Dataset of 3D high-resolution μCT scan of fossil specimens of <i>Qinglongtriton gangouensis</i>, a basal salamandroid (Amphibia, Urodela) from the Upper Jurassic of Hebei Province, China

Biodiversity in China Zone II • Versions EN2 Vol 3 (1) 2018.

Dataset of 3D high-resolution μCT scan of fossil specimens of Qinglongtriton gangouensis, a basal salamandroid (Amphibia, Urodela) from the Upper Jurassic of Hebei Province, China

Jia Jia, Gao Ke-Qin

DOI: 10.11922/csdata.2017.0004.zh
: 10.11922/sciencedb.527

： 2017 - 11 - 17

： 2017 - 12 - 11

： 2018 - 02 - 26

735 37 0

Abstract & Keywords

Abstract: It comes the digital era for paleontological research. High-resolution X-ray tomography (or μCT) has several advantages (high resolution, high efficiency and non-destructive detection) over traditional mechanical preparation and serial sectioning techniques when used to investigate fossil specimens. Thus, this new technique has been widely used by paleontologists in their study of fossils. This paper provides a methodological description of μCT scanning of fossils of a Jurassic salamander, Qinglongtriton gangouensis, and provides the μCT source data of the holotype (PKUP V0226) and two referred specimens (PKUP V0228, PKUP V0254) of this fossil taxon. Qinglongtriton gangouensis is a primitive salamander classified in the suborder Salamandroidea. Specimens of this taxon were discovered from the Upper Jurassic Tiaojishan Formation of Hebei Province, China, and the fossil beds have been dated at ~160 million years. A 3D printable stl formatted file of the upper body skeleton of PKUP V0226, together with CT images and videos of the three specimens, was provided to display the reconstructed skeleton of the three specimens. This is the first attempt of employing μCT technique in the study of salamander fossils from China. Several unique osteological features were revealed via μCT scan of the specimens; for instance, the absence of an ossified orbitosphenoid provides deep insights in understanding character evolution in Salamandroidea. This dataset offers a methodological reference for the application of μCT scan technique in future research of fossil salamanders, and also opens a window to the public arena for virtual access to the results of our CT scanning of the Jurassic salamander fossils.

Keywords: μCT scan; fossil salamander; Qinglongtritongangouensis; Salamandroidea; Late Jurassic; Tiaojishan Formation; Hebei Province

Dataset Profile

Title	μCT dataset of skeletons of basal salamandroid (Amphibia, Caudata) Qinglongtriton gangouensis
Data authors	Jia Jia, Gao Ke-Qin
Datacorresponding author	Jia Jia(jia_jia@pku.edu.cn)
Time range	Fossil beds of Qinglongtriton pertain to the Upper Jurassic Tiaojishan Formation, which date back to (160.889±0.069)–(160.254±0.045) Ma;1 Specimens were collected in the summer of 2009 and μCT-scanned in the spring of 2015.
Geographical location of fossil site	Specimens of Qinglongtriton were collected from the same fossil horizon at the Gangou fossil site (40°31'52''N/119°29'11''E), located on a hill to the north of the Nanshimenzi Village, Gangou County, Qinglong Manchu Autonomous County, Qinhuangdao City, Hebei Province, China.
CT scan resolution	PKUP V0226 (66.624 μm), PKUP V0228 (118.609 μm), PKUP V0254 (78.569 μm)
Data volume	44.8 GB
Data format	.tif, .stl, *.avi
Data service system	<http://www.sciencedb.cn/dataSet/handle/527>
Sources of funding	China Scholarship Council (201306010049);National Natural Science Foundation of China (41702002, 41072007, 41272016); Shandong Provincial Key Laboratory of Depositional Mineralization & Sedimentary Mineral, Shandong University of Science and Technology (DMSM2017002); Key Laboratory of Economic Stratigraphy and Palaeogeography, Chinese Academy of Sciences (Nanjing Institute of Geology and Palaeontology) (2017KF03).
Dataset composition	The dataset consists of 4 subsets in total. Each of the first to the third subsets includes source data generated from μCT scan of PKUP V0226, PKUP V0228 and PKUP V0254, respectively. The fourth subset comprises reconstructed images and videos of all the three specimens and an stl file of the skull portion of PKUP V0226 for 3D printing.The four subsets has a total of 6 data documents, recorded as PKUPV0226rawdata.zip, PKUPV0228rawdata.zip,PKUPV0254 rawdata.zip, PKUPV0226stl.zip, pics.zip, videos.zip:(1) PKUPV0226rawdata.zip is made up of 1998 tiff images and a text file (PKUPV0226.xtekct) containing parameters of μCT scan, with a data volume of 14.8 GB; (2) PKUPV0228rawdata.zip is made up of 1998 tiff images and a text file (PKUPV0228.xtekct) containing parameters of μCT scan, with a data volume of 14.8 GB; (3) PKUPV0254rawdata.zip is made up of 1998 tiff images and a text file (PKUPV0254.xtekct) containing parameters of μCT scan, with a data volume of 14.8 GB; (4) PKUPV0226stl.zip consists of 1 stl file for 3D printing of the upper body of PKUP V0226, with a data volume of 227 MB; (5) pics.zip comprises 7 tiff images of the reconstructed skeletons of PKUP V0226, PKUP V0228 and PKUP V0254, with a data volume of 15.9 MB; (6) videos.zip is made up of 3 avi formatted video files, each of which displays the rolling motion of PKUP V0226, PKUP V0228 and PKUP V0254; and another avi file showing the rotation of rendered skull of PKUP V0226, with a data volume of 135 MB.

