PhD: The ones that got away: diversification and dispersal in the first neopterygians

Project Highlights:
- Neopterygians are a hugely successful modern group of well over 30,000 species, but their origins are obscured by a limited understanding of their early fossil record
- Incorporating neglected fossils into recent phylogenetic analyses will provide a framework for macroevolutionary studies
- Investigations into patterns of biogeographic dispersal and diversity of body shapes will shed new light onto how early neopterygian evolution paved the way for the staggering diversity of modern forms

Overview:
Neopterygians are a major vertebrate group of over 30,000 extant taxa comprising two radiations: holosteans, with fewer than 10 living species; and teleosts, with over 30,000 living species. The origin of neopterygians lies deep in geological time, over 250 million years ago. Despite an abundance of fossils, patterns of relationships outside of the living groups is poorly understood, with very few taxa incorporated into formal schemes of phylogenetic relationships. This depauperate neopterygian ‘stem group’ is in large part due to major taxonomic reshuffling that has taken place among early ray-finned fish relationships in recent years. The resulting lack of resolution presents a fundamental barrier to resolving patterns of evolution outside of, and leading to, the living neopterygian radiation. As the affinity of key fossils is not known, these forms are typically excluded from morphometric analyses, which instead only include taxa more closely associated with the living radiation. As a result, the amazing disparity of body shapes displayed by the assemblage, encompassing everything from deep-bodied taxa to flying fish, is not taken into consideration when investigating the factors leading to neopterygian asymmetry and success. Uncertainty with regard to the taxonomic affinity of key fossils also calls into question the reliability of their use as calibration points for analyses of divergence. Restudy of the anatomy of the first neopterygians will allow their inclusion in formal phylogenetic analyses for the first time. Once this new phylogenetic hypothesis of relationships has been assembled, detailed macroevolutionary questions can be addressed. The morphology of phylogenetically resolved taxa will be quantified using landmarks and semilandmarks and their diversity analysed in principle component space to investigate rate of body shape evolution. Databasing methods (including compilation of important geographic and environmental data) will be used to investigate patterns of dispersal and ecological expansion. These results will contribute to understanding the patterns and drivers of diversity in the early evolutionary history of neopterygians.

Methodology:
This project incorporates descriptive, phylogenetic and quantitative techniques. Fossil taxa will be examined through a combination of traditional description and computed tomography (CT) scanning. The latter allows the internal and external anatomy of specimens to be investigated in a non-destructive manner. Three-dimensionally and exceptionally preserved taxa will be investigated using CT scanning. This new anatomical data will be incorporated into recent schemes of actinopterygian phylogeny, with maximum parsimony and Bayesian analysis used to investigate their position in the ray-finned fish tree. Quantitative techniques will be used to investigate broader patterns of evolution. Landmarking of body shape outline will be used to quantify patterns and rates of morphological evolution within the group. Databasing methods will be used to collect occurrence, stratigraphic and environmental data, which will be interrogated to understand patterns of biogeographic dispersal.

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 CT scanning and segmentation, comparative anatomy and description, systematics and phylogenetic techniques (including parsimony and Bayesian analyses), database construction and comparative biology. The student will also receive training in how to write and illustrate scientific papers, apply for grants and prizes, present work at conferences and scientific meetings, and network with peers and other scientists. 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 an outstanding student.

Partners and collaboration:
This project will be carried out in collaboration with the Natural History Museum, London and the University of Leeds. Dr Zerina Johanson (NHM) and Dr Graeme Lloyd (Leeds) will provide additional supervision. The collections at the NHM represent a world-leading resource, and specimens from here will form a central component of the specimens studied. Dr Johanson has extensive experience of CT scanning and anatomical interpretation and will assist thw student in these areas. Dr Lloyd is an expert in the development of macroevolutionary techniques and will guide the student in investigating biodiversity metrics and methodological aspects

Possible timeline:
Year 1: Literature review, CT scanning and segmenting, comparative anatomy. database construction.
Year 2: Phylogenetic analysis, database construction and analysis.
Year 3: Morphospace analysis, synthesis, completing thesis, writing manuscripts (although manuscripts will be written throughout project).

Further reading:
Clarke, J.T., Lloyd, G.T. & Friedman, M., (2016). ‘Little evidence for enhanced phenotypic evolution in early teleosts relative to their living fossil sister group’, Proceedings of the National Academy of Sciences, 113 (41), 11531–11536. https://doi.org/10.1073/pnas.1607237113
Clarke, J.T. & Friedman, M., (2018). Body-shape diversity in Triassic–Early Cretaceous neopterygian fishes: sustained holostean disparity and predominantly gradual increases in teleost phenotypic variety, Paleobiology, 1–32. https://doi.org/10.1017/pab.2018.8
Friedman, M. (2015). ‘The early evolution of ray‐finned fishes’, Palaeontology, 58 (2), 213–228. https://doi.org/10.1111/pala.12150.
Giles, S., Xu, G. H., Near, T. J., & Friedman, M. (2017). Early members of ‘living fossil’ lineage imply later origin of modern ray-finned fishes, Nature, 549 (7671), 265–268. https://doi.org/10.1038/nature23654.
Latimer, A.E. & Giles, S., (2018). A giant dapediid from the Late Triassic of Switzerland and insights into neopterygian phylogeny, Royal Society open science, 5 (8), p.180497. doi: 10.1098/rsos.180497
Sallan, L. C. (2014). Major issues in the origins of ray‐finned fish (Actinopterygii) biodiversity, Biological Reviews, 89 (4), 950–971. https://doi.org/10.1111/brv.12086.