seasonal variation in the spontaneous mutation frequency in the NSC growth chamber, and the lower overall frequency, probably related to the minor modification in supplying the nutrient solution, is helpful for conducting mutagenicity tests at low levels, offering a lower background level. The analyses of the sectoring patterns of all these PMEs showed that the most of the 203 cases of multiple (two to five) pink sectors observed in the same stamen hairs (scored as 253 PMEs for calculating mutation frequency) were the results of events involving somatic recombinations occurred in single cells or cell lineages, rather than those of two or more independent somatic mutations occurred in different cells, agreeing with our previous stduy, and the significance of somatic recombinations in causing single PMEs was also reconfirmed.
Substitutions rates are expected to be rather constant when a gene is compared between species. To analyze this feature, Ka/Ks rations have been studied for Alcohol dehydrogenase (Adh) and Alcohol dehydrogenase duplication (Adh-dup) genes in Drosophila species. Adh Ka/Ks values are lower in intrasubgenus comparisons involving species of the Sophophora group than when these species are compared to the D. immigrans and S. lebanonensis, and this difference does not occur in the Adhdup comparisons.