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.     

三维几何形态学概述及其在昆虫学中的应用

长期以来二维（two-dimensional, 2D）数据是几何形态学（geometric morphometrics）分析的最主要的数据类型,在推动几何形态学的发展过程中起到了奠基性的作用,并也解决了很多重大的科学问题,展示了几何形态学强大的科学计算能力与问题解决能力。但有些特殊的科学问题或者特殊的形态结构,无法通过二维数据完美解决,亟需大规模、大尺度三维（three-dimensional, 3D）数据的支持,这对几何形态学的三维化发展提出需求。更重要的是,随着三维数据获取成本的日渐降低,大量三维数据涌现出来。因此,三维几何形态学应运而生。本文对三维几何形态学的原理及其应用进行了概述,重点探讨了三维几何形态学与二维几何形态学的异同点,并对前者的两个发展阶段（少量样本的形态模拟与准定量比较及大量样本的定量比较）进行了概述,评价了四维数据和有限元等方法的应用,指出了该方法在昆虫学领域的发展潜力,最后对该方法在样本量增加、硬件提升、数据分辨率提高、新算法的开发、分析结果的呈现及3D打印等方面的发展趋势进行了展望。     

几何形态测量法在生物形态学研究中的应用

形态分析是生物系统学及其多样性研究中很重要的一部分。随着统计学的发展,我们可以对非常复杂的数据进行分析,这在客观上导致了多变量形态测量的出现。在20世纪80年代,在数据收集和分析上产生了重要突破——标点和标点相对位置的几何信息的匹配,从而可以将多变量分析的标点集叠加到生物原始图上,它不仅仅是生成散点图,而是试图客观反映生物的形态性状。这项研究被称为几何形态测量法(geometricmorphometrics),Rohlf和Marcus(1993)称其为形态测量方法上的一次革命。文章简要介绍了该方法。     

中国古代人骨体质人类学的研究进展与展望

近10年来,中国古代人骨遗存的体质人类学研究迅猛发展,研究内容的广度和深度已完全超越了上世纪以人种类型分析为主的情况。这些研究涉及到古代人群的演化、古代疾病与健康、文化习俗相关的骨骼异常、骨骼功能适应、古人口学等多个领域,并积累了一批重要的古代人群体质人类学数据。这些研究工作丰富了我们对东亚地区全新世人群演化历史的认识,体现了多学科的研究理念和研究方法的创新。本文对我国近10年来全新世古代人骨材料的体质人类学研究进展进行了回顾和展望。     

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。     

Utility of geometric morphometrics for inferring feeding habit from mouthpart morphology in insects: tests with larval Carabidae (Insecta: Coleoptera)

Feeding habits are important life‐history traits in animals; however, methods for their determination are not well established in many species. The larvae of the beetle family Carabidae are an example. The present study tested the utility of geometric morphometrics of mouthpart morphology to infer the feeding habits of carabid larvae. Using Pterostichus thunbergi as a model system, larval feeding habits were inferred using geometric morphometrics of mouthparts and the results were compared with those obtained from rearing experiments. The rearing experiments indicated that P. thunbergi larvae are carnivores that require snails as an essential part of the diet. Through geometric morphometrics, associations between mouthpart morphology and larval feeding habits were confirmed for species in which these two traits are known. A discriminant analysis using these associations classified P. thunbergi larvae as snail/slug feeders, which is a result compatible with the rearing experiments. Geometric morphometrics also revealed that morphological integration and ontogenetic shape change might play roles in the diversification of mouthpart morphology. Overall, these results demonstrate the utility of the geometric morphometrics of mouthparts to infer feeding habit and to clarify the mechanisms of mouthpart morphological diversification in the study group, and the results also serve as a basis for future studies of other insect groups.     

Geometric morphometrics as a tool for understanding Dactylorhiza (Orchidaceae) diversity in European Russia

Geometric morphometric techniques were employed to assess the diversity of lip shapes (305 samples from 83 populations) in flowers of European Russian Dactylorhiza (Orchidaceae: Orchidinae). We found significant agreement between the results from geometric morphometrics, classic morphometrics and the distribution of certain nuclear DNA markers. The lip shapes from Arctic Dactylorhiza samples occupied an intermediate position between D. maculata and D. fuchsii samples from Central Russia, supporting a hybrid origin of 'northern tetraploids'. Lip shapes of the taxonomically controversial allotetraploid D. baltica were found to form a distinct group, with members having definite relationships with diploid D. incarnata samples from the same localities, indicating either their local origin or introgression with D. incarnata . In addition to demonstrating the value of geometric morphometric methods in studies of plant taxonomy and hybridization, we suggest future applications designed to explore pollinator-driven directional selection, developmental constraints and fluctuating asymmetry.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 1–12.     

