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Using Genomics to Restore and Future-Proof Underwater Seaweed Forests

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Using Genomics to Restore and Future-Proof Underwater Seaweed Forests Using genomics to restore and future-proof underwater seaweed forests Georgina V. Wood A dissertation submitted in fulfillment of the requirements for the degree of Doctor of Philosophy Supervised by Ezequiel Marzinelli and Adriana Vergés Evolution & Ecology Research Centre The School of Biological, Earth and Environmental Sciences Faculty of Science UNSW Sydney January 2020 Thesis/Dissertation Sheet Surname/Family Name : WOOD Given Name/s : GEORGINA VALENTINE Abbreviation for degree as give in the University calendar : PhD Faculty : SCIENCE School : BIOLOGICAL, EARTH AND ENVIRONMENTAL SCIENCES USING GENOMICS TO RESTORE AND FUTURE-PROOF UNDERWATER Thesis Title : SEAWEED FORESTS Abstract 350 words maximum: (PLEASE TYPE) Worldwide, foundation species are declining, leading to significant loss of biodiversity and ecosystem goods and services. With anthropogenic pressures predicted to continue to have major effects on foundation species, restoration is emerging as a key management tool to halt or reverse decline. Planning long-term restoration solutions that include population resilience under extant and future conditions as an explicit objective is of utmost importance; yet, it is still in its infancy for marine systems. In this thesis, I investigated approaches that can be used to develop and improve restoration and future-proofing strategies for declining underwater seaweed forests. A literature review identified the most significant challenges predicted to influence marine macrophytes into the next century. The incorporation of novel tools such as genomics emerged as being essential to combat these challenges. I applied genomics to design and experimentally assess the restoration of Phyllospora comosa, a foundational seaweed that has suffered historical declines along the coast of Sydney. Single Nucleotide Polymorphisms (SNPs) were used to characterise genetic diversity and structure on extant populations surrounding Phyllospora’s gap in distribution and subsequently inform restoration, via transplantation, of five Phyllospora populations. Although donor transplant provenance influenced survival of transplanted donors, recruitment was rapid and SNP analyses showed that genetic diversity and structure of the F1 generation successfully resembled extant populations. Landscape genomic tools were then used to characterise overall and potentially adaptive genetic diversity and structure along Phyllospora’s entire latitudinal range. Genetic diversity was unevenly distributed and putative loci under selection that linked to sea temperature were identified and may be useful to assist adaptation. Finally, the potential to harness important host-microbial interactions was investigated. A combination of interdisciplinary tools was used to demonstrate that the environment and host traits together explain 54% of variation in Phyllospora-associated microbial communities, with host genetics explaining half of this. Key genetic loci and phenotypic traits were strongly related to taxa with known associations to seaweed defense, disease and tissue degradation. Overall, my research demonstrates the capacity of genomic data to optimise intervention strategies for marine forests and paves the way for development of innovative solutions to prevent further degradation. Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents a non-exclusive licence to archive and to make available (including to members of the public) my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known. I acknowledge that I retain all intellectual property rights which subsist in my thesis or dissertation, such as copyright and patent rights, subject to applicable law. I also retain the right to use all or part of my thesis or dissertation in future works (such as articles or books). …………………………………………………………… ……….……………………...…….… Signature Date The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years can be made when submitting the final copies of your thesis to the UNSW Library. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed …………………………………………….............. Date …………………………………………….............. INCLUSION OF PUBLICATIONS STATEMENT UNSW is supportive of candidates publishing their research results during their candidature as detailed in the UNSW Thesis Examination Procedure. Publications can be used in their thesis in lieu of a Chapter if: • The candidate contributed greater than 50% of the content in the publication and is the “primary author”, ie. the candidate was responsible primarily for the planning, execution and preparation of the work for publication • The candidate has approval to include the publication in their thesis in lieu of a Chapter from their supervisor and Postgraduate Coordinator. • The publication is not subject to any obligations or contractual agreements with a third party that would constrain its inclusion in the thesis Please indicate whether this thesis contains published material or not: This thesis contains no publications, either published or submitted for publication ☐ (if this box is checked, you may delete all the material on page 2) Some of the work described in this thesis has been published and it has been documented in the relevant Chapters with acknowledgement ☒ (if this box is checked, you may delete all the material on page 2) This thesis has publications (either published or submitted for publication) ☐ incorporated into it in lieu of a chapter and the details are presented below CANDIDATE’S DECLARATION I declare that: • I have complied with the UNSW Thesis Examination Procedure • where I have used a publication in lieu of a Chapter, the listed publication(s) below meet(s) the requirements to be included in the thesis. Candidate’s Name Signature Date (dd/mm/yy) COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents a non-exclusive licence to archive and to make available (including to members of the public) my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known. I acknowledge that I retain all intellectual property rights which subsist in my thesis or dissertation, such as copyright and patent rights, subject to applicable law. I also retain the right to use all or part of my thesis or dissertation in future works (such as articles or books).’ ‘For any substantial portions of copyright material used in this thesis, written permission for use has been obtained, or the copyright material is removed from the final public version of the thesis.’ Signed ……………………………………………........................... Date …………………………………………….............................. AUTHENTICITY STATEMENT ‘I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis.’ Signed ……………………………………………........................... Date …………………………………………….............................. Acknowledgements All theses are the outcome of multiple architects and mine has had exceptionally many. First and foremost, I am enormously grateful to my wonderful supervisors. To Ziggy Marzinelli: your scientific rigour, good humour and level-headedness have carried me throughout this journey. To Adriana Vergés, I owe you many of the opportunities I have had to communicate my love for research and the ocean; thank you for continually supporting and inspiring me. To Mel Coleman, I will never forget you so graciously took me into your home during those initial months; thank you for teaching me how to unravel the secrets of tricky seaweed DNA extraction and for always being on the ball. Many thanks to Alex Campbell; it is largely due to you that I joined Operation Crayweed in the first place; our early days in the field have stuck in my mind. To Peter Steinberg, you have always stepped in at the right time with your wisdom. Thank you all for welcoming me into the crayweed family; you have motivated me greatly and I look forward to being able to continue working with you in the future. I have received generous awards from Holsworth Research Fund, Evolution & Ecology Research Centre, School of BEES and UNSW that went towards genotyping costs, fieldwork equipment, conference costs and an international workshop. This thesis has greatly benefitted from their financial contributions. Over the years I have had the privilege of working and speaking with a fantastic team of scientists. Many thanks are due to Damon Bolton – my crayweed
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