A method for molecular phylogeny construction by direct use of nucleotide sequence data

Summary A method for molecular phylogeny construction is newly developed. The method, called the stepwise ancestral sequence method, estimates molecular phylogenetic trees and ancestral sequences simultaneously on the basis of parsimony and sequence homology. For simplicity the emphasis is placed more on parsiomony than on sequence homology in the present study, though both are certainly important. Because parsimony alone will sometimes generate plural candidate trees, the method retains not one but five candidates from which one can then single out the final tree taking other criteria into account.The properties and performance of the method are then examined by simulating an evolving gene along a model phylogenetic tree. The estimated trees are found to lie in a narrow range of the parsimony criteria used in the present study. Thus, other criteria such as biological evidence and likelihood are necessary to single out the correct tree among them, with biological evidence taking precedence over any other criterion. The computer simulation also reveals that the method satisfactorily estimates both tree topology and ancestral sequences, at least for the evolutionary model used in the present study.     

DNA turnover and the molecular clock

Summary Many detailed studies on the mechanisms by which different components of eukaryotic nuclear genomes have diverged reveal that the majority of sequences are seemingly not passively accumulating base substitutions in a clocklike manner solely determined by laws of diffusion at the population level. It appears that variation in the rates, units, biases, and gradients of several DNA turnover mechanisms are contributing to the course of DNA divergence. Turnover mechanisms have the potential to retard, maintain, or accelerate the rate of DNA differentiation between populations. Furthermore, examples are known of coding and noncoding DNA subject to the simultaneous operation of several turnover mechanisms leading to complex patterns of fine-scale restructuring and divergence, generally uninterpretable using selection and/or neutral drift arguments in isolation. Constancy in the rate of divergence, where observed over defined periods of time, could be a reflection of constancy in the rates and units of turnover. However, a consideration of the generally large disparity between rates of turnover and mutation reveals that DNA clocks, which would be independently driven by turnover in separate genomic components, would tend to be episodic. The utility of any given DNA sequence for measuring time and species relationships, like individual proteins, is proportional to the extent to which all contributing forces to the evolution of the sequence, internal and external, are understood.     

木聚糖酶分子进化的研究进展

木聚糖的降解需要多种水解酶的协同作用,其中βD1,4内切木聚糖酶是最关键的水解酶之一。同一家族木聚糖酶氨基酸序列间有较高的同源性和较近的亲缘关系,这标准通常用于酶的家族归类。不同来源的同种木聚糖酶在相同位置上的氨基酸残基起源于共同祖先或者具有相似的生物学功能,而在进化过程中,对酶分子结构、催化起重要作用的氨基酸残基往往高度保守。综述了木聚糖酶分子进化的研究进展及其应用前景 。     

A contiguous sequence in spinach nuclear DNA is homologous to three separated sequences in chloroplast DNA

Summary A 3.4-kbp nuclear (n) DNA sequence has greater than 99% sequence homology to three segments of the chloroplast (cp) genes rps2, psbD/C, and psaA respectively. Each of these cpDNA segments is less than 3 kbp in length and appears to be integrated, at least in part, into several (>5) different sites flanked by unique sequences in the nuclear genome. Some of these sites contain longer homologies to the particular genes, while others are only homologous to smaller parts of the cp genes. Both the cpDNA fragments found in the nuclear genome and their flanking nDNA sequences are invested with short repeated A-T rich sequences but, apart from a hexanucleotide sequence and a palindromic sequence identified near each recombination point, there is no obvious structure that can suggest a mechanism of DNA transfer from the chloroplast to the nucleus in spinach.     

