Natural selection on EPAS1 (HIF2 alpha) associated with low hemoglobin concentration in Tibetan highlanders

By impairing both function and survival, the severe reduction in oxygen availability associated with high-altitude environments is likely to act as an agent of natural selection. We used genomic and candidate gene approaches to search for evidence of such genetic selection. First, a genome-wide allelic differentiation scan (GWADS) comparing indigenous highlanders of the Tibetan Plateau (3,200 3,500 m) with closely related lowland Han revealed a genome-wide significant divergence across eight SNPs located near EPAS1. This gene encodes the transcription factor HIF2 alpha, which stimulates production of red blood cells and thus increases the concentration of hemoglobin in blood. Second, in a separate cohort of Tibetans residing at 4,200 m, we identified 31 EPAS1 SNPs in high linkage disequilibrium that correlated significantly with hemoglobin concentration. The sex-adjusted hemoglobin concentration was, on average, 0.8 g/dL lower in the major allele homozygotes compared with the heterozygotes. These findings were replicated in a third cohort of Tibetans residing at 4,300 m. The alleles associating with lower hemoglobin concentrations were correlated with the signal from the GWADS study and were observed at greatly elevated frequencies in the Tibetan cohorts compared with the Han. High hemoglobin concentrations are a cardinal feature of chronic mountain sickness offering one plausible mechanism for selection. Alternatively, as EPAS1 is pleiotropic in its effects, selection may have operated on some other aspect of the phenotype. Whichever of these explanations is correct, the evidence for genetic selection at the EPAS1 locus from the GWADS study is supported by the replicated studies associating function with the allelic variants.

稻属C染色体组物种的群体遗传学和物种形成研究

植物近缘物种系统发育和物种形成过程一直以来都是植物进化生物学研究中最基本的问题之一，是人们理解自然界物种多样性产生和变化的前提。近缘物种间通常形态相似，遗传和分子水平的分化很小且常受诸如渐渗杂交、谱系分选、种内重组等微观进化事件的影响，导致植物近缘物种间系统发育和物种形成过程研究极为困难。在过去十多年中，生物技术的革新和理论方法的发展极大地推动了进化生物学研究，促进了人们对一些重要模式生物与其近缘种间的系统发育关系和物种分化过程的认识，如人、果蝇、线虫、拟南芥和玉米等。然而，迄今在植物中，许多重要类群及其近缘种的系统发育和物种形成过程研究仍不多见，包括在具有特殊重要性的栽培作物中，如稻属（Oryza L.）。由于属内包含有重要粮食作物水稻，稻属向来都是禾本科内备受关注的一个类群。本研究中，我们通过多基因序列的方法，探讨了稻属C染色体组三个近缘二倍体物种的系统发育和物种形成过程，主要研究结果如下。 为选择适宜的实验策略和保证序列数据的真实性，我们利用不同聚合酶扩增自交的栽培稻Oryza sativa ssp. japonica和异交的O. longistaminata不同类型的基因片段，采用克隆测序的方法，评估聚合酶链式扩增反应（PCR）中产生的非真实变异的状况。我们使用exTaq、exTaq和Pfu混和酶和PfuUltraTM酶三种不同聚合酶扩增了Adh1、GPA1和Waxy三个基因片段。在检测到的非真实变异中，PCR 错误的类型主要为单碱基变异和不同等位基因间重组，其中以单碱基变异为主，且突变类型以转换占绝大多数。比较不同酶扩增错误的结果表明，高保真PfuUltraTM酶对PCR反应错误有显著的改善，在扩增产物的单克隆中几乎检测不到PCR噪音，错误率仅为0.0001%，而exTaq和混和酶的错误率分别为0.096%和0.073%。从不同物种比较结果来看，exTaq酶和Pfu酶混用时在自交的O. sativa ssp. japonica内对PCR错误也表现明显的改善，但在异交的O. longistaminata中改善效应不太明显。在三个不同基因位点上，PCR扩增错误出现频率随扩增区域增长而变大。在PfuUltraTM酶的扩增产物中发现重组最少，exTaq和混和酶重组较多，且混和酶对重组改善效果不明显。基于不同聚合酶扩增错误对比研究结果，我们认为，由于能保证序列变异的真实性且不遗漏等位基因，核基因的克隆测序较宜于分离杂合个体中不同的等位基因。 基于随机挑取4个叶绿体和10个核基因位点，利用12份Oryza officinalis、8份O. eichingeri和4份O. rhizomatis材料，对稻属C染色体组三个近缘二倍体物种的系统发育关系作了深入分析。利用不同的系统发育分析方法对单基因位点序列和合并序列数据作了分析，结果表明，稻属C染色体组三个近缘种间呈多歧分支。因此，三个二倍体C染色体组物种可能经快速辐射分化形成。在不同核基因和叶绿体基因的系统发育树中各分支枝长均很短，也表明C染色体组的三个物种可能在较短时期内分化出。不同基因间拓扑结构不一致主要受谱系随机分选的影响。此外，C染色体组不同物种间的种间渐渗和不同等位基因重组对系统发育树的冲突也有影响。值得注意的是，C染色体组三个物种的辐射分化不排除由于相邻两次物种形成事件间隔时间太近、目前数据量不够而无法分辨的可能。在本研究中，我们发现，对于系统发育重建困难的类群，利用等位基因构建物种谱系树有助于挖掘不同基因间结果不一致的因素。 基于10个随机选取的核基因序列数据，利用物种水平的取样方式和群体遗传学分析方法，我们研究了稻属C染色体组三个近缘物种O. officinalis、O. eichingeri和O. rhizomatis的核苷酸多态性，并根据多态性水平和式样，推测了三个近缘种分化的历史。结果表明，在C染色体组的三个近缘种中，仅分布于斯里兰卡的O. rhizomatis的核苷酸多态性水平相对最低（θsil = 0.0038），而间断分布于非洲和斯里兰卡的O. eichingeri最高（θsil = 0.0057）。与被子植物其他类群相比，稻属C染色体组三个物种的核苷酸多态性水平显得较低，O. eichingeri的核苷酸多态性仅约为玉米及其近缘野生种的23-46%和拟南芥的35%。C染色体组内三个野生种相对较低的核苷酸多态性水平可能起因于其较小的祖先有效群体。物种形成模型分析表明，O. officinalis和其近缘种从最近共同祖先分化开后可能经历了居群缩减的历史，且自最近共同祖先分开后，三个物种彼此间并无显著的基因交流。基于分子钟粗略估算了C染色体三个物种分化时间，结果表明，三个物种彼此在很短的时期内分开，约0.63-0.68 Myr。同时，O. eichingeri在非洲和斯里兰卡两个地理宗的分异时间约为0.37 Myr，且推测斯里兰卡的O. eichingeri主要由西非经长距离扩散传播到斯里兰卡。

