Andalucia (n. gen.)--the deepest branch within jakobids (Jakobida; Excavata), based on morphological and molecular study of a new flagellate from soil

A new heterotrophic flagellate (Andalucia godoyi n. gen. n. sp.) is described from soil. Earlier preliminary 18S rRNA analyses had indicated a relationship with the phylogenetically difficult-to-place jakobid Jakoba incarcerata. Andalucia godoyi is a small (3-5 mum) biflagellated cell with a ventral feeding groove. It has tubular mitochondrial cristae. There are two major microtubular roots (R1, R2) and a singlet root associated with basal body 1 (posterior). The microtubular root R1 is associated with non-microtubular fibres "I,"B," and "A," and divides in two parts, while R2 is associated with a "C" fibre. These structures support the anterior portion of the groove. Several features of A. godoyi are characteristic of jakobids: (i) there is a single dorsal vane on flagellum 2; (ii) the C fibre has the jakobid multilaminate substructure; (iii) the dorsal fan of microtubules originates in very close association with basal body 2; and (iv) there is no "R4" microtubular root associated with basal body 2. Morphological analyses incorporating the A. godoyi data strongly support the monophyly of all jakobids. Our 18S rRNA phylogenies place A. godoyi and J. incarcerata as a strong clade, which falls separately from other jakobids. Statistical tests do not reject jakobid monophyly, but a specific relationship between Jakoba libera and J. incarcerata and/or A. godoyi is rejected. Therefore, we have established a new genus Andalucia n. gen. with the type species Andalucia godoyi n. sp., and transfer Jakoba incarcerata to Andalucia as Andalucia incarcerata n. comb.     

Franciscideres gen. nov. – a new,highly aberrant kinorhynch genus from Brazil,with an analysis of its phylogenetic position

A new genus and species of Kinorhyncha, Franciscideres kalenesos gen. et sp. nov., is described from tidal and subtidal sandy habitats in Brazil. The new genus and species is characterized by an extremely flexible trunk without pachycycli that appears perfectly circular in cross-section, segments 1, 2 and 11 consisting of closed rings and 3 to 10 of single, bent plates with midventral articulations, a neck without placids that resembles an additional segment, densely packed scale-like, cuticular hairs, and a terminal segment with a middorsal spine and two sets of lateral terminal spines, but no midterminal spine. Phylogenetic analyses of 18S rRNA of Franciscideres kalenesos gen. et sp. nov. and 47 other kinorhynch ingroup taxa suggest that the new genus is a basal homalorhagid, whereas comparison of morphological characters indicates affinities between the new genus and the peculiar cyclorhagid Cateria.

http://zoobank.org/urn:lsid:zoobank.org:pub:64E29D97-DE1D-4511-8683-C969DD2EED43     

苔藓动物18S rRNA基因的分子系统发生初探

本文对我国沿海较为常见的8种唇口目苔藓动物的18SrRNA基因进行了PCR扩增和序列测定。结合已知的其它苔藓动物（包括内肛动物和外肛动物）以及腕足动物和帚虫的相应序列,运用分子系统学方法,研究苔藓动物门的系统发生关系,结果表明,外肛动物和内肛动物构成苔藓动物分子系统树中的二大平行支;本文测定的大室膜孔苔虫与Giribet等测定的膜孔苔虫在系统树中的位置间隔较远。结果也支持外肛动物包含被唇纲和裸唇纲两大类群的形态划分,而关于裸唇纲特别是唇口目内部的系统发生关系。分子数据的分析结果和形态分类之间的分歧有待于进一步研究。     

Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods

Protozoa are common inhabitants of the rumen where they play roles in host nutrition and methanogenesis. Knowledge of how changes in the composition of protozoa communities affect these processes is limited in part due to a lack of efficient methods for protozoa community analysis. In this study, a terminal-restriction fragment length polymorphism (T-RFLP) assay targeting the 18S rRNA gene was developed for comparative analysis of rumen protozoa communities. Comparison of diversity and structure of protozoa communities from hay-fed versus silage/grain-fed cattle via T-RFLP analysis yielded similar overall results to microscopy analysis. According to both methods, Entodinium spp. were more abundant in the silage/grain-fed cattle and protozoa diversity (as calculated using the Shannon index) was higher for the hay-fed cattle due to greater species evenness. Type B protozoa were more prevalent in the hay-fed cattle, whereas Type A protozoa were more prevalent in the silage/grain-fed cattle. Analysis of similarity (ANOSIM) indicated that the protozoa communities from hay-fed and silage/grain-fed cattle were different, and multivariate analysis indicated that pen mates (i.e., cattle fed the same diet and housed together) tended to have similar protozoa communities types. In summary, we present a T-RFLP method for analyzing rumen protozoa communities which complements traditional microscopy approaches but has the advantage of being amenable to high-throughput.     

