EVOLUTION OF AXIAL SKELETAL REGIONALISATION IN VERTEBRATES: INTEGRATING PHYLOGENY, ENVIRONMENT, AND DEVELOPMENTAL MECHANISMS

Lead Research Organisation: UNIVERSITY OF CAMBRIDGE
Department Name: Zoology

Abstract

Evolutionary diversification of the axial skeleton (i.e. vertebrae and ribs) is a key component of the success of vertebrate animals. "Fishes" are generally thought to possess a two-region axial skeleton, with "precaudal" and "caudal" vertebrae, while tetrapods exhibit regionalisation of their vertebral column into distinct cervical, thoracic, sacral, and caudal regions. Conventional wisdom is, therefore, that the evolutionary transition from water to land coincided with increasing anatomical specialisations of the vertebral column. However, recent discoveries of striking axial skeletal complexity in some living and fossil fish groups suggest an alternative scenario: the primitive presence of a regionalised, complex axial skeleton in vertebrates, with repeated loss or augmentation of regionalisation as adaptation to new environments and ecologies. This project will be the first to explicitly and quantitatively reconstruct the evolutionary history of vertebrate axial skeletal complexity, and to test for environmental and developmental correlates of such complexity.

In order to understand the evolution of the vertebral column and its role in diversifications into new environments and ecology, we will combine anatomical and regulatory genetic datasets to undertake a concerted investigation of axial skeletal regionalisation in a broad taxonomic sample of extant and fossil vertebrates. 1) We will quantify axial skeletal regionalization and complexity based on skeletal data derived from Computed Tomography and direct specimen measurement. 2) We will use comparative phylogenetic methods to reconstruct ancestral states for major vertebrate clades and to test for correlations between axial skeletal regionalisation and environmental and ecological factors. 3) We will test for expression of genes that define the amniote cervical-thoracic and thoracic-lumber transitions in embryos of a cartilaginous fish (the skate, Leucoraja erinacea), and we will use fluorescent cell labelling approaches to test whether these genes delineate previously unrecognised axial skeletal regions in this species. By comparing our findings with those from other lineages (e.g. tetrapods), we will be able to infer mechanisms of axial skeletal development at one of the earliest nodes in vertebrate evolutionary history. 4) Finally, we will use evolutionary modelling to combine results of anatomical, evolutionary, and developmental analyses to elucidate the relationships between vertebral morphology and developmental mechanisms in evolutionary transitions into new environments.

Debate surrounding the evolution of the vertebrate axial skeleton has lingered for centuries, with current dogma and "textbook scenarios" stemming largely from speculation, and suffering from poor taxon sampling. Our study will integrate anatomical, developmental and environmental data, within a rigorous phylogenetic framework, in order to accurately reconstruct the evolutionary and ecological history of the vertebrate axial skeleton.

Planned Impact

This project is the first integration of fossil and extant anatomy with Hox expression patterns in a comparative phylogenetic framework across Vertebrata. The complimentary skill sets of the investigators make them uniquely suited to successfully conduct this research, and results will have broad impact on NERC user groups including the general public, students, and researchers (see Academic Beneficiaries).

The researcher co-investigator: The project will provide the Res-CoI, Katharine Criswell, with excellent opportunities for honing transferable skills in project management, networking, team-working, and written and verbal communication. She will also develop skills in bioinformatics, computational biology, statistics and experimental embryological techniques.

The general public: The research proposed here is uniquely positioned to directly educate the general public through exhibition and outreach in the University Museum of Zoology. We will incorporate results of this project in the museum exhibit structure through flexible exhibit space (1500 ft2) for a projected viewership of 100,000/year. The exhibit will also be available for temporary travel to other museums. Thus, through public display, products of this project will educate both the general public and biodiversity decision-makers. We will additionally develop curriculum materials on vertebrate evolution based on this project for the Museum's educational outreach programs to area schools.