高山松（Pinus densata）同倍性杂交物种形成的生态遗传学研究

种间杂交在自然界中普遍存在。杂交可以为群体带来多方面的遗传改变，具有重要的进化生物学意义。越来越多的证据表明，同倍性杂交物种形成是一种重要物种形成途径，在动、植物物种进化中扮演着重要的角色。同倍性杂交物种形成意味着一个稳定的、可育的、与亲本种间形成生殖隔离的杂种群体建立起来，但不改变染色体的数目。这种生殖隔离被认为是通过快速的染色体重组、生态分化、或空间分离形成的。对于现存杂交种的对比分析和对同倍性杂交物种形成的理论模拟都表明，适应性分化和生态转变在同倍性杂交物种形成中起着至关重要的作用。来自于生态成种的研究也表明生态选择自身就可以导致生殖隔离的形成和新物种的形成。尽管如此，我们对同倍性杂交物种形成过程的研究仍然较多地关注于染色体重组及相应的遗传效应；对于自然选择，特别是生态选择在同倍性杂交成种过程中的作用模式缺乏全面地了解。 本研究以同倍性杂交种－高山松为研究对象，利用地理信息学技术、基于天然群体取样的性状对比分析和人工杂交手段，全面地定量描述了高山松及其亲本种间的生态分化、生态转变下的天然群体生殖适应性、以及生态选择下的形态变异和种间杂交可配性。以此探讨了高山松的杂交成种过程，生态转变和自然选择的重要性以及它们与杂交种适应性、形态变异和生殖隔离之间的关系。利用地理信息学手段，对高山松及其亲本种间的生态分化对比分析表明：高山松与其亲本种间形成了明显的生态转变；在自然选择的作用下，高山松已经具备了对于青藏高原东南缘横断山区高山地带独特的生态适应性；相对于亲本种，它的适应性特征体现为混合型，在某些性状上它高出亲本种的适应性，在另一些性状上，它体现出居中、较低或者类似于亲本种适应性；高山松适生区由于地形地貌的复杂性，往往不连续，呈间断状。基于四个反映结实效率的性状、小孢子母细胞减数分裂异常现象及花粉萌发率在种间的对比分析表明，这些反映生殖状态的指标，在三个种及群体间并没有显著差异；相对于亲本种的天然群体，居于青藏高原的高山松群体，表现出了正常的授粉效率和生殖适应性。高山松天然群体正常的生殖效率表明，它经历了生态转变过程中的选择作用，已经具备了在新生境下，繁殖发展下去的生殖适应性。 在大规模群体取样的基础上，通过对反映植物个体发育和营养状态的球果和针叶形态性状的对比分析，我们发现，高山松及其亲本种间的形态变异存在以下特征：第一，绝大多数性状，在种间和种内群体间都存在着显著的差异，并且大部分性状的差异主要体现在种间；第二，高山松在大部分形态性状上介于两个亲本种之间，少数性状表现为超亲分离、类似于某个亲本或无种间差别；第三，在多数性状上，和亲本种相比，高山松群体都拥有较大的变异幅度。第四，在临近亲本种的群体中，高山松的形态特征更类似于所临近的亲本种。上述形态变异特征及其与气象、土壤、经纬度、海拔等因子间普遍的相关性，意味着生态选择在高山松成种过程中起了重要作用。总的来说，形态性状变异的总体模式揭示出：高山松在选择作用下的遗传和表型的精炼过程中已经形成了自身适应于高原环境的、稳定而有效的形态发育模式和资源利用方式，甚至是恰当的防御机制。 本研究通过云南松×油松的单交实验和油松×高山松部分双列杂交实验，检验了高山松及其亲本种间的杂交可配性。结果表明，就平均水平而言，高山松及其亲本种间的种间杂交结实可配性低于种内杂交，但个别种间杂交组合的结实可配性可能高于种间杂交；高山松及其亲本种间正在或已经形成了部分的合子后生殖障碍；现存的高山松群体及其亲本种间的生态地理隔离可能是很有效的生殖隔离形式，一方面做为合子前生殖隔离，它能避免种间相互传粉、阻碍种间杂交的发生，另一方面做为合子后生殖隔离，它能清除掉可能存在的劣势回交产物。 综合已有的证据，我们提出了高山松同倍性杂交物种形成模型：高山松的同倍性杂交成种是与青藏高原隆升过程以及隆升过程中所产生的全新生态空间紧密相关的；青藏高原隆升导致了生态环境的剧变，创造了全新的生态位，在选择的作用下，拥有综合了双亲遗传基础的杂种基因型开始占领这个全新的生态位；在分化的生态选择的持续作用下，杂种基因型在新的生境下稳定下来，形成了独立于亲本种的资源利用方式、形态特征和繁育系统，具备了完善的生殖和生态适应性；此时，一个与亲本种间以生态隔离存在的同倍性杂交种－高山松形成了；随着分化的生态选择的持续进行,高山松与亲本种间的内在生殖隔离不断加强。

