Project highlights

  • Ray finned fishes have evolutionary roots stretching back nearly 400 million years
  • The dual barriers of deep timescales and fossil preservation present barriers to understanding early anatomical innovations
  • This project will combine taphonomic experiments and refining tomographic techniques to reconstruct the early evolutionary history of ray-finned fishes.


Living ray-finned fishes, which account for over half of all living vertebrate diversity (some 36,000 species), display anatomical innovations of the skeleton and soft tissues. As the living groups diverged from each other around 360 million years ago, fossils are vital for understanding their evolution. These deep evolutionary roots present a number of problems, however. Firstly, soft tissue rarely fossilises, and the processes by which soft tissue is preserved in the vertebrate fossil record are poorly understood. Secondly, fossil fishes are often preserved in dense rocks that are tricky to image using CT scanning and even tricker to digitally dissect. Together, these present a barrier to reconstructing anatomies and relationships at the base of the ray-finned fish tree of life.

Technological advances in CT scanning and synchrotron imaging have revolutionised work on early fossil fishes. Notable recent examples include the discovery of exceptionally preserved soft tissue anatomy: the heart of a Devonian (~380 million years old) placoderm (Trinajstic et al. 2022) and the brain of a Carboniferous (~319 million years old) ray-finned fish (Figueroa et al. 2022). Aside from representing novel preservational styles, these features provide key information regarding anatomical innovations deep in the vertebrate tree. Taphonomic studies in fishes are in their infancy (Sansom et al. 2013), and the mechanisms by which such delicate structures as the brain are preserved in fossils that are well over 300 million years old is far from clear. Despite these exceptional discoveries, many of the rocks that host these fossils have lithologies and geometries that make them challenging to CT scan. This project will combine tomographic techniques and taphonomic experiments to understand how neural soft tissue structures are preserved in fossils, investigate anatomical innovations revealed by fossilised soft tissues, and refine CT scanning practices for fossil specimens. This research will provide new insights into exceptional three-dimensional preservation of soft tissues in vertebrate fossils, as well as the use of CT scanning to investigate mechanisms of taphonomy and decay.

Photo of a fossil fish and smaller inset of a CT section through the skull The brain is visible as a symmetrical white object.
Figure 1: Fossil of the exceptionally preserved Carboniferous ray-finned fish Coccocephalichthys (a) and a CT slice through the skull showing the symmetrical, x-ray dense brain (b).


University of Birmingham


  • Organisms and Ecosystems


Project investigator

Dr. Sam Giles, University of Birmingham ([email protected])


How to apply


This project will focus on performing taphonomic experiments and refining tomographic techniques in order to understand exceptional fossil preservation. The student will survey museum collections (initially at the Natural History Museum, with potential travel worldwide) for taphonomically promising horizons in which vertebrate soft tissues may be preserved. CT scanning and/or synchrotron scanning of these specimens will focus on internal anatomy (e.g. braincase) and soft tissues (e.g. heart, brain), as well as specimens with challenging compositions (e.g carbonates, ironstones) and geometries (e.g. high aspect ratios). Best practice protocols will be quantitatively investigated throughout, an area of immature research in palaeontology. In conjunction with identifying soft tissues in fossils, the student will perform experimental taphonomy work on extant fish to investigate potential pathways for preserving soft tissue. This work will be complemented by description of the soft and hard tissue anatomy of key specimens, feeding into revisions of their taxonomy and relationships.

Training and skills

Students will be awarded CENTA2 Training Credits (CTCs) for participation in CENTA2-provided and ‘free choice’ external training. One CTC equates to 1⁄2 day session and students must accrue 100 CTCs across the three years of their PhD.

The student will be trained in the entire CT workflow from selecting specimens to scanning to segmentation, comparative anatomy and description, taxonomic and phylogenetic analyses, statistical methods, and taphonomic experimental design. The student will also receive training in how to write and illustrate scientific papers, apply for grants and awards, present work at conferences and scientific meetings, and network with peers. There may also be opportunities for undergraduate teaching and research supervision. These form the basis of an outstanding skill set, combining traditional and state- of-the-art techniques, that will facilitate a successful research career for the student.

Partners and collaboration

This project will be carried out in collaboration with Dr Paul Wilson at the University of Warwick, Dr Rob Sansom at the University of Manchester and Dr Zerina Johanson at the Natural History Museum, London. Dr Wilson is an X-Ray CT Specialist and will provide support on optimising tomographic techniques. Dr Sansom will provide supervision and advice relating to experimental taphonomic design. The collections at the NHM represent a world-leading resource, with exceptionally preserved material that is of key importance to this project. Dr Johanson has extensive experience of CT scanning and anatomical interpretation and will assist in these areas.

Further details

Dr Sam Giles, University of Birmingham ([email protected]). We particularly encourage applications from backgrounds underrepresented in geology/palaeontology and allied subjects, and welcome informal enquiries.

If you wish to apply to the project, applications should include:

  • A CV with the names of at least two referees (preferably three and who can comment on your academic abilities)
  • Submit your application and complete the host institution application process via: and go to Apply Now in the PhD Geography and Environmental Science (CENTA) section. Please quote CENTA23_B7 when completing the application form.

Applications to be received by the end of the day on Wednesday 11th January 2023. 

Additional information for international applicants

  • All international applicants must ensure they can fulfil the University of Birmingham’s international student entry requirements, which includes English language requirements.  For further information please visit
  • Please be aware that CENTA funding will only cover University fees at the level of support for Home-fee eligible students.  The University is only able to waive the difference on the international fee level for a maximum of two successful international applicants.

Possible timeline

Year 1

Literature review, museum visits, preliminary scanning and experimental design.

Year 2

Taphonomic experiments, detailed investigation of scanning parameters, segmentation and descriptions.

Year 3

Completion of taphonomic runs, synthesis, completing thesis, writing manuscripts (although manuscripts will be written throughout project).

Further reading

  • Camilieri-Asch, V., Shaw, J.A., Mehnert, A., Yopak, K.E., Partridge, J.C. and Collin, S.P., 2020. Dicect: a valuable technique to study the nervous system of fish. Eneuro, 7(4).
  • Figueroa, R.T., Goodvin, D., Kolmann, M.A., Coates, M.I., Caron, A.M., Friedman, M. and Giles, S., 2022. Exceptional fossil preservation and evolution of the ray-finned fish brain. bioRxiv.
  • Sansom, R.S., Gabbott, S.E. and Purnell, M.A., 2013. Atlas of vertebrate decay: a visual and taphonomic guide to fossil interpretation. Palaeontology56(3), pp.457-474.
  • Trinajstic, K., Long, J.A., Sanchez, S., Boisvert, C.A., Snitting, D., Tafforeau, P., Dupret, V., Clement, A.M., Currie, P.D., Roelofs, B. and Bevitt, J.J., 2022. Exceptional preservation of organs in Devonian placoderms from the Gogo lagerstätte. Science377(6612), pp.1311-1314.


A resurgence of covid-19 could impact international travel, for example to view museum collections. This can be mitigated by arranged for loans from these museums to the NHM or University of Birmingham. During the last pandemic and lockdown, CT-facilities were kept open and staffed, as much as possible, for time-limited projects, such as PhD theses. NHM workstations can be accessed remotely. Preliminary CT data has already been collected for several specimens, and can be worked on in the event that travel is not possible.