Chromosome-specific subsets of human alpha satellite DNA: Analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat

Summary The centromeric regions of human chromosomes are characterized by diverged chromosome-specific subsets of a tandemly repeated DNA family, alpha satellite, which is based on a fundamental monomer repeat unit 171 bp in length. We have compared the nucleotide sequences of 44 alphoid monomers derived from cloned representatives of the multimeric higher-order repeat units of human chromosomes 1, 11, 17, and X. The 44 monomers exhibit an average 16% divergence from a consensus alphoid sequence, and can be assigned to five distinct homology groups based on patterns of sequence substitutions and gaps relative to the consensus. Approximately half of the overall sequence divergence can be accounted for by sequence changes specific to a particular homology group; the remaining divergence appears to be independent of the five groups and is randomly distributed, both within and between chromosomal subsets. The data are consistent with the proposal that the contemporary tandem arrays on chromosomes 1, 11, 17, and X derive from a common multimeric repeat, consisting of one monomer each from the five homology groups. The sequence comparisons suggest that this pentameric repeat must have spread to these four chromosomal locations many millions of years ago, since which time evolution of the four, now chromosome-specific, alpha satellite subsets has been essentially independent.     

Identification and chromosomal distribution of DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis

DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis were identified, using the GenBank sequence database. Chromosomal locations of the conserved segments were compared between the two bacteria, and the following three features were observed. (1) Although the two genomes are nearly identical in size, chromosomal arrangements of the conserved segments are considerably different from each other. (2) In many cases, chromosomal locations of a conserved segment in the two species have deviated from each other by a multiple of 60°. (3) There are many instances in which a contiguous segment in one genome is split into two or more segments located at distinct positions in the other genome, and these split segments were found to tend to lie on the E. coli or B. subtilis genome separated by distances of multiples of 60°. On the basis of these observations, genome organizations of the two bacteria were discussed in terms of genome doublings as well as random chromosomal rearrangements.     

Extreme rates and heterogeneity in insect DNA evolution

Summary DNA-DNA hybridization studies of insects, more specificallyDrosophila and cave crickets, have revealed interesting patterns of genome evolution that contrast markedly with what has been seen in other taxa, especially mammals and birds. Insect genomes are composed of sections of single-copy DNA with extreme variation in rates of evolutionary change. This variation is more extreme than between introns and exons; introns fall into the relatively conserved fraction of the genome. Attempts to calculate absolute rates of change inDrosophila DNA have all led to estimates some 5–10 times faster than those found in most vertebrates; this is true even for the more conservative part of the nuclear genome. Finally we point out that morphological similarity, chromosomal similarity, and/or ability to form interspecific hybrids is often associated with quite high levels of single-copy DNA divergence in insects as compared to mammals and birds.     

Knob heterochromatin homology in maize and its relatives

Summary We have characterised the major DNA sequence component of knob heterochromatin in maize, teosinte andTripsacum. Sequence analysis of this DNA gives strong support to the proposal that maize originated by selection of variants in teosinte. In situ hybridization has confirmed that this repeating DNA sequence, which is the major component of maize knob heterochromatin, is also the major component of knobs in teosinte,Zea diploperennis andTripsacum. In Southern blot hybridizations the repeat has a similar basic organization in all taxa;Tripsacum, however, is differentiated from maize and teosinte by a number of sequence features. Maize and teosinte knob heterochromatin are indistinguishable with regard to the distribution of mutations in the 180-bp repeat and the presence and organization of a 202-bp variant sequence. The knob DNA sequence was not detectable in three species ofCoix, an Old World genus of the Maydeae.Within the repeat unit is a 27-bp region that shows no sequence changes in maize, teosinte orTripsacum. The remainder of the repeat unit has randomly distributed nucleotide changes. The presence of the conserved sequence region suggests that knob DNA may have a functional role in the nucleus.     

