METHODS IN GEOMETRIC MORPHOMETRICS AND THEIR APPLICATIONS IN ONTOGENETIC AND EVOLUTIONARY BIOLOGY OF ANIMALS

简要回顾了几何形态学的发展历史,介绍了30多年来该领域使用的主要方法及其在生物发育与进化研究中的实际应用.除目前应用最为广泛的标点法和轮廓线法外,基于三维数据的表面特征分析和有限元分析也在该领域得到推广.这些方法可运用于分析两性分化、异速生长、种群分化、种上进化以及复杂功能结构的形态集成等科学问题.几何形态学与生物信息学的综合运用还将有利于探讨表型变化与遗传物质变化的相关性.随着生物成像技术和海量数据计算技术的进步,几何形态学将由目前以二维数据为主的研究向三维重建和分析的方向发展.     

几何形态学方法及其在动物发育与系统进化研究中的应用

简要回顾了几何形态学的发展历史,介绍了30多年来该领域使用的主要方法及其在生物发育与进化研究中的实际应用。除目前应用最为广泛的标点法和轮廓线法外,基于三维数据的表面特征分析和有限元分析也在该领域得到推广。这些方法可运用于分析两性分化、异速生长、种群分化、种上进化以及复杂功能结构的形态集成等科学问题。几何形态学与生物信息学的综合运用还将有利于探讨表型变化与遗传物质变化的相关性。随着生物成像技术和海量数据计算技术的进步,几何形态学将由目前以二维数据为主的研究向三维重建和分析的方向发展。     

蜣螂后胸叉骨的几何形态学分析及其适应进化研究

【目的】甲虫的后胸叉骨是基部位于后足基节关节处,端部游离在胸腔内的几丁质构成的内骨骼。后胸叉骨作为胸腹部运动肌肉的联结点,在甲虫运动过程中扮演了重要角色,同时也承载了分类和系统发育信息。蜣螂根据其习性可分为滚粪球和直接掘洞两类行为类型。通过传统的比较形态学方法,我们无法得知滚粪球或直接掘洞的行为对后胸叉骨形态的影响。本研究旨在利用定量的几何形态学方法探究蜣螂后胸叉骨形态对不同行为选择压力的响应关系。【方法】对76种蜣螂后胸叉骨的形态多样性进行二维几何形态学定量评估;利用显微CT和计算机三维重建方法,对直接掘洞类蜣螂和滚粪球类蜣螂的代表种西班牙粪蜣螂Copris hispanus和忠诚泽蜣螂Kheper devotus的后胸叉骨进行三维重建,用于比较两者的三维形态差异。【结果】经过几何形态学分析可知,两类蜣螂后胸叉骨背面观和侧面观的马氏距离和普氏距离的p值均低于0.0001,表明两类蜣螂的后胸叉骨的形态存在显著性差异;通过对C.hispanus和K.devotus后胸叉骨3D模型的比较发现,两类蜣螂后胸叉骨的最大区别在于后胸叉骨的端半部(叉臂和中突)。前者的叉臂细长,中突面积大,背立脊呈窄条状且不发达;后者的叉臂宽扁,叉臂基半部十分宽大,中突面积小,背立脊呈鳍状且十分发达。【结论】滚粪球或直接掘洞的行为会对蜣螂后胸叉骨的形态有显著性影响,蜣螂后胸叉骨形态与滚粪球和直接掘洞两种行为的选择压力显著相关,这与后胸叉骨所附着的胸部肌肉参与相关运动关系密切。本研究为探索昆虫形态与功能关系提供了一个有益范例。     

基于流形学习的基因表达谱数据可视化

基因表达谱的可视化本质上是高维数据的降维问题。采用流形学习算法来解决基因表达谱的降维数据可视化,讨论了典型的流形学习算法（Isomap和LLE）在表达谱降维中的适用性。通过类内／类间距离定量评价数据降维的效果,对两个典型基因芯片数据集（结肠癌基因表达谱数据集和急性白血病基因表达谱数据集）进行降维分析,发现两个数据集的本征维数都低于3,因而可以用流形学习方法在低维投影空间中进行可视化。与传统的降维方法（如PCA和MDS）的投影结果作比较,显示Isomap流形学习方法有更好的可视化效果。     

