Fangdong Zou
Sichuan University
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Publication
Featured researches published by Fangdong Zou.
Zoological Science | 2005
Fangdong Zou; Bisong Yue; Liu Xu; Yizheng Zhang
Abstract This study reported the isolation and characterization of eight polymorphic microsatellite loci in endangered forest musk deer Moschus berezovskii. An improved enrichment protocol was used to isolate microsatellites, and polymorphism was explored with samples from wild musk deer population collected in Miyalo of Sichuan Province in China. Approximately 70% of clones from the genomic library constructed in current study contained dinucleotide (AC) repeats. Eight microsatellite loci amplified were highly polymorphic within forest musk deer population. The number of alleles per locus ranged from 6 to 14, and the observed and expected heterozygosities ranged from 0.41~1.0 and from 0.8~0.9, respectively. The average polymorphic information content (PIC) value for these markers was 0.82. This demonstrated that the eight microsatellite loci developed here are highly polymorphic, and can be used as genetic markers for further investigation of musk deer. Also, the results showed that the musk deer distributed in Miyalo had a relatively higher level of genetic variation.
Gene | 2013
Lichun Jiang; Gaochao Wang; Shuai Tan; Shu Gong; Min Yang; Quekun Peng; Rui Peng; Fangdong Zou
The genus Ovis (Bovidae, Artiodactyla) includes six species, i.e. Ovis ammon, Ovis aries, Ovis canadensis, Ovis dalli, Ovis nivicola and Ovis vignei. Based on morphology, geographical location, habitat, etc., the species O. ammon is divided into nine subspecies. The near threatened Tibetan argali is distributed across the Tibetan Plateau and its peripheral mountains, and believed to be one of the O. ammon subspecies (O. a. hodgsoni). However, considering its morphological features and distributions, a question has been proposed by some researchers about the subspecies status of Tibetan argali. In this study, we employed complete mitochondrial DNA (mtDNA) to explore the phylogenetic relationship and population genetic structure of Tibetan argali. The results revealed that the nucleotide composition, gene arrangement and codon usage pattern of the mitochondrial genome of Tibetan argali are similar to those of other caprines. Phylogenetic analyses showed that Tibetan argali was clustered with O. ammon. Interestingly, five Tibetan argali individuals and one of the three Gansu argali (O. a. dalailamae) individuals were clustered in the same branch, which is a sister group to other two Gansu argali individuals. Together with morphological characteristics, our results suggested that Tibetan argali and Gansu argali may belong to the same subspecies (O. a. hodgsoni) of O. ammon, rather than two different subspecies.
Molecular Phylogenetics and Evolution | 2010
Rui Peng; Peng Zhang; Jian-Li Xiong; Hai-Jun Gu; Xiaomao Zeng; Fangdong Zou
The mysterious Asian hynobiid salamander, Protohynobius puxiongensis, was described based on a single specimen collected in 1965 and never found again since then. Because the specimen had an internasal bone, Pr. puxiongensis was thought to retain a primitive character lost by a common ancestor of all other hynobiid salamanders, and it was thus considered to be not only a new genus, but also a new subfamily. This conclusion bothered herpetologists for decades because it was based on only one specimen and one character without other living specimens being rediscovered. After years of field effort, we rediscovered living individuals of Pr. puxiongensis at its type locality. All characters observed in rediscovered specimens are identical to the original description of the holotype except the internasal bone, implying that the internasal bone observed in the holotype may be just an individual variation. To examine the phylogenetic position of Pr. puxiongensis, we sequenced complete mitochondrial genomes for this species, together with two Pseudohynobius species. By combining 18 published hynobiid mitochondrial genomes and our new sequences, we reconstructed a comprehensive phylogenetic relationship of Hynobiidae at the genus level. Our results indicate that Pr. puxiongensis is deeply nested within the hynobiid phylogeny. It is the sister group of the Pseudohynobius species, and the validity of subfamily Protohynobiinae is not supported.
