全球锹甲的几何形态学数据集
A geometric morphometric dataset of stag beetles
通讯作者: * E-mail:baim@ioz.ac.cn;yangxk@ioz.ac.cn
第一联系人: #共同第一作者
编委: 黄晓磊
责任编辑: 闫文杰
收稿日期: 2021-04-26 接受日期: 2021-05-21
基金资助: |
|
Corresponding authors: * E-mail:baim@ioz.ac.cn;yangxk@ioz.ac.cn
First author contact: #Co-first authors
Received: 2021-04-26 Accepted: 2021-05-21
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。 数据库(集)基本信息简介
数据库(集)名称 全球锹甲的几何形态学数据集 作者 佟一杰, 张萌娜, Josh Jenkins Shaw, 万霞, 杨星科, 白明 通迅作者 杨星科(yangxk@ioz.ac.cn), 白明(baim@ioz.ac.cn) 时间范围 2019年 地理区域 全球 文件大小 929.48 KB 数据格式 .tps,.xlsx 数据链接 http://www.dataopen.info/article/204
http://doi.org/10.24899/do.202104001
https://www.biodiversity-science.net/fileup/1005-0094/DATA/2021160.zip 数据库(集)组成 数据集共包括3个文件: (1) Morphological dataset of pronotum.zip, 是所有锹甲测试样本的前胸背板的标点数据, 数据量274.65 KB; (2) Morphological dataset of elytron.zip, 是所有锹甲测试样本的鞘翅的标点数据, 数据量499.83 KB; (3) Classification.zip, 是所有锹甲测试样本的分类信息数据, 数据量155 KB。
关键词:
Stag beetles (Coleoptera: Lucanidae) have become an important model group for morphological research due to their sexual dimorphism, male polymorphism, and unique behaviors. Here we present a preliminary database of geometric morphometrics for 1,302 stag beetles, which includes nearly 99% of described species from around the world. This new dataset comprises morphological information from two continuous traits, the curves of the pronotum and elytron, both of which are typical characters of stag beetles. Two curves were measured from the left contours of the pronotum and elytron to represent their external forms. Curve 1 was measured from the middle of the anterior margin of the pronotum to the middle of the posterior margin of the pronotum. Curve 2 started from the anterior margin of the left elytron and terminated at the rear edge. Each curve was resampled into 25 and 50 equally spaced semi-landmarks, respectively. Our dataset provides a baseline for future research in several disciplines, including biodiversity, phylogeny and evolutionary biology. Database/Dataset Profile
Title A geometric morphometric dataset of stag beetles Authors Yijie Tong, Mengna Zhang, Josh Jenkins Shaw, Xia Wan, Xingke Yang, Ming Bai Corresponding authors Xingke Yang (yangxk@ioz.ac.cn), Ming Bai (baim@ioz.ac.cn) Time range 2019 Geographical scope Global File size 929.48 KB Data format .tps,.xlsx Data link http://www.dataopen.info/article/204
http://doi.org/10.24899/do.202104001
https://www.biodiversity-science.net/fileup/1005-0094/DATA/2021160.zip Database/Dataset composition The dataset consists of 3 subsets in total: Morphological dataset of pronotum.zip is the punctuation data of the pronotum of all stag beetle test samples, the data volume is 274.65 KB; (2) Morphological dataset of elytron.zip is the punctuation data of the elytra of all stag beetle test samples, the data volume is 499.83 KB; (3) Classification.zip is the classification information data of all the stag beetle test samples, the data volume is 155 KB.
