Research Collection Doctoral Thesis The genome of the trematode parasite Atriophallophorus winterbourni, Blasco-Costa et al., 2019: A macro- and microevolutionary perspective Author(s): Zajac, Natalia Publication Date: 2021 Permanent Link: https://doi.org/10.3929/ethz-b-000475035 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 27280 The genome of the trematode parasite Atriophallophorus winterbourni, Blasco-Costa et al., 2019: A macro- and microevolutionary perspective A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by Natalia Halina Zając MSc, Uppsala University Born on 01.07.1992 citizen of Poland Accepted on the recommendation of Prof. Dr. Roger Butlin, Department of Animal and Plant Sciences, University of Sheffield Prof. Dr. Christophe Dessimoz, Computational Evolutionary Biology, University of Lausanne Prof. Dr. Jukka Jokela, D-USYS, ETH Zurich Prof. Dr. Hanna Hartikainen, Faculty of Medicine & Health Sciences, University of Nottingham 2020 Table of Contents Summary 5 Zusammenfassung 8 Introduction 11 Chapter 1 34 Gene duplication and gain in the trematode Atriophallophorus winterbourni contributes to adaptation to parasitism Chapter 2 96 Divergence of gene structure in genes originating through duplication Chapter 3 128 Genomic footprint of divergence under high gene flow in the trematode parasite Atriophallophorus winterbourni Chapter 4 182 Genomic signature of local adaptation to a host population in a connected parasite population of the trematode, Atriophallophorus winterbourni Concluding remarks 225 Acknowledgments 228 Curriculum Vitae 230 Summary Summary Macro- and microevolutionary processes impact the structure and the function of a genome. Macroevolution mediates character state transitions that diagnose evolutionary differences of major taxonomic rank. The study of genomic features that have evolved on a macroevolutionary scale, including gene duplications or evolution of novel genes, reveals outcomes of evolutionary processes affecting species as a whole. On the other hand, microevolutionary processes, including natural selection, mutation, gene flow and genetic drift, affect changes in allele frequencies within and among populations of a species. The study of genomic regions impacted by those processes reveals their impact on fitness- correlated trait values and the diversity of a genome within a species. Ultimately, the two processes inevitably work in concert: macroevolution restricts the repertoire of genes microevolutionary processes can act on; but accumulation of small modifications has an impact over longer evolutionary time scales. A genome of an organism at any point in time is the product of them both. Ideal model systems for the study of macro- and microevolutionary processes are parasitic species as transition to parasitism is a macroevolutionary event but rapid evolutionary responses to hosts with which the parasites co-evolve, diversification and specialization as well as evolution of complex population structures are a result of microevolution. This thesis addresses the genomic signature of macro- and microevolutionary processes that have shaped the genome of the trematode parasite, Atriophallophorus winterbourni (Blasco-Costa et al.,2019). Firstly, we sequenced, assembled de novo and annotated a reference genome for A. winterbourni, creating a resource and an opportunity for the subsequent whole genome research. Secondly, through comparative genomic analysis with other major parasitic worms and reconstruction of three ancestral genomes in the trematode phylogeny, we investigated gene families that might have contributed to adaptation of A. winterbourni to parasitism. We inferred the timing of these evolutionary changes through the inference of a robust phylogeny of 18 Platyhelminthes and a time tree with divergence times of the trematode speciation events. In order to better understand the trematode genome architecture, we studied the gene structure of conserved genes, genes evolved through duplication and novel genes since the trematode ancestor in the 13 focal trematode species. The research was performed in collaboration with the authors of OMA 5 Summary (“Orthologous MAtrix”) which is a method and a database for the inference of orthologs among complete genomes. The results indicated that A. winterbourni split from the Opisthorchiata suborder approximately 237.4 MYA (± 120.4 MY). We found that since that speciation event, 24% of A. winterbourni genes have arisen through duplication events and 31.9% have been newly acquired, suggesting a high contribution of novelty in lineage-specific adaptation. Among those genes, we found 