Durham E-Theses Adaptation in the Deep Sea: How Depth Aects Morphology and Protein Function in Coryphaenoides rupestris and its Congeners STEEDS, NATASHA,JANE How to cite: STEEDS, NATASHA,JANE (2020) Adaptation in the Deep Sea: How Depth Aects Morphology and Protein Function in Coryphaenoides rupestris and its Congeners, Durham theses, Durham University. Available at Durham E-Theses Online: http://etheses.dur.ac.uk/13841/ Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in Durham E-Theses • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full Durham E-Theses policy for further details. Academic Support Oce, Durham University, University Oce, Old Elvet, Durham DH1 3HP e-mail: [email protected] Tel: +44 0191 334 6107 http://etheses.dur.ac.uk 2 Adaptation in the Deep Sea: How Depth Affects Morphology and Protein Function in Coryphaenoides rupestris and its Congeners Natasha Steeds Submitted to the Department of Biosciences, Durham University in fulfilment of the requirements for the degree MSCR Biological Sciences C1A009 March 2020 Material Abstract Adaptation in the Deep Sea: How Depth Affects Morphology and Protein Function in Coryphaenoides rupestris and its Congeners Natasha Steeds Although the deep sea is the largest habitat on Earth, there is little understanding of how adaptation and speciation occur across depth gradients. The roundnose grenadier, Coryphaenoides rupestris, has demonstrated genetic segregation according to habitat depth across several functional loci. In this study, 139 C. rupestris individuals were sampled for morphological analysis, and the protein OBSL1 was modelled to explore the impact of non-synonymous single nucleotide polymorphisms (SNPs) across the species’ depth range. It was confirmed that the genetic segregation is mirrored by morphological differences in deeper-living individuals. C. rupestris sampled from deeper habitats were smaller and had more slender body forms, along with larger eyes and mouth gapes. Lipid stores in the liver and swimbladder both increased with habitat depth. OBSL1, the modelled muscle protein, was shown to have tighter intra-domain boning in fish from shallower habitats. These changes were linked to changes in foraging strategy and an increased demand for energy conservation in deeper habitats. Analyses were extended to explore adaptation to even deeper habitats. OBSL1 was modelled for 13 additional Coryphaenoides species from abyssal and non-abyssal habitats. These analyses suggested that hydrostatic pressure was the key selection pressure for this protein as habitat depths increase to reach the abyssal zone. This finding was contrasted with those from the single-species analysis of C. rupestris to illustrate how selection pressures for adaptation and speciation change across a depth gradient in the deep sea. i Table of contents Material Abstract ................................................................................................................................................... i Table of Contents .................................................................................................................................................. ii Statement of Copyright ..................................................................................................................................... iv Acknowledgements ............................................................................................................................................. v Chapter 1: Introduction and Background .............................................................................................. 1 Potential for adaptation in the deep sea ................................................................................. 1 Phenotypic responses to environmental factors ...................................................................... 2 The study species Coryphaenoides rupestris ........................................................................... 5 Fishery, conservation and management ................................................................................. 8 Project rationale and aims .................................................................................................... 10 Chapter 2: Morphometric Analysis of C. rupestris ......................................................................... 11 Introduction ........................................................................................................................... 11 The mesopelagic-bathypelagic boundary ............................................................................ 11 Expected morphological trends in C. rupestris .................................................................... 12 Methods .................................................................................................................................. 18 Measurement and dissection protocol ................................................................................. 19 Otolith preparation and sectioning ....................................................................................... 21 Statistical analysis ................................................................................................................. 23 Results .................................................................................................................................... 27 Demographic and general trends.......................................................................................... 27 Single trait tests .................................................................................................................... 30 Principal component analysis .............................................................................................. 36 Clustering analyses ............................................................................................................... 41 Discussion ............................................................................................................................... 43 Demographic and general trends.......................................................................................... 43 Body size ............................................................................................................................... 44 Body shape ........................................................................................................................... 46 Energy storage ..................................................................................................................... 49 Conclusion ............................................................................................................................ 51 Chapter 3: Changes to Protein Function Across the Meso-Bathypelagic Boundary in C. rupestris ............................................................................................................................................................ 53 Introduction ........................................................................................................................... 53 Known protein adaptations to life in the deep sea ................................................................ 53 Initial exploration of potential study proteins ....................................................................... 56 OBSL1 and its function ......................................................................................................... 59 ii Methods ................................................................................................................................. 62 Initial analysis ...................................................................................................................... 62 OBSL1 size analysis ............................................................................................................. 63 SNP modelling ...................................................................................................................... 64 Results .................................................................................................................................... 66 Initial analysis ...................................................................................................................... 66 OBSL1 size analysis ............................................................................................................. 68 SNP modelling ...................................................................................................................... 69 Discussion .............................................................................................................................. 74 Chapter 4: Beyond C. rupestris: Changes to Protein Structure and Function Across the Abyssal Boundary in Coryphaenoides .......................................................................................... 82 Introduction .......................................................................................................................... 82 The abyssal zone 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