Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus

As the only remainder type of phycobiliproteins in Prochlorococcus, the actual role of phycoerythrin still remains unknown. Previous studies revealed that two different forms of phycoerythrin gene were found in two ecotypes of Prochlorococcus that are specifically adapted to either high light (HL) or low light (LL) conditions. Here we analyze patterns of phycoerythrin nucleotide variation in the HL- and LL-Prochlorococcus populations. Our analyses reveal a significantly greater number of non-synonymous fixed substitutions in peB and peA than expected based on interspecific comparisons. This pattern of excess non-synonymous fixed substitutions is not seen in other five phycoerythrin-related genes (peZ/V/Y/T/S). Several neutrality statistical tests indicate an excess of rare frequency polymorphisms in the LL-Prochlorococcus data, but an excess of intermediate frequency polymorphisms in the HL-Prochlorococcus data. Distributions of the positively selected sites identified using the likelihood ratio test, when mapped onto the phycoerythrin tertiary structure, reveal that HL- and LL-phycoerythrin should be under different selective patterns. These findings may provide insights into the likely role of selection at the phycoerythrin locus and motivate further research to unveil the function of phycoerythrin in Prochlorococcus.

Population genetics of Crassostrea ariakensis in Asia inferred from microsatellite markers

Crassostrea ariakensis is an important aquacultured oyster species in Asia, its native region. During the past decade, consideration was given to introducing C. ariakensis into Chesapeake Bay, in the United States, to help revive the declining native oyster industry and bolster the local ecosystem. Little is known about the ecology and biology of this species in Asia due to confusion with nomenclature and difficulty in accurately identifying the species of wild populations in their natural environment. Even less research has been done on the population genetics of native populations of C. ariakensis in Asia. We examined the magnitude and pattern of genetic differentiation among 10 wild populations of C. ariakensis from its confirmed distribution range using eight polymorphic microsatellite markers. Results showed a small but significant global theta (ST) (0.018), indicating genetic heterogeneity among populations. Eight genetically distinct populations were further distinguished based on population pairwise theta (ST) comparisons, including one in Japan, four in China, and three populations along the coast of South Korea. A significant positive association was detected between genetic and geographic distances among populations, suggesting a genetic pattern of isolation by distance. This research represents a novel observation on wild genetic population structuring in a coastal bivalve species along the coast of the northwest Pacific.

Mitochondrial control region and population genetic patterns of Nycticebus bengalensis and N-Pygmaeus

Bengal slow lorises (Nycticebus bengalensis) and pygmy slow lorises (Nycticebus pygmaeus) are nocturnal which creates difficulties to study them in the field. There is a scarcity of data on them and their population genetics are poorly understood. We sequ

中国普通野生稻（Oryza rufipogon Griff.）群体遗传学及保护策略的研究

普通野生稻的基因资源对水稻的育种已经起过并将继续起至关重要的作用。所以，研究和保存其遗传多样性具有重要的意义。首先对普通野生稻在我国的分布现状作了较为全面的野外调查。采集了69个群体，近2000个个体的硅胶干燥叶片。研究了从硅胶干燥的小量叶片中高效率、高质量制备DNA的方法。并用此方法制备了44个代表群体，1168个个体的总DNA，建立了中国普通野生稻的总DNA库。随机选取19个引物对29个群体、651个个体的总DNA进行了RAPD扩增。统计出群体和地区内的多态性片段百分比（PPB），RAPDistance和WINAMOVA程序联用分析遗传变异在地区间、地区内群体间和群体内的组成。广西濠江流域5个野生群体的分析结果表明了中下游群体的PPB值显著高于中上游群体。从而从分子水平上证实了水流对无性繁殖体的传播影响了沿江分布群体的遗传多样性和遗传结构。6个现有原位保护群体的分析结果说明了5个群体值得进一步原位保护，而另一个群体适合异位保护。中国境内29个群体的统计分析揭示出群体间的遗传多样性差异很大（PPB值从23.29%到46.18%）。广东具有的PPB值最高（79.12%），其次是海南（77.11%）和广西（68.67%）。因而，华南是我国普通野生稻的遗传多样性中心。18个群体AMOVA分析结果均表明了遗传变异主要存在于群体内，但群体间业已有较大的遗传分化。从175个随机引物中筛选出9个引物，成功地鉴定出5个群体的克隆多样性和克隆结构。这二者与群体的生态环境，特别是水分状况密切相关。也同时受人类干扰强度的影响。而与群体所处的纬度没有明显的相关性。 根据以上结果，普通野生稻原位保护的策略是选取分布在不同地理区域、遗传多样性水平高的群体。分布在广东、海南和广西的6个群体，具有很高的遗传多样性，建议加以原位保护。此外，孤岛状隔离在我国普通野生稻分布区边缘的3个小群体也应立即进行原位保护。此外，原位保护的群体应给予适度的干扰以维系较高的克隆多样性和遗传多样性。在进行遗传多样性研究和异位保护时，每群体的取样个体数应不少于25株，相邻取样个体间的距离应大于12米。