内唇在蜉金龟亚科中用于分属和分族的分类学价值

【目的】蜉金龟亚科（鞘翅目：金龟科）成虫外部形态高度趋同,种间相似性大,属族等高级阶元的鉴别特征混乱,因此构建新的形态指标系统极为重要。近年来内唇形态广泛应用于蜉金龟的分类学研究,并能有效区分部分种类,然而内唇在高级阶元的分类学价值和应用范围仍未可知。【方法】本文选取276属818种金龟为研究对象,其中包括蜉金龟亚科7族259属799种,以及外群样本17属19种（蜣螂亚科13属14种,沙金龟亚科4属5种）,利用几何形态学手段量化蜉金龟内唇的形态学信息,评估了属级和族级的区分度,并联合支序系统学方法,重建了蜉金龟祖先内唇形态。【结果】根据主成分分析显示,属级阶元的形态总方差为0.032 131 27,族级为0.032 914 63,内唇在属族间变异程度接近（两者相差约3%）,揭示了内唇形态在高级阶元间基本保持稳定,适合用于分类鉴定。为了进一步探索内唇在高级阶元的分类归属是否也接近,随之对样本进行判别函数分析。结果显示,仅基于内唇形态,98.49%的属可被正确鉴定,族级有98.41%的正确率,表明内唇在属级阶元间的判别归类略胜于族级阶元,内唇适合应用于高级阶元的判别归类。结合系统发育树,重建的内唇祖先形态显示其多变区域包括上内唇根基部、侧缘,内唇前区和内唇外缘等6个特征,不仅验证了前人对内唇的部分特征应用,也发现了新的形态指标。【结论】本研究利用定量形态学方法证实了内唇适用于蜉金龟高级阶元分类,同时为外部形态趋同类群提供了新的特征筛选与评估范式。     

PCA 和PLS 应用于胃癌亚型分类研究

文章研究了基于微阵列基因表达数据的胃癌亚型分类。微阵列基因表达数据样本少、纬度高、噪声大的特点,使得数据降维成为分类成功的关键。作者将主成分分析(PCA) 和偏最小二乘（PLS）两种降维方法应用于胃癌亚型分类研究,以支持向量机（SVM）、K- 近邻法（KNN）为分类器对两套胃癌数据进行亚型分类。分类效果相比传统的医理诊断略高,最高准确率可达100%。研究结果表明,主成分分析和偏最小二乘方法能够有效地提取分类特征信息,并能在保持较高的分类准确率的前提下大幅度地降低基因表达数据的维数。     

染色体三维结构重建方法研究

染色体三维结构重构问题是近年生物领域中基因组学的热点研究问题,是以二维交互频率数据为基础来预测其三维空间结构。最新相关实验表明染色质的三维空间结构对于基因表达、调控等方面都具有重要意义。而Hi-c数据能利用染色质交互信息形成二维接触矩阵重构出染色体三维结构。本综述以染色体三维结构重建方法为研究对象,通过对染色体三维结构重建方法进行比较分析,综述了目前基于Hi-c数据在染色体三维结构重建中的经典方法,系统介绍了染色体三维结构重建技术的发展脉络,以促进染色体三维结构重建的进一步研究。     

全球锹甲的几何形态学数据集

几何形态学是通过定量分析手段对生物的形态特征在几何空间中的变化进行测量, 并将这些测量得到的信息转变为数字信息进行统计学分析以达到形态特征间比较的目的, 目前被越来越多地用于探索生物的特征进化和多样性研究。先前的研究通常提取、比对生物的间断性特征信息用以类群之间的划分, 针对连续性特征研究的缺乏使得有关生物进化和形态学的相关知识变得匮乏。锹甲(鞘翅目: 锹甲科)由于其性二型、雄虫多型性和独特的习性成为形态学研究的重要类群。基于此, 本研究中我们提供了一个包含1,302种锹甲成虫(涵盖全世界99%已知种)的形态学数据集, 数据集包含锹甲的典型的连续性特征, 即前胸背板和鞘翅的外轮廓形态。我们提供的数据集为甲虫的生物多样性、系统发育和进化生物学在内的多个学科的研究提供基础。     