Molecular Phylogenetics and Evolution | 2008
Bo Zeng; Liu Xu; Bisong Yue; Zhijun Li; Fangdong Zou
Within the genus Pseudois (Bovidae, Artiodactyla), two challenges are faced by taxonomists. First, the designation of the two subspecies of blue sheep, Pseudois nayaur nayaur and Pseudois nayaurszechuanensis, tends to be questionable with the accumulation of morphological and molecular data. Second, the taxonomic status of the dwarf blue sheep (Pseudois schaeferi) has been controversial since its discovery, and molecular analyses with relatively small sample sizes have not painted a clear picture. We collected samples and DNA sequence data from a broad geographic range in China to investigate the population structure of Pseudois nayaurszechuanensis and its phylogenetic relationship with Pseudois schaeferi. Employing mitochondrial cytochrome b and control region sequences, as well as the nuclear gene zona pellucida glycoprotein 3, further investigation was performed to extend upon previous studies. We found that the population of Helan Mountain of Ningxia Hui Autonomous Region has significantly differentiated from the populations in Qinghai, Gansu and Sichuan provinces, and may be classified as a new subspecies according to the 75% rule. The dwarf blue sheep was found to be some individuals of Pseudois nayaurszechuanensis with morphological variations and is not a species or subspecies, since they did not fall into a monophyletic group in the phylogenetic analyses with blue sheep. Gene flow between dwarf blue sheep and common blue sheep might have occurred in different areas of western Sichuan, which would result in the paraphyly of dwarf blue sheep.
Animal Genetics | 2009
Hongyuan Peng; S. Liu; Fangdong Zou; Bo Zeng; Bisong Yue
Forest musk deer (Moschus berezovskii) were once distributed widely in China. However, wild populations have declined dramatically because of poaching and habitat loss. Captive breeding populations have been established for several decades, but the genetic backgrounds of most captive populations were unclear and the population sizes increased very slowly. To provide useful information for conservation and management of this species, we investigated the genetic diversity and population structure of forest musk deer by analysing a 582-bp fragment of the mitochondrial DNA (mtDNA) control region (CR) in three captive breeding populations in Sichuan Province, China. Ninety-four variable sites and 27 haplotypes were observed in 109 individuals, and the nucleotide and haplotype diversities were relatively high compared with those of other endangered mammals. Of the three investigated populations, the Maerkang population had the highest nucleotide diversity (pi=0.0568), haplotype diversity (h=0.836) and average intra-population genetic distance (0.062). The analysis of molecular variance demonstrated that most variation occurred within samples and that there was significant differentiation of the three populations. Estimates of gene flow indicated that there were few genetic exchanges among the three populations. Building pedigree records and increasing gene flow between populations will be helpful for conserving these populations and this species.
Gene | 2014
Lichun Jiang; Gaochao Wang; Rui Peng; Quekun Peng; Fangdong Zou
The Swinhoes Pheasant (Lophura swinhoii) is an endemic and most endangered species to Taiwan, China. It belongs to the genus Lophura, family Phasianidae. To further investigate the evolutionary history of L. swinhoii, we determined its complete mitochondrial genome and reconstructed a single, robust phylogenetic tree. Our results showed that L. swinhoii is clustered with Lophura nycthemera and forms a sister group of Lophura ignita. The genus Lophura is strongly supported as the sister taxon of the genus Crossoptilon. The molecular clock analysis showed that the genetic divergence of L. swinhoii occurred in 2.71 (1.31-4.22) Mya. The most common ancestor of L. swinhoii might have migrated from mainland of South East Asia to Taiwan Island by the land bridge at 2.71 Mya ago. Taiwan Island is separated from the mainland by the sea (Taiwan Strait) and formed a separate island at around 2.5 Mya because of the transgression and regression. Therefore, geographical isolation and climate change may accelerate the evolution of L. swinhoii. In this study, we propose a biogeographic hypothesis for speciation of the L. swinhoii based on known events of the geographic and geological history of South East Asia and southeast China, which would benefit the understanding of evolutionary history of L. swinhoii as well as other galliform birds.
