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| 1 | Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling显示文摘The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future cli-matic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent mo-lecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data. | Richard L. MAYDEN Kevin L. TANG Robert M. WOOD Wei-Jen CHEN Mary K. AGNEW Kevin W. CONWAY Lei YANG Andrew M. SIMONS Henry L. BART Phillip M. HARRIS Junbing LI Xuzhen WANG Kenji SAITOH Shunping HE Huanzhang LIU Yiyu CHEN Mutstmi NISHIDA Masaki MIYA | 2008 | 植物分类学报2008，46，3： | 5 |
| 2 | Phylogenetic relationships and estimation of divergence times among Sisoridae catfishes显示文摘Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyzed separately and combined into a single data set to reconstruct phylogenetic relationships among Chinese sisorids. Both Chinese Sisoridae as a whole and the glyptosternoid taxa formed monophyletic groups. The genus Pseudecheneis is likely to be the earliest diverging extant genus among the Chinese Sisoridae. The four Pareuchiloglanis species included in the study formed a monophyletic group. Glaridoglanis was indicated to be earliest diverging glyptosternoid, followed by Glyptosternon maculatum and Exostoma labiatum. Our data supported the conclusion that Oreoglanis and Pseudexostoma both formed a monophyletic group. On the basis of the fossil record and the results of a molecular dating analysis, we estimated that the Sisoridae diverged in the late Miocene about 12.2 Mya. The glyptosternoid clade was indicated to have diverged, also in the late Miocene, about 10.7 Mya, and the more specialized glyptosternoid genera, such as Pareuchiloglanis, originated in the Pleistocene (within 1.9 Mya). The speciation of glyptosternoid fishes is hypothesized to be closely related with the uplift of the Qinghai-Tibet Plateau. | YU MeiLing HE ShunPing | 2012 | Science China(Life Sciences)2012，55，4： | 5 |
| 3 | Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning显示文摘1140 bp of cytochrome b gene were amplified and sequenced from 14 species of primitive cyprinid fishes in East Asia. Aligned with other ten cytochrome b gene sequences of cyprinid fish from Europe and North America retrieved from Gene bank, we obtained a matrix of 24 DNA sequences. A cladogram was generated by the method of Maximum likelihood for the primitive cyprinid fishes. The result indicated that subfamily Leuciscinae and Danioninae do not form a monophyletic group. In the subfamily Danioninae, Opsariichthys biden and Zacco platypus are very primitive and form a natural group and located at the root. But the genera in subfamily Danioninae are included in different groups and have not direct relationship. Among them, Aphyocypris chinensis and Yaoshanicus arcus form a monophyletic group. Tanichthys albonubes and Gobiocypris rarus have a close relation to Gobioninae. The genus Danio is far from other genera in Danioninae. In our cladogram, the genera in Leuciscinae were divided into two groups that | HE Shunping CHEN Yiyu Nakajiama Tsuneo | 2001 | Chinese Science Bulletin2001，46，8： | 5 |
| 4 | Mitochondrial cytochrome b sequence variations and phylogeny of the East Asian bagrid catfishes显示文摘The mitochondrial DNA cytochrome b gene was sequenced from 8 bagrid catfishes in China. Aligned with cytochrome b sequences from 9 bagrid catfishes in Japan, Korea and Russia retrieved from GenBank, and selected Silurus meridionalis, Liobagrus anguillicauda, Liobagrus reini and Phenacogrammus interruptus as outgroups, we constructed a matrix of 21 DNA sequences. The Kimura's two-parameter distances were calculated and molecular phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The results show that (i) there exist 3-bp deletions of mitochondrial cytochrome b gene compared with cypriniforms and characiforms; (ii) the molecular phylogenetic tree suggests that bagrid catfishes form a monophyletic group, and the genus Mystus is the earliest divergent in the East Asian bagrid catfishes, as well as the genus Pseudobagrus is a monophyletic group but the genus Pelteobagrus and Leiocassis are complicated; and (iii) the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%~0.30% sequence divergence per million years. | PENG Zuogang, HE Shunping and ZHANG Yaoguang(1. Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China 2. School of Life Science, Southwest China Normal University, Chongqing 400715, China) | 2002 | Progress in Natural Science:Materials International2002，12，6： | 5 |
