Biodiversity in China Zone II Versions EN2 Vol 2 (4) 2017
3D morphological data of Pauropetalichthys magnoculus from the Early Devonian of Qujing, Yunnan, China
: 2017 - 09 - 25
: 2017 - 10 - 17
: 2017 - 12 - 22
2006 20 0
Abstract & Keywords
Abstract: Placodermi is a diversified jawed vertebrate group that underwent a highly successful radiation in the Devonian period (419.2 – 358.9 Ma). Recent anatomical and systematic studies, along with new fossil findings, have shown that placoderms represent an assemblage of primitive jawed vertebrates, which form the paraphyletic crownward part of the gnathostome stem group. As such, placoderms illuminate the step-wise character acquisition in the origin of crown gnathostomes or modern jawed vertebrates (including chondrichthyans, bony fishes, and tetrapods). Pauropetalichthys magnoculus, an early member of petalichthyids (a subgroup of placoderms), was discovered from the late Emsian (Early Devonian) of Qujing, Yunnan, China. We scanned Pauropetalichthys speciemen using the high-resolution computed tomography (HRCT) apparatus at the Key Laboratory of Vertebrate Evolution and Human Origins, and reconstructed the skull roof and neurocranium using Mimics (version 18.0). We found that Pauropetalichthys preserved part of the nasal capsules surrounded by perichondral bones. When the neurocranium was not preserved in placoderms, its shape was only inferred from the depression on the visceral surface of skull roof. By means of HRCT, we obtained anatomical details of the neurocranium by reconstructing the preserved perichondral bones and showed for the first time the perichondral lining of the nasal capsules in petalichthyids. This study on Pauropetalichthys adds to our understanding on the morphological diversity of placoderms and helps to evaluate the interrelationships of petalichthyids.
Keywords: petalichthyids; placoderms; Yunnan; Devonian; HRCT; 3D reconstruction
Dataset Profile
English title3D morphological data of Pauropetalichthys magnoculus from the Early Devonian of Yunnan, China
Data corresponding authorZhu Min (
Data authorsPan Zhaohui, Zhu Min
Time range407.6 – 393.3 Ma
Geographical scope25°35'4.78''N & 103°45'33.11''E; Shangshuanghe Village, Zhanyi District, Qujing City, Yunnan Province
Resolution per pixel8.63 μmData volume12.0 GB for *.raw, 1.87 GB for *.mcs.
Data format*.raw, *.mcs
Data service system<>
Sources of fundingNational Natural Science Foundation of China (41530102),
Key Research Program of Frontier Sciences of Chinese Academy of Sciences (QYZDJ-SSW-DQC002)
Dataset compositionThe dataset consists of 2D image data and 3D image data, which are recorded as *.raw and *.mcs, respectively:
① *.raw stores the raw tomographic image data, made up of 1538 tomography pictures totaling a data volume of 12.0 GB;
② *.mcs stores the 3D reconstructed data, with a data volume of 1.87 GB.
1.   Introduction
Placoderms, the most primitive jawed vertebrates, comprise diverse groups from various habitats and show large morphological disparity. Originated in the Silurian, placoderms underwent a successful evolutionary radiation and had a global distribution in the waters during the Devonian period (419.2 – 358.9 Ma).1–3 It was believed that Placodermi was a monophyletic group that had disappeared by the end of the Devonian. Recent studies regard placoderms as an assemblage of primitive jawed vertebrates, which form the paraphyletic crownward segment of the gnathostome stem group. In other words, placoderms were not extinct during the end-Devonian Mass Extinction, because one placoderm lineage evolved into crown gnathostomes or modern jawed vertebrates (Figure 1). Since placoderms are phylogenetically positioned at the stem of the gnathostome clade next to the common ancestor of modern jawed vertebrates,4–8 studies on their anatomy will help to illuminate the acquisition sequence of the key characters of modern jawed vertebrates.