Mitochondrial DNA | 2014
Xiang Shan; Yun Xia; Yuchi Zheng; Fangdong Zou; Xiaomao Zeng
Abstract Quasipaa boulengeri, an Asian spiny frog that belongs to Neobatrachia, has been reported as a de novo case of chromosomal rearrangements. In this paper, we determined the whole mitochondrial DNA (mtDNA) sequence of Q. boulengeri. The complete mtDNA sequence of Q. boulengeri is 17,741 bp in length, which contains 13 protein-coding genes (PCGs), two rRNAs, 23 tRNAs and one control region. The overall nucleotides base composition of the complete mtDNA is A (28.86%), G (14.43%), C (26.09%), T (30.62%), with a much higher A + T content. Compared to other Neobatrachia species, the mtDNA genome of Q. boulengeri shows a novel gene order at WANCY region.
Journal of Natural History | 2009
Hongyuan Peng; Shichang Liu; Bo Zeng; Fangdong Zou; Xiuyue Zhang; Bisong Yue
The complete mitochondrial genome sequence of the forest musk deer (Moschus berezovskii) was determined. Sequence analysis revealed that the organization of the mitochondrial genome in the forest musk deer was consistent with that of other reported mammals. Molecular phylogenetic analysis of the forest musk deer and 22 other species of the order Cetartiodactyla was conducted using maximum parsimony and Bayesian inference methods based on the 12 heavy‐strand protein‐coding genes, RNA genes and their combination. Both the consensus phylogenetic trees and the topologies test supported the monophyly of Cervidae, Bovidae and Cetancodonta, and placed Moschidae as a sister group to Cervidae/Bovidae. †These two authors contributed equally to this work.
Mitochondrial DNA | 2016
Xiang Shan; Yun Xia; Ryosuke Kakehashi; Atsushi Kurabayashi; Fangdong Zou; Xiaomao Zeng
Abstract Sichuan torrent frog, Amolops mantzorum (family Ranidae, suborder Neobatrachia), possesses heteromorphic sex chromosomes unusual characteristics among amphibians. We determined the complete nucleotide sequence of the A. mantzorum mitogenome. This genome is 17,744 bp in length and contains 37 genes, 1 control region, and 1 light strand replication origin typically found in vertebrate mtDNAs. In the A. mantzorum mitogenome, a novel gene arrangement is observed within the WANCY tRNA gene cluster region. This mt gene arrangement seems to be usable as a molecular maker to distinguish to this species from other species in the genus Amolops.
Mitochondrion | 2012
Quekun Peng; Lei Tang; Shuai Tan; Zhigang Li; Jifei Wang; Fangdong Zou
The genus Pseudois includes two variable taxa, blue sheep (Pseudois nayaur) and dwarf blue sheep (Pseudois schaeferi), that exhibit notable geographic variation in morphology and ecological niche, suggesting the potential for significant adaptive differentiation between these two goats. Blue sheep are broadly distributed in the Tibetan Plateau and peripheral mountains through Central Asia, while dwarf blue sheep are only found in the gorges of the upper Yangtze River (Jinsha River) near Batang county, Sichuan province and adjacent mountains. Although they are all adapted to high altitude environments, endangered dwarf blue sheep show unique morphological variation and niche shifts compared to blue sheep. Mitochondria play important roles in oxygen usage and energy metabolism. The energetically demanding lifestyles of these high altitude species may have altered the selective regimes on mitochondrial genes encoding proteins related to cellular respiration. Here, we compared the sequences of 13 protein-coding genes in the mitochondrial genome of dwarf blue sheep with those of blue sheep to understand the genetic basis of morphological variation. Using neighbor-joining, maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (d(S)) and nonsynonymous (d(N)) substitutions. Independent analyses showed that no ω ratio was larger than 1, suggesting that all mitochondrial 13 genes were under the purifying selection. Surprisingly, we found that the ω ratio (d(N)/d(S)) of the ATP synthase complex (ATP6 and ATP8) in blue sheep is sixteen times that of dwarf blue sheep (0.340 compared to 0.021). This result was confirmed by a separate analysis of ATP synthase genes from two additional P. schaeferi individuals and two P. nayaur individuals. We hypothesize that the large body size and diverse feeding styles are factors influencing the nonsynonymous substitutions in the ATP synthase complex of blue sheep.