Phylogenetic Analysis Reveals Rapid Evolutionary Dynamics in the Plant RNA Virus Genus Tobamovirus

Early studies on the evolutionary dynamics of plant RNA viruses suggested that they may evolve more slowly than their animal counterparts, sometimes dramatically so. However, these estimates were often based on an assumption of virus–host codivergence over time-scales of many millions of years that is difficult to verify. An important example are viruses of the genus Tobamovirus, where the assumption of host–virus codivergence over 100 million years has led to rate estimates in the range of ~1 × 10⁻⁸ nucleotide substitutions per site, per year. Such a low evolutionary rate is in apparent contradiction with the ability of some tobamoviruses to quickly overcome inbred genetic resistance. To resolve how rapidly molecular evolution proceeds in the tobomaviruses, we estimated rates of nucleotide substitution, times to common ancestry, and the extent of congruence between virus and host phylogenies. Using Bayesian coalescent methods applied to time-stamped sequences, we estimated mean evolutionary rates at the nucleotide and amino acid levels of between 1 × 10⁻⁵ and 1.3 × 10⁻³ substitutions per site, per year, and hence similar to those seen in a broad range of animal and plant RNA viruses. Under these rates, a conservative estimate for the time of origin of the sampled tobamoviruses is within the last 100,000 years, and hence a far more recently than proposed assuming codivergence. This is supported by our cophylogeny analysis which revealed significantly discordant evolutionary histories between the tobamoviruses and the plant families they infect.     

斯库台涡虫属一新种(单肠目,斯库台科)及其分子系统学分析

本研究报道单肠目Rhabdocoela斯库台科Scutariellidae斯库台涡虫属Scutariella新种:中国斯库台涡虫,新种Scutariella sinensis sp.nov.,对其进行了形态学、分子系统学等研究。新种的主要鉴别特征:(1)二支卵黄腺在背部两侧沿肠管分布,在近肠后部愈合,整体呈"U"型;(2)生殖孔位于肠前端腹侧;(3)咽腺丰富,位于咽肠交界处的两侧;(4)精巢、卵巢位于肠道前1/3腹侧。新种的18S rDNA和28S rDNA分子系统发生研究首次提供了切头类斯库台科的分子数据,确定切头亚目Temnocephalida的分类地位及该亚目与吸虫类的进化关系。     

Phylogenetic Analysis Reveals a Novel Protein Family Closely Related to Adenosine Deaminase

Adenosine deaminase (ADA) is a well-characterized enzyme involved in the depletion of adenosine levels. A group of proteins with similarity to ADA, the adenosine deaminase-related growth factors (ADGF; known as CECR1 in vertebrates), has been described recently in various organisms. We have determined the phylogenetic relationships of various gene products with significant amino acid similarity to ADA using parsimony and Bayesian methods, and discovered a novel paralogue, termed ADA-like (ADAL). The ADGF proteins share a novel amino acid motif, “MPKG,” within which the proline and lysine residues are also conserved in the ADAL and ADA subfamilies. The significance of this new domain is unknown, but it is located just upstream of two ADA catalytic residues, of which all eight are conserved among the ADGF and ADAL proteins. This conservation suggests that ADGF and ADAL may share the same catalytic function as ADA, which has been proven for some ADGF members. These analyses also revealed that some genes previously thought to be classic ADAs are instead ADAL or ADGFs. We here define the ADGF, ADAL, ADA, adenine deaminase (ADE), and AMP deaminase (AMPD) groups as subfamilies of the adenyl-deaminase family. The availability of genomic data for the members of this family allowed us to reconstruct the intron evolution within the phylogeny and strengthen the introns-late hypothesis of the synthetic introns theory. This study shows that ADA activity is clearly more complex than once thought, perhaps involving a delicately balanced pattern of temporal and spatial expression of a number of paralogous proteins. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Martin Kreitman]     

Molecular Cloning and Phylogenetic Analysis of New Human Endogenous Retrovirus HERV-W Family in Cancer Cells