Keywords:
本文引用格式
佟一杰, 张萌娜, 万霞, 杨星科, 白明 (2021)
Yijie Tong, Mengna Zhang, Josh Jenkins Shaw, Xia Wan, Xingke Yang, Ming Bai (2021)
形态比较的起源可以追溯到史前时期, 由其发展出的形态学是自然科学、材料科学和工程学的重要基础和信息来源(MacLeod, 2017)。几何形态学(Geometric Morphometrics)兴起于20世纪80年代至90年代(Bookstein, 1986, 1989, 1991; Rohlf & Bookstein, 1990), 研究者们试图从复杂的形态信息 (Bookstein, 1997; Ricklefs, 2012; Farré et al, 2013; Kozak & Wiens, 2016)中提取待测样本的形状数据集(shape dataset), 从而将形态分析手段综合于统一的方法中进行分析(MacLeod, 2017)。基于这种定量的分析手段, 传统形态学研究受到主观因素(Bouchard et al, 2011)以及二维线性距离分析(Fisher, 1938; Rao, 1948)的影响, 所面临的难于标准化获取、比较特征的形态信息(Smith, 1988; Vihelmsen, 2019; Polidori et al, 2020)等问题得到解决。几何形态学通过种内及种间固有的可比性, 在拓扑同源点的位置上呈现小范围差异(MacLeod, 2017), 从而为长久以来不易获取和进行比较的连续性特征的差异分析提供了新的思路。当前的大部分几何形态学研究基于间断性特征对地理种群间的形态差异进行比较(索中毅等, 2015; Francoy et al, 2016; Zhang et al, 2019), 尚无关于连续性特征在高级阶元的形态学和生物进化研究中是否具有重要意义的探究工作(Zhang et al, 2019; Tong et al, 2021)。
锹甲科昆虫广泛分布于除南极洲以外的各大洲(Mizunuma, 1994; Kim & Farrell, 2015), 全世界已有100属1,300种的锹甲被记录(Benesh, 1960; Pinratana & Maes, 2002; Fujita, 2010)。锹甲特殊的性二型和雄虫多型现象长期以来吸引了大量学者关注(Fujita, 2010; Bai et al, 2015; Monte et al, 2016; 佟一杰等, 2016), 多样的形态结构变化也使得这一类群成为了很好的形态学研究对象。前胸背板(pronotum)和鞘翅(elytron)是甲虫背面观占比最大的连续性特征, 因其丰富的形态多样性及强大的功能, 在锹甲进化和分类学研究中具有重要意义, 前者为前胸内肌肉系统和前足的运动(Evans, 1977; Chapman, 1998)提供了重要的支持作用; 后者的形成使得锹甲的后翅及柔软的腹部受到更好的保护, 从而对周围环境的适应能力大大提升(Van de Kamp & Greven, 2010; Beutel & Leschen, 2011)。
本文中, 我们首次提供了一份基于几何形态学手段获取的前胸背板及鞘翅的形态数据集, 该数据集涵盖全世界99%已描述的锹甲物种。本文的目的是通过该数据集提高对连续性特征的标准化获取和分析的认识, 同时为后续的多特征比较研究或其他类群的形态学分析工作创造条件, 对连续性特征形变的意义进行更为系统的评估。本数据集可用于多方面的探索工作: (1)量化后的连续性特征所包含的形态信息在昆虫分类中的应用; (2)生物进化过程中连续性特征和间断性特征的加权策略的探究; (3)结合几何形态学和系统发育信息获取生物祖先的特征信息。
1 数据采集和处理方法
1.1 数据预处理
表1 测试亚科类群的取样信息
Table 1
测试亚科级类群 Test subfamily-level group | 族级阶元样本量 Number of tribes sampled | 属级阶元样本量 Number of genera sampled | 种级阶元样本量 Number of species sampled |
---|---|---|---|
斑纹锹甲亚科 Aesalinae | 3 | 7 | 41 |
金锹甲亚科 Lampriminae | 2 | 5 | 11 |
锹甲亚科 Lucaninae | 4 | 89 | 1,225 |
Syndesinae | 0 | 3 | 25 |
总计 Total | 10 | 104 | 1,302 |
1.2 数据的采集
首先, 数据集中的形态学信息取自锹甲样本的前胸背板和鞘翅的左侧外轮廓(图1)。曲线1(Curve 1)由前胸背板前缘的中点起至前胸背板的后缘中点止; 曲线2 (Curve 2)由鞘翅的前缘与小盾片末端交界处起至鞘翅侧缘端点止。前胸背板和鞘翅的外轮廓曲线分别按照长度均等分为25/50个半标点(semi-landmark)以保证其形态信息被完整地提取(图1)。通过软件TPS-Utility (Version: 1.64)和TPS- DIG (Version: 2.05) (Rohlf, 2005; Bai et al, 2014; Tong et al, 2021)将所有曲线和半标点数据化。其次, 通过文本编辑器打开TPS文件, 将数据中的曲线标号以及半标点信息删除并将半标点信息替换为标点信息(Rohlf, 2010; Zhang et al, 2019), 获得的新数据集保存用于后续几何形态学分析。同时, 本研究展示了锹甲科下的族级类群的前胸背板和鞘翅的形态变化情况(由前三个主要成分表示: PC1-PC3), 用于指示分散在形态空间(PC coordinates' space)中的测试特征沿主成分轴正方向上的形变趋势(图2)。特征的形变图由主成分轴负极值处的红色逐渐过渡至正极值处的蓝色, 以便更加直观地展示各测试类群对应的形态变化程度。
图1
图1
几何形态学分析中的测试曲线(a)及半标点(SLM)(b)的标注(图示为Pristoderus viridipictus)
Fig. 1
Description of the curves (a) and semi-landmarks (SLM) (b) used in the geometric morphometric analysis (Pristoderus viridipictus)
图2
图2
锹甲科的测试特征的形态变化(族级阶元)。a, 前胸背板沿主成分轴1和主成分轴2的形态变化; b, 前胸背板沿主成分轴2和主成分轴3的形态变化; c, 鞘翅沿主成分轴1和主成分轴2的形态变化; d, 鞘翅沿主成分轴2和主成分轴3的形态变化。
Fig. 2
Deformation trend of test characters (tribe-level test) in lucanid beetles. a, Deformation trend of the pronotum along PC1 and PC2. b, Variation of the pronotum along PC2 and PC3. c, Variation of the elytron along PC1 and PC2. d, Variation of the elytron along PC2 and PC3.
