中国哺乳动物形态、生活史和生态学特征数据集

物种特征是生物对生存环境适应和响应的表现, 反映了物种的生态位、适合度和生态功能。特征数据库的建立和共享是研究生物多样性维持与丧失、物种进化与适应、生态过程与生态系统功能、物种对气候变化和人类干扰响应、种内与种间关系等的基础。中国是世界哺乳动物物种数最多的国家之一, 然而目前中国还没有包含哺乳动物形态、生活史、生态学和地理分布等物种特征的数据库。我们系统查阅了文献和各种数据资料, 共收集整理出中国有分布记录的754种哺乳动物(包括近些年野外绝灭种、分布存疑种)的体重、脑容量、体长、尾长、前臂长(翼手目)、后足长、耳长、性成熟时间、妊娠期、窝崽数、年窝数、世代长度、食性、活动模式、是否特有种、濒危等级、海拔范围、栖息地类型、栖息地宽度、动物地理界、生物群系、分布型、动物地理区划和分布省份或水域等24个生态特征数据。在这些特征中, 除了分布省份或水域及是否特有种外, 其余特征数据均存在不同程度的缺失, 数据的完整度为30%‒100%。本数据库收录的哺乳动物种数为目前中国哺乳动物种数的上限, 为中国哺乳动物研究提供了基础数据, 推进中国哺乳动物多样性信息共享和深度挖掘。     

中国银口天竺鲷属鱼类的分类厘定

本研究检视了采自中国沿海的银口天竺鲷属标本314尾, 形态学鉴定为8种: 斑鳍银口天竺鲷(Jaydia carinata (Cuvier, 1828))、细条银口天竺鲷(J. lineata (Temminck & Schlege, 1842))、新几内亚银口天竺鲷(J. novaeguineae (Valenciennes, 1832))、黑鳃银口天竺鲷(J. poeciloptera (Cuvier, 1828))、史密斯氏银口天竺鲷(J. smithi Kotthaus 1970)、横带银口天竺鲷(J. striata (Smith & Radcliffe, 1912))、印度洋银口天竺鲷(J. striatodes (Gon, 1997))和黑边银口天竺鲷(J. truncata (Bleeker, 1854))。结合GenBank中的同种序列, 对史密斯氏银口天竺鲷进行DNA条形码分析, 发现中国群体和地中海群体分为两个组群, 两者平均组间遗传距离为0.044, 表明其中存在隐存种。因该种模式产地为亚丁湾, 推测中国种群为隐存种Jaydia sp.。结合标本和文献考证, 我们认为中国已知有银口天竺鲷属鱼类9种, 未采集到的烟台银口天竺鲷J. tchefouensis (Fang, 1942)可能为J. lineata次定同种异名。我们整理了各种的同种异名、形态特征和地理分布, 编制了检索表, 探讨了分类问题, 修订了错误。中国已记录物种J. ellioti、J. arafurae、J. albomarginata实际为J. truncata、J. poeciloptera和J. novaeguineae。     

