鱼类线粒体DNA(mtDNA)及其在分子系统学中的应用

应用线粒体DNA标记,分析种群间的遗传关系、确定种群地理格局、确定种群间的基因流以及确定物种进化显著性保护单元（EsU）,从而为分子系统学研究提供了一个新的具有很强操作性的科学手段。文中论述了鱼类线粒体DNA研究的最新进展,重点介绍了线粒体DNA标记在分子系统学研究中的广泛应用。     

基于文献数据比较研究东北针阔混交林群落叶绿体遗传多样性

第四纪气候变化对植物群落产生深远影响,然而植物群落如何响应气候变化,群落内不同物种是否具有一致的响应,对于这些问题仍缺乏更系统和完整的答案．中国东北针阔混交林位于凉温带,对气候变化十分敏感,是研究物种对第四纪气候变化响应的理想区域．本研究利用文献检索调查东北针阔混交林物种谱系地理研究现状,并基于文献数据分析东北针阔混交林群落及其周边群落的遗传多样性空间分布情况．结果发现,2020年前,仅有23篇文章对27个东北针阔混交林群落物种进行谱系地理研究．无论是群落水平还是物种水平,均未发现遗传多样性的纬度梯度格局．现有的数据表明,长白山西部和大兴安岭北部地区具有较高的群落遗传多样性．这些结果表明冰期“原位避难”可能是东北针阔混交林群落物种的普遍模式,但是具体的冰期避难所位置可能存在物种差异．由于文献数据是独立而分散的谱系地理研究,存在取样种群和分子标记以及覆盖度的差异,从而导致基于文献分析的群落水平遗传多样性格局结论仍存在不确定性．未来应开展以群落遗传多样性和群落形成历史问题为导向的系统设计,以期系统性地回答群落如何响应第四纪气候变化．      

杂草稻杂种F_2代群体等位基因非随机分离和位点间连锁不平衡的研究

杂交-渐渗在物种进化过程中起到了重要作用,本研究对人工杂交和自交构建的3个杂草稻杂种F2代群体进行遗传分析,了解各群体中来自双亲不同位点等位基因的遗传规律,并以此揭示在杂草稻的杂交-渐渗过程中双亲基因的传递是否受到自然选择而发生非随机分离.采用微卫星(SSR)和插入/缺失(InDel)分子标记,检测了F2群体各位点等位基因和基因型频率,以连续卡方(X2)方法,检验了F2代群体各位点等位基因和基因型频率的观察比值和理论比值是否相符,检测配子或合子选择对偏态分离造成的影响,对3个F2群体分子标记的各两两位点进行了连锁不平衡分析和卡方统计检验.结果显示3个群体均出现显著的等位基因非随机分离,配子选择对非随机分离影响较大,某些基因位点存在显著关联关系,表明杂草稻的杂种后代群体在杂交分离过程明显受到了自然选择,这一结果为杂交-渐渗在杂草稻适应性进化过程中的作用提供了遗传和分子证据.     

青藏高原特有植物分子谱系地理学研究现状

分子谱系地理学是研究物种或近缘物种遗传谱系地理格局和历史成因机制的一种研究方法.通过重建物种进化历史过程可探讨以往地质事件、地形地貌和气候变化对生物物种形成、分化和扩散的影响.文章通过对近几年来青藏高原特有植物分子谱系地理学研究所取得重要成果的介绍,探讨了高原特有植物谱系地理结构,分析和总结了冰期高原植物微型避难所分布格局、居群各分支分化时间和冰期后回迁和扩散模式等.这些研究结果表明,青藏高原不同植物物种具有不同的冰期避难所分布格局和历史扩散特征.     

青藏高原特有植物分子谱系地理学研究现状

分子谱系地理学是研究物种或近缘物种遗传谱系地理格局和历史成因机制的一种研究方法.通过重建物种进化历史过程可探讨以往地质事件、地形地貌和气候变化对生物物种形成、分化和扩散的影响.文章通过对近几年来青藏高原特有植物分子谱系地理学研究所取得重要成果的介绍,探讨了高原特有植物谱系地理结构,分析和总结了冰期高原植物微型避难所分布格局、居群各分支分化时间和冰期后回迁和扩散模式等.这些研究结果表明,青藏高原不同植物物种具有不同的冰期避难所分布格局和历史扩散特征.     