A human endogenous retroviral family (HERV-W) has recently been described that is related to multiple sclerosis-associated retrovirus (MSRV) sequences. By using the PCR approach with human genomic DNA derived from cancer cell lines (HepG2, Jurkat, MCF7, UO-31), five env fragments of HERV-W family were newly identified and analyzed. They showed a high degree of nucleotide sequence similarity (94–99%) with that of the HERV-W. Translation of the env fragments showed no frameshift and termination codon by deletion/insertion or point mutation in clones HepG2-1 and JUR-3. The ratio of synonymous to non-synonymous substitutions indicated that negative selective pressure is acting on HepG2-1 and JUR-3 sequences. These env gene sequences could be associated with an active provirus in human cancer cells (HepG2 and Jurkat). The HepG2-1 and JUR-3 showed sister relationship with the HERV-W and W-7-1 derived from human Chromosome (Chr) 7. Phylogenetic analysis from the HERV-W family indicated close relationships of the env gene sequences across human chromosomes. Received: 12 March 2001 / Accepted: 12 July 2001     

天南星属的系统发育分析

运用分支分类学方法对天南星属进行了系统发育分析,以天南星属13个组为13个分支分类单位,选择菖蒲属作为外类群,从天南星属植物特征中选取13个性状作为建立数据矩阵的基本资料,并以外类群比较和通行的形态演化规律为依据这些性状进行极化,采用改进后的最大同步法和最小平行进化法进行分类运算,按照最简约的原则,选出演化长度较短的最大同步法谱分支图,作为本文讨论的基础,并在此基础上,探讨了天南星属各组的系统关系。     

Phylogenetic Analysis of the Family Taxodiaceae

In the present paper,both cladistic analysis and phenetic analysis were conducted to evaluate the phylogenetic relationships of the Taxodiaceae based on an extensive literature review and study of herbarium． In the cladistic analysis,the Sciadopityaceae was chosen as outgroup．The polarity of characters was determined mainly according to outgroup comparison,fossil evidence and generally accepted viewpoints of morphological evolution．By the result of compatibility analysis,character 2(leaf type),which possessed a much higher coefficient than others whether or not its polarity was altered,was deleted． Finally,a data matrix consisting of all the extant nine genera and 24 characters was analyzed using Maximal Same Step Method,Synthetic Method,Evolutionary Extremal Aggregation Method and Minimal Parallel Evolutionary Method,and four cladograms were generated,of which only the most parsimonious one (Fig．1)was presented for discussion. The cladogram shows that the Taxodiaceae are assorted along five lines of evolution： 1)Metasequoia;2)Sequoiadendron,Sequoia;3)Cryptomeria;4)Glyptostrobus and Taxodium;5)Cunninghamia,Athrotaxis and Taiwania． Ten genera(including Sciadopitys)and 59 characters were used in the phenetic analysis．The phenogram(Fig．2)indicates that Sciadopitys is a very distinct group with remote affinity to the other genera,and the Taxodiaceae are divided into four groups：1)Sequoia,Sequoiadendron;2)Athrotaxis,Cunninghamia and Taiwania;3)Cryptomeria,Glyptostrobus and Taxodium;4)Metasequoia． Based primarily on the result of cladistics,with reference to that of phenetics,the main conclusions were drawn as follows：(1)Generic relationships：Cryptomeria should be considered the most primitive genus in the extant groups of the Taxodiaceae. Glyptostrobus and Taxodium, close to Cryptomeria, are sister taxa and relatively primitive groups. Sequoiadendron and Sequoia are closely related and intermediate advanced. Metasequoia is a more or less isolated taxon, relatively close to Sequoiadendron and Sequoia. Cunninghamia. Athrotaxis and Taiwania might represent a single lineage and form a very advanced group, of which Taiwania may be the most specialized. (2) Systematic treatments: The authors support the viewpoint that Sciadopitys should be treated as an independent family, and suggest that the Taxodiaeae should be divided into five tribes. Systematic arrangements are as follows: Taxodiaceae Warming Trib. 1. Cryptomerieae Vierhapper Gen. 5. Sequoia Endl. Gen. 1. Cryptomeria D. Don Trib. 4. Metasequoieae Pilger et Melchior Trib. 2. Taxodieae Benth. et Hook. Gen. 6. Metasequoia Miki ex Hu et Cheng Gen. 2. Glyptostrobus Endl. Trib. 5. Cunninghamieae Zucc. Gen. 3. Taxodium Rich. Gen. 7. Cunninghamia R. Br. Trib. 3. Sequoieae Wettstein Gen. 8. Athrotaxis D. Don Gen. 4. Sequoiadendron Buchholz Gen. 9. Taiwania Hayata     

