Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation

Background: Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family repre

Paraphyly of Chinese Amolops (Anura, Ranidae) and phylogenetic position of the rare Chinese frog, Amolops tormotus

In order to evaluate the five species groups of Chinese Amolops based on morphological characteristics, and to clarify the phylogenetic position of the concave-eared torrent frog Amolops tormotus, we investigated the phylogeny of Amolops by maximum parsim

Phylogenetic relationships of the Chinese brown frogs (Genus rana) inferred from partial mitochondrial 12S and 16S rRNA gene sequences

Based on partial sequences of the 12S and 16S ribosomal RNA genes, we estimated phylogenetic relationships among brown frogs of the Rana temporaria group from China. From the phylogenetic trees obtained, we propose to include Rana zhengi in the brown frog

Application of the phylogenetic analysis in mitochondrial disease study

Mitochondrial disease currently received an increasing concern. However, the case-control design commonly adopted in this field is vulnerable to genetic background, population stratification and poor data quality. Although the phylogenetic analysis could

Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys

Evidence of incongruence between mitochondrial and nuclear gene trees is now becoming documented with increasing frequency. Among the Old World monkeys, this discordance has been well demonstrated in the Cercopithecinae, but has not yet been investigated

The complete mitochondrial genomes of two species from Sinocyclocheilus (Cypriniformes: Cyprinidae) and a phylogenetic analysis within Cyprininae

We determined the complete mitochondrial DNA sequences for two species of surface- and cave-dwelling-cyprinid fishes, Sinocyclocheilus grahami and S. altishoulderus. Sequence comparison of 13 protein-coding genes shows that the mutation pattern of each single gene is quite similar to those of other vertebrate animal species. Analysis of the ratios of Ka/Ks at these loci between Sinocyclocheilus and two other cyprinid species (Cyprinus carpio and Procypris rabaudi) show that Ka/Ks ratios are differed, consistent with purifying selection and variation in functional constraint among genes. Bayesian analysis and maximum likelihood analysis of the concatenated mitochondrial protein sequences for 14 cyprinid taxa support the monophyly of the family Cyprininae, and further confirm the monophyly of the genus Sinocyclocheilus. The two Sinocyclocheilus species fall within the Cyprinion-Onychostoma lineage, including Cyprinus, Carassius, and Procypris, rather than among the Barbinae, as previously suggested on morphological grounds.

Ribosomal DNA gene and phylogenetic relationships of Diplura and lower Hexapods

The monophyly of Diplura and its phylogenetic relationship with other hexapods are important for understanding the phylogeny of Hexapoda. The complete 18SrRNA gene and partial 28SrRNA gene (D3-D5 region) from 2 dipluran species (Campodeidae and Japygidae), 2 proturan species, 3 collembolan species, and 1 locust species were sequenced. Combining related sequences in GenBank, phylogenetic trees of Hexapoda were constructed by MP method using a crustacean Artemia salina as an outgroup. The results indicated that: (i) the integrated data of 18SrDNA and 28SrDNA could provide better phylogenetic information, which well supported the monophyly of Diplura; (ii) Diplura had a close phylogenetic relationship to Protura with high bootstrap support.

Phylogenetic relationships in genus Niviventer (Rodentia : Muridae) in China inferred from complete mitochondrial cytochrome b gene

Chinese species of the genus Niviventer, predominantly distributed in the southeastern Tibetan Plateau and in Taiwan, are a diverse group and have not yet received a thorough molecular phylogenetic analysis. Here, we reconstructed the phylogenetic relatio

A survey on relation of morphological, molecular and phylogenetic structure of zoanthids of the islands located in the Hormoz Strait (Hormoz, Qeshm, Larak, Hengam)

The order Zoantharia (Zoanthids) is one of the most neglected orders of cnidarians in the Persian Gulf. The present study aims to investigate the biodiversity of this order with morphological and molecular examination in the Persian Gulf. For this purpose, 123 colonies of zoanthids with variety of shape and colors have been collected from intertidal and shallow water zone of four islands, i. e. Hengam, Qeshm, Larak and Hormoz. After sampling, morphological characteristics of each specimen were recorded based on in situ photographs. Then DNA was extracted using the cetyl trimethyl ammonium bromide (CTAB) method. Both mitochondrial 16S ribosomal DNA (mt 16S rDNA) and cytochrome oxidase subunit I (COI) gene fragments were amplified and sequenced. The results of preliminary morphological identification integrated with two mitochondrial markers sequencing demonstrated the presence of five different species in this region; Zoanthus sansibaricus, Palythoa mutuki, Palythoa cf. mutuki, Palythoa tuberculosa and Neozoanthus persicus?. Although at first sight, morphological properties were not successful to delineate zoanthid species, they become reliable criteria to identify and delineate species in field studies after molecular identification.

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.