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.     

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。     

植物内生固氮菌系统发育进化新进展

在植物内生固氮菌系统发育进化关系研究中,常用的方法有形态学与蛋白质水平法、数值分类和自动化鉴定法、化学分类法、分子遗传学方法等。本文简要介绍了常用方法的关键技术,并归纳了它们的优缺点。生物学的研究进入基因组时代后,随着高通量DNA测序技术在微生物学领域应用的迅速发展,全基因组测序被应用到微生物系统发育进化研究中,然而目前并未发现对已测全基因组序列的植物内生固氮菌进行系统总结。本文在对已测序植物内生固氮菌进行归纳的基础上,又详细研究了基于基因组数据的几种具有代表性的新方法(ANI分析法、最大唯一匹配指数法、核心基因组分析、组分矢量法、基因流动性分析),并结合目前系统发育进化研究常用方法,对植物内生固氮菌系统发育进化研究趋势进行总结和展望,旨在使植物内生固氮菌的系统发育进化关系研究在精确度、可靠性等方面有所突破。     

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。     

生物多样性起源与进化研究进展

生物多样性的起源与进化是生命科学领域最重要的科学问题之一。多组学数据的积累和相关分析技术的发展, 极大地推动了人们对生物多样性起源与进化的理解和研究, 使得阐明生物进化事件发生的过程与机制成为可能。值此《生物多样性》创刊30周年之际, 本文简要回顾生物多样性起源与进化相关研究在近年来取得的重要研究进展, 以期帮助读者了解该研究方向的发展现状。过去10年中, 生物多样性起源与进化相关研究在生命之树重建、生物多样性时空分布格局、物种概念、物种形成与适应性进化以及新性状起源与多样化等方面取得了许多重要进展, 并在此基础上厘清了许多分类单元间的系统发育关系、揭示了生物多样性分布格局的部分历史成因、提出了新的物种概念和物种形成模型、阐明了新性状和新功能发生的部分分子机制。我们认为, 更精准地重建生命之树、深入挖掘基因组数据以及多学科交叉融合将是今后生物多样性研究的主要趋势。     

生态基因组学研究进展

生态基因组学是一个整合生态学、分子遗传学和进化基因组学的新兴交叉学科。生态基因组学将基因组学的研究手段和方法引入生态学领域,通过将群体基因组学、转录组学、蛋白质组学等手段与方法将个体、种群及群落、生态系统不同层次的生态学相互作用整合起来,确定在生态学响应及相互作用中具有重要意义的关键的基因和遗传途径,阐明这些基因及遗传途径变异的程度及其生态和进化后果的特征,从基因水平探索有机体响应天然环境(包括生物与非生物的环境因子)的遗传学机制。生态基因组学的研究对象可以分为模式生物与非模式生物两大类。拟南芥、酿酒酵母等模式生物在生态基因组学领域发挥了重要作用。随着越来越多基因组学技术的开发与完善,越来越多的非模式生物生态基因组学的研究将为生态学的发展提供重要的理论与实践依据。生态基因组学最核心的方法包括寻找序列变异、研究基因差异表达和分析基因功能等方法。生态基因组学已广泛渗透到生态学的相关领域中,将会在生物对环境的响应、物种间的相互作用、进化生态学、全球变化生态学、入侵生态学、群落生态学等研究领域发挥更大的作用。     

甲虫形态学研究现状及态势分析

为了解甲虫形态学的研究概况和发展趋势,本文检索Zoological Record(ZR)数据库中该领域的研究论文,利用Thomson Data Analyzer(TDA)分析工具进行统计分析和数据挖掘。分析表明,该研究在20世纪六七十年代得到了快速发展,近十年以来,数量又有所增加。从事该研究的主要国家有美国、德国、日本、中国、法国等,热点主要内容集中在翅、生殖系统、结构大小、触角、口器等方向。新方法应用的领域各不相同,几何形态学和TEM的发文量较多,其次为显微CT和三维重建,MRI、CLSM、FIB/SEM发文量较少。甲虫形态学研究进入了一个新的发展阶段,显微CT、计算机三维重建、几何形态学等新方法的作用越来越突出。中国的研究数量表现不俗,但是论文影响力较弱,相关研究有待深入。     

生物多样性国际研究态势分析

生物多样性研究是综合性和高度交叉性的跨学科研究领域,是1997年底Science周刊上预测的1998年及近期的6个重大科学热点之一。检索1986—2008年间SCIE文献数据库中关于生物多样性的研究论文(article,proceedings paper和review),利用Thomson Data Analyzer(TDA)分析工具和Aureka分析平台进行数据挖掘。分析表明,该研究涉及多个学科领域,近年来在生态学领域的论文数量增加最多,而生物多样性保护、进化生物学、生物化学与分子生物学方面的论文增长速度较快。生物多样性研究越来越重视全球变化和人类社会对生物多样性的影响,DNA技术和基因工程等先进技术在生物多样性研究和保护中的作用也更加突出。     