| 5 | Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes显示文摘The mitochondrial DNA control region is amplified and sequenced from 8 genera and 10 species of gobiobotine fishes. The phylogenetic tree of Gobiobotinae and some representative species of other Cyprinid subfamilies obtained by the method of neighborhood joining, maximum likelihood and maximum parsimony with Danio rerio as an outgroup indicates that Gobiobotinae fishes are a monophyletic group which is close to Gobioninae subfamily. Gobiobotinae should be included into subfamily Gobioninae in terms of phylogenetic analysis. The research result supports that Gobiobotinae can be divided into genus Xenophysogobio and Gobiobotia. Xenophysogobio is the most primitive genera in the subfamily. | WANG Wei, HE Shunping and CHEN Yiyu(Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China) | 2002 | Progress in Natural Science:Materials International2002，12，11： | 4 |
| 6 | Diversification of Sisorid catfishes(Teleostei: Siluriformes)in relation to the orogeny of the Himalayan Plateau显示文摘Sisorid catfishes are primarily limited in distribution to rivers of the Himalayan region and Tibetan Plateau. These species have external morphologies that are adapted for extremely fast-flowing riverine systems. Given the diversity of the group and the above qualities of these catfishes, this lineage serves as an ideal group for inferring the geological history of this region based on their phylogenetic relationships reflecting evolutionary history. We sequenced the complete mitochondrial genome and four nuclear genes of representative sisorids distributed across river systems in China. Phylogenetic analyses strongly support the monophyly of the Sisoridae and the glyptosternoids. An analysis of the reconstructed ancestral states derived from inferred genealogical relationships suggests that the evolution of this lineage was accompanied by convergent evolution in morphological traits that were presumably in response to environmental pressure involving the rapid flowing river system that were generated during the uplift of the Tibetan Plateau(UTP).Molecular dating indicates that the Chinese sisorids and the glyptosternoids originated at the later Miocene(*10.9–9.8Mya), and with further biogeographic analyses indicates that the species of Sisoridae likely originated from a widely distributed ancestor. Moreover, the divergence of the Sisoridae in China can be divided into two phases consistent with the UTP. All of these results indicate that the diversification and dispersal events in this lineage occurred as a result of drainage systems formed during and after the UTP in the late Miocene and Quaternary periods. | Chuanjiang Zhou Xuzhen Wang Xiaoni Gan Yaping Zhang David M.Irwin Richard L.Mayden Shunping He | 2016 | Science Bulletin2016，61，13： | 4 |
| 7 | Phylogenetic relationships of Cypriniformes and plasticity of pharyngeal teeth in the adaptive radiation of cyprinids显示文摘The Cypriniformes comprise approximately 4,200 species accounting for 25% of the diversity of all freshwater fish, which is widely distributed across the world's continents except Antarctica, South America, and Australia. The highest species diversity is found in Southeastern Asia. Despite its remarkable species diversity and broad-scale geographic patterns of distribution, the evolutionary history of this major freshwater fish group remains largely unresolved. To gain insight of the evolutionary history of Cypriniformes, we present a phylogeny of this group using 1 mitochondrial gene and 15 nuclear genes comprising a total of14,061 bp. Bayesian inference using all gene fragments yielded a well resolved phylogeny, which