1. Introduction

In paleontological research, fossil specimens have to be prepared in a laboratory where rock matrixes are removed to fully expose the fossil for observation. This can be done by manual or mechanical preparation, or by acid treatment of specimens. However, these traditional means of specimen preparation are not only unable to fully reveal three-dimensional structures of the fossil, but often cause irretrievable damage on the specimen. If enough number of specimens are available, serial-sectioning technique can be employed to examine the interior structures of fossil specimens.³ Nevertheless, the lost part between thin sections also precludes the recovery of a complete morphology of the specimen.

High-resolution X-ray tomography (high-resolution micro-CT or μCT) features as an established technique that is capable of acquiring the complete three-dimensional morphology of a physical object via X-rays within a short time period. Obviously, μCT technique bears several advantages (high resolution, high efficiency and non-destructive detection) over the laborious and tedious mechanical preparation or serial-sectioning techniques, and thus it has been extensively used to investigate a number of key transitional groups of vertebrates, including sarcopterygian Eusthenopteron,^4–5 basal tetrapod Ichthyostega,⁶ pelobatid frog Prospea,⁷ stem snake Dinilysia,⁸ ctenochasmatid pterosaur Liaodactylus,⁹ tyrannosauroid dinosaur Alioramus,¹⁰ early bird Confuciusornis¹¹ and early mammal Vilevolodon.¹² μCT technique not only facilitates the observation and measurement of specimens, but also allows investigators to conduct functional morphological studies based on digital models, such as biomechanical analysis of the limb mobility of the early tetrapod Ichthyostega.⁶ Furthermore, three-dimensional digital models can be printed to produce physical casts, which are ideal for both research and museum exhibition.

This paper provides the μCT source data of a primitive salamandroid Qinglongtriton gangouensis. Salamanders are a group of tailed amphibians, including three suborders: Cryptobranchoidea (70 species, 11 genera, 2 families), Salamandroidea (633 species, 55 genera, 7 families) and Sirenoidea (4 species, 2 genera, 1 family). Salamanders are classified in the subclass Lissamphibia along with frogs and caecilians.¹³ Previous studies based on molecular data show that salamanders are an ancient lineage, originated about 262.5~357.0 million years ago.^14–15 Since 1990s, tens of thousands of salamander specimens have been found from the Mesozoic strata in northern Hebei Province, western Liaoning Province and southeastern Inner Mongolia, China. These fossils are remarkably well preserved and show quite a rich taxonomic diversity. To date, 10 species in 8 genera have been identified as cryptobranchoids and 2 species in 2 genera as salamandroids.^16–18 This paper, our recent publication of the salamandroid Qinglongtriton, represents the first application of μCT and 3D printing in the research of fossil salamanders from China.¹⁷ By using these new techniques, we were able to provide a more thorough morphological account of this significant Jurassic fossil taxon than previous studies on fossil salamanders from China, and hence shed new lights on the early evolution of Salamandroidea.¹⁷

Publication of high-quality μCT source data in paleontological research makes an easy way for researchers to share digital models of important fossil specimens in a global scale. We realize that several online libraries, like Dryad or DigiMorph, have already archived the μCT source data and 2D and 3D visualizations of several important fossil specimens. Therefore, this paper provides the μCT source data of the holotype (PKUP V0226) and two referred specimens (PKUP V0228, PKUP V0254) of the early salamandroid Qinglongtriton gangouensis from the Upper Jurassic Tiaojishan Formation of Hebei Province, China. This paper is also supplemented with a 3D printable stl file of the upper body skeleton of the holotype (PKUP V0226), as well as images and videos displaying the reconstructed skeleton of the three specimens.