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

DNA accessibility is an important layer of regulation of DNA-dependent processes. Methods that measure DNA accessibility at local and genome-wide scales have facilitated a rapid increase in the knowledge of chromatin architecture in animal and yeast systems. In contrast, much less is known about chromatin organization in plants. We developed a robust DNase I-polymerase chain reaction (PCR) protocol for the model plant Arabidopsis (Arabidopsis thaliana). DNA accessibility is probed by digesting nuclei with a gradient of DNase I followed by locus-specific PCR. The reduction in PCR product formation along the gradient of increasing DNase I concentrations is used to determine the accessibility of the chromatin DNA. We explain a strategy to calculate the decay constant of such signal reduction as a function of increasing DNase I concentration. This allows describing DNA accessibility using a single variable: the decay constant. We also used the protocol together with AGRONOMICS1 DNA tiling microarrays to establish genome-wide DNase I sensitivity landscapes.Chromatin has a major impact on genome organization and gene activity. Differential accessibility of DNA is thought to be a major consequence of locally different chromatin composition and structure (Li et al., 2007). Chromatin sensitivity to nucleases has proven to be a powerful tool to probe DNA accessibility in chromatin. Frequently used nucleases include DNase, micrococcal nuclease, and restriction enzymes. The resolution of restriction enzymes is limited by their sequence specificity, and micrococcal nuclease is more often used to determine nucleosome occupancy (Schones and Zhao, 2008). Chromatin sensitivity to DNase I has often been used to define the “openness” of chromatin relative to its higher order structures. Its applicability has been manifested by detecting regulatory elements, such as promoters, enhancers, and insulators, as DNase I-hypersensitive sites (Wang and Simpson, 2001; Crawford et al., 2004, 2006; Dorschner et al., 2004; Sabo et al., 2006; Boyle et al., 2008; Naughton et al., 2010; Pique-Regi et al., 2011). DNase I sensitivity can also be used as a measure for the general accessibility of chromatin (Weil et al., 2004).Initially, the chromatin accessibility of local genomic regions to DNase I was probed by Southern blotting (Mather and Perry, 1983; Bender et al., 2000; Wang and Simpson, 2001; Bulger et al., 2003). However, Southern blotting is tedious and lacks sensitivity, and the interpretation of results can be challenging. Therefore, analysis methods based on PCR have been developed (Pfeifer and Riggs, 1991; Feng and Villeponteau, 1992; McArthur et al., 2001; Dorschner et al., 2004; Martins et al., 2007). In recent years, DNase I assays were coupled to high-throughput genome-wide profiling strategies such as genome tiling arrays and next-generation sequencing (Crawford et al., 2004, 2006; Sabo et al., 2004, 2006; Weil et al., 2004). While much has been learned about the accessibility of chromatin in animal and yeast systems, our knowledge of chromatin accessibility in plants is limited. Most studies have focused on selected genomic regions such as the general regulatory factor1 (GRF1) gene and the alcohol dehydrogenase1 (Adh1) and Adh2 genes in maize (Zea mays; Paul and Ferl, 1998a, 1998b) or the GRF gene, the Adh gene, and an 80-kb genomic region harboring 30 protein-coding genes in Arabidopsis (Arabidopsis thaliana; Vega-Palas and Ferl, 1995; Paul and Ferl, 1998a, 1998b; Kodama et al., 2007). The technique used in these reports was exclusively DNase I treatment and analysis of accessibility using Southern blotting. More recently, we have combined the DNase I sensitivity assay with whole-genome tiling arrays in Arabidopsis to generate a genome-wide chromatin accessibility profile (Shu et al., 2012).Here, we present a robust, optimized DNase I sensitivity assay protocol for Arabidopsis tissues based on PCR. This protocol can be adapted to different samples or experimental objectives; the strategies for optimizing each step are also discussed. Analysis of relatively large fragments by PCR has proven to be highly robust as a first step in probing DNase I sensitivity in any region of the genome. We also introduce a new strategy for presenting the DNase I sensitivity of the tested regions using a decay constant calculated by fitting PCR product intensity values from a gradient digestion. In this way, the sensitivity of each region is characterized by a single value, facilitating comparisons between different regions or samples. Finally, we describe how our protocol can be combined with genomic techniques for genome-wide profiles of chromatin accessibility.     

木论喀斯特常绿落叶阔叶混交林群丛数量分类及稳定性

加深对喀斯特顶极群落植物组成、群落结构和群落分布的认识可以为该区域生物多样性保护和森林管理提供参考。本文基于广西木论喀斯特常绿落叶阔叶混交林25 ha森林动态监测样地地形、土壤和物种组成数据, 采用多元回归树对该群落进行群丛分类, 并分析各群丛多样性和稳定性。结果表明, 群落可分为6个群丛, 分别为群丛I: 长序厚壳桂+栀子皮+香叶树群丛(Ass. Cryptocarya microcarpa + Itoa orientalis + Lindera communis), 群丛II: 长序厚壳桂+灰岩棒柄花+罗伞群丛(Ass. Cryptocarya microcarpa + Cleidion bracteosum + Brassaiopsis glomerulata), 群丛III: 圆果化香树+密花树+齿叶黄皮群丛(Ass. Platycarya longipes + Rapanea neriifolia + Clausena dunniana), 群丛IV: 圆果化香树+滇丁香+齿叶黄皮群丛(Ass. Platycarya longipes + Luculia intermedia + Clausena dunniana), 群丛V: 长序厚壳桂+罗伞+伞花木群丛(Ass. Cryptocarya microcarpa + Brassaiopsis glomerulata + Eurycorymbus cavaleriei), 群丛VI: 小叶栾树+长管越南茜+圆果化香树群丛(Ass. Boniodendron minus + Rubovietnamia aristate + Platycarya longipes)。除群丛I外, 各群丛总体的多样性指数较高。Shannon-Wiener指数、Simpson指数以及Pielou均匀度指数表现出一致的变化趋势: 群丛VI > 群丛V > 群丛IV > 群丛III > 群丛II > 群丛I, 而丰富度则为群丛VI > 群丛IV > 群丛V > 群丛I > 群丛III > 群丛II, 物种多样性在中海拔群丛最高。中上坡部位群丛稳定性最高, 洼地群丛稳定性最低。海拔在群落结构及组成中起重要作用, 可能是影响群落分布的重要因素。     