is mostly consistent with topologies obtained from Maximum Likelihood analyses. Our results further confirmed the monophyly of Cypriniformes and seven constituent subclades including Cyprinidae, Catostomidae, Gyrinocheilidae, Balitoridae, Cobitidae, Nemacheilidae, and Botiidae. Bayesian divergence time analysis indicated that the origin of the Cypriniformes was about 193 Mya during the early Jurassic, coinciding with the onset of the Pangaea breakup. The basal divergence of Cypriniformes is 154 Mya during the late Jurassic. Our findings from molecular divergence and biogeographical analysis indicate the most likely initial geographical range of the ancient Cypriniformes was both East and South Asia(Southeastern area of Mesozoic Laurasia). Moreover, the burst in species diversity in Cyprinidae afforded by the nearly worldwide colonization is possibly in response to the plasticity of pharyngeal dentition. The present study demonstrates that the Cypriniformes was about 193 Mya during the early Jurassic,coinciding with the onset of the Pangaea breakup. The plasticity of pharyngeal dentition of cyprinids might contribute to the burst and radiation of this lineage. The phylogenetic and biogeographic analyses in this study help to improve our understanding of the evolutionary history of this diverse and important freshwater fish group. | Wenjing Tao Lei Yang Richard L.Mayden Shunping He | 2019 | Science China(Life Sciences)2019，62，4： | 4 |
| 8 | Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau显示文摘Origin and diversification of the Tibetan polyploid cyprinids(schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that(i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins;(ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau. | Xuzhen Wang Xiaoni Gan Junbing Li Yiyu Chen Shunping He | 2016 | Science China(Life Sciences)2016，59，11： | 4 |
| 9 | Comparative study on pattern recognition receptors in non-teleost ray-finned fishes and their evolutionary significance in primitive vertebrates显示文摘Pattern recognition receptors(PRRs) play important roles in innate immunity system and trigger the specific pathogen recognition by detecting the pathogen-associated molecular patterns. The main four PRRs components including Toll-like receptors(TLRs), RIG-I-like receptors(RLRs), NOD-like receptors(NLRs) and C-type lectin receptors(CLRs) were surveyed in the five genomes of non-teleost ray-finned fishes(NTR) including bichir(Polypterus senegalus), American paddlefish(Polyodon spathula), alligator gar(Atractosteus spatula), spotted gar(Lepisosteus oculatus) and bowfin(Amia calva), representing all the four major basal groups of ray-finned fishes. The result indicates that all the four PRRs components have been well established in these NTR fishes. In the RLR-MAVS signal pathway, which detects intracellular RNA ligands to induce production of type I interferons(IFNs), the MAVS was lost in bichir particularly. Also, the essential genes of recognition of Lipopolysaccharide(LPS) commonly in mammals like MD2, LY96 and LBP could not be identified in NTR fishes. It is speculated that TLR4 in NTR fishes may act as a cooperator with other PRRs and has a different pathway of recognizing LPS compared with that in mammals. In addition, we provide a survey of NLR and CLR in NTR fishes. The CLRs results suggest that Group V receptors are absent in fishes and Group II and VI receptors are well established in the early vertebrate evolution. Our comprehensive research of PRRs involving NTR fishes provides a new insight into PRR evolution in primitive vertebrate. | Yuming He Hailin Pan Guojie Zhang Shunping He | 2019 | Science China(Life Sciences)2019，62，4： | 4 |
