Rapid divergent evolution of internal female genitalia and the coevolution of male genital morphology revealed by micro-computed tomography

Data from: Rapid divergent evolution of internal female genitalia and the coevolution of male genital morphology revealed by micro-computed tomography Nadia S. Sloan1, Mark S. Harvey1,2, Joel A. Huey1,2,3 and Leigh W. Simmons1 1Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley 6009, Australia. 2Department of Terrestrial Zoology, Western Australian Museum, Welshpool 6986, Australia. 3Biologic Environmental, East Perth 6004, Australia. ORCID iD NSS, 0000-0002-4081-5031; MSH, 0000-003-1482-0109; JAH, 0000-0001-7108-0552; LWS, 0000-0003-0562-1474 The data necessary to conduct the analyses reported in Sloan et al. are provided within this zip file. When expanded the folder contains two folders, “PLY files females” and “PLY files males”, two nexus files, and 6 csv files containing data. Each PLY file (polygon file format) contains the 3D scan data for each male gonopod and each female receptaculum for all samples of the species used in the comparative analysis. Each file is labelled with the species name and the West Australian Museum Voucher number (e.g. DIP015T150043) except A. variabilis which has the collection location (e.g. variabilisSerpNPfem2, Serpentine National Park female 2). These files can be entered into the Generalized Procrustes Surface Analysis (GPSA) software available in Pomidor et al. (2016) The files “male_gpsa_ordination_projections_all” and “female_gpsa_ordination_projections_all” are .csv files that are outputs from the GPSA software, and contain scores on the axes of variation (135 axes for males, 130 axes for females) that describe the shape of male and female genital structures. These data files can be used to conduct all of the analyses described in Sloan et al. 2024, Proceedings of the Royal Society of London: B. Two summary files are also provided, “male.ord.summary” and “female.ord.summary”, which provide the eigenvalue (value) for each axis of variation from the GPSA, the proportion of variance explained by that axis (pro) and the cumulative proportion of variance explained (cum). These data can be used to recreate Figure S5 found in the online supporting material of Sloan et al. Data on collum area (mm^2) for each species can be found in the csv files “male_collum” and “female_collum” and can be used in analyses of trait shape to control for species body size. The two nexus files, “1.4% run 1 nexus” and 2.3% run 1 nexus” provide the phylogenies calibrated with divergence rates of 1.4%/Ma and 2.3%/Ma required for the phylogenetic analyses described in Sloan et al. Molecular data used to construct phylogenies are available at Genbank using the accession numbers provided in Table S5 of the online supporting material of Sloan et al. Pomidor B.J., Makedonska J., Slice D.E. 2016 A landmark-free method for three-dimensional shape analysis. PLOS ONE 11(3), e0150368. (doi:10.1371/journal.pone.0150368).

数据集来源：基于显微计算机断层扫描（micro-computed tomography）揭示的雌性内生殖器快速趋异演化与雄性生殖器形态协同演化
作者：Nadia S. Sloan¹, Mark S. Harvey¹,², Joel A. Huey¹,²,³ 与 Leigh W. Simmons¹
¹ 西澳大利亚大学生物科学学院进化生物学中心，克劳利 6009，澳大利亚；² 西澳大利亚博物馆陆生动物学部，威尔士波 6986，澳大利亚；³ Biologic Environmental公司，东珀斯 6004，澳大利亚。
ORCID标识符：NSS：0000-0002-4081-5031；MSH：0000-0003-1482-0109；JAH：0000-0001-7108-0552；LWS：0000-0003-0562-1474

本压缩包包含Sloan等人本研究分析所需的全部数据。解压后内含两个子文件夹："雌性PLY文件"与"雄性PLY文件"，两份nexus格式文件，以及6份包含实验数据的逗号分隔值（CSV）文件。

每份PLY文件（多边形文件格式，PLY format）存储了本比较分析所用全部物种类群的雄性生殖肢与雌性纳精器的三维扫描数据。所有文件均以物种名与西澳大利亚博物馆凭证编号命名（例如DIP015T150043），仅A. variabilis例外，其文件名采用采集地点命名（例如variabilisSerpNPfem2，即蛇纹石国家公园雌性个体2）。

此类文件可导入由Pomidor等人（2016）开发的广义普罗克汝斯忒斯表面分析（Generalized Procrustes Surface Analysis, GPSA）软件中进行分析。文件"male_gpsa_ordination_projections_all"与"female_gpsa_ordination_projections_all"为GPSA软件生成的CSV格式输出文件，存储了描述雌雄生殖器形态的变异轴得分（雄性共135个变异轴，雌性共130个变异轴）。上述数据文件可用于复现Sloan等人2024年发表于《英国皇家学会学报B辑》的研究中所有分析内容。

本数据集同时提供两份摘要文件："male.ord.summary"与"female.ord.summary"，分别记录了GPSA分析得到的各变异轴的特征值、该轴解释的方差比例，以及累计方差解释比例。利用这些数据可复现Sloan等人在线补充材料中的图S5。

各物种类群的颈区面积（单位：平方毫米）数据存储于"male_collum"与"female_collum"两个CSV文件中，可用于形态性状分析时控制物种体型大小的变量。

两份nexus格式文件"1.4% run 1 nexus"与"2.3% run 1 nexus"分别存储了以1.4%/百万年（Ma）与2.3%/百万年（Ma）为分化速率校准的系统发育树，用于Sloan等人本研究中的系统发育分析。用于构建系统发育树的分子数据可通过基因银行（GenBank）检索获取，检索号详见Sloan等人在线补充材料的表S5。

参考文献：
Pomidor B.J., Makedonska J., Slice D.E. 2016 一种无标志点的三维形态分析方法. PLoS ONE 11(3), e0150368. (doi:10.1371/journal.pone.0150368).