2 数据描述
样本图片主要来源于本实验室的历史积累, 含历届研究生毕业论文、专著、世界各主要博物馆馆藏标本、重要文献等(Fujita, 2010)。
一份记录锹甲前胸背板和鞘翅的主文件已上传至数享(Data-Open), 这份文件中包含22份TPS格式的测试特征形态信息文件, 以及11份Excel格式的记录锹甲分类地位的说明文件:
(1) 20份几何形态学标点文件(.tps)。代表了9个族级类群以及分类系统中不含有族级阶元的Syndesinae亚科的前胸背板和鞘翅的形态学数据。所有的形态学数据依据前胸背板/鞘翅进行了25/50个分布于形态空间的地标点的划分。
(2)与几何形态学标点文件对应的10份测试类群分类地位的说明文件(.csv)。每份说明文件中包含对该类群中所有测试样本的分类地位的展示, 样本的分类地位统一进行整理: 亚科-族-属-种, 以便其他科研人员更好地使用对应的标点文件。分类地位说明文件中的样本的列表顺序即为对应的标点文件中的顺序, 以便快速确定标点文件中测试样本的分类学地位。
(3) 2份整合后的几何形态学标点数据(.tps)及1份对应的样本分类地位说明文件(.csv)同样被上传至数享(Data-Open), 整合标点数据分别包含了所有测试样本的前胸背板形态学信息及鞘翅的形态学信息, 方便科研人员根据需要自行选择整合标点数据/测试类群标点数据。
3 数据质量控制和评估
4 数据使用方法和建议
当使用前胸背板及鞘翅的形态学数据(.tps格式)时, 请引用本文。该数据集将具有探索不同锹甲类群间形态差异和系统发育关系的潜在用途。例如, 将几何形态学数据映射到系统发育树上实现锹甲祖先前胸背板和鞘翅的形态特征的重建, 从而通过定量分析手段可视化测试特征的形态演化(Zhang et al, 2019); 通过挖掘测试特征在主成分空间中的最大形变程度可以探索锹甲进化的多元化模型。此外, 除本研究提供的数据集外, 还可以整合更多的几何形态学软件对数据进一步分析。例如, 通过Morpho J 1.06a (Klingenberg, 2011)对数据集进行主成分分析(principal component analysis)获取测试类群的Procrustes变异值(通常被视为形态多样性数值), 从而为该数据集在生物多样性研究中的使用提供支撑; 通过Morpho J 1.06a (Klingenberg, 2011)对数据集进行典型变量分析(canonical variance analysis)以及判别分析(discrimination function analysis)探究不同阶元类群之间的差异。
致谢
感谢中国科学院动物研究所鞘翅目形态与进化研究组为这项研究提供的科研平台, 同时衷心感谢深圳职业技术学院阮用颖博士为本研究提供的富有成效的建议。
作者分工
佟一杰和张萌娜构建数据集; 张萌娜收集锹甲类群的形态信息; Josh Jenkins Shaw对文稿正文进行审阅; 佟一杰和万霞对数据集中样本的分类学地位进行厘定; 杨星科对文稿正文进行审阅; 白明设计本课题思路。
参考文献
Description of a new species of Glaresidae (Coleoptera: Scarabaeoidea) from the Jehol Biota of China with a geometric morphometric evaluation
Mandible evolution in the Scarabaeinae (Coleoptera: Scarabaeidae) and adaptations to coprophagous habits
DOI:10.1186/s12983-014-0093-6 URL [本文引用: 1]
Size and shape spaces for landmark data in two dimensions
Principal warps: Thin-plate splines and the decomposition of deformations
DOI:10.1109/34.24792 URL [本文引用: 1]
Family-group names in Coleoptera (Insecta)
DOI:10.3897/zookeys.88.807 URL [本文引用: 3]
Locomotion in the Coleoptera Adephaga, especially Carabidae
DOI:10.1111/j.1469-7998.1977.tb03237.x URL [本文引用: 1]
Geometric morphology as an alternative for measuring the diversity of fish assemblages
DOI:10.1016/j.ecolind.2012.12.005 URL [本文引用: 1]
The statistical utilization of multiple measurements
DOI:10.1111/j.1469-1809.1938.tb02189.x URL [本文引用: 1]
Wing morphometrics indicates the existence of two distinct phenotypic clusters within population of Tetragonula iridipennis (Apidae: Meliponini) from India
DOI:10.1007/s00040-015-0442-2 URL [本文引用: 1]
Phylogeny of world stag beetles (Coleoptera: Lucanidae) reveals a Gondwanan origin of Darwin's stag beetle
DOI:10.1016/j.ympev.2015.02.015 URL [本文引用: 2]
MorphoJ: An integrated software package for geometric morphometrics
DOI:10.1111/j.1755-0998.2010.02924.x
PMID:21429143
[本文引用: 2]
Increasingly, data on shape are analysed in combination with molecular genetic or ecological information, so that tools for geometric morphometric analysis are required. Morphometric studies most often use the arrangements of morphological landmarks as the data source and extract shape information from them by Procrustes superimposition. The MorphoJ software combines this approach with a wide range of methods for shape analysis in different biological contexts. The program offers an integrated and user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. MorphoJ is written in Java and versions for the Windows, Macintosh and Unix/Linux platforms are freely available from http://www.flywings.org.uk/MorphoJ_page.htm.© 2010 Blackwell Publishing Ltd.