稻属A基因组的分子系统发育--兼论亚洲栽培稻的起源

稻属Oryza隶属禾本科Poaceae，包括20多个野生种和2个栽培种(亚洲栽培稻O. sativa L和非洲栽培稻O. glaberrima Steud) ，广泛分布于全球热带和亚热带。稻属物种可划分为10个基因组(又称染色体组)类型：A, B, C, BC, CD, E, F, G, HJ 和 HK。栽培稻所属的A基因组是稻属中物种数目最多、地理分布最广的基因组类型，由8个种组成。由于栽培稻属于A基因组，故A基因组物种是栽培稻遗传改良的巨大基因源。数十年来，国际上许多学者对A基因组类群开展了大量涉及形态、细胞、同工酶和分子标记方面的研究，但由于A基因组物种间遗传关系十分接近，形态上差异小且地理分布重叠，使得A基因组物种的系统发育、物种起源和生物地理学等方面存在诸多悬而未决的问题，是稻属中分类和鉴定困难较多的类群。本文利用核基因内含子序列，结合转座子插入分析，重建了A基因组的系统发育，估测了各类群的分化时间;与此同时，基于多克隆测序和基因谱系分析，探讨了O. rufipogon和O. nivara遗传关系以及亚洲栽培稻起源。主要研究结果如下： 1. A基因组的系统发育 在水稻全基因组数据库搜索的基础上，测定了4个单拷贝核基因（Adh1 及3个未注释基因）的内含子序列，构建了稻属A基因组8个种的系统发育关系。基于最大简约法和贝叶斯法的系统发育分析表明：1）澳大利亚的O. meridionalis为A基因组的基部类群;2）亚洲栽培稻两个亚种O. sativa ssp. japonica 和 O. sativa ssp. indica分别和不同的野生类群聚为独立的两个分支，支持japonica 和 indica为多次起源;3）O. rufipogon和O. nivara在系统发育树上完全混在一起，显示出二者间不存在遗传分化;4）非洲一年生野生种O. barthii是非洲栽培稻O. glaberrima的祖先，而非洲多年生野生种O. longistaminata与O. glaberrima/O. barthii.亲缘关系较远;5）分子钟方法估测A基因组类群约在2百万年前（2.0MYA）开始分化，亚洲栽培稻和非洲栽培稻，以及亚洲栽培稻的两个亚种则分别在0.7和 0.4 MYA左右开始分化。此外，通过核基因内含子序列与其它常用片段如ITS，matK等对比分析表明，进化速率相对较快的核基因内含子序列可以有效地用于近缘类群的系统发育研究。 2. Oryza rufipogon 和O. nivara群体遗传研究及亚洲栽培稻起源 对于亚洲野生类群O. rufipogon和O. nivara是合并为一个种还是处理为两个独立的种一直存在争议。在系统发育研究基础上，我们选取4个核基因内含子或5’-UTR区（Waxy, LHS，CatA和1个未注释基因），对采自整个分布区的群体样品进行了多克隆测序，结果表明：1）检测到O. rufipogon和O. nivara均有较高的核苷酸多态性，4个位点上π值和θw值平均分别为0.011和0.014;2）且二者在遗传上没有明显分化，两个类群在4个核基因位点上均检测到大量共享多态（shared polymorphism），未发现固有差异(fixed difference)，表明它们历史上可能属于一个大群体，支持将二者作为种内不同生态型或亚种处理;3）基因谱系树表明亚洲栽培稻的两个亚种indica和japonica分别和不同的O. rufipogon (包括O. nivara)群体聚在一起，进一步从基因谱系角度支持亚洲栽培稻多次起源假说。 3．转座子在群体遗传与系统发育研究中的应用 鉴于目前植物谱系地理学研究中缺乏具有足够信息量的分子标记用于检测种内遗传变异，我们选取3个核基因中的转座子，通过对取自O. rufipogon和O. nivara整个分布区的37份样品的克隆测序，探讨了进化速率快、信息含量丰富的转座子序列在群体遗传上的应用。结果表明：1）无论在物种水平还是群体水平，转座子能检测到比包括内含子在内的其它DNA区域高得多的遗传变异;2）在物种水平上，异交多年生的O. rufipogon和自交一年生的O. nivara多样性均较高，且2个种间相差很小，二者在3个位点上平均核苷酸多样性π值均为0.013，差别主要表现在O. rufipogon杂合位点比例（46.1%）明显高于O. nivara（9.1%），说明交配系统不同并不一定和物种多样性水平相关;3）是否发生转座子序列插入是有价值的系统发育信息，发生在不同染色体上3个基因中的转座子插入进一步证实A基因组基部类群是O. meridionalis;通过叶绿体中3个转座子的插入现象推断了稻族一些四倍体物种，如稻属BC基因组的一些类群的母本来源。

