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Introgression in Betula Species of Different Ploidy Levels and the Analysis of the Betula Nana Genome

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Introgression in Betula Species of Different Ploidy Levels and the Analysis of the Betula Nana Genome Introgression in Betula Species of Different Ploidy Levels and the Analysis of the Betula nana Genome JASMIN ZOHREN School of Biological and Chemical Sciences Queen Mary University of London Mile End Road London E1 4NS Supervisors: Dr Richard J. A. Buggs Prof Richard A. Nichols November 2016 Submitted in partial fulfilment of the requirements of the Degree of Doctor of Philosophy 1 Statement of Originality I, Jasmin Zohren, confirm that the research included within this thesis is my own work or that where it has been carried out in collaboration with, or supported by others, that this is duly acknowledged below and my contribution indicated. Previously published material is also acknowledged below. I attest that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge break any UK law, infringe any third party’s copyright or other Intellectual Property Right, or contain any confidential material. I accept that the College has the right to use plagiarism detection software to check the electronic version of the thesis. I confirm that this thesis has not been previously submitted for the award of a degree by this or any other university. The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without the prior written consent of the author. Signature: Date: Details of collaboration and publications Chapter 2 is published in Zohren et al. (2016): Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, Buggs RJA (2016). ’Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by RAD markers.’ Molecular Ecology, 25(11): 2413-2426. Nian Wang, James Borrell, and Richard Buggs sampled the data; Nian Wang and James Borrell extracted DNA for sequencing; Igor Kardailsky co-developed genotyping method; Anika Joecker co-developed analysis pipeline; Richard Nichols helped to do cline analysis using mixed-effect models and developed the beta-binomial method; Richard Buggs super- vised the project and helped putting together the manuscript. All authors contributed to editing and commenting on the original manuscript. 2 And hark, the noise of a near waterfall! I pass forth into light - I find myself Beneath a weeping birch (most beautiful Of forest trees, the lady of the woods) Hard by the brink of a tall, weedy rock That overflows the cataract. SAMUEL TAYLOR COLERIDGE Acknowledgements First, I would like to thank Richard Buggs for his supervision and guidance during the last years. Our weekly meetings often provided me with fresh ideas and food for thought. Your feedback on the thesis chapters was very valuable. Thanks as well for teaching me how to drive a tractor, feed a lamb, and for introducing me to Egremont Russet apples. Second, my thanks go to Richard Nichols for setting up the INTERCROSSING network and his support throughout the years. He helped me with many mathematical aspects of my thesis (especially for chapter 2) and offered lots of advice during lab chat and beyond. Thank you for taking me to the Arsenal match, your efforts in teaching us the rules of Cricket (I hope we will see a match together one day), and many enlightening conversations about the English language and culture. Thanks to everyone in the Buggs Lab, especially to Lizzy for being my buddy in many ways, to James for your contributions to chapter 2 and many helpful discussions e.g. about introgression and structure, to Nian also for your contributions to chapter 2 and for your expertise on birches in general, and to Laura for helping me with the repeat analysis in chapter 3. I would also like to thank Igor Kardailsky, Anika Joecker, and everyone else at CLC bio, Qiagen Aarhus, for being very welcoming during my time in Aarhus and for your important contributions towards this thesis and chapter 2 in particular. A special thanks to the European Union for the Marie-Curie FP7 framework INTER- CROSSING funding. And thanks to the whole INTERCROSSING gang for many mem- orable weeks of training courses and hours of Skype conferences. Being on this journey together with so many interesting, fun, and inspiring people is something very special and incredibly helpful. Personal thanks to: Andrea for just everything. We pushed ourselves through these years and you were always there for me whenever I needed you. An adequate list of things I want to thank you for would probably fill a second thesis. Jeannine for encouraging hugs and not letting my German fall into pieces, to Roddy for help with R, samtools, and much more, to Hannes