New symbiotic hypothesis on the origin of eukaryotic flagella

The origin of eukaryotic flagella has long been a mystery. Here we review the possibility that flagella sprouted evolutionarily from the eukaryotic cell proper seems very unlikely because it is hard to imagine what function and benefit in natural selection the flagella would have provided to the cells when they first emerged as simple buds. Lynn Margulis' 1970 spirochete hypothesis, though popular still, has never been confirmed. Moreover, the absence of tubulin and axonemal dynein in the spirochetes and the incapability of the bacterial and eukaryotic membranes' making a continuum now suggest that the hypothesis is outdated. Tubulin genes were recently identified in a new bacteria division, verrucomicrobia, and microtubules have also been found in one of these species, epixenosomes, the defensive ectosymbionts. On the basis of these data, we propose a new symbiotic hypothesis: that the mid-ancestor of eukaryotic cells obtained epixenosomelike verrucomicrobia as defensive ectosymbionts and the ectosymbionts later became endosymbiotic. They still, however, protruded from the surface of their host to play their role. Later, many genes were lost or incorporated into the host genome. Finally, the genome, the bacterial membrane, and the endosymbiotic vesicle membrane were totally lost, and fingerlike protrusions with microtubules formed. As the cells grew larger, the defensive function of the protrusions eventually weakened and then vanished. Some of the protrusions took on a new role in cell movement, which led them to evolve into flagella. The key step in this process was that the dynein obtained from the host evolved into axonemal dyneins, attaching onto the microtubules and forming motile axonemes. Our hypothesis is unproven, but it offers a possible explanation that is consistent with current scientific thought. We hope that our ideas will stimulate additional studies on the origin of eukaryotic flagella and on investigations of verrucomicrobia. Whether such studies confirm, refine, or replace our hypothesis, they should nevertheless further our understanding of the origin of eukaryotic cells.

Molecular phylogeny of Sinocyclocheilus (Cypriniformes : Cyprinidae) inferred from mitochondrial DNA sequences

More than 10 species within the freshwater fish genus Sinoncyclocbeilus adapt to caves and show different degrees of degeneration of eyes and pigmentation. Therefore, this genus can be useful for studying evolutionary developmental mechanisms, role of natural selection and adaptation in cave animals. To better understand these processes, it is indispensable to have background knowledge about phylogenetic relationships of surface and cave species within this genus. To investigate phylogenetic relationships among species within this genus, we determined nucleotide sequences of complete mitochondrial cytochrome b gene (1140 bp) and partial ND4 gene (1032 bp) of 31 recognized ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony. Bayesian, and maximum likelihood analyses. Our phylogenetic results showed that all species except for two surface species S. jii and S. macrolepis clustered as five major monophyletic clades (I, II, III, IV, and V) with strong supports. S. jii was the most basal species in all analyses, but the position of S. macrolepis was not resolved. The cave species were polyphyletic and occurred in these five major clades. Our results indicate that adaptation to cave environments has occurred multiple times during the evolutionary history of Sinocyclocheilus. The branching orders among the clades I, II, III, and IV were not resolved, and this might be due to early rapid radiation in Sinocyclocheilus. All species distributed in Yunnan except for S. rhinocerous and S. hyalinus formed a strongly supported monophyletic group (clade V), probably reflecting their common origins. This result suggested that the diversification of Sinocyclocheilus in Yunnan may correlate with the uplifting of Yunnan Plateau. © 2005 Published by Elsevier Inc.

Adaptive evolution of energy metabolism genes and the origin of flight in bats

Bat flight poses intriguing questions about how flight independently developed in mammals. Flight is among the most energy-consuming activities. Thus, we deduced that changes in energy metabolism must be a primary factor in the origin of flight in bats. The respiratory chain of the mitochondrial produces 95% of the adenosine triphosphate (ATP) needed for locomotion. Because the respiratory chain has a dual genetic foundation, with genes encoded by both the mitochondrial and nuclear genomes, we examined both genomes to gain insights into the evolution of flight within mammals. Evidence for positive selection was detected in 23.08% of the mitochondrial-encoded and 4.90% of nuclear-encoded oxidative phosphorylation (OXPHOS) genes, but in only 2.25% of the nuclear-encoded nonrespiratory genes that function in mitochondria or 1.005% of other nuclear genes in bats. To address the caveat that the two available bat genomes are of only draft quality, we resequenced 77 OXPHOS genes from four species of bats. The analysis of the resequenced gene data are in agreement with our conclusion that a significantly higher proportion of genes involved in energy metabolism, compared with background genes, show evidence of adaptive evolution specific on the common ancestral bat lineage. Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting our hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.

