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Endochondral bone in an Early Devonian ‘placoderm’ from Mongolia

Abstract

Endochondral bone is the main internal skeletal tissue of nearly all osteichthyans—the group comprising more than 60,000 living species of bony fishes and tetrapods. Chondrichthyans (sharks and their kin) are the living sister group of osteichthyans and have primarily cartilaginous endoskeletons, long considered the ancestral condition for all jawed vertebrates (gnathostomes). The absence of bone in modern jawless fishes and the absence of endochondral ossification in early fossil gnathostomes appear to lend support to this conclusion. Here we report the discovery of extensive endochondral bone in Minjinia turgenensis, a new genus and species of ‘placoderm’-like fish from the Early Devonian (Pragian) of western Mongolia described using X-ray computed microtomography. The fossil consists of a partial skull roof and braincase with anatomical details providing strong evidence of placement in the gnathostome stem group. However, its endochondral space is filled with an extensive network of fine trabeculae resembling the endochondral bone of osteichthyans. Phylogenetic analyses place this new taxon as a proximate sister group of the gnathostome crown. These results provide direct support for theories of generalized bone loss in chondrichthyans. Furthermore, they revive theories of a phylogenetically deeper origin of endochondral bone and its absence in chondrichthyans as a secondary condition.

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Fig. 1: MPC-FH100/9.1, a ‘placoderm’ skull roof and braincase from the Early Devonian of Mongolia.
Fig. 2: Endoskeletal mineralization in fossil gnathostomes.
Fig. 3: Braincase endocavity of MPC-FH100/9.1, Minjinia turgenensis.
Fig. 4: Strict consensus tree from equal weights parsimony analysis of early gnathostomes showing distribution of endochondral bone and exoskeletal armour.

Data availability

The holotype specimen of M. turgenensis will be permanently deposited in the collections of the Institute of Paleontology, Mongolian Academy of Sciences. Original tomograms are available at https://doi.org/10.6084/m9.figshare.12301229 and rendered models are available at https://doi.org/10.6084/m9.figshare.12301223. The phylogenetic character list and dataset are available as Supplementary Information and Supplementary Data 1. The LifeScience Identifier for M. turgenensis is urn:lsid:zoobank.org:act:82A1CEEC-B990-47FF-927A-D2F0B59AEA87

Code availability

R code for generating partitions based on character fits and code for likelihood ancestral state reconstructions and plots are available in the Supplementary Data 1 and 2.

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Acknowledgements

M. Bolortsetseg generously assisted M.D.B. with contacts and field experience in Mongolia. Fieldwork was supported by National Geographic Society grants CRE 8769-10 and GEFNE35-12 to M.D.B. The field contributions of A.J. were supported by funds from the Anna Maria Lundin’s stipend from Smålands Nation, Uppsala University. The field contributions of R.S. were supported by a Royal Society Research Grant and the University of Manchester. The majority of this work was supported by the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement number 311092 to M.D.B. R.P.D. was also supported by the Île-de-France DIM (Domaine d’Intérêt Majeur) Matériaux Anciens et Patrimoniaux grant PHARE. S. Walsh is thanked for access to and loan of a specimen at the National Museums of Scotland. Synchrotron tomography was performed at the European Synchrotron Radiation Facility (application LS 2451) with the assistance of P. Tafforeau. S.G. was supported by a Royal Society Dorothy Hodgkin Research Fellowship. M. Friedman is thanked for undertaking the X-ray computed microtomography analysis. This study includes data produced in the CTEES facility at University of Michigan, supported by the Department of Earth and Environmental Sciences and College of Literature, Science, and the Arts. TNT was made available with the support of the Willi Hennig Society.

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Contributions

M.D.B. conceived and designed the study. M.D.B., A.J., Y.A. and E.Z. participated in all field seasons. R.P.D. and A.J. undertook preliminary computed tomography scanning and segmentation that revealed the fossil was a ‘placoderm’ and had endochondral bone. R.S. discovered the first vertebrate remains in the first field season at Yamaat Gol in 2010. S.G. undertook the segmentation of Minjinia with input from M.D.B. A.J. performed segmentation of Diplacanthus tissue. M.C. provided input on occipital comparative morphology of ‘placoderms’. R.P.D. provided data and comparative analyses and data for endoskeletal tissue. Y.A. provided background on the geology, palaeontology and stratigraphy of the type location; E.Z. and Y.A. organized field logistics and permitting. M.D.B., S.G., M.C., R.P.D. and A.J. undertook the anatomical interpretation and prepared the figures. M.D.B. and S.G. conducted the phylogenetic analyses. R.S. conducted the parsimony branch support analyses. T.G. wrote the script for generating MrBayes partitions from TNT’s character fits table and conducted the likelihood and model-fitting analyses. The manuscript was written by M.D.B., R.P.D. and S.G.