Advances in insectivore and rodent systematics due to geometric morphometrics

• 1 Morphometrics, the study of the variation and change in form amongst organisms, serves as a basic methodological tool in various fields of biological research, including systematics. Because it includes information about spatial relationships amongst anatomical landmarks, geometric morphometrics is more suitable for analyzing morphometric variation than methods based on distance measurements.
• 2 Geometric morphometrics allows us to answer general ecological and evolutionary questions about shape.
• 3 In this paper, landmark‐based methods are described and illustrated, based on a dataset of measurements from 295 Apodemus mandibles, and the applications of such methods in the systematics of insectivores (Eulipotyphla) and rodents (Rodentia) are summarized.

     

Can members of the south‐western Gila robusta species complex be distinguished by morphological features?

The goal for this project was to re‐examine key morphological characters hypothesized to differentiate Gila intermedia, Gila robusta and Gila nigra and outline methods better suited for making species designations based on morphology. Using a combination of meristic counts, morphological measurements and geometric morphometrics, morphological dissimilarities were quantified among these three putative species. Traditional meristic counts and morphological measurements (i.e. distances between landmarks) were not useful for species identification. Geometric morphometrics, however, identified differences among species, while also suggesting an effect of geographic location on morphological variation. Using canonical variate analysis for the 441 fish sampled in this study, geometric morphometrics accurately predicted true group membership 100% of the time for G. nigra, 97% of the time for G. intermedia and 91% of the time for G. robusta. These results suggest that geometric morphometric analysis is necessary to identify morphological differences among the three species. Geometric morphometric analysis used in this study can be adopted by management officials as a tool to classify unidentified individuals.     

Discrimination of Eubazus (Hymenoptera, Braconidae) sibling species using geometric morphometrics analysis of wing venation

Abstract.  Complexes of sibling and cryptic species are encountered frequently in parasitic Hymenoptera. Geometric morphometrics is a useful tool to detect minimal morphological variations, which often are undetectable by traditional morphological studies and even by classical morphometric approaches. We applied geometric morphometrics to wing venation to assess a complex case of sibling species in the genus Eubazus (Hymenoptera, Braconidae), parasitoids of conifer bark weevils of the genus Pissodes (Coleoptera, Curculionidae). The results and methods were compared with previous taxonomic studies on the same species, involving classical multivariate morphometrics, isoenzyme analyses, cross-mating experiments and biological observations. Geometric morphometrics confirmed the previous division into four distinct species. However, this approach enabled the four species to be separated simultaneously, with a reliability of 98.6% for well-classified females and 93.1% for males. A similar result in previous studies was obtained only by combining isoenzyme analyses and several canonical variate analyses, including many morphometric characters. Furthermore, measurements of wing venation were less time-consuming, more reliable and required less prior knowledge of braconid taxonomy than the measurements needed for the classical morphometrics methods. Geometric morphometrics was used also to test the effect of host species on wing shape. Several female populations of Eubazus semirugosus originating from three different Pissodes spp. were compared. Significant differences were found in wing shape between conspecific Eubazus from different host species. The results are discussed in relation to reproductive isolation and genetic flow between the four species.     

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。     

中国履行生物多样性公约的成就和展望

2004年是生物多样性公约实施10周年。中国于1993年1月7日作为第7个国家正式加入“公约”。接着就由国家环境保护总局牵头组建国家履约协调组和许多联络点,下设办公室负责日常工作。可见,国家对生物多样性工作的重视和认真的态度。10年来,中国在履约方面做了大量工作,成绩显著。例如,完成了“中国生物多样性国情研究报告”和“中国生物多样性保护行动计划”等一大批重要文件,建立了“生物多样性委员会”、“生物多样性保护基金会”和相应的科学与教育部门,开展了许多科研项目和讲授相关的课程,出版了系列丛书和“中国生物多样性”学术刊物,重视开展学术交流,建立了生物多样性数据库和相关的管理政策,生物多样性保护实体和产业日益增加和发展等就是明显的事例。履约10年的经验在于下列三个方面(1)保护和发展必须密切结合;(2)“统一协调、分散管理”的方针需要进一步完善;(3)基础性和综合性研究需要加强。展望未来,只有在加强基础和综合研究以及提高管理水平方面下一番功夫,履约工作才能取得更大的成绩。     