一种在核苷酸水平检测自然选择的新方法

非编码区序列在基因表达调控中起着重要作用, 但其在进化过程中是否受到选择作用一直较难检 测。最近有一些研究使用平均的核苷酸替换速率与中性序列的核苷酸替换速率的比值(ω) 作为检测非编码区 总体受选择作用的指标; 但是对于非编码区而言, 了解具体哪些核苷酸受到选择作用更具有意义。我们借鉴 Nielsen & Yang (1998) 检测单个氨基酸位点是否受选择作用的思路, 在最大似然法的模型下, 提出一种在核苷 酸位点水平上对自然选择作用检测的方法。本方法能够检测在进化过程中对功能分化有重要贡献的核苷酸位 点, 包括编码和非编码区。将此方法应用于熟知的受到正选择作用的蛋白编码基因序列( HIV21 包装蛋白基因 编码区) , 均能够检测到那些已知的受到正选择的核苷酸(密码子) 位点, 说明此方法可以有效地在核苷酸位 点水平检测选择作用; 又将此方法应用于非编码区( CTGF 基因5′UTR) , 也得到了良好的结果。

DNA 水平自然选择作用的检测

上个世纪60 年代, Kimura 提出的“中性进化”假说使经典的达尔文自然选择学说遭遇了前所未有 的挑战。但新近的研究表明: 在DNA 水平, 越来越多的证据支持“自然选择”的进化理论。这些研究成果得益 于近年来大量群体和基因组DNA 数据的积累, 以及理论群体遗传学的发展。在DNA 水平检测选择作用是否存 在的方法包括两大类: 种内多态性检验和种间差异度检验。前者以Tajima (1989) 提出的D 检验为代表, 后者 大都基于“中性条件下, 种内与种间进化速率一致”的原理。这些方法以中性假说作为零假设, 结合统计检验 方法分析DNA 数据, 被称为“中性检验”。这些方法对于解决一些有关进化的基础理论问题和人类遗传学及生 物信息学的深入研究都具有重要意义。本文介绍几个应用广泛的检测方法, 以使国内的读者了解它们的基本思 路和操作方法。

Margulis' theory on division of labour in cells revisited

Division of labour is a marked feature of multicellular organisms. Margulis proposed that the ancestors of metazoans had only one microtubule organizing center (MTOC), so they could not move and divide simultaneously. Selection for simultaneous movement and cell division had driven the division of labour between cells. However, no evidence or explanation for this assumption was provided. Why could the unicellular ancetors not have multiple MTOCs? The gain and loss of three possible strategies are discussed. It was found that the advantage of one or two MTOC per cell is environment-dependent. Unicellular organisms with only one MTOC per cell are favored only in resource-limited environments without strong predatory pressure. If division of labour occurring in a bicellular organism just makes simultaneous movement and cell division possible, the possibility of its fixation by natural selection is very low because a somatic cell performing the function of an MTOC is obviously wasting resources. Evolutionary biologists should search for other selective forces for division of labour in cells.

