Subset selection from multi-experiment data sets with application to milk fatty acid profiles

The development of routine analyses to allow for the handling of large amounts of samples and to avoid cost and time expensive analytical techniques is of high value. These routine analyses most often require calibration using the detailed analyses as reference values. A representative subset reflecting the complete range of the variables of interest is required for this purpose. In this paper this subset selection problem is tackled for multi-experiment data sets. Conventional techniques such as the Kennard and Stone algorithm and OptiSim are compared to a new approach based on Genetic Algorithms. The challenge here is to find an adequate objective function and to modify the standard crossover and mutation operators to keep the number of desired samples fixed. These techniques are applied on a data set containing the concentration of 45 fatty acids, determined by a simplified reference method, in 1033 milk samples, stemming from six different experiments. The objective is to select a subset of 100 samples in which each of the six different experiments is sufficiently represented. While there is no obvious way to generalize the conventional methods for multi-experiment data sets, this can quite easily be accomplished for Genetic Algorithms by modifying the objective function. Our results indicate that Genetic Algorithms are very capable of handling the subset selection problem for multi-experiment data sets.     

基因组时代的植物系统发育研究进展

系统发育研究是进化生物中的基本问题,也是其他众多生物学分支学科的基础问题,其核心在于研究不同生物类群间的亲缘关系与进化命运。利用分子数据研究生物之间的进化关系是系统发育研究的重要手段。随着测序技术的提升和测序成本的持续下降,系统发育研究由早期基于单基因或联合少数片段逐步发展到现阶段利用大规模基因组数据对个体、群体、物种以及更高水平的进化关系进行探讨。讨论了目前植物体内的3套基因组(叶绿体基因组、线粒体基因组与核基因组)在系统发育研究中的代表性成果,总结了植物不同基因组的特征及其在系统发育研究中的优势与局限,探讨了系统发育树构建的主要方法,并对未来研究进行了展望。目前,植物体内的3套基因组适用于不同阶元和类群的系统发育研究,不同基因组之间的遗传特性差异使其在系统发育研究中具备不同的优势和应用:① 叶绿体基因组结构相对简单,序列保守,不易重组,单亲遗传,是广泛应用于系统发育学和进化生物学等研究领域的理想分子数据资源;②植物线粒体基因组序列进化速率较慢,目前仅适用于早期植物和大尺度水平的系统发育研究;③核基因组为双亲遗传,可综合揭示双亲谱系及系统网状进化关系,在系统发育研究中具有巨大的应用潜力。不同建树方法适用于不同特征的数据集,在建树过程中应采用合理的方法避免长枝吸引和不完全谱系分选带来的影响。未来核基因组将成为系统发育研究的主流方向,其双亲遗传特性能够为物种形成过程中的杂交和基因组渗入等事件提供充分的见解。随着越来越多的类群系统位置被确定,物种形成和进化过程中的杂交、回交等双亲遗传,以及核质互作、多倍化、功能适应和趋同进化等问题将会成为系统发育研究的重点。表1参78     

家蚕分子系统学研究之中外群的作用与影响

以33个家蚕品种、10个不同导区的野桑蚕、5个柞蚕品种AFLP分子数据为例,分析探讨了家蚕分子系统学研究中外群对构建系统发生树的作用与影响。结果表明：⑴不同的构树方法中外群的作用是不同的;⑵同一构树方法研究,因外群规模不同对构建的系统发生树有较大影响,而不同规模的复合外群所构建得系统发生树几乎没有差异;⑶以亲缘关系不同对野桑蚕和柞蚕作外群对照,在对照规模相同（或相近）时,其两种外群对系统发生树的重建几乎没有影响。     

Whole-genome analysis of photosynthetic prokaryotes

The process of photosynthesis has had profound global-scale effects on Earth; however, its origin and evolution remain enigmatic. Here we report a whole-genome comparison of representatives from all five groups of photosynthetic prokaryotes and show that horizontal gene transfer has been pivotal in their evolution. Excluding a small number of orthologs that show congruent phylogenies, the genomes of these organisms represent mosaics of genes with very different evolutionary histories. We have also analyzed a subset of "photosynthesis-specific" genes that were elucidated through a differential genome comparison. Our results explain incoherencies in previous data-limited phylogenetic analyses of phototrophic bacteria and indicate that the core components of photosynthesis have been subject to lateral transfer.     

