Lifu Qian

Complete sequence and gene organization of the mitochondrial genome of Asio flammeus (Strigiformes, strigidae).

Abstract The complete sequence of the mitochondrial genome was determined for Asio flammeus, which is distributed widely in geography. The length of the complete mitochondrial genome was 18,966 bp, containing 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes (PCGs), and 1 non-coding region (D-loop). All the genes were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The D-loop of A. flammeus contained many tandem repeats of varying lengths and repeat numbers. The molecular-based phylogeny showed that our species acted as the sister group to A. capensis and the supported Asio was the monophyletic group.

The complete mitochondrial genome of Glaucidium brodiei (Strigiformes: Strigidae)

Abstract In this paper, the complete mitochondrial genome of Glaucidium brodiei is sequenced and reported for the first time. The mitochondrial genome is a circular molecule of 17,318 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Overall base composition of the complete mitochondrial DNA is A (29.9%), G (14.1%), C (32.1%) and T (23.9%), the percentage of A and T (53.8%) is slightly higher than G and C (46.2%). All the genes in G. brodiei are distributed on the H-strand, except for the ND6 subunit gene and nine tRNA genes, which are encoded on the L-strand.

The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification

Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus.

Mitochondrial genome of Dinodon rufozonatum (Squamata: Colubridae: Dinodon)

Abstract Dinodon rufozonatum is a species of nocturnal snake in the family Colubridae, which is native to East Asia. In this study, we determined the complete mitochondrial genome of D. rufozonatum. The results showed that the total length of the mitogenome was 17,188 bp and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, 2 control regions and 1 stem-loop region. Overall base composition of the complete mitochondrial DNA was A (34.37%), G (12.61%), C (28.24%), and T (24.78%), so the percentage of A and T (59.15%) was slightly higher than G and C. All the genes in D. rufozonatum were distributed on the H-strand, except for the ND6 subunit gene and ten transfer RNA genes which were encoded on the L-strand.

Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

BackgroundMitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes.ResultsIn total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome.ConclusionsThe WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.

Phylogeny of Asian Bufonids inferred from mitochondrial DNA sequences (Anura: Amphibia): implication for the speciation of East Asian Bufonids.

Abstract Many bufonidae species distributed in Asia are inhabited in a variety of environments. However, there are few studies focusing on the speciation of Asia Bufonidae. In this study, we reconstruct the phylogeny tree of Asia Bufonidae with timescale in BEAST based on a multiple sequence alignment of 12S gene and 16S gene sequences from 13 Bufonidae species and whole mtDNA from five Bufonidae species. The results show that the bufonids split into two major clades. In general, there are two lineages mainly distributed on different sides of the Himalayas. According to the divergence time and distribution of the two lineages, we imply that the differentiation of Bufonidea may be closely linked to the uplift of QTP and consequent monsoon climate.

Complete mitochondrial genome of Motacilla alba and implications for Motacillidae taxonomy.

Abstract Motacilla alba is a species of small and passerine songbird in the Family Motacillidae, which is widely distributed. In this study, we determined the complete mitochondrial genome of M. alba. The result showed that the total length of the mitogenome was 16 826 bp and contained 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and one control region. All the genes in M. alba were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree was reconstructed using maximum-likelihood analysis and divided into three major clades. The species from genus Anthus were clustered into clade A. The clade B contained M. alba and other seven Motacilla species. Dendronanthus indicus as one species from Dendronanthus comprised the clade C, and received strong support.

Complete mitochondrial genome of Lycodon flavozonatum and implications for Colubridae taxonomy

Abstract Lycodon flavozonatum, a species of Colubcridae family, is mainly inhabited in hilly region of forest in South China, India, Myanmar, and Vietnam. In this study, the complete mtDNA of L. flavozonatum is 17 172 bp long, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA (12S and 16S rRNA), and two control regions and a stem-loop region. Most of these genes are encoded in the H-strand; only ND6, stem-loop and other nine tRNA genes are on the L-strand. The phylogenetic tree among the 14 Serpentiformes species was divided into three major clade; Lycodon makes up the first clade, which showed a sister relationship to the second clade, Elaphe; Hypsiglena forms the third clade and is sister to Lycodon and Elaphe. And the species of L. flavozonatum which we studied belongs to the first clade.

The mitochondrial genome of Ixobrychus flavicollis (Ardeidae: Ixobrychus)

Abstract Ixobrychus flavicollis is the largest bittern in Ixobrychus which has very wide geographical range. In our results, the complete mitochondrial genome of I. flavicollis is 17,016 bp in length. Thirteen protein-coding genes, two rRNA genes, twenty-two tRNA genes and one non-coding region (D-loop) are present in this mitochondrial genome. No special arrangement when compared with other typical mitochondrial of vertebrates. The percentage of A and T (56.7%) was slightly higher than G and C.

The complete mitochondrial genome of Tylototriton anhuiensis and implications for its taxonomy

Abstarct Tylototriton anhuiensis (Salamandridae, Urodela), collected from Yaoluoping Nature Reserve, was identified as a new species. The complete mitogenome sequence of T. anhuiensis is 16,259 by in length, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and D-loop region. The base composition of the mitogenome was 33.6%A, 26.3% C, 14.5% G, and 25.6% T. The ND6 subunit gene and eight tRNA genes were encoded on the L-strand, the others were encoded on the H-strand.