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。

盐渍条件下野大豆群体的DNA变异

当前分子生物学的方法以惊人的速度渗透到生命科学研究的各个领域。植物对不断变化的环境逐步适应的过程中，积累了丰富的遗传多样性。与此同时，人类活动空间的不断扩大已经严重威胁到其他生命的生存和繁衍，越来越多的物种以越来越快的速度在我们还没有来得及认识它们时就已经永远地消失了。加快物种鉴定和保护的步伐就必须发展更多能充分揭示物种遗传多样性的实验技术，从具有丰富遗传多样性的野生资源中寻找到更多能够服务于人类可持续发展的基因资源。本文以杨树杂交后代过氧化物同工酶和RAPD分析为基础，论证了我们改进的RAPD方法用于遗传分析的可行性。在前期工作的基础上，进一步测定了野大豆自然群体的耐盐性变异，并且用微卫星和RAPD分析的方法研究分子标记与DXA变异、植株耐盐性之间的关系。对四个可能与抗盐性有关的RAPD片段进行克隆、测序，并进行序列比较。由此得出以下结论： 1、在本文的实验条件下，杨树同工酶和RAPD分析均表明，RAPD标记在亲本及其杂交后代中性状比例符合孟德尔遗传规律，尽管有时也会出现遗传负载等机制引起的基因分布扭曲现象。 2、初步研究了个体发育阶段和环境条件对植株耐盐性的影响。结果表明，植物耐盐性不仅仅与外界的盐度有关，而且受发育阶段和其它环境条件（如，温度）的影响。但也发现了某些个体在各种条件下都具有较高的耐盐性，而且，不易受到其它环境条件的影响。 3、微卫星标记的结果表明，10对引物中的8对引物共检测到时17个等位基因，平均每对引物2.125个等位基因。本文的实验条件下，双核苷酸和三核苷酸的引物对扩增产物都没有出现“ghosts"条带或“打滑”现象。 4、有4个RAPD标记可能与野大豆群体的耐盐性有关，分别是OPCO8460bp、OPCO8213bp、OPCO2690bp、以及OPCO5270bp。测序结果与GenBank中的序列作同源性比较，结果显示，OPCO2_(690bp)与小麦、松树等植物的吉普赛性的逆转录转座子的部分区域（24－－53）有很高的同源性（86－89％）。此外，OPCO2690bp与栽培大豆胞质谷氨酰胺合成酶（gs15）基因的启动子有高达95％的同源性。 5、本文实验条件下，RAPD扩增产物在限制性内切酶消化后，消化产物的多态性未见增大，也没有发现与耐盐性相关的多态位点。 6、野大豆自然群体DNA变异的研究中也可以应用SWAPP方法。

基于线粒体控制区的滇金丝猴群体遗传学研究

滇金丝猴(Rhinopithecus bieti)是我国著名的濒危保护动物.迄今为止,关于滇金丝猴并基于DNA序列的群体遗传学研究还没有报道.文章测定了来自于云南省维西县滇金丝猴群体样本的线粒体控制区全序列以及部分个体的细胞色素b全序列.在排除了核线粒体假基因存在的可能性之后,滇金丝猴维西群体内部被确认存在着两个序列分歧较大的分枝.即使如此,如果考虑到群体结构和迁移的影响,维西群体的遗传多样性水平可能并不高.