2. Data collection and processing

2.1 Data collection

Before μCT scanning, specimens of Qinglongtriton were mechanically prepared under microscope to be better fit onto the object stage of the μCT scanner for high-resolution images. A total of 46 specimens of this taxon were collected during the field season in 2009, all of which were prepared at the School of Earth and Space Sciences, Peking University, Beijing, China.¹⁷ Among these, the holotype (PKUP V0226) and two referred specimens (PKUP V0228 and PKUP V0254) were scanned using the Nikon XT H 320 LC scanner at the Industrial Micro-CT Laboratory of China University of Geosciences (Beijing). Visualization, segmentation and 3D reconstruction of these specimens were undertaken by using the software package VG Studio Max 2.2 (Volume Graphics, Heidelberg, Germany). It is noteworthy that VG Studio is not the only, but a widely used software package for dealing with image stack. Readers who are interested in learning about other commercial or free software are recommended to refer to the work of Richard Leslie Abel et al.¹⁹

2.1.1 Specimens preparation and μCT scan

Both the holotype (PKUP V0226) and the referred specimens (PKUP V0228 and PKUP V0254) of Qinglongtriton were broken into several blocks of different sizes during field collection. The surrounding matrix of each block of the specimen was carefully removed to expose the fossil skeleton by using fine needles under microscope. In order to enhance the penetrating power of X-rays, the matrix on both sides of specimens along the longitudinal axis was removed as much as possible by using a hand-hold electric grinder to narrow the width of the specimen. Specimen surfaces were spread with varnish and acetone mixtures to prevent fragmentation of the bony skeleton. Then the blocks of each specimen were pieced together using a mixture of soda powder and 2-cyanoacrylate adhesive.

The whole specimen was placed onto the object stage with its long axis set to be perpendicular to the stage. The source-to-object distance was adjusted to enlarge the projection of the specimen onto the X-ray detector. Rotate the object stage for 360° to ensure that the complete projection of the specimen was documented by the detector. Considering different thicknesses of the fossil specimens, voltages and currents of the scanner were adjusted for each specimen to reinforce the contrast between the fossil and its surrounding matrix.

2.1.2 Data generation

When conducting μCT scan, the X-ray detector generated a 2D radiograph image (tiff formatted) that contained the gray value of the fossil specimens each time the object stage rotated by 0.11457670273711° along a single axis. In total, each scan produced a sequential of 3142 radiographs (tiff formatted) of 2D projections and a parameter file in xtekct format. All of the tiff files were imported into the 3D pro software that comes with the Nikon XT H 320 scanner, to reduce the artefacts along the edge of the specimen that resulted from specimen shaking or X-ray beam-hardening (cupping artefacts). Then, an image stack consisting of 1998 16-bit tiff images along the longitudinal axis (z axis) of the specimen were exported, namely, PKUPV0226rawdata.zip, PKUPV0228rawdata.zip, PKUPV0254rawdata.zip for the three specimens respectively (Figure 1).

Figure 1 Workflow of specimens of Qinglongtriton gangouensis in preparation, μCT scan and data processing

2.2 Data processing

First, the image stack of 1998 tiff files (16 bit) was imported into VG Studio Max 2.2. The contrast between the fossil and its surrounding matrix, as observed in cross sections, was strengthened by assigning a relatively low value to the background (air) and a relatively high value to the material (fossilized bone). After these files were read, the fossil material was shown in four windows, with three windows displaying transverse sections (X-Y axis, Y-Z axis, X-Z axis) and a fourth window showing a 3D digital model arbitrarily orientable. Take the X-Y axis window as an example: a region of interest (ROI, Figure 2) of a certain bone was created by drawing the outline of the bone that appeared on each slice in this window. The ROI was extracted as a maneuverable 3D model. 3D printable stereolithography (stl) files were exported after surface determination was conducted on the 3D model, namely, the PKUPV0226stl.zip file in this dataset, which contains an stl file of the upper body of the holotype (PKUP V0226). In addition, the fossil skeleton of each specimen was segmented along the transverse section, and a complete structure of the fossil was numerically generated. High-resolution tiff images (pics.zip) and avi videos (videos.zip) were created to show the dorsal and ventral views of the fossil.

Figure 2 Color rendering and the regions of interest (ROIs) of the skull in the holotype of Qinglongtriton gangouensis

Notes: A, B, C are three transverse sections.

3. Sample description

The holotype (PKUP V0226) specimen and two referred specimens (PKUP V0228 and PKUP V0254) are all adult individuals (Figures 3 & 4). In PKUP V0226, the skull length (SKL, distance between premaxilla and the posterior extremity of exoccipital) is 45.11 mm, the skull width (SKW, maximum distance between the cranio-mandibular joints) is 40.35 mm, and the snout-pelvic length (SPL, distance between premaxilla and the posterior border of ischium) is 155.71 mm. The SKL and SKW are 40.79 mm and 35.78 mm in PKUP V0228, and 46.18 mm and 44.23 mm in PKUP V0254. The SPL is 148.47 mm in PKUP V0228, while it is unmeasurable in PKUP V0254 as the posterior part of its trunk region is lost. The holotype is preserved in dorsal view, whereas the two referred specimens are both preserved in ventral view (Figure 3). μCT imagery of Qinglongtriton shows that the ribs are bicapitate and the angular is fused with the prearticular in the lower jaw, both of which are diagnostic features of the suborder Salamandroidea. Cladistic analysis shows that Qinglongtriton gangouensis and the previously reported salamandroid Beiyanerpetonjianpingensis²⁰ form a clade, which in turn forms the sister group taxon to the rest of salamandroids.¹⁷