粗枝云杉( Picea asperata Mast.)天然群体的遗传变异

西南地区在我国的经济发展和生态环境建设中占重要地位，但也是我国生态环境最脆弱的地区之一，生态系统退化，生态功能减弱，严重制约着西南林业的可持续经营与发展。本项目采用DNA 分子标记SSR 研究不同生境条件下粗枝云杉群体的遗传变异及其时空分布格局，考察遗传变异与复杂的山地生态环境间的潜在联系，系统地揭示粗枝云杉天然群体与环境系统相互作用的生态适应与分子进化机制。粗枝云杉适应性强，生长迅速，在植树造林和工业用材方面占有重要地位，研究成果可为中国西南部亚高山天然林的可持续经营及退化生态系统的恢复与重建提供理论依据和科学指导。主要研究结果如下： 1. SSR 位点变异丰富，等位基因频率的分布格局多样。7 个SSR 标记全是多态位点，每位点的等位基因数变化范围为13~24，平均为19.9 个。SSR 位点的等位基因片段长度范围变化较大。73.1%的等位基因变异遵循逐步突变模型(SSM)而发生1 个重复基元的变化，22.3%和4.6%的变异分别按两阶段突变模型(TMP)发生1 个重复基元以上的变化和在SSR 位点侧翼区发生1 个碱基变化的插入-删除事件。 2. 粗枝云杉拥有中等偏高水平的遗传多样性和相对大的群体间遗传分化。通过分析代表10 个群体的250 个个体在7 个SSR位点的变化，调查了源自中国西南山区的粗枝云杉的微卫星变异。相当高的遗传多样性和强烈的群体分化发生在粗枝云杉中， 其群体平均Nei's 期望杂合度为0.707 ， 群体间遗传距离为0.121~0.224(FST)和0.100~0.537(RST)。然而，群体间遗传距离与地理距离之间无相关性，从而排除了简单的距离分离模式并暗示迁移不是影响粗枝云杉遗传变异格局的主要因素。事实上，使用私有等位基因估算的基因流数量非常低，仅等于0.753。等位基因置换检验(Allele permutation tests)揭示逐步突变及遗传漂变都对群体间分化有贡献。另外，在多数位点检测到显著的群体间遗传差异，这个结果说明自然选择，假设通过环境压力，是引起粗枝云杉微地理分化的主要因素之一。根据SSR基因型，250 个粗枝云杉个体的70%被正确地归类入其各自的来源群体，结果表明微卫星(SSR)对区分来自中国不同生态地理位点的粗枝云杉基因型是有效的。 3. 在SSR、RAPD 和AFLP 位点，显著的群体间遗传结构被发现的，但三种标记间遗传分化程度和群体遗传关系有差异。利用来自10 个群体的247 个个体，我们报告了关于样本粗枝云杉群体间遗传关系的总体看法。根据各自对评价遗传关系的信息能力和适用性，SSR、RAPD 和AFLP 标记被选用，三种技术非常有效地区别这些基因型。使用的SSR、RAPD 和AFLP 标记分别估计平均Dice 相似性系数。Mantel 检验产生显著但相对低的共表型适合度(RAPD = 0.63£AFLP = 0.60和SSR = 0.75)。比较三种标记系统，RAPD 和AFLP 共表型指数相对高地相关(r =0.59)，而RAPD 和SSR 及SSR 和AFLP 之间的相关系数分别是0.53 和0.35。所有系统树，包括不同标记资料结合获得的系统树，反映了多数群体依据它们的地理条件而成某种特定关系。结果暗示单个或结合标记系统能用来深入洞察粗枝云杉遗传研究，并且不同标记系统合并资料能提供更可靠的信息。 Southwestern region plays an important role in economic developmentand ecological construction in China. Yet, it is also one of the weak regionsof ecological environment in China with degraded ecosystem and imperfectfunction, which restricts the sustaining management and development ofsouthwestern forestry. The genetic variation and spatial distribution patternof P. asperata populations originating from different habitats wereinvestigated using SSR molecular markers in this study. The correlationsbetween genetic variation and ecological and environmental conditionswere detected, and the interaction between P. asperata populations andenvironmental system and the mechanism of ecological adaption -molecular evolution were revealed. Given the significant ecological andeconomic roles of the fast-growing and wide-adaptive species in reforestation and production of pulp wood and timber, the study couldprovide a strong theoretical evidence and scientific direction for thesustaining management of subalpine natural forest, and the afforestationand rehabilitation of degraded ecosystem. The results are as follows: 1. The genetic variation at SSR loci was abundant and the distributionof allelic frequencies was uneven. All seven loci were polymorphic, and thenumber of alleles per locus varied from 13 to 24 with a mean valueequaling 19.9. The allele sizes at SSR loci were found to vary widely.73.1% of allelic variation followed stepwise mutation model (SSM) whichresults increase or decrease by one repeat type, and 22.3% and 4.6% wereresulted from two-phase mutation model (TMP) with allele size varying bymore than one repeat type and from insertion-deletion events in theflanking regions at SSR loci with a single basepair changing, respectively. 2. P. asperata possessed a moderate to high level of genetic diversityand considerable genetic differentiation. Microsatellite variation of P.asperata. originating from the mountains of southwestern China wasinvestigated by analyzing variation at seven SSR loci in 250 individualsrepresenting ten populations. A fair degree of genetic diversity and strongpopulation subdivision occurred with the mean gene diversity (H) of 0.707,and genetic distances among populations varying between 0.121 and 0.224(FST) and between 0.100 and 0.537 (RST). However, inter-populationgenetic distances showed no correlation with geographic distances between the population sites. This ruled out a simple isolation by distance modeland suggested that migration does not have a great impact. In fact, theamount of gene flow, detected using private alleles, was very low, equalingonly 0.753. Allele permutation tests revealed that stepwise-like mutations,coupled with genetic drift, could contribute to population differentiation.Moreover, significant genetic differences between populations weredetected at most loci. The results indicate that natural selection, presumablythrough environmental stress, may be one of the main factors causingmicro-geographical differentiation in the genetic structure of P. asperata.Based on SSR genotypes, 70% of the 250 individuals were correctlyclassified into their sites of origin. This suggests that microsatellites (SSRs) are effective in distinguishing genotypes of P. asperata originating fromdiverse eco-geographical sites in China. 3. Using a set of 247 individuals from ten P. asperata populations wereport an overview on the genetic relationship among the sampled P.asperata populations. RAPD, AFLP and SSR were used in terms of theirinformativeness and applicability for evaluate relationship and all threetechniques discriminated the genotypes very effectively. Mean Dicesimilarities coefficient were estimated using RAPD, AFLP and SSR,respectively. The Mantel test resulted in a significant but relatively low fit(RAPD = 0.63, AFLP = 0.60 and SSR = 0.75) of cophenetic values.Comparing the three marker systems to each other, RAPD and AFLP cophenetic indices were highly correlated (r = 0.59), while correlationcoefficient between RAPD and SSR was r = 0.53 and between SSR andAFLP was r = 0.35. For all markers a relatively high similarity indendrogram topologies was obtained although some differences wereobserved. All the dendrograms, including that obtained by the combineduse of all the marker data, reflect some relationships for most of thepopulations according to their geographic conditions. The results indicatethat single or combined marker system could be used to insight into geneticstudy in P. asperata and the combined data of different marker systems canprovide more reliable information.