A New Orchid Genus,Danxiaorchis, and Phylogenetic Analysis of the Tribe Calypsoeae

Background

Orchids have numerous species, and their speciation rates are presumed to be exceptionally high, suggesting that orchids are continuously and actively evolving. The wide diversity of orchids has attracted the interest of evolutionary biologists. In this study, a new orchid was discovered on Danxia Mountain in Guangdong, China. However, the phylogenetic clarification of this new orchid requires further molecular, morphological, and phytogeographic analyses.

Methodology/Principal Findings

A new orchid possesses a labellum with a large Y-shaped callus and two sacs at the base, and cylindrical, fleshy seeds, which make it distinct from all known orchid genera. Phylogenetic methods were applied to a matrix of morphological and molecular characters based on the fragments of the nuclear internal transcribed spacer, chloroplast matK, and rbcL genes of Orchidaceae (74 genera) and Calypsoeae (13 genera). The strict consensus Bayesian inference phylogram strongly supports the division of the Calypsoeae alliance (not including Dactylostalix and Ephippianthus) into seven clades with 11 genera. The sequence data of each species and the morphological characters of each genus were combined into a single dataset. The inferred Bayesian phylogram supports the division of the 13 genera of Calypsoeae into four clades with 13 subclades (genera). Based on the results of our phylogenetic analyses, Calypsoeae, under which the new orchid is classified, represents an independent lineage in the Epidendroideae subfamily.

Conclusions

Analyses of the combined datasets using Bayesian methods revealed strong evidence that Calypsoeae is a monophyletic tribe consisting of eight well-supported clades with 13 subclades (genera), which are all in agreement with the phytogeography of Calypsoeae. The Danxia orchid represents an independent lineage under the tribe Calypsoeae of the subfamily Epidendroideae. This lineage should be treated as a new genus, which we have named Danxiaorchis, that is parallel to Yoania. Both genera are placed under the subtribe Yoaniinae.     

Molecular Phylogenetic Characterization of Streptomyces Protease Inhibitor Family

We previously found that proteinaceous protease inhibitors homologous to Streptomyces subtilisin inhibitor (SSI) are widely produced by various Streptomyces species, and we designated them ``SSI-like proteins' (Taguchi S, Kikuchi H, Suzuki M, Kojima S, Terabe M, Miura K, Nakase T, Momose H [1993] Appl Environ Microbiol 59:4338–4341). In this study, SSI-like proteins from five strains of the genus Streptoverticillium were purified and sequenced, and molecular phylogenetic trees were constructed on the basis of the determined amino acid sequences together with those determined previously for Streptomyces species. The phylogenetic trees showed that SSI-like proteins from Streptoverticillium species are phylogenetically included in Streptomyces SSI-like proteins but form a monophyletic group as a distinct lineage within the Streptomyces proteins. This provides an alternative phylogenetic framework to the previous one based on partial small ribosomal RNA sequences, and it may indicate that the phylogenetic affiliation of the genus Streptoverticillium should be revised. The phylogenetic trees also suggested that SSI-like proteins possessing arginine or methionine at the P1 site, the major reactive center site toward target proteases, arose multiple times on independent lineages from ancestral proteins possessing lysine at the P1 site. Most of the codon changes at the P1 site inferred to have occurred during the evolution of SSI-like proteins are consistent with those inferred from the extremely high G + C content of Streptomyces genomes. The inferred minimum number of amino acid replacements at the P1 site was nearly equal to the average number for all the variable sites. It thus appears that positive Darwinian selection, which has been postulated to account for accelerated rates of amino acid replacement at the major reaction center site of mammalian protease inhibitors, may not have dictated the evolution of the bacterial SSI-like proteins. Received: 23 August 1996 / Accepted: 20 November 1996     

