Supporting Material, Supporting Figures S1-S4, Supporting Tables S1-S6 from Polyclonal symbiont populations in hydrothermal vent tubeworms and the environment

Horizontally transmitted symbiosesusually house multiple and variable symbiont genotypes that are acquired from a much more diverse environmental pool via partner choice mechanisms. However, in the deep-sea hydrothermal venttubeworm Riftia pachyptila(Vestimentifera, Siboglinidae), it has been suggested that the CandidatusEndoriftia persephone symbiont is monoclonal. Here, we show with high-coverage metagenomicsthat adult R. pachyptilahouse a polyclonal symbiont population consisting of one dominant and several low-frequency variants. This dominance of one genotype is confirmed by multilocus gene sequencing of amplified housekeeping genesin a broad range of host individuals where three out of four loci (atpA, uvrD and recA) revealed no genomic differences, while one locus (gyrB) was more diverse in adults than in juveniles. We also analysed a metagenomeof free-living Endoriftia and found that the free-living population showed greater sequence variability than the host-associated population. Most juveniles and adults shared a specific dominant genotype, while other genotypes can dominate in few individuals. We suggest that although generally permissive, partner choice is selective enough to restrict uptake of some genotypes present in the environment.