Molecular phylogenetics of mastodon and Tyrannosaurus rex

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.     

缠绕植物手性的系统发育分析(英文)

利用matK、rbcL与trnL基因,分析了中国薯蓣属植物缠绕手性的系统发生关系;利用matK基因,从大分类单元角度进一步分析了缠绕植物的系统特征。结果显示左、右旋缠绕植物物种存在显著的系统发育特征:matK数据中的右旋薯蓣聚成独立的进化枝与rbcL基因的分析共同支持右旋物种的单系性;rbcL和trnL的数据均较好地显示了右旋薯蓣的单系特征[除多毛叶薯蓣(D.decipiens)和甘薯(D.esculenta)外];在大分类单元上,缠绕植物手性性状则呈现出明显的多系特征。结果表明在中国区薯蓣属的分类中,手性特征是较可靠的性状特征,《中国植物志》薯蓣属章节直接将右旋物种归入周生翅组(sect.Enantiophyllum)较合理。但在世界范围上看,在小分类单元的薯蓣属内和薯蓣科及其他大分类单元内,手性特征都具有单独多次起源的性质,因此在执行分类时应当慎用这个性状。对于手性特征的起源问题,最新的观点倾向于否定南北半球物理差异相关的假说,但其结论的正确性有待商榷。结合地质事件研究薯蓣属等具有两种手性方向的小分类单元,以及构建突变体的方法,有助于最终解决植物手性的起源问题。     

缺省值问题中一种新的比较补充方法的方法

讨论了当缺省值问题中有多种补充方法时,从补充完整样本的损失的角度,并引进了统计决策理论来比较这些补充方法.当补充风险r(X ,X)=∫∫f(X (x)-x)dPXmisθxmis)dPθ(xobs)在决策空间是最小时,相应的补充方法就是容许决策法则.     

面向风云静止卫星地表温度产品的缺失数据修复方法对比

静止卫星地表温度数据是研究昼夜温度变化规律及全球气候变化的重要参数。但常见的静止卫星地表温度数据,如风云二号F星地表温度产品(FY-2F LST)由于受到云、雾霾和气溶胶等大气因素的影响,往往会出现数值缺失的现象。针对该问题,一系列基于温度昼夜变化模型(diurnal temperature cycle,DTC)的静止卫星地表温度产品空值数据修复方法被提出,如VAN2006方法;此外,常见的三次样条插值(Cubic spline)和智能的反向传播网络(back-propagation network,BP)利用像元时间连续性原理,通过温度预测实现地表温度产品空值数据修复在理论上也是可行的。模拟不同类型的像元缺失情况分析和比较了3种方法的温度修复结果。研究表明,在空值数量较少的情况下,3种方法修复结果都比较理想,其中Cubic spline方法效果最好;随着空值数量增加,3种方法修复效果都不同程度变差,其中VAN2006衰退较缓慢,Cubic spline衰退最快;当空值数目继续增多且达到一定数量时,VAN2006仍可以较为真实的还原地表温度数据,并且优于BP,其中Cubic spline修复结果最差,难以反映实际地表温度。对14种不同空间大小空值区域实验研究进一步说明3种方法对地表温度空值修复具有可行性,但修复效果与空值区域大小无关,时间序列中空值数量是最主要的影响因素。     

Molecular Phylogeny of the ＂True Citrus Fruit Trees＂ Group （Aurantioideae,Rutaceae） as Inferred from Chloroplast DNA Sequence

The genus Citrus L.has a long controversial taxonomy history,and a well-resolved molecular phylogeny of the "true citrus fruit trees" group in the future will provide new information for advancing breeding techniques and developing better conservation strategies.In the present study,three cpDNA fragments(TrnL-TrnF,PsbH-PetB,and TrnS-TrnG)of 30 genotypes chosen from the six genera of the "true citrus fruit trees" group were analyzed.A molecular phylogenetic tree of the "true citrus fruit trees" group was reconstructed based on plastid DNA sequences.The results confirmed that the "true citrus fruit trees" group was monophyletic,and thereby the group was divided into genera as previously suggested based on morphological characters.The cpDNA data also suggested that Poncirus might be the first genus separated from the other five genera in the group.The genus Fortunella were of hybrid origin and Citrus might be as its putative paternal parent.The genera Microcitrus,Eremocitrus,and Clymenia were possibly monophyletic and their common ancestor might branch out from Citrus.Furthermore,the phylogenetic relationships within the Citrus genus were discussed.     