微卫星标记在Ⅱ型糖尿病基因定位上的应用

微卫星是以几个碱基(一般为1～6个)为重复单位组成的简单的串联重复序列,遍布真核生物基因组中,具有丰度高、多态性高、共显性标记、选择中性、可自动检测等优点,已经成为人类遗传学研究中被广泛应用的分子遗传标记.Ⅱ型糖尿病是糖尿病中最普遍的一种形式,它以胰岛素抗性活动紊乱为特征.该病与遗传因素、肥胖以及缺少运动行为等生活方式相关.为有效阻止或至少延缓疾病的进程,对Ⅱ型糖尿病的基因定位研究是必要的.微卫星DNA标记技术在动物亲缘关系的鉴定、特定基因定位、群体遗传结构的分析、物种的进化和系统发生以及遗传基因连锁图谱的构建等方面已得到了广泛的应用.因此,就微卫星DNA遗传标记在Ⅱ型糖尿病基因定位上应用的原理、方法等方面进行综述.     

分子细胞遗传学及其在动物遗传育种中的应用

分子细胞遗传学的建立和发展是与细胞遗传学和分子遗传学密切相关的,是细胞遗传学的微观深入和分子遗传学的宏观发展。其在动物遗传育种中的广泛应用主要表现在基因定位和构建基因图谱、分子标记及标记辅助选择、杂种优质预测以及物种起源、分类和进化等几个方面的研究中。     

基于RNA-Seq技术的日本七鳃鳗(Lampetra japonica)肝脏转录组从头组装及分析

采用RNA-seq技术对日本七鳃鳗肝脏进行高通量转录组测序.经从头(de novo)组装,最终获得了47 293个Unigenes,N50为1 447bp.通过与多个数据库的同源比对,65.04%的Unigenes得到了功能注释.在KEGG分析中,从肝脏转录组中挖掘鉴定到了众多参与固有免疫相关防御途径的Unigene,表明七鳃鳗的肝脏可能在抵御病原体侵袭的早期防御中发挥了重要作用.基于该转录组,全面认识了七鳃鳗补体与凝集级联系统的遗传构成,为深入探索它们的起源进化以及重要基因的功能适应性研究提供了依据.应用拼接的转录组,批量筛选了大量的SSR分子标记,为以后的遗传多样性研究和种质保护工作提供了候选材料.为今后深入认识七鳃鳗早期肝脏的免疫防御功能,探索该物种适应复杂水生生活的免疫进化以及群体多样性保护,奠定了重要的理论和实践基础.     

利用SSR及ISSR分子标记研究苜蓿属及其近缘植物的亲缘关系

利用30对SSR引物和12个ISSR引物对苜蓿属(Medicago)及其近缘植物共11个物种的亲缘关系进行研究。通过遗传多样性研究及UPGMA聚类分析显示,"阔荚类群"(subgen.Platycapos)的4个种在两种分子标记下都聚为一支,符合其相似的形态学特征;"阔荚类群"在SSR分子标记中与胡卢巴属(Trigonella)聚成一支,网脉胡卢巴(T.cancellata)在ISSR分子标记中聚在"阔荚类群"中;两种分子标记中,"紫花苜蓿复合体"(Medicago sativa complex)3个种间的遗传距离都最短;南苜蓿(M.polymorpha)在两种分子标记下的聚类结果有所不同,SSR分子标记下与胡卢巴属的亲缘关系更近。研究说明苜蓿属与胡卢巴属具有很近的亲缘关系,苜蓿属内不同物种与胡卢巴属的亲缘关系有远有近,其中苜蓿属中的"阔荚类群"与胡卢巴属的关系最近,苜蓿属中其他物种与胡卢巴属的亲缘关系较远。     

中华稻蝗种群遗传关系研究

对我国中华稻蝗若干种群进行了基于形态分类学重要特征、染色体C带核型和RAPD分子标记的种群遗传学关系研究.结果表明,我国中华稻蝗从形态上来看东部沿海种群体型较大,前翅较长,尾须较钝,而内陆及东北种群则体型较小,前翅较短,尾须较尖;但从外生殖器基本结构来看,不同种群具有相似的形态特征.其次,不同种群在染色体数目、着丝粒位置以及C带带型等方面具有明显恒定的结构特点.从RAPD分子标记研究结果来看,不同种群拥有明显一致的分子标记数据.由此可见,我国中华稻蝗是稻蝗属中一个广布物种,其外部形态结构的差异可能与其分布地环境条件相适应,然而其外生殖器结构能够反映物种的基本特征.从种群遗传学角度来看,染色体带型结构和分子标记结果的稳定性更能体现物种遗传结构的本质,因此,文章支持Ho llis将无齿稻蝗等合并入中华稻蝗的主张.     

