Bothriolepis (Placodermi, Arthrodira) from Iveragh Peninsula (Ireland) - CT-Data, 3D-Models, and Phylogenetic Analyses Files

The current data set refers to the study of fossil fish material from Southwest Ireland (Placodermi, Antiarchi; Givetian of the Iveragh Peninsula). The data consist of SEM elemental mapping (section 1), CTscan image stacks and subsequent working files (i.e. segmentation, visualisation files, STLs and 3D PDF files; sections 2-5), as well as phylogenetic analyses related to the genus Bothriolepis studied in the article (section 6).
* Zoobank LSID for article: urn:lsid:zoobank.org:pub:0438B3D4-AEAA-4000-A1CB-B5DA0ECA466F
* Zoobank LSID for taxon Bothriolepis dairbhrensis: urn:lsid:zoobank.org:act:B577F075-1EF6-48A5-8C7C-E64E36E2BC4E

The dataset corresponding to the article

Dupret, Byrne, Castro, Hammer, Higgs, Long, Niedźwiedzki, Qvarnström, Stössel & Ahlberg. In Press. The Bothriolepis (Placodermi, Antiarcha) material from the Valentia Slate Formation of the Iveragh Peninsula (middle Givetian, Ireland): morphology, evolutionary and systematic considerations, phylogenetic and palaeogeographic implications. PLOS ONE.
with the LSID urn:lsid:zoobank.org:pub:0438B3D4-AEAA-4000-A1CB-B5DA0ECA466F
and the species Bothriolepis dairbhrensis Dupret, Byrne, Castro, Hammer, Higgs, Long, Gzegorz Niedźwiedzki, Qvarnström, Stössel & Ahlberg
with the LSID urn:lsid:zoobank.org:act:B577F075-1EF6-48A5-8C7C-E64E36E2BC4E

is composed of the following files:

1. Elemental analysis (SEM)
equipment: Hitachi S–3600N Scanning Electron Microscope (SEM); JPGS are original output.

2. CT-scans datasets
In London, the material was CT-scanned with a Nikon HMX ST 225 system, Nikon Metrology, Leuven, Belgium, with a tungsten reflection target. Detailed settings files were adjusted for each specimen and are given in associated documentation "S2 Table-scan properties.xlsx". Two specimens required stitching performed with an in-house NHM script written in Octave. In Oslo, the scanning was carried out with a Nikon Metrology XT H 225 ST microfocus CT instrument at the Natural History Museum, University of Oslo, at 160-220 kV, 1 s exposure time, 3016 projections, and with tin filters of varying thickness. Voxel resolution was 75 µm or better. Detailed settings are given in in associated documentation "S2 Table-scan properties.xlsx".

3. Drishti and Mimics files (segmentation)

4. STL files

5. 3D pdfs
In Mimics, each individual structure corresponding to a mask was used to generate a high quality 3D object, itself transformed into an STL file. Each 3D object was duplicated and relocated in the 3D space; once again STLs were generated. The STL files were then imported into Materialise 3-matic (v. 15.0) and were reorganised into anatomical ensembles (head, fin, etc.) in both original and correct positions. Each STL surface was then simplified and corrected using the following functions: Filter Sharp Triangles with filter distance 0.01; Filter Small Edges with filter distance 0.01; Improve Mesh with shape quality high/medium, maximum geometrical error 0.07, and maximal edge length 20.0. A 3D pdf file was finally generated and open in Adobe Acrobat to take pictures used in figures of the current article.

for the following specimens
a. NMING:F35203-UU210ab_HQ
Bothriolepis dairbhrensis sp. nov. Incomplete lateral plate and fragment of indeterminate plate. Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm.
Please note that within the Mimics project files for this specimen µm is incorrectly given as a base of measurement when it should be mm (millimeters). All other processing has been performed treating the source data as being scaled in millimeters.

b. NMING:F35229-CH003
Bothriolepis dairbhrensis sp. nov. Assemblage of indeterminate plate and indeterminate scavenging gastropods. Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm.

c. NMING:F35216-UU SFB001
Bothriolepis dairbhrensis sp. nov. Proximal segment of the pectoral fin, with AVL and articular condyle. [ORG] corresponds to plates in original position; [RELOC] corresponds to plates relocated in life position. Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm.

d. NHM P 59677 (complete, ORG end RELOC files)
Bothriolepis dairbhrensis sp. nov. Incomplete head (and endocranial processes), ventral body armour and proximal segment of the pectoral fin. [ORG] corresponds to plates in original position; [RELOC] corresponds to plates relocated in life position. Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm.

e. NHM P 59678
Bothriolepis dairbhrensis sp. nov. Incomplete lateral and indeterminate plates of an adult individual. The scale of the reference cube edges is 10 mm.

f. NHM P 59679
Bothriolepis dairbhrensis sp. nov. Two indeterminate fragments. The scale of the reference cube edges is 10 mm.

g. NHM P 59687
Bothriolepis dairbhrensis sp. nov. Indeterminate fragments and burrows. The scale of the reference cube edges is 10 mm.