区域生命之树及其在植物区系研究中的应用

区域生命之树是对一个区域内的所有物种进行生命之树重建,在最近10年已成为生命科学领域的研究热点。生命之树反映了物种间的亲缘关系和进化信息,可以将生物区系形成与发展过程中的进化和生态因素联系起来,是揭示区系来源和演化规律的有效手段。本文从3个方面总结了区域生命之树在植物区系研究中的应用:(1)在时间维度上,通过生命之树类群分化时间和进化速率估算,反映区系演化历史,揭示区系的时间分化格局;(2)在空间维度上,结合系统发育信息与物种分布数据,揭示区系内生物多样性的空间格局,并在此基础上进行区系分区;(3)整合生物地理信息和气候环境数据,分析区系中生物类群对古地理事件以及气候变化的响应机制,以揭示形成现存生物多样性格局的生态、地理和历史因素。此外,我们阐述了区域生命之树与全球生命之树之间的关系;指出由于类群取样不全而造成的时间估算偏差是区域生命之树研究中需要注意的问题;建议对生物多样性热点地区从不同尺度进行大数据的整合分析。     

ITS序列的特点及其在昆虫学研究中的应用

随着PCR技术和DNA测序技术的成熟及广泛应用,分子数据的分析和利用逐渐成为生物学研究的重要手段。基因组中含有丰富的遗传信息,运用核基因序列或将核基因与线粒体基因序列相结合作为遗传标记,研究昆虫的系统发育,已成为分子系统学领域的发展趋势。由于长度适中、易于扩增、进化速度快、变异性高等优点,核糖体基因中内转录间隔区(ITS)已在昆虫系统学研究中得到广泛的应用。本文介绍了ITS序列的结构特点,重点对ITS序列在近缘种及种型快速鉴定、属及属上高级阶元系统学研究、谱系生物地理学及与其它基因联合分析昆虫系统进化关系等研究中的应用及前景进行了综述。     

Testing heterochrony: Connecting skull shape ontogeny and evolution of feeding adaptations in baleen whales

Ontogeny plays a key role in the evolution of organisms, as changes during the complex processes of development can allow for new traits to arise. Identifying changes in ontogenetic allometry—the relationship between skull shape and size during growth—can reveal the processes underlying major evolutionary transformations. Baleen whales (Mysticeti, Cetacea) underwent major morphological changes in transitioning from their ancestral raptorial feeding mode to the three specialized filter-feeding modes observed in extant taxa. Heterochronic processes have been implicated in the evolution of these feeding modes, and their associated specialized cranial morphologies, but their role has never been tested with quantitative data. Here, we quantified skull shapes ontogeny and reconstructed ancestral allometric trajectories using 3D geometric morphometrics and phylogenetic comparative methods on sample representing modern mysticetes diversity. Our results demonstrate that Mysticeti, while having a common developmental trajectory, present distinct cranial shapes from early in their ontogeny corresponding to their different feeding ecologies. Size is the main driver of shape disparity across mysticetes. Disparate heterochronic processes are evident in the evolution of the group: skim feeders present accelerated growth relative to the ancestral nodes, while Balaenopteridae have overall slower growth, or pedomorphosis. Gray whales are the only taxon with a relatively faster rate of growth in this group, which might be connected to its unique benthic feeding strategy. Reconstructed ancestral allometries and related skull shapes indicate that extinct taxa used less specialized filter-feeding modes, a finding broadly in line with the available fossil evidence.     

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.     

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。     

Allometry and ontogeny in Callibia diana Stål (Mantodea: Acanthopidae)

The life-cycle of Callibia diana St?l is described and linear and geometric morphometrics are used for studying allometrics and shape changes throughout this neotropical mantid species' life-cycle. Significant changes were expected in the allometry and shape of the raptorial leg and abdomen, given the importance of hunting and reproduction. The allometric slopes were obtained by using total length as the independent variable. Geometric morphometrics of landmarks were used for frontal femur and tibia. Hunting and reproduction-related structures had the steepest slopes and positive allometries. Negative growth of both disc width and head width found in the last moulting event may be a consequence of prothoracic muscle growth which is responsible for predatory strike strength. The tibial claw and femur of the raptorial leg become larger, while their spines become more orthogonal to the longitudinal axes which may facilitate prey retention. These changes in mantid shape throughout ontogeny were consistent and suggested the resource allocation and development programming of the body that improved reaching distance and prey retention.     