通过红色名录评估研究中国哺乳动物受威胁现状及其原因

依据中国哺乳类野生种群与生境现状, 我们利用IUCN Red List Categories and Criteria (Version 3.1), Guidelines for Using the IUCN Red List Categories and Criteria和Guidelines for Application of IUCN Red List Criteria at Regional and National Levels (Version 4.0), 评价了中国所有已知的673种哺乳动物的濒危状况。本次评估了71种《IUCN濒危物种红色名录(2015)》没有评估的哺乳动物, 还评估了60种《IUCN濒危物种红色名录(2015)》误认为中国没有分布的哺乳动物。发现中国有3种哺乳动物“野外灭绝”, 3种“区域灭绝”。受威胁中国哺乳动物共计178种, 约占评估物种总数的26.4%, 高于IUCN濒危物种红色名录的物种平均受威胁率(21.8%)。中国哺乳动物1/4的特有种属于受威胁物种。受威胁比例最高的目是灵长目、食肉目与鲸偶蹄目。多数省区的受威胁哺乳动物物种占本省区哺乳动物总数的20-30%。中国哺乳动物种类多分布在中国第二级地理阶梯。生活在高海拔地区的哺乳动物虽然种类少, 但是受威胁哺乳动物的种类比例高。过度利用、生境丧失和人类干扰名列受威胁哺乳动物致危因子的前3位。自从1989年《中华人民共和国野生动物保护法》实施以来, 一些中国濒危哺乳动物的生存状况得到了改善。然而, 鉴于中国哺乳动物区系的独特性和多样性, 以及中国地形地貌的复杂性, 如何拯救这些濒危物种仍是中国生物多样性保护的一项艰巨任务。     

Two Fundamentally Distinct PCNA Interaction Peptides Contribute to Chromatin Assembly Factor 1 Function