| 10 | Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei: Cyprinidae)显示文摘起源和种系发生的模式为 G 被估计。przexvalskii 和 G。由分析完全的 mtDNA 细胞色素 b 基因顺序(1140bp ) 的 eckloni。种系发生的分析进一步支持了那有三个 mtDNA 系(交流) ,在 G 识别。przewalskii 和 G。eckloni,证明第一鳃的外部 rakers 在 Gymnocypris 的发展史有很少意义钓鱼。建立的网络显示出那 G。黄河特定的 haplotype 艾尔的 eckloni 是一个创始人,它散发了 G 的所有 haplotypes。建议了 G 的 przexvalskii。przexvalskii 可能仅仅从 G 的二 maternals 之一发源。从黄河的 eckloni。F 测试和失配分析在 G 的人口显示出至少二个扩大事件。przexvalskii 大约 0.2734 妈并且 0。0658 妈,当时 G。ecklonifrom Qaidam 盆能经历了严重瓶颈效果大约 0.0693 妈。人口扩大与最近的普通祖先(TMRCA ) 在 subclades 艾尔和 A21 被检测大约 0.2308 ± 0 .01 妈和 0.1319 ± 0 .015 妈,分别地它在从上面的黄河引起了金海湖的分离的 Gonghe 运动事件的地质的年龄范围以内。这些结果建议了鱼多样化的效果由快速在迟了的更新世 Qing-hai-Tibetan 高原高举。 | Zhao Kai Duan Ziyuan Yang Gongshe Peng Zuogang He Shunping Chen Yiyu | 2007 | Progress in Natural Science:Materials International2007，17，5： | 3 |
| 11 | Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae)显示文摘The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodonti- dae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this ge- nus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsi- mony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the mo- lecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our re- sults also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data. | ZHANG YuBo HE ShunPing | 2008 | Chinese Science Bulletin2008，53，2： | 3 |
| 12 | Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae: Sinocyclocheilus)显示文摘The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed mo-lecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed diver-gence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed. | LI ZhiQiang GUO BaoCheng LI JunBing HE ShunPing CHEN YiYu | 2008 | Chinese Science Bulletin2008，53，15： | 3 |
| 13 | The c-myc coding DNA sequences of cyprinids (Teleostei:Cypriniformes):Implications for phylogeny显示文摘The family Cyprinidae is one of the largest fish families in the world,which is widely distributed in East Asian,with obvious difference in characteristic size among species. The phylogenetic analysis of cy-prinid taxa based on the functionally important genes can help to understand the speciation and functional divergence of the Cyprinidae. The c-myc gene is an important gene regulating individual growth. In the present study,the sequence variations of the cyprinid c-myc gene and their phylogenetic significance were analyzed. The 41 complete sequences of the c-myc gene were obtained from cyprinids and outgroups through PCR amplification and clone. The coding DNA sequences of the c-myc gene were used to infer molecular phylogenetic relationships within the Cyprinidae. Myxocyprinus asiaticus (Catostomidae),Misgurnus anguillicaudatus (Cobitidae) and Hemimyzon sinensis (Homalopteridae) were assigned to the outgroup taxa. Phylogenetic analyses using maximum parsimony (MP). maximum likelihood (ML),and Bayesian retrieved similar topology. Within the Cyprinidae,Leuciscini and Barbini formed the monophyletic lineage respectively with high nodal supports. Leuciscini comprises Xeno-cyprinae,Cultrinae,East Asian species of Leuciscinae and Danioninae,Gobioninae and Acheilog-nathinae,and Barbini contains Schizothoracinae,Barbinae,Cyprininae and Labeoninae. Danio rerio,D. myersi and Rasbora trilineata were supposed to separate from Leuciscinae and Barbini and to form another lineage. The positions of some Danioninae species were still unresolved. Analyses of both amino acid variation with parsimony information and two high variation regions indicated that there is no correlation between variations of single amino acid or high variation regions and characteristic size of cyprinids. In addition,the species with smaller size were usually found to be basal within clades in the tree,which might be the results of the adaptation to the primitive ecology and survival pressure. | KONG XiangHui WANG XuZhen GAN XiaoNi HE ShunPing | 2007 | Chinese Science Bulletin2007，52，11： | 3 |
