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University of Southampton Research Repository University of Southampton Research Repository Copyright © and Moral Rights for this thesis and, where applicable, any accompanying data are retained by the author and/or other copyright owners. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis and the accompanying data cannot be reproduced or quoted extensively from without first obtaining permission in writing from the copyright holder/s. The content of the thesis and accompanying research data (where applicable) must not be changed in any way or sold commercially in any format or medium without the formal permission of the copyright holder/s. When referring to this thesis and any accompanying data, full bibliographic details must be given, e.g. Thesis: Author (Year of Submission) "Full thesis title", University of Southampton, name of the University Faculty or School or Department, PhD Thesis, pagination. Data: Author (Year) Title. URI [dataset] University of Southampton Faculty of Natural and Environmental Sciences School of Ocean and Earth Science The Roles of Hybridisation, Contemporary Climate Change, and Recent Range Shifts on the Redistribution of Marine Biodiversity. by Jamie Hudson ORCID ID 0000-0002-2294-1616 Thesis for the degree of Doctor of Philosophy March 2020 University of Southampton Abstract Faculty of Natural and Environmental Sciences School of Ocean and Earth Science Thesis for the degree of Doctor of Philosophy The Roles of Hybridisation, Contemporary Climate Change, and Recent Range Shifts on the Redistribution of Marine Biodiversity by Jamie Hudson Global change as a result of human activities has caused unprecedented alterations to biodiversity. One consequence of such alteration is the redistribution of species. Understanding the mechanisms that determine and maintain species’ ranges is at the forefront of ecological and evolutionary research. Current drivers of the redistribution of biodiversity include natural range expansions, anthropogenic transport of species, and contemporary climate change. These can alter both species ranges and evolutionary trajectories in multiple ways. A notorious example is when changes in species distributions bring divergent genotypes into secondary contact, facilitating hybridisation. Despite each of these topics being well studied individually, there remains a dearth of research studying these factors in combination to understand how they reshape biodiversity patterns in the marine environment. It is predicted that an integrative approach studying these factors in combination would enable further understanding how they interact to affect the redistribution of biodiversity. This thesis used a multidisciplinary approach that combined population genomic data, controlled experimental crosses of divergent genotypes, and environmental datasets to investigate the role of different factors on past, current, and future changes in species distributions. My research has shown that whilst hybridisation can be beneficial for range expansions, this is not always the case. I found evidence that some species that have spread as a result of human mediated transport have undergone secondary contacts, facilitating the colonisation of distant habitats. Conversely, other species with transoceanic distributions may be expected to undergo secondary contact due to anthropogenic transport and the presence of two native lineages, though I found no evidence that range expansion had been preceded by hybridisation. Finally, species that are able to currently hybridise may not perform as well as parental crosses under thermal stress, suggesting that under CCC, hybridisation may not be such a dominant driver of species redistribution. Taken together, this thesis demonstrates the utility in using a multidisciplinary approach to study factors that can combine to determine species ranges. I have shown that different mechanisms can have dissimilar consequences on species ranges that can be difficult to predict, and that by studying multiple factors can one successfully disentangle the role each one plays in the redistribution of marine biodiversity. Table of Contents Table of Contents Table of Contents ...................................................................................................................... i Table of Tables ......................................................................................................................... v Table of Figures ...................................................................................................................... vii List of Accompanying Materials ............................................................................................... xi Research Thesis: Declaration of Authorship ........................................................................... xiii Acknowledgements ................................................................................................................ xv Definitions and Abbreviations ............................................................................................... xvii Chapter 1 Introduction......................................................................................................... 1 1.1 Species redistribution ............................................................................................................. 1 1.1.1 Natural range expansions .............................................................................................. 2 1.1.2 Biological invasions ........................................................................................................ 3 1.2 Contemporary climate change ............................................................................................... 4 1.3 Hybridisation ........................................................................................................................... 5 1.3.1 The costs associated with hybridisation ........................................................................ 5 1.3.2 The benefits associated with hybridisation ................................................................... 6 1.4 Hybridisation and contemporary climate change leading to species redistributions............ 9 1.5 Ascidians: a unique group to study changes in marine ecosystems ....................................10 1.5.1 Ecology of ascidians .....................................................................................................12 1.5.2 Ascidians as invaders ...................................................................................................14 1.6 Thesis structure and author contributions ...........................................................................15 Chapter 2 Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrate...................................................................................... 21 2.1 Abstract .................................................................................................................................21 2.2 Introduction ..........................................................................................................................22 2.3 Materials and Methods ........................................................................................................25 2.3.1 Field sampling ..............................................................................................................25 2.3.2 DNA extraction and genotyping ...................................................................................28 2.3.3 Analysis of genotyping-by-sequencing data ................................................................28 2.3.4 Population structure ....................................................................................................29 2.3.5 Reconstructing invasion routes ...................................................................................30 i Table of Contents 2.4 Results................................................................................................................................... 31 2.4.1 Loci assembly and detection of outlier loci ................................................................. 31 2.4.2 Heterozygosity and population structure .................................................................... 31 2.4.3 Reconstructing invasion routes ................................................................................... 35 2.5 Discussion ............................................................................................................................. 36 2.6 Acknowledgements .............................................................................................................. 40 Chapter 3 Using oceanographic and genomic data to study regionally constrained distributions of non-indigenous species .............................................................. 41 3.1 Abstract................................................................................................................................. 41 3.2 Introduction .......................................................................................................................... 42 3.3 Methods................................................................................................................................ 44 3.3.1 Study species and distribution ..................................................................................... 44 3.3.2 Sampling......................................................................................................................
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