Genome-wide scan reveals the molecular mechanisms of functional differentiation of Myotis lucifugus and Pteropus vampyrus

小棕蝠(MyOTIS luCIfuguS)和大狐蝠(PTErOPuS VAMPyruS)在生理和行为上有诸多差异,应被诉诸于分子水平并加以系统探讨。该研究对包括小棕蝠和大狐蝠在内的7个哺乳动物全基因组同源编码序列进行了高质量比对,使用比对序列进行了分别以两个蝙蝠枝为前景枝的全基因组水平选择压力分析,并对两种蝙蝠中的正选择基因进行了富集聚类分析。结果表明,在小棕蝠枝受到正选择的基因数高于大狐蝠枝;两种蝙蝠中独立受到正选择的基因富集于不同的功能类别;且正选择基因的富集差异与小棕蝠和大狐蝠在免疫、运动协调、能量代谢和感觉器官发育等关键生物学功能方面的分化大体吻合。The physiological and behavioral differences between Myotis lucifugus and Pteropus vampyrus should be attributed to molecular mechanisms and deserve intensive investigation.We conducted genome-wide scan for coding sequences from the orthologue genes of seven mammalian species.Selection analyses were carried out by setting the branches leading to Myotis lucifugus and Pteropus vampyrus as foreground branches, respectively.Enrichment analyses were conducted for positively selected genes.Our results indicated that more genes exhibited positive selection in Myotis lucifugus than that in Pteropus vampyrus.The positively selected genes of the two species were enriched in different functions.The differences between Myotis lucifugus and Pteropus vampyrus represented their differentiation in biological functions, especially the functions of immunity, motor ability, energetic metabolism and sensory organ development.国家自然科学基金(31172080;91231202

非正交曲线坐标下二维水流计算的SIMPLEC算法

本文采用Laplace方程坐标变换方法生成正交曲线网格，并对浅水流动的控制方程进行坐标变换，方程离散时采用B型交错网格。利用“水位扫描法”结合壁面函数法来处理移动边界，用SIMPLEC算法解非正交曲线坐标下的κ-ε双方程紊流模型，修正了由网格的非正交性引起的误差，通过对美国Colorado洲Fall River的资料进行流场验证，计算结果与实测资料基本符合，显示了本模型在不规则水域计算中的实用价值

Assessing DNA Barcoding as a Tool for Species Identification and Data Quality Control

National Natural Science Foundation of China [31172080]; Key Program of West Light Foundation; Youth Innovation Promotion Association of the Chinese Academy of Sciences; Engineering Research Council [3148]In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating deep intraspecific and shallow interspecific divergences to discover possible taxonomic problems and other sources of error. We use the mitochondrial DNA gene encoding cytochrome b (Cytb) from turtles to test the utility of barcoding for pinpointing potential errors. This gene is widely used in phylogenetic studies of the speciose group. Intraspecific variation is usually less than 2.0% and in most cases it is less than 1.0%. In comparison, most species differ by more than 10.0% in our dataset. Overlapping intra-and interspecific percentages of variation mainly involve problematic identifications of species and outdated taxonomies. Further, we detect identical problems in Cytb from Insectivora and Chiroptera. Upon applying this strategy to 47,524 mammalian CoxI sequences, we resolve a suite of potentially problematic sequences. Our study reveals that erroneous sequences are not rare in GenBank and that the DNA barcoding can serve to confirm sequencing accuracy and discover problems such as misidentified species, inaccurate taxonomies, contamination, and potential errors in sequencing

Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins

National Natural Science Foundation of China [2007CB411600, 2008GA001]; Bureau of Science and Technology of Yunnan Province [31061160189]Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We resequenced some of the positively selected sites (PSSs), within the positively selected genes, and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment

Adaptive Evolution of the Hox Gene Family for Development in Bats and Dolphins

National Basic Research Program of China (973 Program) [2007CB411600]; National Natural Science Foundation of China [30621092, 31172080]; Key Program of West Light Foundation of the Chinese Academy of Sciences [Y102281081]; Bureau of Science and Technology of Yunnan ProvinceBats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation

2009年阿克苏河枯水年水文特征及其对塔里木河干流生态环境的影响

塔里木河流域2009年4—8月0℃层高度平均为4290 gpm,较12 a平均值偏低52 gpm,偏低幅度位居近19 a(1991—2009年)同期第5位.而夏季(6—8月)4站平均高度偏低129 gpm,偏低幅度位居近19 a(1991—2009年)同期第1位.2009年阿克苏河流域年径流量69.28×108m3为偏枯水年;经两支流灌区后,阿克苏河西大桥站年径流量为52.34×108m3,为枯水年.由于塔里木河阿拉尔站以上阿克苏河、叶尔羌河、和田河三条源流2009年入塔里木河水量仅为12.01×108m3,使阿拉尔站年径流量仅为14.08×108m3,为历史最小值,属特枯水年.新渠满站年径流量仅为8.374×108m3,为历史最小值,属特枯水年,并于6月1日—7月22日河道断流52 d,该站至台特玛湖河道断流长达1 100km,占塔里木河干流总长1 321 km的83%,这在历史上是罕见的