Figure 1   Evolution of jawed vertebrates
Notes: The last common ancestor of modern jawed vertebrates (including chondrichthyans and osteichthyans) and all of its descendants form the crown group of jawed vertebrates (modern gnathostomes). The conventional Placodermi is an assemblage of primitive jawed vertebrates, which form the paraphyletic crownward part of the gnathostome stem group.
Petalichthyida, an important group of Placodermi, consists of Macropetalichthyidae, Quasipetalichthyidae, and basal petalichthyids including Diandongpetalichthys, Xinanpetalichthys, and Neopetalichthys.9–12 Petalichthyids are characterized by an elongated nuchal plate on which the supraorbital sensory canals and the posterior pit lines meet to form an X-shaped pattern.13 Among Petalichthyida, only Macropetalichthyidae is cosmopolitan, while Quasipetalichthyidae and basal petalichthyids are endemic in China. Research on Pauropetalichthys magnoculus has provided crucial evidence for studying the relationships of petalichthyids and corroborate, which supports that Petalichthyida was originated in China. 14Pauropetalichthys is the first petalichthyid taxon studied by the high-resolution computed tomography (HRCT) (Figure 2), whose morphological details render important data for the comparative anatomy of Placodermi. In addition, Pauropetalichthys preserved the perichondral bones of neurocranium. Reconstruction of the perichondral bones in Pauropetalichthys revealed a pair of the nasal capsules, which was discovered for the first time among Petalichthyida. As nasal capsule is an important part of the neurocranium, accumulation of similar data helps to reconstruct the neurocranial pattern of early vertebrates, and adds to our understanding of the evolution of early vertebrate neurocranium. The data were generated by the 225kV HRCT apparatus at the Key Laboratory of Vertebrate Evolution and Human Origins of CAS, and the scanning parameters herein could be used as a reference in other fossil scannings.

Figure 2   Pauropetalichthys magnoculus , Holotype IVPP V 20160
Notes: A. Photograph of the holotype; B. Digital reconstruction of the skull roof in ventral view; C. Digital reconstruction of the skull roof in dorsal view; D. Digital reconstruction of the skull roof in ventral view, with perichondral bones highlighted in yellow; E. Restoration of the neurocranium in ventral view. (scale: 2 mm)
To date, HRCT and three-dimensional (3D) reconstructions are widely used in research on the comparative anatomy and palaeohistology of Paleozoic fishes. Gai et al. reconstructed almost the whole neurocranium, sensory organs, nerves and vessels of a tiny galeaspid, which provided key fossil evidence to illuminate the origin of jaws.15 Rücklin et al. visualized a composite of distinct teeth that developed in succession in the jaw of Compagopiscis, comparable to tooth families in modern jawed vertebrates. They proposed that successional teeth evolved amongst the gnathostome stem-lineage soon after the origin of jaws.16 Dupret et al. proposed a novel hypothesis on the origin of the jawed vertebrate face by reconstructing the Romundina model.17 Zhu et al. provided critical evidence on the paraphyly of Placodermi and proposed a hypothesis on vertebrates' transition from primitive gnathal jaws to advanced maxillate jaws, partly based on HRCT reconstructions of Entelognathus and Qilinyu6, 8 of the Silurian Xiaoxiang Fauna. In sum, new HRCT technologies have supported significant breakthroughs of recent studies on early vertebrate evolution.
2.   Data collection and processing
2.1   Methods of data collection
Packaged in appropriate Styrofoam, the specimen was then placed on the platform of the 225 kV HRCT, where the center of the specimen matched the axis of the platform. The specimen was scanned with a beam energy of 130keV and a flux of 100 µA at a detector resolution of 8.6 µm per pixel, using a 720°rotation with a step size of 0.5° and an unfiltered aluminum reflection target.
2.2   Resolution calculation
The file "params.ini" in the "slices" folder recorded the parameters of this scan. According to the formula , we calculated the resolution of the data was 8.63 μm. In the formula, sod is the distance between the beam source and the sample, f is the distance between the beam source and the unfiltered aluminum reflection target, and dl is the pixel size of the target.