瑞香狼毒（Stellera chamaejasme L.）对高寒草甸系统生长和非生长季节碳氮循环的影响及其花粉化感效应

瑞香狼毒（Stellera chamaejasme L.）是瑞香科（Thymelaeaceae）狼毒属的一种多年生野草，有毒。据调查，从20 世纪60 年代开始至今，狼毒在青藏高原东缘的高寒草甸上不断蔓延、密度不断变大，在一些地段甚至成为优势物种。有关狼毒在高寒草甸蔓延的生态系统效应的研究尚未见报道。本文从系统碳、氮循环的角度，分别研究狼毒在生长和非生长季节对高寒草甸生态系统的影响。同时，从花粉化感的角度，深入研究狼毒对当地同花期物种有性繁殖的影响。系统地研究高寒草甸生态系统物质循环过程，特别是非生长季节微生物和土壤碳氮库的动态变化，有助于揭示狼毒在系统物质循环方面的“物种效应”以及这种效应的季节变化，为丰富有关高海拔生态系统，特别是其非生长季的物质循环的科学理论做出贡献。同时，碳氮循环和花粉化感的研究还有助于深刻地理解狼毒作为一种入侵性很强的杂草的特殊的蔓延机制，从而为狼毒的有效防治、高寒草甸的科学管理提供依据。 针对狼毒在青藏高原高寒草甸上蔓延的生态系统碳氮循环方面的影响，开展以下2 方面的研究：（1）在生长季，研究松潘县尕米寺附近（北纬32°53'，东经103°40'，海拔3190 m）的两种地形（平地和阳坡）条件下狼毒对土壤碳氮循环影响及可能的原因。狼毒和其它几个主要物种（圆穗蓼（Polygonummacrophyllum D. Don var. Macrophyllum），草地早熟禾（Poa pretensis L.），四川嵩草（Kobresia setchwanensis Hand.-Maizz.），鹅绒委陵菜（Potentilla anserina L.var. anserine）和鳞叶龙胆（Gentiana squarrosa Ledeb.）的地上凋落物产量以及地上凋落物和根的化学组成被测量。在有-无狼毒斑块下，各种土壤的库（比如，铵态氮、硝态氮、无机磷和微生物生物量）和周转率（包括净矿化、净硝化、总硝化、反硝化和微生物呼吸速率）被测量和比较。（2）在非生长季节，尤其是春季冻融交替期，选取了两个研究地点——尕米寺和卡卡沟（北纬32°59'，东经103°41'，海拔3400 m），分别测定有狼毒和无狼毒斑块下土壤微生物生物量碳和氮、可溶性有机碳和氮以及铵态氮和硝态氮的动态变化。同时，分别在上述两个地点有-无狼毒的样地上，研究6 个主要物种（狼毒、圆穗蓼、草地早熟禾、四川嵩草、鹅绒委陵菜和鳞叶龙胆）从秋季开始、为期1 年的凋落物分解过程。 针对狼毒花粉化感对同花期其它物种可能的花粉化感作用开展以下工作：在实验室中，用一系列浓度的狼毒花粉水浸提液对与它同花期的其它物种以及自身花粉进行测试，测定花粉萌发率；在野外自然条件下的其它物种的柱头上施用上述浓度的狼毒花粉水浸提液，观测种子结实率，同时，观察狼毒花粉的种间花粉散布数量。 生长季节的研究结果表明，狼毒地上凋落物氮含量比其它几个主要物种更高，而木质素-总氮比更低。狼毒显著地增加其斑块下表层土壤中有机质的含量，而有-无狼毒的亚表层土壤在有机碳和总磷方面没有显著差异。狼毒表土中硝态氮含量在平地和阳坡比无狼毒土壤分别高113%和90%。狼毒表土中微生物生物量碳和氮量显著高于无狼毒表土。无论是平地还是阳坡，狼毒土壤的总硝化和微生物呼吸速率显著高于无狼毒土壤；而它们的反硝化速率只在平地有显著的差异。狼毒与其它物种间地上凋落物的产量和质量的差异可能是导致有-无狼毒土壤碳氮循环差异的原因。我们假设，狼毒可能通过增加贫氮生态系统土壤中的有效氮含量提高其入侵能力。 非生长季的研究结果表明，在青藏高原东缘的高寒草甸上，土壤微生物生3物量在11 月的秋-冬过渡期达到第一个峰值；在春季的冻融交替期，微生物生物量达到第二个峰值后又迅速降低。无机氮以及可溶性有机碳氮与微生物生物量有相似的变化过程。微生物碳氮比呈现显著的季节性变化。隆冬季节的微生物生物量碳氮比显著高于生长旺季的微生物碳氮比。这种变化可能暗示冬、夏季微生物的群落组成和对资源的利用有所不同。有-无狼毒斑块下土壤微生物和土壤碳、氮库一般只在秋-冬过渡期有显著差异，有狼毒土壤微生物生物量和土壤碳、氮库显著高于无狼毒土壤；而在之后的冬季和春季没有显著差异。所有6 个物种凋落物在非生长季分解率为24%-50%，均高于生长季的10%到30%。其中在秋-冬过渡期，凋落物开始埋藏的两周时间内，分解最快，达10%-20%。不同物种凋落物全年的分解率和分解过程有显著差异。圆穗蓼在全年的分解都较缓慢（非生长季26%，生长季15%），草地早熟禾和四川嵩草等全年的分解速率比较均匀（非生长季和生长季均为30%，非生长季略高），而狼毒在非生长季分解较快（约50%），而在接下来的生长季分解变得缓慢（约12%）。所有物种的凋落物氮含量在非生长季下降，而在随后的生长季上升。 实验室的花粉萌发试验证明，狼毒花粉对自身花粉萌发没有自毒作用，而其它受试的所有物种（圆穗蓼，秦艽（Gentiana macrophylla Pall. var. fetissowii），湿生扁蕾（Gentianopsis paludosa (Hook. f.) Ma var. paludosa），鳞叶龙胆，椭圆叶花锚（Halenia elliptica D. Don var. elliptica），蓝钟花（Cyananthus hookeri C. B.Cl. var. grandiflorus Marq.），小米草（Euphrasia pectinata Ten.），川西翠雀花（Delphinium tongolense Franch.），高原毛茛（Ranunculus tanguticus (Maxim.)Ovcz. var. tanguticus）和鹅绒委陵菜）的花粉萌发率随着狼毒花粉浸提液浓度的增加呈显著的非线性降低。大约3 个狼毒花粉的浸提液就可以抑制受试的多数物种的50%的花粉萌发。在鳞叶龙胆和小米草柱头上狼毒花粉的数量分别为5.76 个和3.35 个。狼毒花粉散布数量的差异最可能的原因在于是否有共同的传粉昆虫。花的形状（辐射对称VS 左右对称）、植株或花的密度以及花期重叠性可以部分解释这种差异。在野外试验中，我们发现6 个物种（秦艽、湿生扁蕾、鳞叶龙胆、椭圆叶花锚、蓝钟花和小米草）的种子结实率随狼毒花粉浸提液浓度的增加呈显著的非线性降低。鳞叶龙胆和小米草柱头上狼毒花粉的数量（分别是5.76 个和3.35 个）分别达到了抑制它们63%和55%种子结实率的水平。因此，狼毒对鳞叶龙胆和小米草可能存在明显的花粉化感抑制作用。狼毒周围的物种可能通过花期在季节或昼夜上的分异避免受到狼毒花粉化感的影响或者通过无性繁殖来维持种群繁衍，因此狼毒通过花粉化感作用对其周围物种繁殖的影响程度还需要进一步地研究。如果狼毒的花粉化感抑制作用确实存在，那么它可能成为一种自然选择压力，进而影响物种的进化。 Stellera chamaejasme L., a perennial toxic weed, has emerged and quicklydominated and spread in the high-frigid meadow on the eastern Tibetan Plateau ofChina since the 1960s. In the present study, effects of S. chamaejasme on carbon andnitrogen cycles on the high-frigid meadow on the eastern Qinghai-Tibetan Plateau ingrowing and non-growing season, and its pollen allelopathic effects on the sympatricspecies were determined. The present study that focused on carbon and nitrogencycles, especially on microbial biomass and pools of carbon and nitrogen innon-growing season, could profoundly illuminate plant-species effects on carbon andnutrient cycles and its seasonal pattern and help to understand spread mechanism ofS. chamaejasme as an aggressive weed. The present study also contributed to furtherunderstand carbon and nutrient cycles on alpine regions in non-growing season andprovide a basis on weed control of S. chamaejasme and scientific management in thehigh-frigid ecosystem. Effects of S. chamaejasme on carbon and nitrogen cycles on the high-frigidmeadow on the eastern