There is tremendous public interest in evolutionary transitions recorded in the fossil record and extant anatomy (e.g., the transition of vertebrates from water to land, the origin of snakes, the evolution of sharks, evolution of extreme body sizes), and a major focus of this project is on axial skeletal evolution in these events. Additionally, chondrichthyan fishes (sharks, skates, rays) have tremendous public appeal, and studies using chondrichthyan embryos as a model for understanding animal evolution have garnered considerable popular media attention. For example, previous work by the CI on chondrichthyan skeletal development has been the topic of media coverage in The Times, National Geographic, Washington Post, USA Today, MSNBC, IFL, and Discovery Channel. This research therefore presents an exceptional opportunity to convey the importance of evolutionary and developmental biology research to the general public. Our public demonstrations on shark and skate embryology during Cambridge Science Week's "Science on Saturday" are very popular, and receive considerable attention from both adults and children. We will use the Cambridge Science Festival to test a new and improved demonstration on chondrichthyan biology. A new addition to this demonstration will be live shark embryos (to be purchased from the Station Biologique in Roscoff). We would repeat this demonstration during future Science Festivals and at local schools.

Cambridge Musculoskeletal Sciences Network (CMSN): The CMSN is an interdisciplinary research network that spans the University of Cambridge, and that operates at the interface of biological and physical sciences, technology and clinical medicine to promote musculoskeletal research with translational potential. AG has previously used CMSN functions as a venue for identifying and communicating basic aspects of fish skeletal biology that may have such potential, and will continue to do so with this research.

Undergraduate student researchers: The Department of Zoology, University of Cambridge offers extensive research opportunities to undergraduates as part of degree requirements. Research components of this proposal are amenable to student participation at all academic levels, and students will be able to participate in data acquisition and analysis, as well as devising new research from the outlined deliverables. Research availability for students will facilitate the outlined objectives as well as allow the Res-CoI to develop mentoring skills.
 
Description The project included two primary objectives, with secondary research components associated with each.

Objective 1 ("Are there phylogenetic patterns of axial skeletal regionalization in vertebrates, and are patterns of regionalization correlated to different environments") was delayed due to the loss of access to museum collections and imaging facilities during quarantine. We have resumed work on this objective and anticipate research products in the near future with respect to the overarching question of the objective. A secondary research component that examined skeletal regionalisation in snakes and snake-like tetrapods was recently completed as an MPhil thesis in the Department of Zoology and University Museum of Zoology, University of Cambridge:

Hillian, E. J. 2021. Quantified Axial Regionalisation of the Squamate Ribcage: Implications for the Evolution and Development of the Snake-Like Body Form.

Key findings of this research are that skeletal elements derived from paraxial mesoderm in "deregionalised" axial skeleton of limbless snake-like taxa show the same patterns of regionalisation as in limbed taxa, suggesting the conservation of regulatory gene systems that underpin regional divisions, contrary to prevailing theories of the evolution of elongate, limb-reduced skeletons.

We have completed Objective 2 ("Do Hox genes mediate vertebral column regionalization within gnathostomes") By combining morphometric analysis with cell line lineage mapping of Hox gene expression, we demonstrate that the developmental mechanisms previously thought to be unique to tetrapods in driving the evolution of specialized heterogenous and regionalized axial skeletons as adaptations terrestrial environments are actually present ancestrally in jawed vertebrates:

Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51).

Thus far, the project has challenged prevailing hypotheses of skeletal transitions in vertebrate evolution and there ecological and environmental correlates, and has provided a new understanding of the relationship between morphology and regulatory genes at the origin of jawed vertebrates. Objective 1 is nearing publication and will provide greater taxonomic sampling and the crucial examination of the relationships between axial skeletal novelty and ecological specialization with environmental change throughout the diversity of vertebrates.
Exploitation Route Datasets produced by this project include gene sequences and digitised morphology which will be widely useful for research spanning evolutionary ecological, phylogenetic, comparative anatomical, developmental, and potential biomedical research. Conclusions will provide new evolutionary context for the developmental mechanisms that pattern the vertebral column, which will likely have impacts for medical studies.
Sectors Education