The complete nucleotide sequence of the mitochondrial DNA of the fin whale,Balaenoptera physalus

Summary The composition of the mitochondrial DNA (mtDNA) of the fin whale,Balaenoptera physalus, was determined. The length of the molecule is 16,398 bp, and its organization conforms with that of other mammals. The general similarity between the mtDNA of the fin whale and the cow is greater than the similarity between the fin whale and other species (human, mouse, rat) in which the composition of the entire molecule has been described. The D-loop region of the mtDNA of the fin whale is 81% identical to the D-loop of dolphin DNA, and the central portion of the D-loop is similar to the bovine D-loop. The accumulation of transversions and gaps in the 12S and 16S rRNA genes was assessed by comparing the fin whale, cow, and human. The sequence difference between human and the whale and human and the cow was at the same level, indicating that the rate of evolution of the mtDNA rRNA genes is about the same in artiodactyls and cetaceans. In the 12S rRNA gene an accumulation rate of 0.05% per million years places the separation of cetaceans and artiodactyls at about 55 million years ago. The corresponding figure for human and either the whale or the cow is about 80 million years. In the 16S rRNA gene a 0.08% accumulation rate of transversions and gaps per million years yields concurring figures. A comparison between the cytochromeb gene of the fin whale and cytochromeb sequences in the literature, including dolphin (Stenella) sequences, identified the cetaceans as monophyletic and the artiodactyls as their closest relatives. The comparison between the cytochromeb sequences of the fin whale andStenella showed that differences in codon positions one or two were frequently associated with a change in another codon position.     

The distribution and divergence during evolution of families of repetitive DNA sequences inLathyrus species

Summary Evolution and divergence among, species within the genusLathyrus have involved an approximately fivefold increase in the amounts of nuclear DNA. Most species inLathyrus are diploids with the same chromosome number, 2n=14. Significant changes in the amounts of repetitive sequences have accounted for much of the evolutionary DNA variation between species. Seven diploidLathyrus species with a twofold variation in nuclear DNA amounts between them were investigated. Using higher derivative analysis of the thermal denaturation profiles of the reassociated repetitive DNA, the reiteration frequency and divergence of repetitive families were compared. Much variation in the reiteration frequency was observed within and between species. In species with larger 2C DNA amounts repetitive families had on average greater amounts of DNA. Despite the massive differences in DNA amounts, six species were consistently similar in the number of repetitive families in their genomes, and they showed a similar pattern in base sequence divergence. In terms of base sequence relationships the repetitive families appeared to be heterogeneous. The evolutionary significance is discussed.     

The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout,Oncorhynchus mykiss

The complete nucleotide sequence of the mitochondrial DNA of the rainbow trout, Onchorynchus mykiss, has been determined. The total length of the molecule is 16,660 bp. The rainbow trout mitochondrial DNA has the same organization described in eutherian mammals, the clawed frog (Xenopus laevis), and the two fish species, Oriental stream loach (Crossotoma lacustre) and carp (Cyprinus carpio). Alignment and comparison of the deduced amino acid sequences of the 13 proteins encoded by rainbow trout and other vertebrate mitochondrial genomes allowed us to estimate that COI is the most conserved mitochondrial subunit (amino acid identity ranging from 85.6% to 94.8%) whereas ATPase 8 is the most variable one (amino acid identity ranging from 30.8% to 70.4%). Putative secondary structures for the 22 tRNAs found in the molecule are given along with an extensive comparison of tRNA sequences among representative species of each major group of vertebrates. In this sense, an unusual cloverleaf structure for the tRNA^Ser(AGY) is proposed. A stem-loop structure inferred for the origin of the L-strand replication (O_L) and the presence of a large polycytidine tract in the O_L loop is described. The existence of this stretch instead of the usual T-rich sequence reported so far in mammal mtDNAs is explained in terms of a less-strict template dependence of the RNA primase involved in the initiation of L-strand replication. Correspondence to: J.M. Bautista     

Single copy DNA and structural gene sequence relationships among four sea urchin species