三维几何形态测量方法在石制品分析中的应用

几何形态测量方法是生物学研究中用于形态特征分析和形态比较研究的一种常用方法。其核心思想是利用空间坐标点获取研究对象的形态数据,再通过坐标数据的多元统计分析,定量探讨研究对象的形态特征及影响其形态变异的因素。近年来,随着三维扫描技术的广泛应用以及对于石制品形态特征量化分析要求的提高,基于三维模型的几何形态测量方法开始出现在相关的旧石器考古研究中。本文首先对三维几何形态测量分析方法及其在石制品研究中的应用情况进行介绍,随后具体阐述了该方法的分析流程。为便于国内学者更好地了解这一方法,本文进一步以广西百色盆地南坡山遗址发现的手斧为例,利用三维几何形态测量方法对这些手斧的几何形态特征进行了初步探讨。三维几何形态测量方法为石制品形态研究提供了新思路和新视角,有望成为今后中国旧石器考古研究中一个重要的发展方向。     

用于昆虫分类鉴定的几何形态计量学方法研究:相对扭曲分析

几何形态计量学着重研究生物形态的拓扑结构信息,不受昆虫标本大小和形状等因素的影响.本文提出利用几何形态计量学中的相对扭曲分析来实现昆虫分类鉴定的研究,做为方法论的探索,本文以鳞翅目夜蛾科6种蛾类昆虫的翅脉图像样本为试验材料.首先利用软件TpsDig2获取6种蛾180个右前翅翅脉样本的标记点,再运用软件TpsSuper对其进行普氏叠加分析,消除非形状因素等多余的信息,最后利用软件TpsRelw进行相对扭曲分析,通过分析得到的相对扭曲图像可以使昆虫的分类实现二维可视化,因此可以更直观地做出其种类的鉴定.研究结果表明本文为蛾类昆虫的可视化鉴定提供了一种可行的方法,对于昆虫分类鉴定的形态学测量数据可视化具有重要意义.     

Geometric morphometrics: Current and future in China

Although there were many ancient Chinese mathematicians contributed a lot on geometry,Geometric morphometrics (GM) in modern concept was not firstly proposed by Chinese.The super capability of geometric morphometrics in scientific computing and problem solving has gained a lot of attentions in the world.Until early of 21 centuries,geometric morphometrics was introduced into China.Since then,GM was rapidly applied in many research fields.However,it is a pity that GM is still not well-known in China as many works are published out of China.Thus,the special issue "Geometric morphometrics:Current shape and future directions" is organized.The present issue presents a series of contributions in this scientific field.In future,there will be many considerable new developing fields on GM needed to pay more attentions,for instances,3D geometric morphometrics,4D analysis,visualization of amber,new machine developing,new software developing,automatic identification system,etc.Once these technical bottle-necks on 3D data collecting and merging geometric morphometric data from multiple characters could be solved,the automatic identification system and other fields based on Big Data would come true.     

A web based tool to merge geometric morphometric data from multiple characters

Geometric morphometrics (GM) is an important method of shape analysis and increasingly used in a wide range of scientific disciplines.Presently,a single character comparison system of geometric morphometric data is used in almost all empirical studies,and this approach is sufficient for many scientific problems.However,the estimation of overall similarity among taxa or objects based on multiple characters is crucial in a variety of contexts (e.g.(semi-)automated identification,phenetic relationships,tracing of character evolution,phylogenetic reconstruction).Here we propose a new web-based tool for merging several geometric morphometrics data files from multiple characters into a single data file.Using this approach information from multiple characters can be compared in combination and an overall similarity estimate can be obtained in a convenient and geometrically rigorous manner.To illustrate our method,we provide an example analysis of 25 dung beetle species with seven Procrustes superimposed landmark data files representing the morphological variation of body features:the epipharynx,right mandible,pronotum,elytra,hindwing,and the metendosternite in dorsal and lateral view.All seven files were merged into a single one containing information on 649 landmark locations.The possible applications of such merged data files in different fields of science are discussed.     

ShapeRotator: An R tool for standardized rigid rotations of articulated three‐dimensional structures with application for geometric morphometrics

The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures. While there are existing methods for analyzing shape variation in articulated structures in two‐dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research. Here, we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space, so it can be applied to any morphometric problem that also uses 3D coordinates (e.g., spherical harmonics). We demonstrate the method by applying it to a landmark‐based dataset for analyzing shape variation using geometric morphometrics. We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.     