Culture

Heritage

Museums and Collections

Pharmaceuticals and Medical Biotechnology

 
Description NSFGEO-NERC: VERTEBRATE FUNCTIONAL TRAITS AS INDICATORS OF ECOSYSTEM FUNCTION THROUGH DEEP AND SHALLOW TIME-Jason Head -NSF-NERC (NSF is the lead)
Amount £242,134 (GBP)
Funding ID NE/W007576/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 03/2022 
End 08/2025
 
Title GenBank: MZ712109.1 Leucoraja erinacea homeobox a5 mRNA, partial cds 
Description mRNA sequence of Leucoraja erinacea homeobox gene a5 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Data for: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/MZ712109
 
Title GenBank: OK360936.1 Leucoraja erinacea homeobox a10 mRNA, partial cds 
Description mRNA sequence of Leucoraja erinacea homeobox gene a10 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360936
 
Title GenBank: OK360937.1 Leucoraja erinacea homeobox a11 (hoxa11) mRNA, 3' UTR 
Description mRNA sequence for Leucoraja erinacea homeobox gene a11 3' UTR 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360937
 
Title GenBank: OK360938.1 Leucoraja erinacea homeobox b5 mRNA, partial cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene b5 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360938
 
Title GenBank: OK360939.1 Leucoraja erinacea homeobox b6 mRNA, complete cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene b6 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360939
 
Title GenBank: OK360940.1 Leucoraja erinacea homeobox b7 mRNA, partial cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene b7 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360940
 
Title GenBank: OK360941.1 Leucoraja erinacea homeobox b8 mRNA, partial cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene b8 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360941
 
Title GenBank: OK360942.1 Leucoraja erinacea homeobox b10 mRNA, partial cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene b10 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360942
 
Title GenBank: OK360943.1 Leucoraja erinacea homeobox d8 mRNA, partial cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene d8 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360943
 
Title GenBank: OK360944.1 Leucoraja erinacea homeobox d10 mRNA, partial cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene d10 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360944
 
Title GenBank: OK360945.1 Leucoraja erinacea homeobox d11 mRNA, partial cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene d11 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? No  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360945
 
Title GenBank: OK360945.1 Leucoraja erinacea homeobox d11 mRNA, partial cds 
Description mRNA sequence for Leucoraja erinacea homeobox gene d11 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360945
 
Title GenBank: OK360946.1 Leucoraja erinacea homeobox A9 mRNA, partial cds 
Description mRNA sequence of Leucoraja erinacea homeobox gene A9 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Data published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://www.ncbi.nlm.nih.gov/nuccore/OK360946
 
Title Morphological and morphometric data on the axial skeleton of the little skate, Leucoraja erinacea 
Description CT scans of adult little skates (Leucoraja erinacea). These scans consist of series of tiff images that can be imported into CT segmenting software to reconstruct their shape in three dimensions. Supplemental files include CT scanning parameters, landmark coordinates for each vertebra in each skate, up to vertebra 70, as well as an R script with code for analysing vertebral shape using morphometrics and segmented linear regression tests. Computed tomography scans of three adult little skates were obtained in order to quantitatively study vertebral column morphology and regionalization. The skate fins were removed to facilitate shipping to our scanning facility, and so the scans include only the head, gill basket, and axial column. The specimens are now housed in the University of Cambridge Museum of Zoology (specimen identification numbers 2021.50.1, 20201.50.2, and 2021.50.3). 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact This dataset provided morphological and morphometric information on axial regionalisation of the chondrichthyes fish Leucoraja. Analysis of this dataset in conjunction with Hox gene expression data has demonstrated that skeletal regionalisation of the vertebral column occurs across jawed vertebrates, in contrast to prevalent theories that it is restricted to tetrapods. These analyses were published in: Criswell, K.E., Roberts, L.E., Koo, E.T., Head, J.J. and Gillis, J.A., 2021. hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences, 118(51). 
URL https://catalogue.ceh.ac.uk/id/9d7810c7-92af-47b2-81ec-365aafc39691
 