MHC II DRB variation and trans-species polymorphism in the golden snub-nosed monkey (Rhinopithecus roxellana)

Genetic variation is generally believed to be important in studying endangered species’ adaptive potential.Early studies assessed genetic diversity using nearly neutral markers,such as microsatellite loci and mitochondrial DNA(mtDNA),which are very informative for phylogenetic and phylogeographic reconstructions.However,the variation at these loci cannot provide direct information on selective processes involving the interaction of individuals with their environment,or on the capability to resist continuously evolving pathogens and parasites.The importance of genetic diversity at informative adaptive markers,such as major histocompatibility complex(MHC) genes,is increasingly being realized,especially in endangered,isolated species.Small population size and isolation make the golden snub-nosed monkey(Rhinopithecus roxellana) particularly susceptible to genetic variation losses through inbreeding and restricted gene flow.In this study,we compared the genetic variation and population structure of microsatellites,mtDNA,and the most relevant adaptive region of the MHC II-DRB genes in the golden snub-nosed monkey.We examined three Chinese R.roxellana populations and found the same variation patterns in all gene regions,with the population from Shennongjia population,Hubei Province,showing the lowest polymorphism among three populations.Genetic drift that outweighed balancing selection and the founder effect in these populations may explain the similar genetic variation pattern found in these neutral and adaptive genes.     

Field parameterization and experimental test of the neutral theory of biodiversity

Ecologists would like to explain general patterns observed across multi-species communities, such as species-area and abundance-frequency relationships, in terms of the fundamental processes of birth, death and migration underlying the dynamics of all constituent species. The unified neutral theory of biodiversity and related theories based on these fundamental population processes have successfully recreated general species-abundance patterns without accounting for either the variation among species and individuals or resource-releasing processes such as predation and disturbance, long emphasized in ecological theory. If ecological communities can be described adequately without estimating variation in species and their interactions, our understanding of ecological community organization and the predicted consequences of reduced biodiversity and environmental change would shift markedly. Here, I introduce a strong method to test the neutral theory that combines field parameterization of the underlying population dynamics with a field experiment, and apply it to a rocky intertidal community. Although the observed abundance-frequency distribution of the system follows that predicted by the neutral theory, the neutral theory predicts poorly the field experimental results, indicating an essential role for variation in species interactions.     

苏南丘陵山区典型次生森林群落的点格局分析

为研究北亚热带丘陵山区次生森林在不同演替序列中群落的空间结构特征,对江苏省南京市溧水林场区域内36块30 m×30 m样地中的木本植物分布进行了详细调查。在利用典范相关分析(CCA)确定不同演替阶段典型群落类型的基础上,运用点格局分析方法对各类型群落中优势树种的空间分布格局进行研究。结果表明:研究区典型森林群落类型为马尾松-麻栎群落、冬青-马尾松群落、麻栎-栓皮栎群落和杉木-油桐群落,土壤条件是影响该地区植物群落组成差异的首要因素。各群落类型中的优势乔木树种在>3 m的空间尺度上通常都表现为均匀分布格局,推断种内竞争可能是形成这种格局特征的重要原因。主要乔木树种之间的空间关联通常表现为中性关系,而对于麻栎-栓皮栎这种功能属性相近的树种,由于受到种间竞争驱动从而表现出显著的负相关。     

Coral reef diversity refutes the neutral theory of biodiversity

The global decline of coral reefs highlights the need to understand the mechanisms that regulate community structure and sustain biodiversity in these systems. The neutral theory, which assumes that individuals are demographically identical regardless of species, seeks to explain ubiquitous features of community structure and biodiversity patterns. Here we present a test of neutral-theory predictions with the use of an extensive species-level data set of Indo-Pacific coral communities. We show that coral assemblages differ markedly from neutral-model predictions for patterns of community similarity and the relative abundance of species. Within local communities, neutral models do not fit relative abundance distributions as well as the classical log-normal distribution. Relative abundances of species across local communities also differ markedly from neutral-theory predictions: coral communities exhibit community similarity values that are far more variable, and lower on average, than the neutral theory can produce. Empirical community similarities deviate from the neutral model in a direction opposite to that predicted in previous critiques of the neutral theory. Instead, our results support spatio-temporal environmental stochasticity as a major driver of diversity patterns on coral reefs.     