Measurements of the divergence of single copy DNA sequences among four sea urchin species are presented. At a standard criterion for reassociation (0.12 M phosphate buffer, 60° C, hydroxyapatite binding) we observe the following extents of reaction and reductions in thermal stability for single copy DNA reassociation between Strongylocentrotus purpuratus tracer and heterologous driver DNA: S. dröbachiensis 68% and 2.5°C; S. franciscanus 51% and 3.5° C; Lytechinus pictus 12% and 7.5° C. The implied extents of sequence relatedness are consistent with the phylogenetic relationships of these species. The rate of single copy sequence divergence in the evolutionary lines leading to the Strongylocentrotus species is estimated to be 0.06–0.35% per million years. The rate of divergence of total single copy sequence has been compared to that of structural gene sequences represented in S. purpuratus gastrula polysomal messenger RNA. When closely related species, S. purpuratus and S. franciscanus, are compared, these polysomal sequences are found to diverge at a lower rate than does the total single copy sequence. For two very distantly related species, S. purpuratus and L. pictus, a small fraction of the single copy DNA sequence is probably conserved. These conserved sequences are not enriched in their content of structural gene sequences.Also staff member, Carnegie Institution of Washington, Washington, D.C. 20015     

Comparison of fatty acid content and DNA homology of the filamentous gliding bacteriaVitreoscilla,Flexibacter, Filibacter

DNA hybridization experiments showed that there was a high degree of homology amongVitreoscilla strains but not with DNA fromFilibacter limicola. Flexibacter spp were much more heterogeneous indicating a low genetic similarity. These results were also reflected in the membrane fatty acids of the bacteria. TheVitreoscilla strains were very similar with the 16:17c fatty acid being dominant. The membrane fatty acids ofF. limicola were dominated by a15:0 and a17:0 components which provided additional support for its relatedness to the genusBacillus. There was much greater diversity in the fatty acid patterns of theFlexibacter spp.F. aurantiacus, F. ruber andF. elegans shared the common dominant fatty acids 16:17c with theVitreoscilla strains, but this was replaced by the 16:16c acid inF. flexilis. F. ruber was distinguished by the absence of branched odd-chain monounsaturated fatty acids andF. elegans by the dominance of the -OH i15:0 acid. Precise determination of fatty acid double bond positions and geometry are essential for correct interpretation of increasingly complex ecological and taxonomic data sets.     

DNA条形码在淡水红藻中的应用评价——基于串珠藻科植物

研究采用4种DNA序列, 分析了各片段序列特征以及在串珠藻科植物中种属水平的鉴定能力, 包括线粒体COI-5P、cox2-3 spacer序列, 以及叶绿体rbcL、UPA序列。结果表明, COI-5P、cox2-3 spacer、UPA以及rbcL序列的PCR扩增成功率分别为96%、100%、96%和98%。其中, COI-5P、cox2-3 spacer和UPA的片段大小符合标准DNA条形码的判定标准, 即片段大小在300—800 bp, 能够通过单对引物双向测序获得。系统发育分析的结果显示, 这4种DNA片段在串珠藻属植物的鉴定中能够鉴定大部分的种类, 但COI-5P、cox2-3 spacer以及rbcL序列均不能将两种中国特有种洪洞串珠藻B. hongdongense和长柄串珠藻B. longipedicellatum与弧形串珠藻B. arcuatum分开。在种水平的鉴定中, UPA基因的种间差异最大, 显示了较好的分离效果, 在串珠藻科植物的鉴定中可以作为一个标准的DNA条形码。     

Molecular phylogeny of the Chinese ranids inferred from nuclear and mitochondrial DNA sequences

The phylogeny of representative species of Chinese ranids was reconstructed using two nuclear (tyrosinase and rhodopsin) and two mitochondrial (12S rRNA, 16S rRNA) DNA fragments. Maximum parsimony, Bayesian, and maximum likelihood analyses were employed. In comparison with the results from nuclear and mitochondrial data, we used nuclear gene data as our preferred phylogenetic hypothesis. We proposed two families (Ranidae, Dicroglossidae) for Chinese ranids, with the exception of genus Ingerana. Within Dicroglossidae, four tribes were supported including Dicroglossini, Paini, Limnonectini, and Occidozygini. A broader sampling strategy and evidence from additional molecular markers are required to decisively evaluate the evolutionary history of Chinese ranids.