DEVELOPMENT OF MICROSATELLITE LOCI FOR PINUS KORAIENSIS (PINACEAE)

Premise of the study: Microsatellite markers were developed for Pinus koraiensis to characterize its genetic diversity and understand its population structure. Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining (FIASCO) Repeats protocol, 20 primer sets were developed in Chinese populations of P. koraiensis. Three of the markers showed polymorphism with two alleles per locus when assessed in a sample of two populations of P. koraiensis from the Changbai Mountain in the Jilin Province of China. Five and three loci were successfully amplified in P. taiwanensis and P. massoniana, respectively. The amplification size of these loci matches those in P. koraiensis. Conclusions: These markers may be useful for further investigation of population genetics of P. koraiensis.

Origin and evolution of new exons in the rodent zinc finger protein 39 gene

The origin of new structures and functions is an important process in evolution. In the past decades, we have obtained some preliminary knowledge of the origin and evolution of new genes. However, as the basic unit of genes, the origin and evolution of exons remain unclear. Because young exons retain the footprints of origination, they can be good materials for studying origin and evolution of new exons. In this paper, we report two young exons in a zinc finger protein gene of rodents. Since they are unique sequences in mouse and rat genome and no homologous sequences were found in the orthologous genes of human and pig, the young exons might originate after the divergence of primates and rodents through exonization of intronic sequences. Strong positive selection was detected in the new exons between mouse and rat, suggesting that these exons have undergone significant functional divergence after the separation of the two species. On the other hand, population genetics data of mouse demonstrate that the new exons have been subject to functional constraint, indicating an important function of the new exons in mouse. Functional analyses suggest that these new exons encode a nuclear localization signal peptide, which may mediate new ways of nuclear protein transport. To our knowledge, this is the first example of the origin and evolution of young exons.

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

A critical reassessment of the role of mitochondria in tumorigenesis

Background Mitochondrial DNA (mtDNA) is being analyzed by an increasing number of laboratories in order to investigate its potential role as an active marker of tumorigenesis in various types of cancer. Here we question the conclusions drawn in most of these investigations, especially those published in high-rank cancer research journals, under the evidence that a significant number of these medical mtDNA studies are based on obviously flawed sequencing results. Methods and Findings In our analyses, we take a phylogenetic approach and employ thorough database searches, which together have proven successful for detecting erroneous sequences in the fields of human population genetics and forensics. Apart from conceptual problems concerning the interpretation of mtDNA variation in tumorigenesis, in most cases, blocks of seemingly somatic mutations clearly point to contamination or sample mix-up and, therefore, have nothing to do with tumorigenesis. Conclusion The role of mitochondria in tumorigenesis remains unclarified. Our findings of laboratory errors in many contributions would represent only the tip of the iceberg since most published studies do not provide the raw sequence data for inspection, thus hindering a posteriori evaluation of the results. There is no precedent for such a concatenation of errors and misconceptions affecting a whole subfield of medical research.

The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake

Although new empirical evidence shows that sympatric speciation has occurred in some species, there are few indisputable model organisms for this process of speciation. The two subspecies (Gymnocypris eckloni eckloni and G. e. scoliostomus) of the schizothoracine Gymnocypris fish species complex from a small glacier lake in the Tibetan Plateau, Lake Sunmcuo, fit several of the key characteristics of the sympatric speciation model. We used combined mitochondrial control region sequences and the cytochrome b gene (1894 bp) to address the phylogenetics and population genetics of 232 specimens of G. e. eckloni and G. e. scoliostomus, as well as all of its closely related sister species. We found that: (i) a total of four old lineages were uncovered in the widespread G. e. eckloni, of which only one was shown to be shared with all G. e. scoliostomus individuals and (ii) the new subspecies (G. e. scoliostomus) evolved in Lake Sunmcuo from the ancestral G. e. eckloni population within approximately 0.057 Ma. These two taxa of the species complex are morphologically distinct, and reproductive isolation is further suggested. Ecological disruptive selection based on morphological traits (e.g. mouth cleft characters) and food utilization may be a mechanism of incipient speciation of two sympatric populations within Lake Sunmcuo. This study provides the first genetic evidence for sympatric speciation in the schizothoracine fish.