13 gene families with over 10 genes arisen through duplication; all of which have functions potentially relating to host behavioural manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. Interestingly, we found that the process of duplication results in a change in gene structure. In the 13 studied trematodes, duplicated copies of a gene tended to be shorter in length and have fewer exons than the gene they originated from. Additionally, gene families coding for shorter proteins tended to more often evolve through duplication than gene families consisting of longer proteins. Thirdly, with the use of population genomic techniques, we searched for the genomic regions involved in adaptation of A. winterbourni to its intermediate host, New Zealand mud snail, Potamopyrgus antipodarum (Gray, 1843), across different spatial scales. We examined the genomic footprint of divergence and the extent of gene flow between the north-west and south-east populations of A. winterbourni across its native range, the South Island of New Zealand, subject to previous separation by glacial periods and to restricted gene flow across a mountain range, the Southern Alps. We found the divergent genomic regions coding for proteins to be possibly involved in an extracellular vesicle biogenesis pathway. The pathway was found in other trematodes to be playing a role in parasite migration through the host tissue and countering the attack of the host immune system. The functional genomic differentiation between these populations could possibly be due to host-parasite co- divergence and local adaptation. Previous research, however, has not only suggested population structure between the lakes but also within a single lake, an extensively studied Lake Alexandrina, where negative frequency-dependent dynamics between the host and the parasite have been observed. In order to fully understand the geographic mosaic of co- evolution shaping the genomic diversity of the parasite, we searched for genomic signature of divergence in Lake Alexandrina between 6 highly interconnected parts of the lake, encompassing all the lake banks. The study found high level of polymorphism for the parasite populations in the lake, but no clear signature of divergence between any of the sites. We 6 Summary speculated that the population might be undergoing an expansion in diversity after a recent selective sweep caused by adaptation to the most common host genotype. The observations were supported with the investigation of the infected host population using neutral markers. Altogether, the thesis presents a comprehensive study of the different forces shaping a parasite genome, acting either on either the species or the population level, and addresses the levels of complexity of the host-parasite co-evolutionary dynamics. Despite the system being extensively studied, it is the first time the questions of orthology, phylogeny, population structure, population divergence, and the geographic mosaic of co-evolution were addressed using whole genome data. 7 Zusammenfassung Zusammenfassung Makro- und mikroevolutionäre Prozesse beeinflussen die Struktur und Funktion eines Genoms. Makroevolution vermittelt Übergänge zwischen Zuständen von Eigenschaften, welche evolutionäre Unterschiede von grossen taxonomischen Stufen diagnostizieren. Durch Untersuchung von genomischen Merkmalen, die durch makroevolutionäre Prozesse wie Genduplikation oder die Entstehung neuer Gene entstanden sind, erkennt man wie stark evolutionäre Vorgänge die gesamte Art beeinflussen. Anderseits beeinflussen mikroevolutionäre Prozesse, wie natürliche Selektion, Mutation, Genfluss oder genetische Drift Veränderungen in Allelfrequenzen innerhalb und zwischen Populationen einer Art. Untersuchungen an genomischen Regionen, welche durch obengenannte Prozesse beeinflusst werden, zeigen deren Einfluss auf fitnesskorrelierte Merkmale und auf die Diversität eines Genoms innerhalb einer Art. Letztlich arbeiten beide Prozesse unweigerlich zusammen: Makroevolution schränkt das Repertoire der Gene ein, auf welche mikroevolutionäre Prozesse einwirken können, aber die Akkumulation kleiner Veränderungen wirkt sich über einen längeren evolutionären Zeitraum aus. Somit ist das Genom eines Organismus immer das Produkt beider Prozesse. Parasitäre Arten sind ein ideales Modell für die Studie der makro- und mikroevolutionären Prozesse: Der Wechsel zu einer parasitären Lebensform ist ein makroevolutionäres Ereignis, während schnelle, kurzzeitige evolutionäre Anpassungen an den Wirt, mit welchem sich der Parasit koevolviert, Diversifizierung und Spezialisierung, oder auch die Evolution von komplexen