Human auditory frequency-following responses to a missing fundamental

Both a complex tone perceived as a 365-hertz "missing fundamental" and a 365-hertz pure tone evoked 365-hertz far-field frequency-following responses. Narrow-band masking noise centered at 365 hertz attenuated the responses to the pure tone but not to the complex tone. Results support the concept that perception of the missing fundamental is based on periodic neural activity.     

Sexual agglutination of heterothallic yeasts in diverse taxonomic areas

Species in four genera of yeasts produce mating types that clump when brought together in liquid or on solid media. All species of a phylogenetic line of Saccharomyces are sexually agglutinative. Unisexuals of the latter species are believed to have from one to four sets of chromosomes, whereas bisexuals are believed to have from two to eight sets.     

Prevalence and patterns of same-gender sexual contact among men

The prevalence and patterns of same-gender sexual contact among men are key components of models of the spread of HIV infection and AIDS in the U.S. population. Previous estimates by Kinsey et al. from data collected between 1938 and 1948 have been widely criticized for inadequacies of sample design. New lower-bound estimates of prevalence developed from data from a national sample survey conducted in 1970 indicate that minimums of 20.3 percent of adult men in the United States in 1970 had sexual contact to orgasm with another man at some time in life; 6.7 percent had such contact after age 19; and between 1.6 and 2.0 percent had such contact within the previous year. Although these estimates incorporate adjustments for missing data, the likelihood of underreporting suggests that these estimates might be lower bounds on the prevalence of same-gender sex among men. Two sets of alternative estimates are derived to assess the sensitivity of these estimates to the assumptions made in imputing values to missing data. Detailed estimates are presented by frequency of contact, age, education, and marital status; and supporting estimates are derived from a 1988 national survey. Data from both the 1970 and 1988 surveys indicate that never-married men are more likely than other men to have had same-gender sexual contacts within the last year. The 1970 survey also indicates, however, that approximately half the men estimated to have such contacts are found among the more numerous population of currently or previously married men.     

A brief history of seed size

Improved phylogenies and the accumulation of broad comparative data sets have opened the way for phylogenetic analyses to trace trait evolution in major groups of organisms. We arrayed seed mass data for 12,987 species on the seed plant phylogeny and show the history of seed size from the emergence of the angiosperms through to the present day. The largest single contributor to the present-day spread of seed mass was the divergence between angiosperms and gymnosperms, whereas the widest divergence was between Celastraceae and Parnassiaceae. Wide divergences in seed size were more often associated with divergences in growth form than with divergences in dispersal syndrome or latitude. Cross-species studies and evolutionary theory are consistent with this evidence that growth form and seed size evolve in a coordinated manner.     

20种溪蟹线粒体COI基因比较分析及系统发育研究

【目的】比较分析20种溪蟹的线粒体COI基因序列,并基于COI基因序列构建溪蟹科系统发育进化树分析不同种类间的亲缘关系,探究COI基因作为分子标记在溪蟹物种鉴定中的适用性,同时为溪蟹科的物种鉴定及系统发育研究提供理论依据。【方法】测定2种龙溪蟹属（Longpotamon）代表种的线粒体COI基因全序列,结合GenBank中已公布的18种溪蟹科COI基因全序列,利用MEGA X计算其碱基组成、保守位点和遗传距离,采用MatGAT 2.02进行多序列相似性比较分析,并以PhyloSuite构建贝叶斯树（BI）和最大似然树（ML）,探究溪蟹科物种内部的亲缘关系。【结果】20种溪蟹的COI基因序列全长1534~1539 bp,连续编码511~512个氨基酸残基,所有物种均以ATG为起始密码子;碱基含量略有不同,分别为35.9%~40.7%（T）、16.4%~20.2%（C）、26.8%~28.9%（A）和14.7%~17.2%（G）,呈明显的AT偏向性。COI基因核苷酸序列及其推导氨基酸序列比较分析结果显示分别有577和98个变异位点,表明密码子存在简并性。20种溪蟹的线粒体COI基因遗传距离、序列相似性及系统发育进化分析结果均显示,长安龙溪蟹（Longpotamon changanense）与龙溪蟹未定种（Longpotamon sp.）的亲缘关系最近。虽然采用不同方法基于不同数据集构建的系统发育进化树在拓扑结构上有所不同,但所有树型均显示龙溪蟹属（Longpotamon）的小龙溪蟹（L.parvum）并未与该属其他物种聚类在一起,华溪蟹属（Sinolapotamon）、近溪蟹属（Potamiscus）和小石蟹属（Tenuilapotamon）物种也散布在系统发育进化树不同分支中,暗示这些物种在分类鉴定上为非单系群,还需进一步研究确定。【结论】20种溪蟹的线粒体COI基因序列平均种间遗传距离为0.173,均具有区别于其他种类的特异位点,即线粒体COI基因序列可作为溪蟹科物种鉴定的分子标记。     