DNA聚合酶x家族的系统发育分析

随着DNA聚合酶x家族成员数量的增加,家族内部的系统发育需要重新检查,来自病毒和细胞的DNA聚合酶x家族成员顺序第一次被汇编在一起,进行系统发育分析。分析显示：真核生物DNA聚合酶beta(polβ)可能起源于病毒基因的水平转移;DNA聚合酶mu(polμ)基因仅存在于哺乳动物基因中,是脱氧核苷酸末端转移酶（TdT）的重复基因;DNA聚合酶lambda(polλ)可能是polμ和TdT的祖先基因,但在某些物种的进化过程中发生了基因丢失。     

用SSR分子标记研究大豆属种间亲缘进化关系

利用SSR标记技术对大豆属11个种37份材料的遗传多样性进行分析,不同位点在种间的等位基因数为6－29,平均生个位点15．9个等位基因,Soja亚属的等位基因数是Glycine亚属的71．5％,并且Glycine亚属种间指纹 谱的差异大于Soja亚属种间的指纹图谱,SSR等位基因的主成分分析结果表明,大豆属中的Glycine亚属和Soja亚属的分类界限是比较明确的,利用第一主成分和第二主成分可较明显地区分开Glycine 亚属的分类界限是比较明显的,利用第一主成分和第二主成分可较明显地区分开Glycine亚属和Soja亚属,通过UPGMA方法构建了大豆属11个种的遗传进化关系,Soja亚属中G.max,G.soja和G.gracilis3个种在系统分化树上界限是比较明显的,由此看来这3个种是独立存在的。     

中国大萼苔科一新记录属

钝叶苔属(Ｃｌａｄｏｐｏｄｉｅｌｌａ)隶属于苔类植物的大萼苔科(Ｃｅｐｈａｌｏｚｉａｃｅａｅ),本属有2种:Ｃ.ｆｌｕｉｔａｎｓ(Ｎｅｅｓ)Ｓｐｒ.和Ｃ.ｆｒａｎｃｉｓｃｉ(Ｈｏｏｋ.)Ｂｕｃｈ.,广泛分布于欧洲和北美洲,其中前者在日本有记录。本属我国首次记录,仅发现1种:Ｃ.ｆｒａｎｃｉｓｃｉ(Ｈｏｏｋ.)Ｂｕｃｈ.,分布西藏。钝叶苔属ＣｌａｄｏｐｏｄｉｅｌｌａＢｕｃｈ.,Ｍｅｍ.Ｓｏｃ.Ｆ.Ｆｌ.Ｆｅｎｎｉｃａ5:87,1927.Ｔｙｐｅ:Ｃｌａｄｏｐｏｄｉｅｌｌａｆｌｕｉｔａｎｓ(Ｎｅｅｓ)Ｓｐｒ.植物体纤细,淡绿色。茎具腹面分枝,横切…     