for your expertise on repeats and a lot of helpful discussions, to Bruno and Adrian for enduring all my apocrita questions - I would have been lost without you. Thanks to Joanne and Emeline for all the motivating words and comforting hugs, to Michael for refreshing opera and theatre nights, to Chris for having an open ear for me, to Monika for help in the lab, to the IT department for their support, to the WISE committee members for many exciting events, and to everyone else from the SBCS-Evolve group. Thanks to Thomas, Melissa, and Adrian for their help with figures. And finally, I want to thank my family for their unconditional love, patience, and support during some stressful times. Ohne euch hätte ich das nicht geschafft! 4 Abstract Two of the most rapid drivers of evolution are hybridisation and polyploidisation. Hybrid- isation allows the rapid introduction of novel genetic material, potentially much faster than mutations, but this process is impeded by reproductive barriers between species. Differ- ences in ploidy level can form such a barrier. Hybridisation as well as polyploidy are known to occur frequently in the plant kingdom, including the genus Betula, which is investigated in this thesis. Three species of the Betula genus that exist in the United Kingdom are studied here: B. nana (dwarf birch), B. pendula (silver birch), and B. pubescens (downy birch). They differ in ploidy: B. nana and B. pendula are diploid and B. pubescens is a tetraploid. Hybridisation and gene flow between these three species was analysed by using a RAD-seq dataset derived from 196 wild individuals. It was found that introgression acts unidirec- tionally from the diploid into the tetraploid species and that there is a cline of introgression between the north and south of the UK. This result suggests a range shift of the species from different distributions in the past. Gene flow from B. nana to B. pubescens could be a neutral or even maladaptive con- sequence of their past species distributions. Alternatively, it could be an adaptive process: alleles from B. nana could be helping B. pubescens to adapt to harsher, more northerly populations. To gain a preliminary understanding of the possible effects of introgression, the loci in close linkage to RAD tags introgressed from B. nana into B. pubescens were investigated and their putative function inferred by comparing their homologs in related species. To enhance the analyses, a draft whole genome sequence assembly of a B. nana individual was improved with long read data generated by PacBio sequencing, as well as the addition of RNA-seq data. This produced a more contiguous and complete reference sequence, enabling a closer look at more genes in linkage to the RAD tags. 5 Contents 1 General introduction 15 1.1 Summary . 15 1.2 The genus Betula ............................... 18 1.2.1 Focal Betula species . 19 1.2.2 Relevance of Betula species . 20 1.3 Initiation of a new genome project . 20 1.3.1 Genome assembly methods . 21 1.3.2 The process of genome annotation . 21 1.4 Speciation vs species extinction through hybridisation . 23 1.4.1 Definition and mechanisms . 23 1.4.2 Methods to detect hybridisation . 24 1.4.3 Impact of hybridisation on evolution . 25 1.4.4 Role in extinction . 25 1.4.5 Conclusion and examples . 26 1.5 Distinguishing between introgression and incomplete lineage sorting . 27 1.5.1 Definitions . 27 1.5.2 Methods to detect allele sharing . 28 1.5.3 Differences between introgression and ILS . 28 1.5.4 Conclusion and examples . 29 1.6 SNP calling and RAD sequencing . 29 1.7 Outlook on this thesis . 30 6 2 Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by RAD markers 32 2.1 Summary . 32 2.2 Introduction . 33 2.3 Materials and methods . 36 2.3.1 Sampling . 36 2.3.2 DNA sequencing . 36 2.3.3 Read mapping and variant calling . 36 2.3.4 Allelic ratios at heterozygous sites . 38 2.3.5 Genotyping . 40 2.3.6 Population structure . 41 2.3.7 Comparison of RAD and microsatellite data . 41 2.4 Results . 42 2.4.1 Read mapping and variant calling . 42 2.4.2 Allelic ratios at heterozygous sites . 42 2.4.3 Genotyping . 43 2.4.4 Population structure . 43 2.4.5 Comparison of RAD and microsatellite data . 45 2.5 Discussion . 46 2.6 Conclusion . 49 3 Improvement of the B. nana genome assembly with PacBio and RNA-seq data 50 3.1 Summary . 50 3.2 Introduction . 51 3.3 Materials and methods . 54 3.3.1 Data sets . 54 3.3.2 Genome assembly . 56 3.3.3 Quality assessment . 57 3.3.4 Repeat analysis . 58 7 3.4 Results . 59 3.4.1 Genome assembly . 59 3.4.2 Quality assessment . 60 3.4.3 Repeat analysis . 61 3.5 Discussion . 63 3.6 Conclusion . 64 4 Functional characterisation of loci introgressed from B.
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