6. taxon*character matrices with different sets of analyses (readible in MESQUITE)

**LINKS TO PREVIOUSLY MENTIONED SOLUTIONS**
MESQUITE (construction of data matrix, visualisation):
https://www.mesquiteproject.org/
https://github.com/MesquiteProject/
Maddison, W. P. and D.R. Maddison. 2021. Mesquite: a modular system for evolutionary analysis. Version 3.70 http://www.mesquiteproject.org

ZEPHYR (Mesquite package for interacting with external phylogeny inference programs)
http://zephyr.mesquiteproject.org/
Maddison, D.R., & W.P. Maddison. 2021. Zephyr: a Mesquite package for interacting with external phylogeny inference programs. Version 3.20. http://zephyr.mesquiteproject.org

TNT (phylogenetic analysis)
https://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2008.00217.x
Goloboff, P.A., Farris, J.S. and Nixon, K.C. (2008), TNT, a free program for phylogenetic analysis. Cladistics, 24: 774-786. https://doi.org/10.1111/j.1096-0031.2008.00217.x

MATERIALISE MIMICS and 3-MATIC (segmentation, 3D modelling):
https://www.materialise.com/en/healthcare/mimics-innovation-suite

DRISHTI (3D visualisation):
https://github.com/nci/drishti
Ajay Limaye; Drishti: a volume exploration and presentation tool. Proc. SPIE 8506, Developments in X-Ray Tomography VIII, 85060X (October 17, 2012)

当前数据集涉及爱尔兰西南部（伊维拉半岛吉维特期（Givetian）；盾皮鱼纲（Placodermi）、反弓亚纲（Antiarchi））的鱼类化石材料研究。数据包含扫描电子显微镜（SEM）元素图谱（第1部分）、计算机断层扫描（CT）图像堆栈及后续工作文件（即分割、可视化文件、STL文件和3D PDF文件；第2-5部分），以及与文章中研究的沟鳞鱼属（Bothriolepis）相关的系统发育分析（第6部分）。
* 文章的Zoobank LSID：urn:lsid:zoobank.org:pub:0438B3D4-AEAA-4000-A1CB-B5DA0ECA466F
* 分类单元Bothriolepis dairbhrensis的Zoobank LSID：urn:lsid:zoobank.org:act:B577F075-1EF6-48A5-8C7C-E64E36E2BC4E

本数据集对应以下文章：

Dupret, Byrne, Castro, Hammer, Higgs, Long, Niedźwiedzki, Qvarnström, Stössel & Ahlberg. 待刊. 《爱尔兰伊维拉半岛瓦伦提亚板岩组（中吉维特期）的沟鳞鱼属（Placodermi, Antiarcha）材料：形态学、演化与系统学考量，及系统发育与古地理意义》. PLOS ONE.
其LSID为urn:lsid:zoobank.org:pub:0438B3D4-AEAA-4000-A1CB-B5DA0ECA466F
且物种Bothriolepis dairbhrensis由Dupret, Byrne, Castro, Hammer, Higgs, Long, Gzegorz Niedźwiedzki, Qvarnström, Stössel & Ahlberg命名，其LSID为urn:lsid:zoobank.org:act:B577F075-1EF6-48A5-8C7C-E64E36E2BC4E

本数据集包含以下文件：

1. 元素分析（SEM）
设备：日立S–3600N扫描电子显微镜（SEM）；JPG文件为原始输出。

2. CT扫描数据集
在伦敦，使用比利时鲁汶尼康计量（Nikon Metrology）的尼康HMX ST 225系统对材料进行CT扫描，采用钨反射靶。每个标本的详细设置文件均已调整，并在相关文档“S2 Table-scan properties.xlsx”中提供。两个标本需使用伦敦自然历史博物馆（NHM）内部用Octave编写的脚本进行拼接。在奥斯陆，于奥斯陆大学自然历史博物馆使用尼康计量XT H 225 ST微焦点CT仪器扫描，参数为160-220 kV电压、1秒曝光时间、3016次投影及不同厚度的锡滤光片。体素分辨率为75微米（µm）或更高。详细设置见相关文档“S2 Table-scan properties.xlsx”。