Molecular Phylogenetic Analysis of Candida krusei

Revealing the phylogenetic relationships of Candida krusei strains (sexual form Pichia kudriavzevii) is a prerequisite for understanding the evolution of its virulence-associated mechanisms and ecological lifestyles. Molecular phylogenetic analyses based on entire internal transcribed spacer region (ITS) and multilocus sequence typing (MLST) data were carried out with sequences available in public databases and Hungarian isolates from animals obtained for the study. The ITS haplotype network yielded a high frequency haplotype at the centre of the network (H1; n?=?204) indicating that various selective pressure might resulted in population expansion from H1. MLST analysis identified three new genotypes among animal-derived isolates, therefore overall 203 sequence types were investigated to determine the population structure of C. krusei. The most commonly encountered sequence types were ST 17 and ST 67. Phylogenetic analyses showed diverse genetic construction of C. krusei population. Evidence of potential recombination events were also observed that might play some role in high intraspecies genetic variability among strains, however, the limited data of C. krusei genotypes from different countries prevented us to identify accurate evolutionary routes of commensal and pathogenic strains or species-specific lineages. Further expansion of C. krusei MLST database may promote the better understanding of the mixed evolutionary history of this species.

     

Redescription of Robustodorus megadorus with Molecular Characterization and Analysis of Its Phylogenetic Position within the Family Aphelenchoididae

Based on a new record of the rare species Robustodorus megadorus from Utah, the generic diagnosis was amended to include the following characters: a labial disc surrounded by six pore-like sensilla; the absence of a cephalic disc; a lobed cephalic region devoid of annulation; a hexagonal inner cuticular structure of the pouch surrounding the stylet cone; large stylet knobs, rounded in outline and somewhat flattened on their lateral margins; a large spermatheca with an occluded lumen and lacking sperm; the excretory pore located between the median bulb and nerve ring. The stylet orifice consists of an open, ventral, elongate slit or groove. These characters distinguish the genus from the closely related genus Aphelenchoides. A lectotype and paralectotypes were designated. Results of phylogenetic analyses of the 18S and D2-D3 of 28S rRNA gene sequences revealed that R. megadorus occupies a basal position within one of the two main clades of the subfamily Aphelenchoidinae and shares close relationships with a species group of the genus Aphelenchoides that includes A. blastophthorus, A. fragariae, A. saprophilus, A. xylocopae, and A. subtenuis. Several specimens in our collection of R. megadorus were infected with Pasteuria sp. as were some of the paralectotypes.     

Phylogenetic Reappraisal of the Genus Monomorphina (Euglenophyceae) Based on Molecular and Morphological Data

A morphological and molecular examination of the genus Monomorphina was conducted on 46 strains isolated mainly from Korea. The strains were divided into two types based on morphological data: Monomorphina aenigmatica and M. pyrum ‐ like species. Phylogenetic analysis based on a combined data set of nuclear SSU and LSU and plastid SSU and LSU rDNA showed that the strains could be divided into eight clades: Clade A of M. aenigmatica, Clade B of the isolates (M. pyropsis) from Michigan, USA, Clade C of M. pseudopyrum, Clade D of the isolates (M. pyroria) from Bremen, Germany, Clade E of M. soropyrum, Clade F of M. pyriformis, Clade G of M. parapyrum, and Clade H of M. pyrum. Six of these clades came from strains that would be considered M. pyrum sensu Kosmala et Zakry?, one of which could be recognized as a traditional species (M. pyrum) and five were designated as new species; each species had unique molecular signatures at nr SSU rDNA helix 17 and 17′ and spacer E23_14′‐E23_15. The species of Monomorphina had a wide range of genetic diversity with interspecies sequence similarity of 85.6%–97.1% and intraspecies similarity of 96.4%–99.9%. Our results suggested that genetic diversity found in the M. pyrum complex justifies the recognition of a minimum of eight species within this genus, based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.     

Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures

The existence of evolutionary conservation in base pairing is strong evidence for functional elements of RNA structure, although available tools for rigorous identification of structural conservation are limited. R-scape is a recently developed program for statistical prediction of pairwise covariation from sequence alignments, but it initially showed limited utility on long RNAs, especially those of eukaryotic origin. Here we show that R-scape can be adapted for a more powerful analysis of structure conservation in long RNA molecules, including mammalian lncRNAs.