带有缺失数据的一种动态聚类方法

【目的】探讨实际问题研究中的不完全数据聚类。【方法】利用相关变量的辅助信息,对缺失数据进行推估,确定其合理的替代值,从而构造出一个“完全”数据集。在此基础上以EM算法循环迭代,参数的估计值和缺失数据的替代值都将逐渐收敛,以相应的贝叶斯后验概率判别个体的归类,进而实现动态聚类。【结果】模拟研究表明,缺值替代法具有较好的收敛性,对有缺失的数据基本都可正确地聚类。【结论】Fisher的鸢尾花花类识别数据验证了缺值替代法的可行性,其聚类的准确性高于缺值删除法,基本接近完全数据聚类。     

耕地质量评价缺失数据填充方法研究

在耕地质量数据调查与采集过程中会由于人为、环境等因素造成数据缺失,而目前数据缺失填充方法都存在适用性不足的问题,为完善耕地质量数据库从而提高耕地质量评价精度,对耕地质量评价缺失数据填充方法的研究是十分重要的。本研究以广州市从化区耕地质量数据库为样本集,根据空间相关性和空间分布将数据集划分为空间关联性数据集和非空间关联性数据集,利用多种填充方法对其进行缺失填充模拟,采用十字交叉法进行精度验证。结果表明：选取数据整体异常值比例不足1.2%,且高程、气温、有效锌等25组因素具有空间相关性。对空间关联性数据填充精度最高的是四象最近邻算法,在缺失率20%以下时精度仍高达80%,精度随缺失率增大而降低,其次为K最邻近（KNN）算法、期望最大化法、多重填充法、回归模型算法,四象最近邻算法相较于KNN算法在数据密集时精度更好。对非空间关联性数据填充精度最高的是相似聚集填充算法,在缺失率25%以下时精度超过80%,其次为期望最大化法、多重填充法、回归模型算法。综上,本研究提出的四象最近邻算法和相似聚集填充算法相比其他算法在耕地质量评价缺失数据填充中精度更高,效果更稳定,且实用性更广。     

基于BP神经网络的缺测降水数据插补

 缺测降水数据的插补可以有效改善数据系列的完整性,以元江境内的元江、洼垤、因远、街子河、阿支、磨房河等水文和雨量站点逐月及年降水数据为基础,研究缺测降水数据的插补。站点之间月降水数据相关分析表明：各站点之间相关性较差,相关分析难以满足本研究流域内部分月降水数据插补精度,故尝试采用BP神经网络模型对研究流域降水数据进行插补。研究表明：基于本流域降水数据建立的神经网络模型检测样本合格率达到89.6%,具有较好的插补精度,说明神经网络可以用于本研究流域的缺测降水数据插补,为降水数据缺测的插补提供了新的途径。     

Paleontology. Tiny, feathered dino is most birdlike yet

Chinese paleontologists studying the fossil known as Microraptor describe it as both the smallest and the most birdlike dinosaur yet discovered. In this week's issue of Nature, they say the crow-sized, feathered creature--whose fossilized tail once formed part of a now-discredited "missing link" between birds and dinosaurs known as Archaeoraptor--belongs to the dromaeosaurs, dinosaurs that many paleontologists consider the closest dinosaurian relatives of birds.