3. Drishti与Mimics文件（分割）

4. STL文件

5. 3D PDF文件
在Mimics中，每个对应掩码的独立结构用于生成高质量3D对象，再转换为STL文件。每个3D对象被复制并在3D空间重新定位，再次生成STL文件。随后将STL文件导入Materialise 3-matic（v.15.0），按原始位置与正确位置重组为解剖集合（头部、鳍等）。接着使用以下功能简化与校正每个STL表面：过滤尖锐三角形（过滤距离0.01）；过滤小边（过滤距离0.01）；优化网格（形状质量高/中，最大几何误差0.07，最大边长20.0）。最终生成3D PDF文件，在Adobe Acrobat中打开以获取本文图中所用图像。

以下为涉及的标本：
a. NMING:F35203-UU210ab_HQ
新种沟鳞鱼（Bothriolepis dairbhrensis sp. nov.）。不完整侧片及未定种骨片碎片。在Mimics中分割，在3-matic中处理STL文件并导出3D PDF。参考立方体边长比例为10毫米。请注意：该标本的Mimics项目文件中错误地将微米（µm）作为测量单位，正确单位应为毫米（mm）。所有其他处理均将源数据视为以毫米为单位缩放。
b. NMING:F35229-CH003
新种沟鳞鱼（Bothriolepis dairbhrensis sp. nov.）。未定种骨片与未定种食腐腹足类集合。在Mimics中分割，在3-matic中处理STL文件并导出3D PDF。参考立方体边长比例为10毫米。
c. NMING:F35216-UU SFB001
新种沟鳞鱼（Bothriolepis dairbhrensis sp. nov.）。胸鳍近端节段，含AVL与关节髁。[ORG]对应原始位置的骨片；[RELOC]对应复位至生活位置的骨片。在Mimics中分割，在3-matic中处理STL文件并导出3D PDF。参考立方体边长比例为10毫米。
d. NHM P 59677（完整，含ORG与RELOC文件）
新种沟鳞鱼（Bothriolepis dairbhrensis sp. nov.）。不完整头部（及颅内突起）、腹甲与胸鳍近端节段。[ORG]对应原始位置的骨片；[RELOC]对应复位至生活位置的骨片。在Mimics中分割，在3-matic中处理STL文件并导出3D PDF。参考立方体边长比例为10毫米。
e. NHM P 59678
新种沟鳞鱼（Bothriolepis dairbhrensis sp. nov.）。成体个体的不完整侧片与未定种骨片。参考立方体边长比例为10毫米。
f. NHM P 59679
新种沟鳞鱼（Bothriolepis dairbhrensis sp. nov.）。两块未定种碎片。参考立方体边长比例为10毫米。
g. NHM P 59687
新种沟鳞鱼（Bothriolepis dairbhrensis sp. nov.）。未定种碎片与钻孔。参考立方体边长比例为10毫米。

6. 分类单元-特征矩阵（含多组分析，可在MESQUITE中读取）

**前述软件链接**
MESQUITE（数据矩阵构建、可视化）：
https://www.mesquiteproject.org/
https://github.com/MesquiteProject/
Maddison, W. P. & D.R. Maddison. 2021. Mesquite：一款模块化演化分析系统。版本3.70 http://www.mesquiteproject.org

ZEPHYR（Mesquite扩展包，用于与外部系统发育推断程序交互）
http://zephyr.mesquiteproject.org/
Maddison, D.R., & W.P. Maddison. 2021. Zephyr：一款用于与外部系统发育推断程序交互的Mesquite扩展包。版本3.20. http://zephyr.mesquiteproject.org

TNT（系统发育分析）
https://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2008.00217.x
Goloboff, P.A., Farris, J.S. & Nixon, K.C. (2008). TNT：一款免费系统发育分析程序。Cladistics, 24: 774-786. https://doi.org/10.1111/j.1096-0031.2008.00217.x

MATERIALISE MIMICS与3-MATIC（分割、3D建模）：
https://www.materialise.com/en/healthcare/mimics-innovation-suite

DRISHTI（3D可视化）：
https://github.com/nci/drishti
Ajay Limaye；Drishti：一款体数据探索与展示工具。Proc. SPIE 8506, X射线断层扫描进展VIII, 85060X（2012年10月17日）