Evolutionary patterns of hind wing morphology in dung beetles (Coleoptera: Scarabaeinae)

The shape of wings can be a good predictor of adaptations to different selective pressures and the value of wing features in taxonomy and phylogeny has long been recognized. In our investigation of the hind wing evolution of dung beetles (Scarabaeinae) we use geometric morphometrics combined with a cladistic approach. The variations of entire hind wings and of three specific regions of 80 dung beetle species were investigated using 19 landmarks and outline data. Extensive evidence indicates that the wing as a whole and the three separate regions were under different selective pressures. The detailed evolutionary patterns of the three regions and the reconstruction of the ancestral forms were computed by mapping the geometric morphometrics data onto a tree based on a cladistic character analysis.     

人类股骨断面面积与形状的不对称性——基于三维激光扫描的形态测量分析

人类股骨横断面面积、形状及其左右侧差异记载的人类演化、人群差异及生存活动的重要信息一直为古人类学研究所关注。多年来, 对股骨断面的研究通常采用破坏性地切割或者制作模型的方法。本文利用三维激光表面扫描技术, 无损、快捷、方便地获取了20对现代中国人左右侧股骨外轮廓的三维数据, 采用CAD软件及几何形态测量方法对两侧股骨断面轮廓的大小及形状进行了对比和分析。初步研究结果发现: 两侧股骨的横断面相对面积差异极其显著, 绝对面积差异不显著, 不对称方式表现为波动不对称性, 而不是偏向不对称性; 个体之间两侧股骨横断面外轮廓形状的波动不对称性极其显著, 偏向不对称性虽有差异但不显著; 平均形状和面积分析结果似乎表明股骨稍有偏左侧优势。虽然本文所采用的标本量有限, 所得出的结论需要更多标本的进一步验证, 但是, 本文的研究结果提示利用三维激光扫描技术获取股骨横断面外轮廓数据, 并采用形态测量方法分析确实能够揭示出一些以往研究方法不能发现的重要信息, 这种研究骨骼不对称性的新方法值得进一步的应用。     

The Evolution of Wing Shape in Ornamented-Winged Damselflies (Calopterygidae, Odonata)

Flight has conferred an extraordinary advantage to some groups of animals. Wing shape is directly related to flight performance and evolves in response to multiple selective pressures. In some species, wings have ornaments such as pigmented patches that are sexually selected. Since organisms with pigmented wings need to display the ornament while flying in an optimal way, we might expect a correlative evolution between the wing ornament and wing shape. We examined males from 36 taxa of calopterygid damselflies that differ in wing pigmentation, which is used in sexual displays. We used geometric morphometrics and phylogenetic comparative approaches to analyse whether wing shape and wing pigmentation show correlated evolution. We found that wing pigmentation is associated with certain wing shapes that probably increase the quality of the signal: wings being broader where the pigmentation is located. Our results also showed correlated evolution between wing pigmentation and wing shape in hind wings, but not in front wings, probably because hind wings are more involved in signalling than front wings. The results imply that the evolution of diversity in wing pigmentations and behavioural sexual displays might be an important driver of speciation due to important pre-copulatory selective pressures.     

Combined methods to detect pollution effects on shell shape and structure in Neogastropods

Tributyltin (TBT) has been widely used as antifouling in marine environments, producing imposex in gastropod females (i.e. neoformation of a vas deferens and/or a penis) and shell malformations in bivalves. However, effects of TBT and other pollutants from high marine traffic zones on the shell of gastropods have been little explored. Shell shape in volutids Odontocymbiola magellanica from a harbor polluted site (P) has been compared with that of animals from a non-polluted location (NP) using 3D geometric morphometrics. Also, the microstructure and density of shells from both populations were analyzed. Prior studies made in the same area (Golfo Nuevo, Patagonia, Argentina) based on traditional multivariate morphometrics showed some differences in size but was unable to detect differences in shell shape among O. magellanica from P and NP areas. Departing from 3D geometric morphometrics, scanning electron microscopy (SEM) and computed tomography (CT) techniques, we have registered the presence of patent differences on shell shape and structure in animals from polluted (P) and non-polluted (NP) areas. In 100% of shells from the NP area we register three calcium carbonate layers (prismatic, cross lamellar and amorphous) and higher densities, while in 50% of the shells collected at the P area the external layer (amorphous) was lacking. Furthermore, a body weight loss of around 30% and a shell weight loss of 20% were registered in animals from the P area. Our combined results suggest that the coordinated use of 3D geometrics morphometrics, CT scan and SEM could be of great utility in order to detect the effect of environmental variables on Neogastropods shell shape and structure.     

Geometric morphometrics: recent applications to the study of evolution and development

The field of morphometrics is developing quickly and recent advances allow for geometric techniques to be applied easily to many zoological problems. This paper briefly introduces geometric morphometric techniques and then reviews selected areas where those techniques have been applied to questions of general interest. This paper is relevant to non-specialists looking for an entry into geometric morphometric methods and for ideas of how to incorporate them into the study of variation within and between species, the measurement of developmental stability, the role of development in shaping evolution and the special problem of measuring the shape of fossil specimens that are deformed from their original shape.