Title Morphological and morphometric data on the axial skeletons of vertebrates from museum specimens 
Description Computed tomography (CT) scans of 212 museum specimens, including mostly cartilaginous and bony fishes as well as several reptiles and amphibians, were obtained to quantitatively study vertebral column morphology and regionalisation. The specimens are housed in the University of Cambridge Museum of Zoology or the Natural History Museum in London (specimen identification numbers can be found in the supporting documentation). These data consist of 1) series of tiff images that can be imported into CT segmenting software to reconstruct their shape in three dimensions; 2) STL files of each vertebra for a subset of the specimens scanned; 3) 3D landmark coordinates or measurements for each vertebra for a subset of taxa scanned; 4) tables of results from regionalisation analyses, and 5) photographs of eight fossil fish specimens Supplemental files include details of the data collection procedures, specimen identification numbers and updated taxonomy, and CT scanning parameters for all scans. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact This dataset forms the basis for multiple studies on the evolution of the axial skeleton across Vertebrata. These studies are in progress or in submission to high-impact journals. 
URL https://catalogue.ceh.ac.uk/id/1c76e443-da02-4bc4-a041-0f79adc016be
 
Description "Growing a backbone: Rise of the Vertebrates" A public exhibition in the University Museum of Zoology, Cambridge 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact "Growing a backbone: Rise of the Vertebrates" is an exhibit focusing on major events in vertebrate evolution, including the origin of jaws, teeth, and the axial skeleton, as well as the evolution of giant body sizes, specialised feeding adaptations, and unique body forms such as the elongate, limb-reduced bodies of snakes and the specialised shells of turtles. The exhibit incorporates research results from the award, and utilises the unique collections of the University Museum of Zoology, including a complete, disarticulated Python skeleton, a 4-m long strand of baleen from a bowhead whale, a diversity of shark jaws, vertebrate spines, and different types of teeth to educate the public viewership and university students on the roles of regulatory gene systems in patterning new body forms and how the origin of Neural Crest has led to the evolution of a diversity of vertebrate specialisations including the facial skeleton and soft tissues. The exhibit includes seven new large displays for specimens, as well as new text and highlights distributed throughout the 2500 square-meter permanent exhibit space.
The exhibit opened to the public on February 1, 2024. In the first six weeks it has been seen by 19,740 museum visitors, including 14094 adults and 5646 children. It has been very well-received with multiple news features, including the BBC:

https://www.bbc.co.uk/news/uk-england-cambridgeshire-68156881
Year(s) Of Engagement Activity 2024
URL https://www.museum.zoo.cam.ac.uk/news/2024-exhibition-growing-backbone-rise-vertebrates
 
Description International Women's Day presentation by Dr. Katharine Criswell 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The International Women's Day event was hosted by the Museum of Zoology and included a set of four presentations and a panel discussion over Zoom, open to the public. The event was intended to highlight women researchers in the Zoology Department and provide inspiration to women interested in careers in science. It included a presentation about Dr. Criswell's background, scientific inspiration, and research, and after the presentation participants asked questions about her research and career path. There were 50 total attendees who asked eight questions, ranging from experimental techniques to experiences with postgraduate programs.
Year(s) Of Engagement Activity 2022
 
Description Public lecture by Dr. Katharine Criswell, Arthur Rank Hospice Charity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Patients, carers and/or patient groups
Results and Impact The presentation to the Arthur Rank Hospice Charity was intended to educate and provide stimulation for adults in hospice care. It was done over Zoom and included a short presentation about Dr. Criswell's research and the animals she studies, as well as a live camera feed on a skate embryo removed from the egg case. A total of 10 participants attended and asked 17 questions, ranging from the process of cartilage development to the life cycle of the skates. We received highly positive feedback from the charity reporting that the event had piqued participants interest and stimulated discussion.
Year(s) Of Engagement Activity 2021