| 14 | Methodology for fish biodiversity monitoring with environmental DNA metabarcoding:The primers,databases and bioinformatic pipelines显示文摘Environmental DNA(eDNA)originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology,which is revolutionizing fish biodiversity monitoring.Several reviews concerning fish eDNA have focused on standard sampling methods and its applications,though a systematic review focused on marker genes,databases,and bioinformatic pipelines has not yet been published.Here,we present a comprehensive literature review of studies applying metabarcoding technology to fish eDNA for the purpose of fish biodiversity monitoring.We systematically provide the available universal primers used to amplify barcoding sequences from fish eDNA,and then discuss reference barcoding databases,relevant bioinformatic analyses,as well as developed pipelines.The performances of universal primers and their relevant reference databases are summarized.Combined use of multiple primer pairs targeted for more than one gene marker(e.g.,12S,16S,Cytb,COI),and use of both local and public databases are recommended as approaches to improve the sensitivity and reliability of fish eDNA analyses.We also compare the effectiveness of eDNA metabarcoding to traditional approaches for monitoring fish biodiversity and highlight challenges and future perspectives associated with this new tool.Ultimately,we advocate for greater incorporation of eDNA analysis into fish biodiversity assessments to assist environmental managers. | Fan Xiong Lu Shu Honghui Zeng Xiaoni Gan Shunping He Zuogang Peng | 2022 | Water Biology and Security2022，1，1： | 3 |
| 15 | Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data:implications for Cyprinidae systematics显示文摘Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylogenetic analyses on phylogeny reconstruction of cyprinid fishes; (ii) provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or-supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major monophyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family. | WANG XuZhen GAN XiaoNi LI JunBing MAYDEN Richard L. HE ShunPing | 2012 | Science China(Life Sciences)2012，55，9： | 2 |
| 16 | The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata)显示文摘The mitochondrial genome complete sequence of Achalinus meiguensis was reported for the first time in the present study. The complete mitochondrial genome of A. meiguensis is 17239 bp in length and contains 13 protein-coding genes, 22 tRNA, 2 rRNA, and 2 non-coding regions (Control regions). On the basis of comparison with the other complete mitochondrial sequences reported, we explored the characteristic of structure and evolution. For example, duplication control regions independently occurred in the evolutionary history of reptiles; the pseudo-tRNA of snakes occurred in the Caenophidia; snake is shorter than other vertebrates in the length of tRNA because of the truncations of TΨC arm (less than 5 bp) and 'DHU' arm. The phylogenic analysis by MP and BI analysis showed that the phylogenetic position of A. meiguensis was placed in Caenophidia as a sister group to other advanced snakes with the exclusion of Acrochordus granulatus which was rooted in the Caenophidia. Therefore we suggested that the subfamily Xenodermatinae, which contains A. meiguensis, should be raised to a family rank or higher rank. At the same time, based on the phylogenic statistic test, the tree of Bayesian was used for estimating the divergence time. The results showed that the divergence time between Henophidia and Caenophidia was 109.50 Mya; 106.18 Mya for divergence between Acrochordus granulatus and the other snakes of the Caenophidia; the divergence time of A. meiguensis was 103 Mya, and Viperidae diverged from the unilateral of Elapidae and Colubridae was 96.06 Mya. | WANG GuangLi HE ShunPing HUANG Song HE Miao ZHAO ErMi | 2009 | Chinese Science Bulletin2009，54，10： | 2 |
| 17 | Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae显示文摘Whole-genome duplications(WGDs)are an important contributor to phenotypic innovations in evolutionary history.The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates.In this study,the evolutionary changes of hemoglobin(Hb)repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish,including eight diploid and four tetraploid species.Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species.Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes.Data were integrated with the expression profiles of the genes during ontogeny.Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family;each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications.This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression.Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems. | Yi Lei Liandong Yang Haifeng Jiang Juan Chen Ning Sun Wenqi Lv Shunping He | 2021 | Science China(Life Sciences)2021，64，7： | 2 |
