The phylogenetic relationships among Primates, Artiodactyla, Cetacea, Carnivora, and Rodentia were estimated from the amino acid sequences of proteins encoded by the mitochondrial genomes, for which entire nucleotide sequence data are available, using Marsupialia, Aves, and Amphibia as outgroups. The overall evidence of the maximum likelihood, as well as maximum parsimony, analyses strongly suggests that Rodentia is an outgroup to the other four eutherian orders, and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon, consistently with the molecular phylogenetic studies of previous authors. However, analyses of individual proteins do not necessarily conform to this conclusion, and some of the proteins reject the putatively correct tree with nearly 5% significance. Furthermore, the 12S mitochondrial ribosomal RNA sequences do not give the putatively correct tree irrespective of the alignments and of the phylogenetic methods, although the tree is not rejected with a statistical significance. The 16S ribosomal RNA sequences give the putatively correct tree with our sequence alignment when the ML method is used, but the result depends on the alignment and on the choice of outgroup species. These results illustrate the limitation of the ribosomal RNA data alone in phylogenetic inference, and suggest that we must analyze as many genes as possible and synthesize the results to draw a reliable conclusion.
In this paper, we reviewed our recent works on a possible link between molecular evolution and tissue evolution. The evolutionary rates of genes that are expressed tissue specifically were shown to differ widely to one another, depending on tissues: Brain specific genes evolve with significantly slower rate than immune specific genes. The tissue dependence of molecular evolutionary rate strongly suggests the presence of functional constraints against molecular changes from tissue level. A molecular phylogenetic analysis of tissue specific isoforms that are identical to one another in function, but differ only in tissue distribution revealed frequent gene duplications and rapid accumulations of amino acid substitutions during the early evolution of chordates, where rapid evolution at the tissue or organ levels is thought to have occurred. On the basis of functional constraints, a possible explanation for the correlation between evolution at the two levels was presented.
For pathogenic viruses such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human influenza A virus, and human T-cell leukemia virus type I (HTLV-I), the evolutionary features were briefly reviewed with special reference to the rates of synonymous and nonsynonymous substitutions. In particular, these rates were discussed in connection with the neutral theory of molecular evolution. It was common to all the five pathogenic viruses that the rate of synonymous substitution was higher than that of, nonsynonymous substitution particularly when the entire gene regions were compared between different isolates. This suggests that the viral proteins are quite conservative to functional and structural changes even though most of theses viral genomes are evolving at a speed extraordinarily higher than their host genomes. Thus, this feature is consistent with the neutral theory. However, it is also pointed out that positive selection may be operating on some specific sites such as antigenic sites in order for the pathogenic viruses to escape from the host immune system.
Evolution of glutamine synthetase gene is discussed on the results of DNA sequence analysis of the gene. Thirty DNA sequences of various organisms spanning from prokaryotes to eukaryotes were collected from the DNA data banks and translated first, they were aligned next, then evolutionary distances were computed, and molecular phylogeny was finally estimated. The results of the alignment reveal that functionally important regions of glutamine synthetase have been evolutionarily more conserved than the remaining regions. The evolutionary distances computed also show that the rate of synonymous substitution is higher than that of nonsynonymous substitution. These are well in accordance with the neutral theory of molecular evolution. Besides, the molecular phylogeny obtained shows that the origin of glutamine synthetase gene is much earlier than the divergence between eukaryotes and prokaryotes, suggesting that the gene is one of the oldest genes functioning now.
This note is about the neutralism first proposed by Dr. Motoo Kimura. It consists of two sections. The first section describes how one person became a neutralist. The second section is a preliminary report on the historical research of neutralism based on questionnaire sent to members of the Genetics Society of Japan.
Accurate estimations of nuclear DNA content of rice are important because this crop is being used in many types of molecular studies. The main objective of this study was to estimate the nuclear DNA content in ten rice species by flow cytometry. Most of the values obtained were lower than those obtained in earlier studies using Feulgen microdensitometry. Significant differences in genome size among rice species were found. Oryza glaberrima had the smallest genome (0.73-0.76 pg/2C), while O. minuta and O. latifolia had the largest values (ca. 2.33 pg/2C). Tetraploid species had more nuclear DNA than diploid ones. The AA genome had less DNA (0.86-0.96 pg/2C) than the CC (1.14-1.17 pg/2C) and EE (1.99 pg/2C) genomes. The AA genome of O. saliva was larger than the AgA g genome of O. glaberrima and the A1A 1 genome of O. longistaminata, which had mean values of 0.73-0.76 and 0.78 pg/2C, respectively. Indica (IR36) and japonica (Yukihikari) cultivars of O. saliva also showed significant differences. Three different nuclear DNA levels (1.93, 1.85, and 1.31 pg/2C) were found among five O. ridleyi plants analyzed. Flow cytometry also allowed rapid and reliable determination of the ploidy level of anther culture-derived plants.
Selected stable standard Solanum genotypes and two populations of asymmetric somatic hybrids between Solanum brevidens (2n=2x=24) and dihaploid S. tuberosum (2n=2x=24) were analyzed to test the resolution of flow cytometric determination of nuclear DNA content (2C value) in terms of a loss or gain of chromosomes, and to analyze the correlation between the 2C value and the chromosome number. Correlation was high within the standard genotypes (r=0.99, P<0.001). However, the correlation was low within the two populations of somatic hybrids (r=0.54 and 0.65, 0.01<P<0.05). Highly chimeric , hybrids were readily detected by flow cytometry, whereas microscopic chromosome observations failed to detect them. Data were analyzed regarding their potential usefulness in predicting the flowering capacity. The 2C values deviating from those of the euploid standard genotypes were highly associated with abnormal morphology and lack of flowering. Flowering capacity did not correlate with chromosome number. These results suggest that flow cytometry can be utilized for initial selection of somatic hybrids.