Qinghai-Tibetan Plateau were determined. The study couldbe divided into two parts. (1) In the growing season, we quantified the effects of S.chamaejasme on carbon and nitrogen cycles in two types of topographic habitats, theflat valley and the south-facing slope, where S. chamaejasme was favored to spreadlitter and root were measured to explain the likely effects of S. chamaejasme on soilcarbon and nutrient cycles. The sizes of various soil pools, e.g. nitrite, ammonium,inorganic phosphorus and microbial biomass, and turnover rates including netmineralization, gross nitrification, denitrification and microbial respiration weredetermined. (2) In the non-growing season study, microbial biomass carbon andnitrogen, soluble organic carbon and nitrogen, ammonium and nitrate weredetermined through the non-growing season, especially in the processes offreeze-thaw of spring in two high-frigid sites, i.e. Kaka valley and Gami temple, onthe eastern Qinghai-Tibetan Plateau. Meanwhile, litter decomposition of six commonspecies, including Stellera chamaejasme L., Polygonum macrophyllum D. Don var.Macrophyllum, Poa pretensis L., Kobresia setchwanensis L., Potentilla anserina L.var. anserine and Gentiana squarrosa Ledeb., were also examined under theabove-mentioned experimental design through one whole-year, which began in theautumn in 2006. In the study of pollen allelopathy, several work, including in vitro study oneffects of extract of pollen from S. chamaejasme on sympatric species and pollenfrom itself, field experiments on effects of pollen extract with the same regime ofconcentrations on seed set and field observation on heterospecific pollen transfer ofS. chamaejasme to six of those sympatric species has been done. The results in the growing season showed that aboveground litter of S.chamaejasme had higher tissue nitrogen and lower lignin: nitrogen ratio than thoseco-occurring species. S. chamaejasme significantly increased topsoil organic matter,whereas no significant differences were found for organic C and total P in subsoilbetween under-Stellera and away-Stellera locations. The nitrate in Stellera topsoilwas 113% and 90% higher on the flat valley and on the south-facing slope,respectively. Both microbial biomass C and N were significantly higher in Stelleratopsoil. Gross nitrification and microbial respiration were significantly higher inStellera topsoil both on the flat valley and on the south-facing slope, whereassignificant differences of denitrification were found only on the flat valley. Thedifferences in the quantity and quality of aboveground litter are a likely mechanismresponsible for the changes of soil variables. We assumed that S. chamaejasme couldenhance their spread by increasing nutrient availability in N-deficient ecosystems. The results in the non-growing season showed that microbial biomass achievedthe first summit in late autumn and early winter on the eastern Qinghai-TibetanPlateau. In the stages of freeze-thaw of spring, microbial biomass firstly achieved thesecond summit and subsequently sharply decreased. Inorganic nitrogen, solubleorganic carbon and nitrogen had a similar dynamics with that of microbial biomass.Ratio of microbial biomass carbon and nitrogen had an obviously seasonal pattern.The highest microbial C: N were in the non-growing season, which weresignificantly higher than those in the growing season. The seasonal pattern inmicrobial biomass C: N suggested that large changes in composition of microbialpopulation and in resources those used by microbes between summer and winter.Generally, microbial biomass and pools size of carbon and nitrogen in Stellera soilwere significantly higher than those under adjacent locations in late autumn andearly winter, but there were not significant differences in winter and in spring. Litterof all the focal species (Stellera chamaejasme L., Polygonum macrophyllum D. Donvar. Macrophyllum, Poa pretensis L., Kobresia setchwanensis Hand.