Systematic Paleontology of Qinglongtriton gangouensis:

Class Amphibia Linnaeus, 1758

Subclass Lissamphibia Haeckel, 1866

Superorder Caudata Scopoli, 1777

Order Urodela Duméril, 1806

Suborder Salamandroidea Dunn, 1922

Family Incertae Sedis

Qinglongtritongangouensis Jia and Gao, 2016

Figure 3 Photographs of the three specimens of Qinglongtritongangouensis (A. holotype PKUP V0226; B. referred specimen PKUP V0228; C. referred specimen PKUP V0254)

Several morphological features of Qinglongtriton that are unable to be observed through traditional mechanical preparation were readily recognizable via μCT scan of the three specimens. As Figure 2 illustrates, purple and orange represent the frontal and parietal bone of the skull roof, respectively; and dark green represents the parasphenoid bone in the palate. Orbitosphenoid was confirmed by the μCT imagery to be absent in Qinglongtriton. In most living salamanders, orbitosphenoid is part of the braincase that sets between the frontal and parietal in the skull roof and the parasphenoid in the palate, which firmly supports the skull roof and protects the cartilaginous brain. To our knowledge, orbitosphenoid is absent only in the derived Proteidae and the plethodontid Eurycea. The μCT scan of specimens of Qinglongtriton gangouensis proves the absence of bony orbitosphenoids in the early evolution of the Salamandroidea, and the loss of the orbitosphenoid in Proteidae and Eurycea is likely resulted from convergent evolution.

Figure 4 μCT reconstruction of the referred specimen PKUP V0228 of Qinglongtritongangouensis (A. dorsal view; B. ventral view)

4. Quality control and evaluation

The μCT source data of Qinglongtriton gangouensis were generated by the Nikon XT H 320 LC CT scanner housed at the Industrial Micro-CT Laboratory of China University of Geosciences (Beijing). The X-ray detector of this scanner has a resolution of 2000×2000 pixels. No filter was used during μCT scanning. Settings of the voltage, current and resolution for each scan are summarized in Table 1, with the remaining parameters documented in the parameter file in xtekct format.

Table 1 Parameters of the μCT scan of three specimens of Qinglongtritongangouensis

Catalogue number	Voltage (kV)	Current (μA)	Resolution (μm)
PKUP V0226	180	105	66.62411648599
PKUP V0228	170	63	118.608638745882
PKUP V0254	170	47	78.569482133407

The stl file showing the upper body of the holotype was created after segmentation and smoothing of the ROI. Original ROI of each skeleton was smoothed by setting smooth strength at 1 and depth at 8 bit, which was then extracted and surface-determined.

The videos of the three specimens of Qinglongtriton were all made by using the key frame function in the animation option of VG Studio Max 2.2, and no compression was conducted.

5. Value and significance

Compared with traditional techniques (serial sectioning and mechanical preparation), high-resolution X-ray tomography is non-destructive and efficient in unveiling the interior structures of fossil specimens, offering great convenience for paleontologists to investigate the anatomy of fossil specimens. This work on Qinglongtriton represents the first attempt of applying μCT scan in the study of Mesozoic salamanders from China. The 3D printable stl file of the upper body of the holotype provides an easy access to obtain physical casts of the fossil specimen of Qinglongtriton gangouensis. We hope that this paper is also helpful to researchers who intend to use μCT scanning technique in their research.

Acknowledgments

We are deeply thankful for Dr. Changfu Zhou of Shandong University of Scientific and Technology and Dr. Lijun Zhang of Shenyang Normal University for their generous help in prospecting and specimen collection. We appreciate Dr. Qinfang Fang for CT scanning the specimens of Qinglongtriton. Jia Jia express his gratitude to Dr. Jianye Chen, Dr. Morgan Hill and Mr. Henry Towbin (American Museum of Natural History) and Dr. Hongyu Yi (Institute of Vertebrate Paleontology and Paleoanthropology) for their help in 3D printing the holotype of Qinglongtriton.

Chu Z, He H, Ramezani J et al. High-precision U-Pb geochronology of the Jurassic Yanliao Biota from Jianchang (western Liaoning Province, China): age constraints on the rise of feathered dinosaurs and eutherian mammal. Geochemistry, Geophysics, Geosystems 17 (2016): 1 – 10.