What explains patterns of species richness? The relative importance of climatic-niche evolution, morphological evolution, and ecological limits in salamanders
DOI:10.1002/ece3.2016.6.issue-16 URL [本文引用: 1]
Morphometrics: History, development methods and prospects
Revision of the Australian species of Figulus MacLeay, 1819 (Coleoptera: Lucanidae)
DOI:10.11646/zootaxa.4189.3 URL [本文引用: 1]
Comparative morphology of the antennal ‘release and spread structure' associated with sex pheromone-producing glands in male Cynipoidea
DOI:10.1007/s00435-020-00490-5 URL [本文引用: 1]
The utilization of multiple measurements in problems of biological classification
DOI:10.1111/rssb.1948.10.issue-2 URL [本文引用: 1]
Species richness and morphological diversity of passerine birds
Proceedings of the Michigan Morphometrics Workshop
tpsDig, digitize landmarks and outlines, Version 2.05
tpsUtil. Version 1.47
A synopsis of the sawflies (Hymenoptera: Symphyta) of America south of the United States: Introduction, Xyelidae, Pamphiliidae, Cimbicidae, Diprionidae, Xiphydriidae, Siricidae, Orussidae, Cephidae
DOI:10.1111/sen.1988.13.issue-2 URL [本文引用: 1]
A geometric morphometric analysis of the morphological variations among Chinese populations of Protaetia brevitarsis (Coleoptera: Scarabaeidae) with an inference of the invading source of its Xinjiang populations
中国白星花金龟地理变异的几何形态学分析及其新疆种群的入侵来源推断
Geometric morphometrics evaluation and adaptive evolution study of Scarabaeinae metendosternites
蜣螂后胸叉骨的几何形态学分析及其适应进化研究
The relationship between genus/species richness and morphological diversity among subfamilies of jewel beetles
DOI:10.3390/insects12010024 URL [本文引用: 2]
On the architecture of beetle elytra
Giant sawflies and their kin: Morphological phylogeny of Cimbicidae (Hymenoptera)
The Cimbicidae is a small family including the largest extant true sawflies (Tenthredinoidea). It comprises four subfamilies, three of which have a northern hemisphere distribution (Abiinae, Cimbicinae - Holarctic/Oriental; Corynidinae - Palaearctic), whereas the Pachylostictinae are restricted to South America. No previous attempts have been made to evaluate the subfamily classification in a cladistic context. In the present paper, 144 morphological characters from the adult anatomy for a total of 95 species of Cimbicidae and 26 outgroup taxa are scored. All subfamilies and all genera of Cimbicidae except one are represented; all families of Tenthredinoidea are represented in the outgroup. Equal weights (EW) and implied weights (IW) analyses are conducted in tnt. The results largely corroborate the existing subfamily classification, except for Pachylostictinae which are paraphyletic in IW analyses with low K-values. Abiinae + Cimbicinae is always retrieved and strongly supported; Corynidinae + Pachylostictinae is retrieved in most analyses but weakly supported. Revised diagnoses of the subfamilies are provided. Several genera are retrieved as monophyletic, notable exceptions being Praia and Trichiosoma, which are polyphyletic. The evolution of large body size in Cimbicidae is briefly discussed; possible related phenomena are intrasexual competition and mimicry, i.e. resemblance to large apids or vespids.
Geometric morphometric analysis of the pronotum and elytron in stag beetles: Insight into its diversity and evolution
/
〈 |
|
〉 |