Morphometric comparison of the cephalic region of cultured Acipenser baerii (Brandt, 1869), Acipenser naccarii (Bonaparte, 1836) and their hybrid*

Geometric morphometric techniques were used in the characterization of morphological differences of the cranial region in cultured Acipenser baerii and A. naccarii and their hybrid. Species identification in sturgeons sometimes is difficult, because of the morphological plasticity of individual variability and the small differences between taxa. Identification is also complicated by human intervention and manipulation (e.g. aquaculture, hybridization, pollution). This study indicates how the differences between two species and their hybrids can be quantified and accurately visualized via geometric morphometrics. This technique may serve as a useful methodology to supplement analytical studies on morphometrics and systematics in Acipenseridae.     

Advances in Geometric Morphometrics

Geometric morphometrics is the statistical analysis of form based on Cartesian landmark coordinates. After separating shape from overall size, position, and orientation of the landmark configurations, the resulting Procrustes shape coordinates can be used for statistical analysis. Kendall shape space, the mathematical space induced by the shape coordinates, is a metric space that can be approximated locally by a Euclidean tangent space. Thus, notions of distance (similarity) between shapes or of the length and direction of developmental and evolutionary trajectories can be meaningfully assessed in this space. Results of statistical techniques that preserve these convenient properties—such as principal component analysis, multivariate regression, or partial least squares analysis—can be visualized as actual shapes or shape deformations. The Procrustes distance between a shape and its relabeled reflection is a measure of bilateral asymmetry. Shape space can be extended to form space by augmenting the shape coordinates with the natural logarithm of Centroid Size, a measure of size in geometric morphometrics that is uncorrelated with shape for small isotropic landmark variation. The thin-plate spline interpolation function is the standard tool to compute deformation grids and 3D visualizations. It is also central to the estimation of missing landmarks and to the semilandmark algorithm, which permits to include outlines and surfaces in geometric morphometric analysis. The powerful visualization tools of geometric morphometrics and the typically large amount of shape variables give rise to a specific exploratory style of analysis, allowing the identification and quantification of previously unknown shape features.     

Morphometric Identification of Queens,Workers and Intermediates in In Vitro Reared Honey Bees (Apis mellifera)

In vitro rearing is an important and useful tool for honey bee (Apis mellifera L.) studies. However, it often results in intercastes between queens and workers, which are normally are not seen in hive-reared bees, except when larvae older than three days are grafted for queen rearing. Morphological classification (queen versus worker or intercastes) of bees produced by this method can be subjective and generally depends on size differences. Here, we propose an alternative method for caste classification of female honey bees reared in vitro, based on weight at emergence, ovariole number, spermatheca size and size and shape, and features of the head, mandible and basitarsus. Morphological measurements were made with both traditional morphometric and geometric morphometrics techniques. The classifications were performed by principal component analysis, using naturally developed queens and workers as controls. First, the analysis included all the characters. Subsequently, a new analysis was made without the information about ovariole number and spermatheca size. Geometric morphometrics was less dependent on ovariole number and spermatheca information for caste and intercaste identification. This is useful, since acquiring information concerning these reproductive structures requires time-consuming dissection and they are not accessible when abdomens have been removed for molecular assays or in dried specimens. Additionally, geometric morphometrics divided intercastes into more discrete phenotype subsets. We conclude that morphometric geometrics are superior to traditional morphometrics techniques for identification and classification of honey bee castes and intermediates.     

Do we need the third dimension? Quantifying the effect of the z-axis in 3D geometric morphometrics based on sailfin silversides (Telmatherinidae)

This study investigated the impact of the third dimension in geometric morphometrics (GM) using sailfin silversides (Telmatherinidae) from the Malili Lakes of Sulawesi (Indonesia). The three morphospecies of the monophyletic “roundfin” radiation are laterally compressed and vary in shape traits. The results of 2D and 3D GM were compared and quantified to discuss the advantages and disadvantages of both methods for closely related species and their sexes. This approach focused on the head because it is far more complex and three-dimensionally structured than the trunk or the caudal region. The results revealed no significant benefit concerning repeatability and measurement error in 3D GM compared to 2D GM. The z-axis contributed substantially to the variance of the 3D data set but was irrelevant for discrimination of species and sexes in the approach. Limited gain in information was contrasted by substantially higher effort for 3D compared to the 2D analyses. The study concluded that 2D GM is the more efficient shape analysis approach for discriminating roundfins. Broader studies are needed to test which of the two methods is more efficient in distinguishing laterally compressed fishes in general. For future studies, due to the high investment required, this study recommends carefully evaluating the necessity of 3D GM. If in doubt, this study suggests testing for congruence between 2D and 3D GM with a subsample and consequently applying 2D GM in the case of high congruence.     

