中国黄颡鱼的线粒体DNA多样性及其分子系统学

基于体侧色斑、背鳍前部形态、吻长及尾柄长的差异, Ng和Kottelat(2007)将分布于中国的黄颡鱼群体划为两个物种: 北方群体为Pseudobagrus sinensis, 南方群体为P. fulvidraco。本研究通过对70个黄颡鱼标本相关形态特征的测量及对线粒体cyt b基因序列的分析, 探讨了P. sinensis物种的有效性问题。结果表明: 依据体侧色斑和背鳍前部形态的差异, 可将黄颡鱼分为对应于P. sinensis和P. fulvidraco的两种形态类型, 但对尾柄长、吻长的测量发现二者没有差异。对70条cyt b基因序列的分析结果为: 两种鱼类有1个共同的单倍型; 两种鱼类的单系性在系统发育分析中都没有得到重现, 而二者聚在一起形成获得100%支持率的单系群; 两种鱼类群体之间存在持续的基因交流(Nm = 4.7); 两种鱼类在单倍型的巢式支系分析(nested clade analysis, NCA)中没有形成各自独立的进化谱系, 所有的单倍型以不超过5步的突变全部被纳入同一个进化网络中。因此我们认为P. sinensis不是有效物种, 而应被视为黄颡鱼的一种形态类型。基于cyt b基因的序列变异, 本研究对黄颡鱼群体的遗传多样性和种群结构作了初步分析。群体的核苷酸不配对分布及Tajima’sD中性检验表明, 约在10.1-14.1万年前, 黄颡鱼在其分布范围内经历过群体扩张, 推测这可能是导致黄颡鱼群体单倍型多样度高(h = 0.857 ± 0.0014)而核苷酸多样度低( π = 0.0023 ± 0.0003)的主要原因。此外, 分析结果显示黄颡鱼群体缺乏明显的地理结构, 推测原因可能是历史上水系的连通促进了不同地理群体之间的基因交流。     

中国脊椎动物2020年新增物种

为了及时掌握中国脊椎动物新增物种情况, 本文系统检索和整理了2020年发表的分类学文献, 汇总结果表明: 2020年中国脊椎动物共新增109种, 其中新物种100种, 国家级新记录种9种。包括鱼类新种24种、两栖类新种41种和新记录4种、爬行类新种30种和新记录4种、鸟类新种1种、哺乳类新种4种和新记录1种。上述新增物种中有92种描述报道时应用了分子遗传学证据, 占新增物种数量的84.4%。在新增脊椎动物物种中, 两栖类集中于无尾目、爬行类全部属于有鳞目, 分别有43种和34种, 其累计占比超新增物种总数的70%。在云南、西藏、湖南、贵州、四川等省区发现新物种数量较多, 均有10种及以上, 累计占比超新增物种总数的60%。绝大部分物种为中国学者发表, 绝大多数论文发表于英文期刊。总结数据提示今后需持续加强我国低等脊椎动物多样性的调查研究, 重视运用分子系统学技术进行物种识别。     

Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong)

The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.     

PCR survey of hox genes in the goldfish Carassius auratus auratus

A tetraploidization event took place in the cyprinid lineage leading to goldfishes about 15 million years ago. A PCR survey for Hox genes in the goldfish Carassius auratus auratus (Actinopterygii: Cyprinidae) was performed to assess the consequences of this genome duplication. Not surprisingly, the genomic organization of the Hox gene clusters of goldfish is similar to that of the closely related zebrafish (Danio rerio). However, the goldfish exhibits a much larger number of recent pseudogenes, which are characterized by indels. These findings are consistent with the hypothesis that dosage effects cause selection pressure to rapidly silence crucial developmental regulators after a tetraploidization event.     

Association of the DNMT3B polymorphism with colorectal adenomatous polyps and adenocarcinoma

DNMT3B is an important enzyme to modulate the methylation status in mammalian cells. The aim of this study is to investigate the correlation of the DNMT3B G39179T polymorphism with the susceptibilities of colorectal adenomatous polyps and adenocarcinoma. This case-control study included 146 colorectal adenomatous polyps, 170 colorectal adenocarcinoma patients, and 157 normal controls. DNMT3B polymorphism was analyzed by polymerase chain reaction-restriction fragment length polymorphism analysis. Family history of colorectal cancer significantly increases the risk of developing colorectal adenomatous polyps and adenocarcinoma. The genotype frequency of DNMT3B polymorphism (T/T and G/T + G/G) in adenocarcinoma patients was significantly different from that in controls (P value = 0.01). Compared with DNMT3B T/T genotype, the G allelotype (G/T + G/G genotype) had lower risk to develop colorectal adenocarcinoma (OR = 0.50, 95% CI = 0.29–0.87); while there was no significant difference between the colorectal adenomatous polyps patients and controls (OR = 0.63, 95% CI = 0.37–1.09), although descending tendency could be found in this polyps group. In the stratification analysis, a significant association was confined to subgroups of age < 55 (OR = 0.31, 95% CI = 0.12–0.84) and males (OR = 0.35, 95% CI = 0.17–0.71). Meanwhile, combined G/T + G/G genotypes were found to have a lower risk in non-drinkers to develop both colorectal adenomatous polyps and adenocarcinoma (OR = 0.54, 95% CI = 0.31–0.96 and OR = 0.48, 95% CI = 0.27–0.84, respectively). This study also showed a distinct difference in the distribution of DNMT3B G39179T SNP in different ethnics. DNMT3B G39179T SNP may be a potential genetic susceptibility factor for adenocarcinoma of the colon, especially in younger Chinese Han non-drinker men.     

Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae)

The members of the cyprinid subfamily Gobioninae, commonly called gudgeons, form one of the most well-established assemblages in the family Cyprinidae. The subfamily is a species-rich group of fishes, these fishes display diverse life histories, appearances, and behavior. The phylogenetic relationships of Gobioninae are examined using sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. This investigation produced a data matrix of 4114 bp for 162 taxa that was analyzed using parsimony, maximum likelihood, and Bayesian inference methods. The phylogenies our analyses recovered corroborate recent studies on the group. The subfamily Gobioninae is monophyletic and composed of three major lineages. We find evidence for a Hemibarbus-Squalidus group, and the tribes Gobionini and Sarcocheilichthyini, with the Hemibarbus-Squalidus group sister to a clade of Gobionini-Sarcocheilichthyini. The Hemibarbus-Squalidus group includes those two genera; the tribe Sarcocheilichthyini includes Coreius, Coreoleuciscus, Gnathopogon, Gobiocypris, Ladislavia, Paracanthobrama, Pseudorasbora, Pseudopungtungia, Pungtungia, Rhinogobio, and Sarcocheilichthys; the tribe Gobionini includes Abbottina, Biwia, Gobio, Gobiobotia, Huigobio, Microphysogobio, Platysmacheilus, Pseudogobio, Romanogobio, Saurogobio, and Xenophysogobio. The monotypic Acanthogobio is placed into the synonymy of Gobio. We tentatively assign Belligobio to the Hemibarbus-Squalidus group and Mesogobio to Gobionini; Paraleucogobio and Parasqualidus remain incertae sedis. Based on the topologies presented, the evolution of swim bladder specializations, a distinctive feature among cyprinids, has occurred more than once within the subfamily.     

Evolutionary patterns of RNA-based gene duplicates in Caenorhabditis nematodes coincide with their genomic features

ABSTRACT: BACKGROUND: RNA-based gene duplicates (retrocopies) played pivotal roles in many physiological processes. Nowadays, functional retrocopies have been systematically identified in several mammals, fruit flies, plants, zebrafish and other chordates, etc. However, studies about this kind of duplication in Caenorhabditis nematodes have not been reported. FINDINGS: We identified 43, 48, 43, 9, and 42 retrocopies, of which 6, 15, 18, 3, and 13 formed chimeric genes in C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. At least 5 chimeric types exist in Caenorhabditis species, of which retrocopy recruiting both N and C terminus is the commonest one. Evidences from different analyses demonstrate many retrocopies and almost all chimeric genes may be functional in these species. About half of retrocopies in each species has coordinates in other species, and we suggest that retrocopies in closely related species may be helpful in identifying retrocopies for one certain species. CONCLUSIONS: A number of retrocopies and chimeric genes exist in Caenorhabditis genomes, and some of them may be functional. The evolutionary patterns of these genes may correlate with their genomic features, such as the activity of retroelements, the high rate of mutation and deletion rate, and a large proportion of genes subject to trans-splicing.     

Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

The cyprinid tribe Labeonini (sensuRainboth, 1991) is a large group of freshwater fishes containing around 40 genera and 400 species. They are characterized by an amazing diversity of modifications to their lips and associated structures. In this study, a total of 34 genera and 142 species of putative members of this tribe, which represent most of the generic diversity and more than one third of the species diversity of the group, were sampled and sequenced for four nuclear genes and five mitochondrial genes (totaling 9465bp). Phylogenetic relationships and subdivision of this tribe were investigated and the placement and status of most genera are discussed. Partitioned maximum likelihood analyses were performed based on the nuclear dataset, mitochondrial dataset, combined dataset, and the dataset for each nuclear gene. Inclusion of the genera Paracrossochilus, Barbichthys, Thynnichthys, and Linichthys in the Labeonini was either confirmed or proposed for the first time. None of the genera Labeo, Garra, Bangana, Cirrhinus, and Crossocheilus are monophyletic. Taxonomic revisions of some genera were made: the generic names Gymnostomus Heckel, 1843, Ageneiogarra Garman, 1912 and Gonorhynchus McClelland, 1839 were revalidated; Akrokolioplax Zhang and Kottelat, 2006 becomes a junior synonym of Gonorhynchus; the species Osteochilus nashii was found to be a member of the barbin genus Osteochilichthys. Five historical hypotheses on the classification of the Labeonini were tested and rejected. We proposed to subdivide the tribe, which is strongly supported as monophyletic, into four subtribes: Labeoina, Garraina, Osteochilina, and Semilabeoina. The taxa included in each subtribe were listed and those taxa that need taxonomic revision were discussed.     

形态和分子进化研究中的同源概念

在比较生物学中,同源是一个中心概念,是系统学的心脏,同源最基本的意义就是共同祖先。然而,这只是对同源的解释而非告诉我们怎样去发现它。同源又可被看成是特别类群间的联系。形态进化研究中同源比较的对象是生物的结构,而分子进化研究中的同源比较对象是DNA中的核着酸序列,现对这两种层次的同源概念及其相互间的关系进行讨论。