The present PhD thesis, entitled “Gyrodactylids on European salmonids hosts: genomics, phylogeography and speciation”, presents a number of significant contributions to the field of evolutionary biology. It offers novel insights into mechanisms of evolution (PAPER III, PAPER IV), introduces methodological advances (PAPER II) and, overall, provides important foundations for future research (PAPER I, PAPER II, PAPER III, PAPER IV). My work has focused on the biology and evolution of ectoparasites of the genus Gyrodactylus infecting European salmonids and I have applied a variety of methods including large scale bioinformatics approaches. G. salaris, along with its benign sister species G. thymalli, has been in the center of gyrodactylid research for over 30 years, since the first outbreak of the Norwegian salmon epidemics. G. teuchis and G. truttae are non-pathogenic, widely distributed, and largely neglected parasites, which bear striking morphological similarity and overlap in host range with the enigmatic G. salaris. My initial paper demonstrates that the so-called cryptic species G. teuchis can indeed be discriminated from the latter based on a Principal Component Analysis (PCA) of 32 morphometric characters. The G. teuchis population in focus represents the first natural record from a Danubian trout population. We furthermore describe genetic variation in the ribosomal internal transcribed regions, which we interpret as evidence for a non-fully homogenized ribosomal DNA cluster, a possible result of recent introgression. Furthermore, I have devised a novel in silico approach for the reconstruction of animal mitochondrial genomes directly from genomic Next Generation Sequencing (NGS) data. The method was developed with particular emphasis on gyrodactylids and its applicability is demonstrated for two Gyrodactylus species, and their respective hosts, based on real and simulated Illumina data. A further paper presents the first high quality draft genome for G. salaris, representing an important platform for future research. We resolve the disputed interrelationships of the three major parasitic flatworm groups with a large scale phylogenomic approach and find the ectoparasitic Monogenea basal to the endoparasitic tapeworms and flukes, indicating ectoparasitism as the ancestral state in the obligate parasitic Neodermata. Comparative genomic analyses of seven parasitic flatworm genomes identify a number of shared genomic features between endo- and ectoparasitic lineages. In a final paper, I present firm evidence for the co-speciation of G. teuchis with its salmond hosts brown trout and Atlantic salmon, based on extensive European sampling and co-phylogenetic analyses. Although co-speciation represents an intriguing concept in evolutionary biology it has rarely been demonstrated in the literature.
List of papers. Paper II. and III. are included as separate files. Papers I. and IV. are removed due to publisher copyright policies.
I. Hahn C., Bakke T.A., Bachmann L., Weiss S., Harris P. (2011) Morphometric and molecular characterization of Gyrodactylus teuchis Lautraite, Blanc, Thiery, Daniel & Vigneulle, 1999 (Monogenea: Gyrodactylidae) from an Austrian brown trout population. Parasitology International. 60(4):480-7. doi:10.1016/j.parint.2011.08.016.
II. Hahn C., Bachmann L, Chevreux B. (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Research. 41(13):e129. doi:10.1093/nar/gkt371.
III. Hahn C., Fromm B., Bachmann L. (2014) Comparative genomics of flatworms (Platyhelminthes) reveals shared genomic features of ecto- and endoparastic Neodermata. Genome Biology and Evolution. 6(5):1105-17. doi:10.1093/gbe/evu078.
IV. Hahn C., Weiss S., Bachmann L. Co-speciation of the ectoparasitic Gyrodactylus teuchis (Monogenea, Platyhelminthes) and its salmonids hosts. Manuscript.