几何形态测量学方法在小哺乳动物化石分类鉴定中的应用——4种(鼠平)类化石大样本的个案研究

小哺乳动物化石在晚新生代生物地层学和生物年代学研究中具有重要作用,尤其是筛洗法在古生物调查中得到广泛应用后,通常可以采集到数量可观的标本,使得其地位较大型哺乳动物化石更加彰显.因此,小哺乳动物化石标本的分类鉴定也成了一项十分关键的工作.然而,传统形态学方法在对大量标本进行分类鉴定时,往往容易受主观因素影响而将不稳定的细微性状变异作为依据建立新种,或者忽视一些肉眼难于察觉的形态学差异而将两个甚至多个类群合并到一起,导致基于形态学的化石分类鉴定随意性增加,失去客观性.此外,对于不具鉴定意义的非关键性单个牙齿,很难凭借肉眼或显微镜观察进行区分.针对这些问题,本文选取了安徽繁昌人字洞早更新世早期三种(鼠平)类甘肃模鼠Mimomys gansunicus,郑氏异模鼠Heteromimomys zhengi和繁昌维蓝尼鼠Hllanyia fanchangensis的1284件臼齿并以早上新世内蒙古比例克的比例克模鼠Mimomys bilikeensis的163件臼齿作为参考,采用几何形态测量学方法在各个臼齿咬合面上分别选取了7～14个同源landmark对咬合面的形态特征进行了线性判别分析,建立了针对这4个种的臼齿咬合面形态差异判别函数.分析结果表明,根据这些landmark所提供的形态差异信息,人字洞的1284件臼齿标本中的确存在3个可以明显区分且形态学性状稳定的类群,先前的分类鉴定得到了验证.与之不同地点不同时代的比例克模鼠也可以很好区分.因此,建立在大样本基础上的这4种(鼠平)类臼齿咬合面同源形态特征的判别函数可以用来描述这些种类较为稳定的形态特征差异,并用来作为今后对样本较少的标本进行分类鉴定时的判别依据.因为几何形态测量学的方法不仅可以对二维的离散landmark数据以及重要形态学特征的轮廓线进行分析,甚至还可以扩展至三维空间,所以上述方法对于较为容易获得大样本标本的小哺乳物化石分类鉴定具有普遍意义.     

Traditional morphometrics in plant systematics and its role in palm systematics

A review is given of the role of traditional morphometrics in plant systematics. The three most commonly used techniques of data analysis – Cluster Analysis, Principal Component Analysis and Discriminant Analysis – are discussed. The kinds of data that can be taken from palm specimens and the problems of using specimens as data sources are outlined. Published systematic studies of palms using traditional morphometrics are reviewed. More recent studies indicate that: hybrid zones between species may be common; infraspecific diversity is greater than previously suspected; there may be more than double the currently accepted number of species; and our current knowledge of morphological variation in palms is superficial. A procedure for scientific systematics is given, which incorporates traditional morphometric methods.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 103–111.     

A three‐dimensional geometric morphometric study of the development of sulcus versus shell outline in Permian neospiriferine brachiopods

The morphological variation of the sulcal development and shell outline in large Permian neospiriferine brachiopods including Fasciculatia Waterhouse, 2004 is investigated using geometric morphometrics. The sulcal tongues of spiriferide brachiopods can be, in a qualitative sense, categorized into three types according to the degree of their development: short sulcal tongue, long sulcal tongue and geniculated sulcal tongue. All three types have been noted within Fasciculatia striatoparadoxa, regardless of the nature of the substrate which they originally inhabited. To quantify its morphological variation both in sulcal development and shell outline, 51 brachiopod shells were scanned with a three‐dimensional (3‐D) surface imaging device, and their 3‐D models were reconstructed. Using two landmarks and 58 semilandmarks designated on the surface of the reconstructed 3‐D models, a landmark‐based morphometric analysis was performed. Our result demonstrates a significant intraspecific variation of sulcal development in F. striatoparadoxa and its relatives. Local environmental factors, especially the intensity of ambient water flow, are invoked as the most likely cause for this intraspecific variation. Additionally, this study also shows that there are considerable interspecific distinctions in shell outline among Fasciculatia species, independent of the high variation in the sulcal development. The strong stability of overall shell outline at species level implies a decoupled morphological development between sulcal tongue and whole shell outline. The 3‐D morphometric approach applied here demonstrates its great utility as a tool for quantifying and analysing the morphological variation of highly convex brachiopod shells.