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Genomics of Speciation and Hybridisation in the Macaronesian Endemic Genus Argyranthemum (Asteraceae; Anthemideae)

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Genomics of Speciation and Hybridisation in the Macaronesian Endemic Genus Argyranthemum (Asteraceae; Anthemideae) 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 Environmental and Life Sciences School of Biological Sciences Genomics of speciation and hybridisation in the Macaronesian endemic genus Argyranthemum (Asteraceae; Anthemideae) by Oliver William White ORCID ID 0000-0001-6444-0310 Thesis for the degree of Doctor of Philosophy (PhD) January 2018 University of Southampton Abstract Faculty of Environmental and Life Sciences School of Biological Sciences Thesis for the degree of Doctor of Philosophy (PhD) Genomics of Adaptation and Speciation in the Macaronesian endemic genus Argyranthemum (Asteraceae; Anthemideae) By Oliver William White The aim of this thesis was to investigate the evolutionary processes responsible for the diversification of the Macaronesian endemic genus Argyranthemum Webb (Asteraceae), using Next Generation Sequencing (NGS) methodologies. Transcriptome sequences from Macaronesian endemic genera, including Argyranthemum, were used to design primers for simple sequence repeat (SSR) markers. This was necessary to overcome the lack of genetic variation commonly observed in Macaronesian endemic lineages. Morphological, ecological and genetic analyses were then employed to address several unanswered questions surrounding the origin of two putative homoploid hybrid species, A. sundingii and A. lemsii. Specifically, each of the homoploid hybrid species are shown to be morphologically distinct, ecologically separated from their parental progenitors and independently derived from the same parental species. The hypothesis of independent homoploid hybrid speciation events facilitated by ecological isolation is supported by these results. Genotyping-By-Sequencing (GBS) was employed to investigate the processes associated with the diversification of Argyranthemum. The results of the phylogenetic and hybridisation analyses reveal that geographical isolation, habitat shifts and hybridisation have all contributed to the diversification of the group. In addition, morphological convergence has contributed to the diversification of the group. A study focussed on A. broussonetii reveals that the two subspecies (subsp. broussonetii and subsp. gomerensis) are not closely related. Their morphological similarity is likely due to convergence as a result of their occupation of similar habitats. Finally, comparative transcriptomics was used to identify differentially expressed genes with a potential role in the ecological isolation and origin of the homoploid hybrid species in Argyranthemum. Although independently derived, A. sundingii and A. lemsii appear to have converged on similar expression phenotypes, likely a consequence of adaptation to similar habitats. NGS methodologies have revolutionised our ability to study the process of speciation in recently evolved lineages. Argyranthemum is the largest endemic genus of the Macaronesian archipelagos and an ideal model for investigating the processes responsible for diversification in oceanic island endemic lineages. Table of Contents Table of Contents Table of Contents ......................................................................................................... ii List of Tables ............................................................................................................... vii List of Figures ............................................................................................................... ix List of Appendix Tables ............................................................................................... xiv List of Appendix Figures .............................................................................................. xix List of Accompanying Materials ................................................................................. xxv Research Thesis: Declaration of Authorship ............................................................. xxvii Acknowledgements .................................................................................................. xxix Abbreviations ........................................................................................................... xxxi Chapter 1 Introduction............................................................................................... 1 Summary .................................................................................................................... 1 Speciation ................................................................................................................... 1 Hybridisation .............................................................................................................. 1 Hybrid speciation ....................................................................................................... 2 1.4.1 Frequency of polyploid and homoploid hybrid speciation ................................ 3 1.4.2 Models of homoploid hybrid speciation ............................................................ 5 Oceanic archipelagos as natural laboratories for studying evolution ....................... 8 Macaronesia as a model for flowering plant evolution ............................................. 8 Argyranthemum ....................................................................................................... 11 Thesis aims ............................................................................................................... 15 Methods ................................................................................................................... 15 Thesis outline ........................................................................................................... 19 Chapter 2 Transcriptome Sequencing and Simple Sequence Repeat Marker Development for Three Macaronesian Endemic Plant Species ................... 23 Abstract .................................................................................................................... 24 Introduction ............................................................................................................. 24 Methods and Results ............................................................................................... 27 Conclusions .............................................................................................................. 33 ii Table of Contents Chapter 3 Independent Homoploid Hybrid Speciation events in the Macaronesian endemic genus Argyranthemum ............................................................... 37 Abstract .................................................................................................................... 38 Introduction .............................................................................................................. 38 Materials and Methods ............................................................................................ 43 3.3.1 Sampling ........................................................................................................... 43 3.3.2 Morphological analysis ..................................................................................... 46 3.3.3 Ecological niche modelling ............................................................................... 46 3.3.4 DNA extraction ................................................................................................. 47 3.3.5 Polymerase Chain Reaction (PCR) of SSRs ....................................................... 48 3.3.6 Population genetic analyses of nuclear SSRs ................................................... 48 3.3.7 Haplotype analysis of chloroplast SSRs ............................................................ 48 3.3.8 Processing of GBS SNP data ............................................................................. 49 3.3.9 Genome-wide SNP analysis .............................................................................. 49 3.3.10 Testing independent hybrid origins with ABC .................................................. 50 Results ...................................................................................................................... 51 3.4.1 Morphological analyses .................................................................................... 51 3.4.2 Ecological niche modelling ............................................................................... 52 3.4.3 Population genetic analyses of nuclear SSRs ................................................... 56 3.4.4 Haplotype analysis of chloroplast SSRs ............................................................ 57 3.4.5 Processing of GBS
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