A critical evaluation of the digital data of 250 barley metaphase spreads obtained by image analysis revealed the instability of the chromosomal morphology during the mitotic metaphase stage. Both the relative length (RL) and arm ratio (AR) of the chromosomes, which are the two major numerical parameters in karyotype analysis, varied in the different chromosomal spreads. The ranking of the chromosomes for the respective parameters within a complement changed accordingly. The data indicated that karyotype analysis based merely on the numerical parameters RL and AR may lead to the misidentification of chromosomes, causing a misinterpretation of the data from different chromosomes when averaging several data. Thus, most of data of the RL and AR which have so far been reported may need reexamination except for the cases where chromosomes were identified based oh other critical parameters, e.g., banding pattern, condensation pattern, in situ hybridization, etc. Differential condensation between the chromosome arms may be the cause of the instability of the karyotype.
Dynamic changes in the morphology of barley chromosomes during the mitotic metaphase stage were observed and attributed to the differential condensation of the chromosome arms. The mitotic stage of the 250 metaphase spreads was classified into five sub-stages from early metaphase to late metaphase. At each sub-stage, the relative length (RL) and the arm ratio (AR) of the chromosomes were examined and the ranking of the chromosomes for the two parameters was also determined for the respective chromosomal spreads. As a result, the RL and AR values of some of the chromosomes as well as their ranking for the two parameters were found to vary with the progression of the metaphase stage. The dynamic changes in the RL and AR values were closely related to the differences in the condensation rate of the chromosome arm. Factors involved in the differential chromosome condensation are discussed.
On the basis of multiple protein data, the phylogenetic relationships among the major clades of eutherian mammals, Primates, Cetacea, Artiodactyla, Carnivora, Lagomorpha, Myomorpha, and Caviomorpha, were analyzed by the maximum likelihood (ML) method, together with the maximum parsimony (MP) method and the neighbor joining (NJ) method. Using nineteen protein data, we first reexamined the hypothesis of rodent polyphyly proposed by Graur et al. (1991) based on the four taxon system, consisting of human, mouse (or rat), guinea-pig and an outgroup. The ML analysis does not support the rodent polyphyly, but strongly favors the traditional view of rodent monophyly representing the Myomorpha-Caviomorpha association. In the second analysis, the phylogenetic position of Lagomorpha were reexamined using three sets of multiple protein data, 13 mitochondrial DNA-coded proteins from rodents, rabbit, human, seals, bovine, whales and opossum, 25 protein data from human, rabbit and rodents and an outgroup, and 20 protein data from human, rabbit, bovine (or pig) and rodents. Our analysis favors the closer affinity of Lagomorpha to Primates than to Rodentia. The branching sequence of seven mammalian groups revealed by the present analyses is as follows: Myomorpha-Caviomorpha clade (Rodentia), rabbit, Primates, Carnivora, and Artiodactyla-Cetacea clade. Judging from the branch lengths measured by the numbers of synonymous substitutions, a series of divergence of these mammals is likely to be bush-like. The rapid rate of rodent evolution was reexamined in the light of the new phylogeny.
Di-nucleotide microsatellites were isolated from a genomic library of a tropical tree species, Dryobalanops lanceolata, in Sarawak, for the purpose of using them as hypervariable genetic markers to study the pollen-mediated gene flow. Among 1600 recombinant clones, in total 20 clones gave positive signals when hybridized with oligonucleotides with the three different repeat motifs, GT, CA and CT. Estimations of abundance of (GT)n/(CA)n and (GA)n/(CT) n di-nucleotide repeats in D. lanceolata genome revealed to be one in every 84 kb and 80 kb, respectively. Among six sequenced microsatellite loci, one was selected to synthesize PCR primers to amplify the microsatellite. PCR product size of the locus was variable among different individuals, which is attributed to the different number of di-nucleotide repeats. The same microsatellite genotype was detected in the trunk and canopy of a single large tree, indicating the utility of trunk tissue as the source of DNA for the population genetic study of tropical tree species, the canopy of which is usually difficult to approach.
The sectoring patterns of somatic pink mutations were analyzed in the stamen hairs of Tradescantia clone KU 20, a temperature-sensitive mutable clone. This clone is a blue/pink heterozygote, and its spontaneous pink mutation frequency increases up to about 40-fold at lower temperature. In order to elucidate the mutable nature of this clone, the sectoring patterns were analyzed on 1,123 spontaneous pink mutant events and on 2,725 pink mutant events induced by 0.606 and 1.28 Gy of gamma rays. The average number of pink cells per terminal pink mutant event (a row of pink cells including the terminal cell of a hair) occurred spontaneously was 7.40, whereas the number for the terminal pink mutant event induced by gamma rays varied from 3.33 to 9.88 depending on the post-irradiation days, i.e. , increased gradually as the number of days proceeded, then was stabilized at the level of spontaneous mutations after about three weeks. The average number of pink cells per interstitial pink mutant event (a single pink cell or two or more contiguous pink cells between blue cells) was 1.97 for spontaneous mutations, while the number for induced mutations varied also depending on the post-irradiation days. The ratio of the number of interstitial pink mutant events against that of terminal pink mutant events was 1.35 for spontaneous mutations, but the ratio for induced mutations varied also with post-irradiation period reaching 2.89 at the peak, indicating that more interstitial pink mutant events are induced by gamma rays than terminal pink mutant events, as compared with spontaneous mutations. The frequency of multiple pink mutant sectors in a hair was more than four times higher than that expected from independent occurrences in case of spontaneous mutations, while the frequency was close to the expectation in induced mutations, suggesting that somatic recombination is involved as one of the major causes of spontaneous mutations in this mutable clone.