Strong population substructure is correlated with morphology and ecology in a migratory bat

Examining patterns of inter-population genetic diversity can provide valuable information about both historical and current evolutionary processes affecting a species. Population genetic studies of flying and migratory species such as bats and birds have traditionally shown minimal population substructure, characterized by high levels of gene flow between populations. In general, strongly substructured mammalian populations either are separated by non-traversable barriers or belong to terrestrial species with low dispersal abilities. Species with female philopatry (the tendency to remain in or consistently return to the natal territory) might show strong substructure when examined with maternally inherited mitochondrial DNA, but this substructure generally disappears when biparentally inherited markers are used, owing to male-mediated gene flow. Male-biased dispersal is considered typical for mammals, and philopatry in both sexes is rare. Here we show strong population substructure in a migratory bat species, and philopatry in both sexes, as indicated by concordance of nuclear and mtDNA findings. Furthermore, the genetic structure correlates with local biomes and differentiation in wing morphology. There is therefore a close correlation of genetic and morphological differentiation in sympatric subspecific populations of this mammalian species.     

Density dependence explains tree species abundance and diversity in tropical forests

The recurrent patterns in the commonness and rarity of species in ecological communities--the relative species abundance--have puzzled ecologists for more than half a century. Here we show that the framework of the current neutral theory in ecology can easily be generalized to incorporate symmetric density dependence. We can calculate precisely the strength of the rare-species advantage that is needed to explain a given RSA distribution. Previously, we demonstrated that a mechanism of dispersal limitation also fits RSA data well. Here we compare fits of the dispersal and density-dependence mechanisms for empirical RSA data on tree species in six New and Old World tropical forests and show that both mechanisms offer sufficient and independent explanations. We suggest that RSA data cannot by themselves be used to discriminate among these explanations of RSA patterns--empirical studies will be required to determine whether RSA patterns are due to one or the other mechanism, or to some combination of both.     

Sky islands of southwest China. I: an overview of phylogeographic patterns

Sky islands are high-elevation areas in continental mountain ranges,which are geographically isolated.We adopted this concept for the mountains in southwest China,which are among the most important biodiversity hot spots on earth.We reviewed the phylogeographic studies of this area and highlighted the sky-island features.We concluded that the genetic structures of species in these islands were shaped by complex topography,climate and habitats.The global climate change,such as Pleistocene climate fluctuations and periodic uplift of the Qinghai–Tibetan Plateau,also have important effects on biodiversity and geographic patterns,when species have responded idiosyncratically by changing their distributions or through adaptation.Future research needs in sky islands include multilocus data and comparative phylogeographic studies,integrating with the methodological advances in the other fields.Using these approaches,we can examine to what degree the geographic,climate and/or biological factors,shape strong geographic patterns,promote diversification/speciation and preserve species/genetic diversity.We hope this paper will inspire future work to uncover the mechanism that has generated the endemic biodiversity and to further resolve the most essential problem:How to protect the biodiversity with limited funding during the coming drastic global climate change.     

Unified spatial scaling of species and their trophic interactions

Two largely independent bodies of scaling theory address the quantitative relationships between habitat area, species diversity and trophic interactions. Spatial theory within macroecology addresses how species richness scales with area in landscapes, while typically ignoring interspecific interactions. Complexity theory within community ecology addresses how trophic links scale with species richness in food webs, while typically ignoring spatial considerations. Recent studies suggest unifying these theories by demonstrating how spatial patterns influence food-web structure and vice versa. Here, we follow this suggestion by developing and empirically testing a more unified scaling theory. On the basis of power-law species-area relationships, we develop link-area and non-power-law link-species models that accurately predict how trophic links scale with area and species richness of microcosms, lakes and streams from community to metacommunity levels. In contrast to previous models that assume that species richness alone determines the number of trophic links, these models include the species' spatial distribution, and hence extend the domain of complexity theory to metacommunity scales. This generality and predictive success shows how complexity theory and spatial theory can be unified into a much more general theory addressing new domains of ecology.     

Cultures in chimpanzees.

As an increasing number of field studies of chimpanzees (Pan troglodytes) have achieved long-term status across Africa, differences in the behavioural repertoires described have become apparent that suggest there is significant cultural variation. Here we present a systematic synthesis of this information from the seven most long-term studies, which together have accumulated 151 years of chimpanzee observation. This comprehensive analysis reveals patterns of variation that are far more extensive than have previously been documented for any animal species except humans. We find that 39 different behaviour patterns, including tool usage, grooming and courtship behaviours, are customary or habitual in some communities but are absent in others where ecological explanations have been discounted. Among mammalian and avian species, cultural variation has previously been identified only for single behaviour patterns, such as the local dialects of song-birds. The extensive, multiple variations now documented for chimpanzees are thus without parallel. Moreover, the combined repertoire of these behaviour patterns in each chimpanzee community is itself highly distinctive, a phenomenon characteristic of human cultures but previously unrecognised in non-human species.