2012酶工程专刊序言

酶工程是酶学与工程科学融合的综合性科学技术,是现代生物技术与未来生物经济的支柱。近年来,随着在合成生物学研究上的突破,作为合成生物学重要核心内容的酶工程研究受到重视与关注,为促进国内酶工程研究的发展,本期"酶工程专刊"介绍了我国酶工程专家与青年学者在新酶的发掘、酶的作用机制及酶的生产与应用方面所取得的最新进展。     

A geometric morphometric and microsatellite analyses of <Emphasis Type="Italic">Scaptotrigona mexicana</Emphasis> and <Emphasis Type="Italic">S. pectoralis</Emphasis> (Apidae: Meliponini) sheds light on the biodiversity of Mesoamerican stingless bees

Geometric morphometrics and molecular methods are effective tools to study the variability of stingless bee populations and species that merit protection given their worldwide decline. Based on previous evidence of cryptic lineages within the Scaptotrigona genus, we tested the existence of multiple evolutionary lineages within the species S. mexicana and we investigated the status of S. pectoralis. By analyzing their population structure, we found differences between the Pacific and Atlantic populations of each of these species, although geometric morphometrics of the wing only confirmed these results in S. mexicana. There was a tendency towards enhanced genetic differentiation over larger distances in the Atlantic populations of both species but not in the Pacific populations. These results revealed a pattern of differentiation among evolutionary units and a specific distribution of genetic diversity within these Scaptotrigona species in Mesoamerica, suggesting the need for future taxonomic revisions, as well as activities aimed at management and conservation.     

Geometric morphometric analysis of the greater sciatic notch in South Africans

The width of the greater sciatic notch of the pelvis is a characteristic commonly used to determine sex in unknown individuals. Recent research on South African skeletal material indicated that this feature may not be so reliable, especially in South African white males. In this study the greater sciatic notches of 115 known skeletons of South African origin were analysed using geometric morphometrics. Geometric morphometrics is a relatively new method that helps to quantify shape. Using this method, it was observed that South African black males have the typical narrow shape, while both the black and white females have typical wide notches. The white males, however, showed a very wide variation and their shapes scattered across the range. The shape of the greater sciatic notch is therefore not reliable to use in sex determination in this population group. Geometric morphometric analysis proved to be a valuable and reliable method to verify morphological characteristics observed with more traditional methods.     

Use of shape to distinguish Chamelea gallina and Chamelea striatula (Bivalvia: Veneridae): Linear and geometric morphometric methods

The commercially fished striped venus clams Chamelea gallina and C. striatula (Bivalvia: Veneridae) are difficult to distinguish by inexperienced observers and the taxonomy of these species is still an issue of discussion. The differences in shape between C. gallina and C. striatula from Portuguese coastal waters were studied through conventional linear and geometric morphometric analysis, using both contour (elliptic Fourier analysis) and landmark-based methods. The relationships shell length vs. height, width, and total weight were significantly different between species. However, because there was a considerable overlap in the data sets, the species could not be distinguished using any combination of those linear measurements. Geometric morphometric methods provided shape variables that led to 0-6% misclassification rates between species; linear morphometric measures led to 16.8% error. Contour analysis revealed differences primarily in the shell umbo and lunular area. The umbo was more "sharp" and the lunula less pronounced in C. striatula than in C. gallina. Generalized procrustes superimposition (landmark analysis) showed that the main differences between species reside in the length of the pallial sinus. Thus, an index was developed (PI: Pallial Index = pallial sinus length/shell length), which was successfully used to separate the species (with 100% correct classification), i.e., specimens with PI lower than 0.119 belonged to C. gallina, whereas greater PI values were attributed to C. striatula. The use of these geometric morphometric methods allowed the detection of differences in shape between these two species and to develop an easy-to-use identification index. We encourage the development of analogous indices that apply the methods of geometric morphometrics to distinguish between other species whose identification is complicated.