新疆典型绿洲经济发展与生态环境建设

科技进步奖三等奖.该成果是中科院“八五”重点科研项目和国家自然科学基金资助项目。分上下篇和专题篇，全文４０万字。对绿洲的形成、演变规律、系统特性、生态经济、生态环境建设、协调发展，作了系统而精辟地论述；对吐鲁番绿洲的资源开发、经济发展、环境建设和优化模式作了深刻提示和分析；对一些专门问题作了剖析研究，周密阐述。是一项重要的绿洲基础理论研究和绿洲开发研究，将使中国的绿洲研究提高到一个新的水平。该成果对绿洲系、绿洲生态经济和环境建设提出了较深刻的新论点，首次提出研究绿洲的方法论。对吐鲁番绿洲研究提出水资源转换规律、经济发展战略和结构转换，有独到见解。绿洲研究涉及面广，时间跨度长。绿洲是一个综合性强的地理区域、生态学、经济学、人口学、历史学、农学和水利学有密切关系。时间上从古代、近代到现代作了动态研究，尤其是近５０年作了细致分析。研究工作量大、难度大。该成果在绿洲的基本理论研究填补了中国绿洲研究方面的空白，对绿洲建设和新疆经济发展有重要理论意义和实践意义，对发展“绿洲学”有重要学术价值，成果达到国内领先水平

Draft genome sequence of the Tibetan antelope

National Basic Research Program of China [2006CB504100, 2007CB411600, 2012CB518200]; Basic Science Research Foundation of Bureau of Science and Technology in Qinghai Provinces [2010-1456]; Program of International S&T Cooperation of China [0S2012GR0195]; National Nature Science Foundation of China [30393133]; Bureau of Science and Technology of Yunnan Province, Chinese Academy of Sciences; Natural Sciences and Engineering Research Council [3148]The Tibetan antelope (Pantholops hodgsonii) is endemic to the extremely inhospitable high-altitude environment of the Qinghai-Tibetan Plateau, a region that has a low partial pressure of oxygen and high ultraviolet radiation. Here we generate a draft genome of this artiodactyl and use it to detect the potential genetic bases of highland adaptation. Compared with other plain-dwelling mammals, the genome of the Tibetan antelope shows signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission. Both the highland American pika, and the Tibetan antelope have signals of positive selection for genes involved in DNA repair and the production of ATPase. Genes associated with hypoxia seem to have experienced convergent evolution. Thus, our study suggests that common genetic mechanisms might have been utilized to enable high-altitude adaptation

The genesis and source of the H7N9 influenza viruses causing human infections in China

National Institutes of Health (National Institute of Allergy and Infectious Diseases) [HSN266200700005C]; Li Ka Shing Foundation; University Grants Committee of the Hong Kong SAR [AoE/M-12/06]; Shenzhen Peacock Plan High-End Talents Program [KQTD201203]; University Development Fund (HKU); Innovation and Technology Commission of the Hong Kong Government; Newton International Fellowship of the Royal Society; US Agency for International Development (USAID) Emerging Pandemic Threats Program, PREDICT project [GHN-A-OO-09-00010-00]; European Union [278433-PREDEMICS]; ERC [260864]; Wellcome Trust [092807]A novel H7N9 influenza A virus first detected in March 2013 has since caused more than 130 human infections in China, resulting in 40 deaths(1,2). Preliminary analyses suggest that the virus is a reassortant of H7, N9 and H9N2 avian influenza viruses, and carries some amino acids associated with mammalian receptor binding, raising concerns of a new pandemic(1,3,4). However, neither the source populations of the H7N9 outbreak lineage nor the conditions for its genesis are fully known(5). Using a combination of active surveillance, screening of virus archives, and evolutionary analyses, here we show that H7 viruses probably transferred from domestic duck to chicken populations in China on at least two independent occasions. We show that the H7 viruses subsequently reassorted with enzootic H9N2 viruses to generate the H7N9 outbreak lineage, and a related previously unrecognized H7N7 lineage. The H7N9 outbreak lineage has spread over a large geographic region and is prevalent in chickens at live poultry markets, which are thought to be the immediate source of human infections. Whether the H7N9 outbreak lineage has, or will, become enzootic in China and neighbouring regions requires further investigation. The discovery here of a related H7N7 influenza virus in chickens that has the ability to infect mammals experimentally, suggests that H7 viruses may pose threats beyond the current outbreak. The continuing prevalence of H7 viruses in poultry could lead to the generation of highly pathogenic variants and further sporadic human infections, with a continued risk of the virus acquiring human-to-human transmissibility