-Maizz.,Potentilla anserina L. var. anserine and G. squarrosa Ledeb.) decomposed about24%-50% in the non-growing season, which were higher than those in the growingseason (ranged from 10% to 30%). Litter decomposed 10%-20% within the first twoweeks in late autumn and early winter. Significant differences in the whole-yeardecomposition rate and in the processes of decomposition were found among species.Polygonum macrophyllum decomposed slowly through the whole year (26% and15% in the non-growing season and in the growing season, respectively). Certainspecies, such as P. pretensis L. and K. setchwanensis, decomposed at a similar rate(30% both in the non-growing and in the growing season, slightly higher in the8growing season than those in the growing season), whereas S. chamaejasmedecomposed more rapidly (about 50%) in the non-growing season and subsequentlydecomposition became slow (about 12%) in the growing season. Litter nitrogencontents of all the focal species firstly decreased in the non-growing season and thenincreased in the growing season. In vitro experiments of pollen allelopathy, the results showed that pollen from S.chamaejasme was not autotoxic, whereas pollen germination in all the sympatricspecies (Polygonum macrophyllum D. Don var. Macrophyllum, Gentianamacrophylla Pall. var. fetissowii, Gentianopsis paludosa (Hook. f.) Ma var. paludosa,Gentiana squarrosa Ledeb., Halenia elliptica D. Don var. elliptica, Cyananthushookeri C. B. Cl. var. grandiflorus Marq., Euphrasia pectinata Ten., Delphiniumtongolense Franch., Ranunculus tanguticus (Maxim.) Ovcz. var. tanguticus andPotentilla anserina L. var. anserina) decreased nonlinearly as the increasingconcentrations of extract of pollen from S. chamaejasme. Pollen Extract of threepollens from S. chamaejasme generally inhibited 50% pollen germination of most ofthe focal species. 5.76 and 3.35 pollens from S. chamaejasme were observed in fieldon stigmas of G. squarrosa and E. pectinata, respectively. Differences inheterospecific pollen transfer of S. chamaejasme could be attributed to the primaryreason whether they shared common pollinators. Flower morphology (e.g.zygomorphic or actinomorphic), plant or floral density and concurrence in floweringphonologies could explain, in part, the differences in heterospecific pollen transfer.In field experiments, the results showed that seed set in six sympatric species(Gentiana macrophylla Pall. var. fetissowii, Gentianopsis paludosa (Hook. f.) Mavar. paludosa, Gentiana squarrosa Ledeb., Halenia elliptica D. Don var. elliptica,Cyananthus hookeri C. B. Cl. var. grandiflorus Marq. and Euphrasia pectinata Ten.)decreased nonlinearly as the increasing concentrations of extract of pollen from S.chamaejasme. According to the nonlinear curves, the amounts of pollens from S.chamaejasme on stigmas of G. squarrosa and of E. pectinata (i.e. 5.76 grains and3.35 grains, respectively) could reduce 63% and 55% seed set of G. squarrosa and ofE. pectinata, respectively. Thus, allelopathic effects of S. chamaejasme on G.squarrosa and E. pectinata could be realistic. The sympatric species of S.chamaejasme could avoid pollen allelopathy of S. chamaejasme to sustainthemselves. This highlights the need to study how much pollen allelopathy in S.chamaejasme influences the sympatric species through divergence in seasonal ordiurnal flowering phonologies or through asexual reproduction. If pollen allelopathyin S. chamaejasme was confirmed, it could be as a pressure of natural selection andthus play an important role in species evolution.

Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Funneled landscape leads to robustness of cellular networks: MAPK signal transduction

We uncover the underlying potential energy landscape for a cellular network. We find that the potential energy landscape of the mitogen-activated protein-kinase signal transduction network is funneled toward the global minimum. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. Funneled landscape is a realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.