A PHYLOGENETIC STUDY OF THE CORALLINALES (RHODOPHYTA) BASED ON NUCLEAR SMALL-SUBUNIT rRNA GENE SEQUENCES

Conflicting classifications for the Corallinales were tested by analyzing partial sequences for the nuclear small-subunit ribosomal RNA (SSU) gene of 35 species of coralline algae. Parsimony and likelihood analyses of these data yielded congruent hypotheses that are inconsistent with classifications for the group that include as many as eight subfamilies. Four major clades are resolved within the order, including the early-diverging Sporolithaceae as well as the Melobesioideae and Corallinoideae. The fourth clade, which is supported robustly, includes both nongeniculate and geniculate species classified in the subfamilies Mastophoroideae, Metagoniolithoideae, Lithophylloideae, and Amphiroideae. Molecular and morphological data support the proposal that the latter two subfamilies are sister taxa. Although relationships among some genera are not resolved clearly, the order of branching of taxa among and within the four principal lineages is concordant with paleontological evidence for the group. Relationships inferred among genera within each of the clades is discussed. Seven morphological characters delimiting higher taxonomic groups within the order were combined with the sequence data, analyzed, and optimized onto the resulting tree(s). Except for the presence or absence of genicula, all other characters were found to be phylogenetically informative. Genicula are nonhomologous structures that evolved independently in the Amphiroideae, Corallinoideae, and Metagoniolithoideae. The phenetic practice of separating coralline algae into two categories solely on the basis of the presence or absence of genicula does not accurately reflect the evolutionary history of the group.     

基于18S rRNA基因序列的直翅目主要类群系统发育关系研究

基于78种直翅目昆虫的18S rRNA基因全序列构建了直翅目各主要类群间的系统发育关系。本研究的结果支持直翅目的单系性,但不支持蝗亚目和螽亚目各自的单系性;直翅目下除蜢总科和蝗总科外各总科的划分多数与Otte系统相一致;蜢总科的单系性得不到支持;蝗总科的剑角蝗科、斑腿蝗科、斑翅蝗科、网翅蝗科和槌角蝗科5科均不是单系群,各物种间的遗传距离差异不大,应合并为一科,即蝗科;本研究支持将Otte系统中蚱总科和螽蟖总科下各亚科级阶元提升为科级阶元;18S rRNA基因全序列可以作为划分科级阶元的工具,当位于同一分支上互成姐妹群的类群间的遗传距离超过1%时,这几个类群属于不同的科;但由于其在进化上的保守性,18S rRNA基因只能用于纲目等高级阶元间关系的研究,而由其获得的总科以下阶元间的关系并不可靠。     

Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences

AIMS: To examine the diversity of protozoa in the rumen contents of cow. METHODS AND RESULTS: Protozoa that inhabit the rumen were detected by PCR using protozoan-specific primers. Libraries of protozoan rDNA sequences were constructed from rumen fluid, solid tissues and epithelium. Twenty-three clones isolated from rumen fluid fell into two genera identified as Entodinium (69.6% of clones) and Epidinium (31.4% of clones). Of the clones isolated from rumen fluid, a moderate number were unidentifiable (30.4%). CONCLUSIONS: The predominant protozoan genus identified in the whole rumen belonged to the Entodinium group (81.1%). Protozoa were not detected in the rumen epithelium. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings suggest that rumen fluid and solid tissues contain different protozoan populations that may play specific roles in rumen function. Quantitative PCR techniques and a more specific set of phylogenetic probes that distinguish between protozoan species are needed to determine the significance of newly identified groups and to determine the distribution of identified protozoan clusters in rumen microbial communities.     

Phylogenetic position of the trichomonad parasite of turkeys, Histomonas meleagridis (Smith) Tyzzer, inferred from small subunit rRNA sequence.