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Correspondence to Martin D. Brazeau.

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Extended data

Extended Data Fig. 1 Tomograms of endoskeletal ossification in MPC-FH100/9.1, Minjinia turgenensis.

Top row: semi-coronal sections through braincase. Double-headed arrows indicate anterior-posterior (a-p) dorsal-ventral (d-v) axes. Bottom row: semi-transverse sections through posterior part of endocranium. Voids of black space represent mouldic preservation. Scale bars, 10 mm and apply across each row of panels.

Extended Data Fig. 2 Right orbital wall and innervation pattern of MPC-FH100/9.1, Minjinia turgenensis.

a, Orbit in anterolateral view showing position of nerve openings (pink infill). b, Endocast in the same perspective showing the relationship between nerve canals and endocast. a.scc, anterior semicircular canal; N.V2,3 trunk of the trigeminal nerve canal for branches 2 and 3; N.VIIhm, hyomandibular branch of facial nerve canal; N.VIIpal, palatine branch of facial nerve canal; sac, sacculus; sup.opht, canal for supra-ophthalmic nerve.

Extended Data Fig. 3 Results of phylogenetic parsimony analysis.

Dataset consists of 95 taxa and 284 characters. Both trees are strict consensus topologies. Equal weights parsimony analysis using the ratchet resulted in 240 trees with a length of 831 steps. Implied weights parsimony analysis using random addition sequence + branch-swapping resulted in 8 optimal trees with score 85.20513. Double-digit figures above internal branches are bootstrap values of 50% and over; single-digit figures below branches are Bremer decay index values. Blue shading: osteichthyan total group (dark blue: crown group); orange shading: chondrichthyan total group (dark orange: crown group).

Extended Data Fig. 4 Results of Bayesian phylogenetic analysis using both partitioned and unpartitioned data.

Majority-rules consensus trees with posterior probabilities shown along branches. Blue shading: osteichthyan total group (dark blue: crown group); orange shading: chondrichthyan total group (dark orange: crown group).

Extended Data Fig. 5 Likelihood ancestral state mapping of endochondral bone on equal weights parsimony results.

a, ARD, all rates different model; b, ER, equal rates model.

Extended Data Fig. 6 Likelihood ancestral state mapping of endochondral bone on unpartitioned Bayesian analysis results.

a, ARD, all rates different model; b, ER, equal rates model.

Supplementary information

Supplementary Information

Full phylogenetic character list and notes, character-state optimization data for a fully resolved parsimony tree, Supplementary Table 1 and references.

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Supplementary Video 1

A transverse section through the otic wall of M. turgenensis showing endochondral bone corresponding to Fig. 1a. Note that the thickness of the trabeculae is exaggerated: the trabeculae are encrusted in a carbonaceous matrix that does not contrast strongly with bone. This resulted in difficulties separating the trabeculae from the matrix with a single consistent threshold value. Indigo-coloured material is cranial exoskeleton. Taupe-coloured material is endoskeletal bone.

Supplementary Video 2

A transverse section through the otic wall of Ligulalepis showing endochondral bone corresponding to Fig. 1c. Data are from Clement et al. (2018) (main-text ref. 56). Indigo-coloured material is cranial exoskeleton. Taupe-coloured material is endoskeletal bone.

Supplementary Data 1

Phylogenetic character data (master Nexus file), command files, R scripts for data partitions and command lists for phylogenetic analyses in TNT.

Supplementary Data 2

R scripts and markdown for generating figures and output tables for ancestral states using maximum likelihood.

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Brazeau, M.D., Giles, S., Dearden, R.P. et al. Endochondral bone in an Early Devonian ‘placoderm’ from Mongolia. Nat Ecol Evol 4, 1477–1484 (2020). https://doi.org/10.1038/s41559-020-01290-2

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