2.3   Methods of data processing
We imported all of the *.raw files into VG Studio (https://www.volumegraph or Drishti ( to generate an image package. We could either continue the 3D reconstruction with these softwares, or export a *.raw image package, then import the image package into Mimics ( to reconstruct the specimen. Note that the *.mcs file is specific to Mimics.
We drew each slice based on the differences of gray values between dermal bones, perichondral bones, and surrounding matrices. Combining all the slices, we generated the 3D model of Pauropetalichthys.
3.   Sample description
Class PLACODERMI McCoy, 1848
Order PETALICHTHYIDA Jaekel, 1911
Family Quasipetalichthyidae Liu, 1991
Genus Pauropetalichthys Pan et al., 2015
Species Pauropetalichthys magnoculus Pan et al., 2015 (Figure 2)
The 3D model consists of six masks. The meaning of each mask is shown in Table 1.
Table 1   Meaning of masks
No.Column 1Column 2
1skull roof+neurocraniumDermalbonesoftheskullroofand perichondral bonesofthe neurocranium
2f.d.endInternalforamenfor the endolymphaticduct
5qp?Possible palatoquadratecartilage
6perichondriumPerichondral bonesofthe neurocranium
4.   Quality control and assessment
The data were collected by the 225kV HRCT apparatus, which was jointly developed by the Institute of High Energy Physics and the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences. This apparatus is suitable to scan objects no larger than 10 cm × 10 cm × 10 cm, and a larger object can be scanned by segment. The study sample, about 1 cm × 1 cm × 0.5 cm in size, falls into the scanning capacity of this apparatus. The minimum rotation angle of HRCT is 0.5°. The resolution of the unfiltered aluminum reflection target is 8 µm/pixel. The error of HRCT is less than 0.5 μm, caused by the screw rod that adjusts the distance between the scanned object and the reflection target. To control the quality of the scan, we tested the resolution of HRCT in advance by using the Resolution Card. After completing the 3D reconstruction, we compared the measurements of the 3D models in the software with the measurements of the specimen by the vernier to evaluate the quality of the scan.
5.   Usage notes
The raw data collected by HRCT can be imported into any 3D reconstruction software. Generally, we import the raw data into VG Studio to cut off the useless region to reduce the size of the image package, and then import the image package into Mimics to conduct the reconstruction. The smaller the image package, the faster the Mimics. Oversized image packages can be reconstructed in VG Studio directly. Compared with Mimics which was designed for the medical industry, VG Studio runs faster. However, Mimics generates better effects in the 3D rendering of organisms. Drishti is an open-source software downloadable on GitHub. Drishti has all the advantages of an open-source software: free, flexible, and accountable, but with little support from its developers, Drishti has only basic functions and does not support large-sized data.
Mimics can export STL format files, which in turn can be imported into any 3D software. We tried to restore the whole nasal capsules of Pauropetalichthys by Mimics, but did not get a satisfactory result because Mimics does not support 3D mesh edits. That said, it is likely that our reconstruction can be further processed to restore the whole nasal capsules by means of Maya or 3D Max. We also recommend using a 3D printer to magnify the head model of Pauropetalichthys in the comparative anatomical studies of placoderms.
We thank Hou Yemao for helping us with HRCT scan.
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Data citation
1. Pan Z & Zhu M. 3D morphological data of Pauropetalichthys magnoculus from the Early Devonian of Qujing, Yunnan, China. Science Data Bank. DOI: 10.11922/sciencedb.487
Article and author information
How to cite this article
Pan Z & Zhu M. 3D morphological data of Pauropetalichthys magnoculus from the Early Devonian of Qujing, Yunnan, China. China Scientific Data 2 (2017). DOI: 10.11922/csdata.2017.16.zh
Pan Zhaohui
3D reconstruction.
PhD candidate, research area: morphology and phylogeny of petalichthyids and antiarchs.
Zhu Min
design of the project.
PhD, Professor; research area: early vertebrate evolution.
Publication records
Published: Dec. 22, 2017 ( VersionsEN2
Released: Oct. 17, 2017 ( VersionsZH1
Published: Dec. 22, 2017 ( VersionsZH3