The phylogenetic position of the trichomonad, Histomonas meleagridis was determined by analysis of small subunit rRNAs. Molecular trees including all identified parabasalid sequences available in data bases were inferred by distance, parsimony, and likelihood methods. All reveal a close relationship between H. meleagridis, and Dientamoeba fragilis. Moreover, small subunit rRNAs of both amoeboid species have a reduced G + C content and increased chain length relative to other parabasalids. Finally, the rRNA genes from H. meleagridis and D. fragilis share a recent common ancestor with Tritrichomonasfoetus, which exhibits a more developed cytoskeleton. This indicates that Histomonas and Dientamoeba secondarily lost most of the typical trichomonad cytoskeletal structures and hence, do not represent primitive morphologies. A global phylogeny of parabasalids revealed significant discrepancies with morphology-based classifications, such as the polyphyly of most of the parabasalid families and classes included in our study.     

基于18S rRNA基因序列分析唇口目苔藓动物主要类群的系统发生关系

对隶属于3亚目、5次目、20科、23属共25个种类的唇口目(裸唇纲)苔藓虫18S rRNA基因部分序列进行了序列测定.结合从GenBank中获得的该类群其它7个种类的18S rRNA基因同源序列,以序列分析软件对其序列组成和变异进行了比较分析;同时,以羽苔虫(被唇纲)和管孔苔虫(窄唇纲)为外类群,以邻接法和最大简约法重建了它们的系统发生树,分析了该目主要类群系统发生关系.序列分析结果显示:经比对后序列长度为884 bp,其中保守位点241个,可变位点643个,简约信息位点357个;A,T,C和G 4碱基平均含量分别为23.8%、22.8%、24.4%和28.9%.分子系统树表明:本研究所有有囊类构成1个单系群,其中檐胞次目的几种苔虫位于皮壳次目内部;无囊类形成1个多系群,其中的亚目级(新唇口亚目)和次目级分类阶元(枝室次目、假软壁次目和隐壁次目)也都为多系发生,这些结果与前人的分子系统学研究结果大体一致,而与传统的形态分类体系间存在明显的冲突.     

凤蝶亚科(凤蝶科,鳞翅目)16S rRNA基因的分子系统发生分析

对15种凤蝶亚科蝶类线粒体16S rRNA基因部分序列进行了测定,并结合GenBank中其它相关类群的序列,采用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯法构建凤蝶亚科的分子系统树,探讨该亚科各类群间的系统发生关系.结果表明,燕凤蝶族构成凤蝶亚科蝶类系统树基部的一个独立分支;燕凤蝶族和裳凤蝶族为单系发生,且裳凤蝶族聚在凤蝶族内部;喙凤蝶族的单系性尚不能确定.综合分子系统学、形态学及寄主植物等相关证据,推测斑凤蝶类为凤蝶族中早期分化的一支;较之裳凤蝶类,斑凤蝶类可能更早从二者最近的共同祖先中分化出来.     

软体动物系统发育研究进展

软体动物是动物界仅次于节肢动物的第二大门类.长期以来,其系统位置及其系统发育关系一直争议颇多.简述了软体动物的分类及系统学研究概况,重点介绍了近年来18SrRNA和28SrRNA基因的分子系统学研究进展.同时就软体动物系统学研究中存在的问题和前景作了分析和展望.     

Archiascomycetes: detection of a major new lineage within the Ascomycota

For phylogenetic analysis of the higher fungi, we sequenced the nuclear small subunit rRNA (18S rRNA) gene fromTaphrina populina, the type species of the genusTaphrina, andProtomyces lactucae-debilis. The molecular phylogeny inferred from these 2 sequences and 75 sequences from the DNA data bank divided the Ascomycota into three major lineages: the hemiascomycetes, the euascomycetes, and the archiascomycetes, newly described herein. The former two lineages are monophyletic, whereas the archiascomycetes, which originated first and are comprised ofTaphrina, Protomyces, Saitoella, Schizosaccharomyces, andPneumocystis, may not be monophyletic. Among the archiascomycetes, theTaphrina/Protomyces branch is monophyletic. Confirmation of the archiascomycetes as a monophyletic taxonomic class will require comparison of additional genetically defined characters.This work was supported in part by grants 05454030 from the Ministry of Education, Science, and Culture of Japan (to J. S.) and 4369 from the Japan Society for the Promotion of Science Fellowship Programs (to H. N.).