Chromatin assembly factor 1 (CAF-1) deposits histones H3 and H4 rapidly behind replication forks through an interaction with the proliferating cell nuclear antigen (PCNA), a DNA polymerase processivity factor that also binds to a number of replication enzymes and other proteins that act on nascent DNA. The mechanisms that enable CAF-1 and other PCNA-binding proteins to function harmoniously at the replication fork are poorly understood. Here we report that the large subunit of human CAF-1 (p150) contains two distinct PCNA interaction peptides (PIPs). The N-terminal PIP binds strongly to PCNA in vitro but, surprisingly, is dispensable for nucleosome assembly and only makes a modest contribution to targeting p150 to DNA replication foci in vivo. In contrast, the internal PIP (PIP2) lacks one of the highly conserved residues of canonical PIPs and binds weakly to PCNA. Surprisingly, PIP2 is essential for nucleosome assembly during DNA replication in vitro and plays a major role in targeting p150 to sites of DNA replication. Unlike canonical PIPs, such as that of p21, the two p150 PIPs are capable of preferentially inhibiting nucleosome assembly, rather than DNA synthesis, suggesting that intrinsic features of these peptides are part of the mechanism that enables CAF-1 to function behind replication forks without interfering with other PCNA-mediated processes.Eukaryotic cells in S phase not only have to replicate their entire genome but also faithfully reproduce preexisting chromatin structures onto the two nascent chromatids. The duplication of chromatin structures during DNA replication is a challenging task for eukaryotic cells. Newly synthesized histones are deposited very rapidly behind replication forks (150 to 300 bp), almost as soon as enough DNA has emerged from the replisome to allow the formation of nucleosome core particles (52). A key protein involved in coupling nucleosome assembly to DNA replication is chromatin assembly factor 1 (CAF-1). CAF-1 is a complex of three polypeptide subunits, known as p150, p60, and RbAp48 in vertebrates, that mediates the first step in nucleosome formation by depositing newly synthesized histone H3/H4 onto DNA (25, 50).In mouse and human cells, CAF-1 localizes to virtually all DNA replication foci throughout the S phase (28, 38, 49, 54). This strongly argues that CAF-1 is a physiologically relevant histone H3/H4 nucleosome assembly factor. In addition, disruption of CAF-1 function in human cells results in a severe loss of viability that is accompanied by spontaneous DNA damage and a block in S-phase progression (20, 40, 60). Thus, unlike in Saccharomyces cerevisiae, the function of CAF-1 in vertebrates cannot be replaced by that of other nucleosome factors, such as members of the Hir protein family or Rtt106 (24, 27, 29). This may be because, unlike CAF-1, HIRA (a human homologue of yeast Hir1 and Hir2) does not associate with core histones that are synthesized during S phase (55). In human cells, the ability to promote nucleosome assembly preferentially onto replicating DNA is thus far unique to CAF-1.This distinctive property of CAF-1 is mediated through proliferating cell nuclear antigen (PCNA), a homotrimeric ring that encircles double-stranded DNA (4) and acts as a sliding clamp to tether DNA polymerases to their DNA substrate and thereby enhance their processivity. Several lines of biochemical and genetic evidence support the role of PCNA in CAF-1-mediated nucleosome assembly. First, CAF-1 colocalizes with PCNA in vivo and binds directly to PCNA in vitro (27, 35, 49, 61). Second, even in the presence of excess unreplicated DNA, CAF-1 can select fully replicated plasmid DNA molecules as preferential substrates for histone deposition, but only when those molecules are associated with PCNA (49). Third, PCNA-driven DNA synthesis can also attract CAF-1 to sites of DNA repair events, such as nucleotide excision repair (12, 15, 32, 35). Fourth, a specific PCNA mutation impairs the role of CAF-1 in telomeric silencing in S. cerevisiae (48, 61). Interestingly, a number of PCNA mutations that reduce its interaction with other PCNA-binding proteins have apparently no effect on CAF-1 function in vivo (48, 61). This implies that the interaction of CAF-1 with PCNA is substantially different from that of other PCNA-binding proteins.Enhancing DNA polymerase processivity is not the only function of PCNA in DNA replication. The sliding clamp also directly binds to other replication enzymes, such as DNA ligase 1, DNA polymerase δ, and FEN1 (14, 21, 37). In addition to its roles in DNA synthesis and nucleosome assembly, PCNA also directly binds to a number of enzymes that continuously monitor and correct the quality of nascent DNA. These include enzymes involved in epigenetic inheritance, such as the maintenance DNA methyltransferase DNMT1 (8), base excision repair (UNG2) (42), mismatch repair (MSH3 and MSH6) (9), DNA lesion bypass (23), and many other processes (31, 36). Even subtle defects in many of these processes, including CAF-1-dependent nucleosome assembly (39), lead to either chromosome rearrangements or mutator phenotypes, which are common features of many human cancers. Surprisingly, many of these enzymes interact with PCNA via canonical PCNA interaction peptides (PIPs) that conform to the consensus sequence QXXhXXaa, where Q is a glutamine, h is a hydrophobic residue (valine, methionine, leucine, or isoleucine), a is an aromatic residue (phenylalanine, tyrosine, tryptophan, or occasionally histidine), and X represents any amino acid. Therefore, regulatory mechanisms must exist to ensure that these fundamentally distinct PCNA-dependent processes occur in a carefully orchestrated manner without mutually interfering with each other.In order to understand how the action of CAF-1 is coordinated with that of other PCNA-binding proteins at replication forks, we carried out a thorough study of CAF-1 PIPs by analyzing their functions using a number of assays. We found that the p150 subunit of CAF-1 contains two fundamentally distinct PIPs. The N-terminal motif (PIP1) binds strongly to PCNA in vitro but is dispensable for nucleosome assembly during simian virus 40 (SV40) DNA replication. In contrast, despite the lack of a key conserved residue, the second PIP (PIP2) of CAF-1 is crucial for replication-dependent nucleosome assembly in vitro and for targeting CAF-1 to DNA replication foci in vivo. Remarkably, although PIP2 exhibits some features of canonical PIPs, it binds only weakly to PCNA in vitro. We suggest that regulated PCNA binding via this peptide may play an important role in ensuring that CAF-1 can efficiently deposit histones behind replication forks without competing with the numerous other enzymes that require continuous access to PCNA during DNA replication. Consistent with this, we show that CAF-1 PIPs possess the ability to preferentially interfere with nucleosome assembly rather than with DNA synthesis.