| 18 | Identification of novel SINEs from Cyprinidae and their evolutionary significance显示文摘短散布原子元素(正弦) 在真核细胞的染色体之中是普遍的。他们是被制动火箭调换放大了的重复 DNA 序列。在这研究,正弦的一个班从 Opsariichthys 出价 ens 染色体被孤立,并且说出 Opsar。顺序分析证实 Opsar 是从 tRNA 分子导出的典型正弦的一个新班。与 Opsar 并且通过 BLASTN 搜索的导出 tRNA 的区域,我们进一步从斑马鱼染色体识别了 Zb 正弦,它包括二个组:Zb-SINE- A 和 Zb-SINE-B。Zb-SINE-A 组包括 -A1-A5, 的亚科, 76-SINE-B 组是一导出 tRNA 的区域和份额更暗淡类似的二聚的 ccrnposition 到算术逻辑单元。76 正弦是三个不同区域的 cxrrnposed:导出 tRNA 的区域,一个 tRNA 无关的区域和 3' 结束的 5' 结束在富有的区域。flanking 区域在富人。76 正弦元素的平均长度是邻接 340 bp。为差不多 0 的 76 正弦报道。1% whde 斑马鱼染色体。大约 70%76 正弦在染色体上 11, 18,和 19。这些 Zb-SINE5 是由 PCR 和点杂交的 characteHzed。在染色体的 76 正弦的分发模式强烈支持基因建模的主人。Opsar 和 76 正弦的导出 tRNA 的区域与 tRNA 翼 基因,和他们显示出 76% 类似,显示那 Opsar 和 76 正弦发源 fiom 不活跃的 tRNA 翼 顺序或 tRNA 翼 相似顺序。鉴于在 Cyprinidae 的斑马鱼的进化地位,我们推断 76 正弦是散布序列的一个很旧的班。 | HAN Yawei HE Shunping CHEN Yiyu | 2007 | Progress in Natural Science:Materials International2007，17，3： | 1 |
| 19 | The new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD+ levels显示文摘The origination of new genes is important for generating genetic novelties for adaptive evolution and biological diversity.However, their potential roles in embryonic development, evolutionary processes into ancient networks, and contributions to adaptive evolution remain poorly investigated. Here, we identified a novel chimeric gene family, the chiron family, and explored its genetic basis and functional evolution underlying the adaptive evolution of Danioninae fishes. The ancestral chiron gene originated through retroposition of nampt in Danioninae 48–54 million years ago(Mya) and expanded into five duplicates(chiron1–5) in zebrafish 1–4 Mya. The chiron genes(chirons) likely originated in embryonic development and gradually extended their expression in the testis. Functional experiments showed that chirons were essential for zebrafish embryo development. By integrating into the NAD^(+) synthesis pathway, chirons could directly catalyze the NAD^(+) rate-limiting reaction and probably impact two energy metabolism genes(nmnat 1 and naprt) to be under positive selection in Danioninae fishes. Together,these results mainly demonstrated that the origin of new chimeric chiron genes may be involved in adaptive evolution by integrating and impacting the NAD^(+) biosynthetic pathway. This coevolution may contribute to the physiological adaptation of Danioninae fishes to widespread and varied biomes in Southeast Asian. | Chengchi Fang Xiaoni Gan Chengjun Zhang Shunping He | 2021 | Science China(Life Sciences)2021，64，11： | 1 |
| 20 | Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish,Tor douronensis显示文摘A PCR survey for Sox genes in a young tetraploid fish Tor douronensis (Teleostei:Cyprinidae) was per-formed to access the evolutionary fates of important functional genes after genome duplication caused by polyploidization event. Totally 13 Sox genes were obtained in Tor douronensis,which represent SoxB,SoxC and SoxE groups. Phylogenetic analysis of Sox genes in Tor douronensis provided evidence for fish-specific genome duplication,and suggested that Sox19 might be a teleost specific Sox gene member. Sequence analysis revealed most of the nucleotide substitutions between duplicated copies of Sox genes caused by tetraploidization event or their orthologues in other species are silent substitutions. It would appear that the sequences are under purifying selective pressure,strongly suggesting that they repre-sent functional genes and supporting selection against all null allele at either of two duplicated loci of Sox4a,Sox9a and Sox9b. Surprising variations of the intron length and similarities of two duplicated copies of Sox9a and Sox9b,suggest that Tor douronensis might be an allotetraploidy. | GUO BaoCheng Li JunBing TONG ChaoBo HE ShunPing | 2008 | Chinese Science Bulletin2008，53，13： | 1 |
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