Phylogenetic and systematic study of the genus Bombina (Amphibia : Anura : Bombinatoridae): New insights from molecular data

Phylogenetic relationships and systematics of the eight currently recognized species of the genus Bombina were investigated using four mitochondrial gene fragments (16S rRNA, 12S rRNA, ND4-tRNA(LEU), and cytochrome b). We prepared two different concatenat

Phylogenetic relationships of the mustache toads inferred from mtDNA sequences

Species of the genus Vibrissaphora are unique among all annurans in that males exhibit external cornified spines in the maxillary region during the breeding season. They were separated from species of the genus Leptobrachium based on this unique character. We construct a phylogeny using the 16S, ND4, and cytochrome b mitochondrial genes of 42 individuals from eight species of Vibrissaphora and five species of Leptobrachium from mainland China, Southeast Asia, and Hainan Island. Species of both Oreolalax and Scutiger were used as outgroups. The results indicate that: L. huashen and L. chapaense form a clade that is nested within Vibrissaphora, and L. hainanense is the sister taxon to the clade comprising all Vibrissaphora plus L. chapaense and L. huashen; V. boringiae is grouped with a clade consisting of V. leishanensis, V. liui, and V. yaoshanensis; and V. yaoshanensis is a species separate from V. liui. We propsed taxonomix changes that reflect these findings. Also based on the resulting phylogenetic trees, we propose that the mustache toads originated in the trans-Himalayan region of southwest China, and that the evolution of maxillary spines, large body size, and reverse sexual size dimorphism in these frogs was influenced by intrasexual selection due to adopting a resource-defense polygyny matting system.

Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhaeophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (

Phylogenetic positions of several amitochondriate protozoa - Evidence from phylogenetic analysis of DNA topoisomerase II

Several groups of parasitic protozoa, as represented by Giardia, Trichomonas, Entamoeba and Microsporida, were once widely considered to be the most primitive extant eukaryotic group - Archezoa. The main evidence for this is their 'lacking mitochondria' and possessing some other primitive features between prokaryotes and eukaryotes, and being basal to all eukaryotes with mitochondria in phylogenies inferred from many molecules. Some authors even proposed that these organisms diverged before the endosymbiotic origin of mitochondria within eukaryotes. This view was once considered to be very significant to the study of origin and evolution of eukaryotic cells (eukaryotes). However, in recent years this has been challenged by accumulating evidence from new studies. Here the sequences of DNA topoisomerase 11 in G lamblia, T vaginalis and E histolytica were identified first by PCR and sequencing, then combining with the sequence data of the microsporidia Encephalitozoon cunicul and other eukaryotic groups of different evolutionary positions from GenBank, phylogenetic trees were constructed by various methods to investigate the evolutionary positions of these amitochondriate protozoa. Our results showed that since the characteristics of DNA topoisomerase 11 make it avoid the defect of 'long-branch attraction' appearing in the previous phylogenetic analyses, our trees can not only reflect effectively the relationship of different major eukaryotic groups, which is widely accepted, but also reveal phylogenetic positions for these amitochondriate protozoa, which is different from the previous phylogenetic trees. They are not the earliest-branching eukaryotes, but diverged after some mitochondriate organisms such as kinetoplastids and mycetozoan; they are not a united group but occupy different phylogenetic positions. Combining with the recent cytological findings of mitochondria-like organelles in them, we think that though some of them (e.g. diplomonads, as represented by Giardia) may occupy a very low evolutionary position, generally these organisms are not as extremely primitive as was thought before; they should be polyphyletic groups diverging after the endosymbiotic origin of mitochondrion to adapt themselves to anaerobic parasitic life.

Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia

The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene, GlTop 2 was identified. It is a single copy gene with a 4476 by long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a similar to 100 as longer central domain; a similar to 200 as shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the "amitochondriate" G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G. lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.

Homologs of eukaryotic Ras superfamily proteins in prokaryotes and their novel phylogenetic correlation with their eukaryotic analogs

Ras superfamily proteins are key regulators in a wide variety of cellular processes. Previously, they were considered to be specific to eukaryotes, and MglA, a group of obviously different prokaryotic proteins, were recognized as their only prokaryotic an

Triosephosphate isomerase genes in two trophic modes of euglenoids (Euglenophyceae) and their phylogenetic analysis

Two different length cDNAs encoding triosephosphate isomerase (TIM) were identified in the two trophic modes of euglenoids, the phototrophic Euglena gracilis and Euglena intermedia and the saprotrophic Astasia longa. Sequence analyses and presequence pred

High Altitude Adaptation and Phylogenetic Analysis of Tibetan Horse Based on the Mitochondrial Genome

研究测定了西藏那曲(4,500 m)、云南中甸(3,300 m)、云南德钦(3,300 m)地区3匹藏马线粒体全基因组序列.3个地区的藏马线粒体基因组全长以及结构均与韩国济州岛的马类似,但比瑞典马线粒体基因组短.藏马基因组在DNA序列上的两两相似性达99.3%.通过对线粒体蛋白编码区的分析发现,NADH6基因的蛋白序列在三匹藏马中均表现快速进化的现象.这表明NADH6基因在藏马高原适应进化过程中扮演着重要角色.此外,利用7匹藏马的D-loop区域序列以及与其亲缘关系较近的马的序列首次构建的藏马的系统发育树显示,那曲藏马与中甸、德钦藏马属于不同的分支,且存在较大的遗传多样性,表明藏马可能为多地区起源.

THE PHYLOGENETIC-RELATIONSHIPS AND CLASSIFICATION OF THE DOUCS AND SNUB-NOSED LANGURS OF CHINA AND VIETNAM

The taxonomy of the douc and snub-nosed langurs has changed several times during the 20th century. The controversy over the systematic position of these animals has been due in part to difficulties in studying them: both the doucs and the snub-nosed langurs are rare in the wild and are generally poorly represented in institutional collections. This review is based on a detailed examination of relatively large numbers of specimens of most of the species of langurs concerned. An attempt was made to draw upon as many types of information as were available in order to make an assessment of the phyletic relationships between the langur species under discussion. Toward this end, quantitative and qualitative features of the skeleton, specific features of visceral anatomy and characteristics of the pelage were utilized. The final data matrix comprised 178 characters. The matrix was analyzed using the program Hennig86. The results of the analysis support the following conclusions: (1) that the douc and snub-nosed langurs are generically distinct and should be referred to as species of Pygathrix and Rhinopithecus, respectively; (2) that the Tonkin snub-nosed langur be placed in its own subgenus as Rhinopithecus (Presbytiscus) avunculus and that the Chinese snub-nosed langur thus be placed in the subgenus Rhinopithecus (Rhinopithecus); (3) that four extant species of Rhinopithecus be recognized: R. (Rhinopithecus) roxellana Milne Edwards, 1870; R. (Rhinopithecus) bieti Milne Edwards, 1897; R. (Rhinopithecus) brelichi Thomas, 1903, and R. (Presbytiscus) avunculus Dollman, 1912; (4) that the Chinese snub-nosed langurs fall into northern and southern subgroups divided by the Yangtze river; (5) that R. lantianensis Hu and Qi, 1978, is a valid fossil species, and (6) the precise affinities and taxonomic status of the fossil species R. tingianus Matthew and Granger, 1923, are unclear because the type specimen is a subadult.