DOI: 10.5061/dryad.d3r64
title: Data from: Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents

description: Background: Chemolithoautotrophic primary production sustains dense
 invertebrate communities at deep-sea hydrothermal vents and hydrocarbon
 seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and
 hydrogen gases nourish bathymodiolin mussels that thrive in these
 environments worldwide. The mussel symbionts are newly acquired in each
 generation via infection by free-living forms. This study examined
 geographical subdivision of the thiotrophic endosymbionts hosted by
 Bathymodiolus mussels living along the eastern Pacific hydrothermal vents.
 High-throughput sequencing data of 16S ribosomal RNA encoding gene and
 fragments of six protein-coding genes of symbionts were examined in the
 samples collected from nine vent localities at the East Pacific Rise,
 Galápagos Rift, and Pacific-Antarctic Ridge. Results: Both of the
 parapatric sister-species, B. thermophilus and B. antarcticus, hosted the
 same numerically dominant phylotype of thiotrophic Gammaproteobacteria.
 However, sequences from six protein-coding genes revealed highly divergent
 symbiont lineages living north and south of the Easter Microplate and
 hosted by these two Bathymodiolus mussel species. High heterogeneity of
 symbiont haplotypes among host individuals sampled from the same location
 suggested that stochasticity associated with initial infections was
 amplified as symbionts proliferated within the host individuals. The
 mussel species presently contact one another and hybridize along the
 Easter Microplate, but the northern and southern symbionts appear to be
 completely isolated. Vicariance associated with orogeny of the Easter
 Microplate region, 2.5–5.3 million years ago, may have initiated isolation
 of the symbiont and host populations. Estimates of synonymous substitution
 rates for the protein-coding bacterial genes examined in this study were
 0.77–1.62%/nucleotide/million years. Conclusions: Our present study
 reports the most comprehensive population genetic analyses of the
 chemosynthetic endosymbiotic bacteria based on high-throughput genetic
 data and extensive geographical sampling to date, and demonstrates the
 role of the geographical features, the Easter Microplate and geographical
 distance, in the intraspecific divergence of this bacterial species along
 the mid-ocean ridge axes in the eastern Pacific. Altogether, our results
 provide insights into extrinsic and intrinsic factors affecting the
 dispersal and evolution of chemosynthetic symbiotic partners in the
 hydrothermal vents along the eastern Pacific Ocean.
description: Geographical structure
 of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern
 Pacific hydrothermal ventsSampling region of
 Bathymodiolus thermophilus and B. antarticus sulfur-oxidizing
 gammaproteobacteria EPR, East Pacific Rise GAR, Galapagos Rift PAR,
 Pacific-Antartic Ridge Information of population and geographic groups
 population group (HA) 11N EPR (HB) 9N EPR (HI) GAR EPR (HC) 7S EPR (HD)
 11S EPR (HE) 17S EPR (HF) 23S EPR (HG) 32S PAR (HH) 38S PAR Folder and
 file information: FASTA folder - 2 folders containing multi loci DNA
 sequences of all the sampled individuals from 9 populations sorted by
 Population and Subpopulation (individual host mussel) Arlequin input files
 (16S) folder - input files used for calculation molecular indices of 16S
 gene at two levels of Population and Subpopulation Arlequin input files
 (Funtional genes, Subpopulation) folder - input files used for calculation
 molecular indices of functional genes at level of Subpopulation
 (individual host mussel) Input files (Functional genetic data, Population)
 folder - input files used for calculation of molecular indices of
 functional genes at level of population, synonymous/nonsynonymous
 substitutions estimation, symbiont isolation-by-distance test, and
 nucleotide substitution rate, generating haplotype networks of functional
 genes Polymorphic tables.xlsx - Polymorphic table of 16S and functional
 genes used in this studyDryad.zipNetworks with OTUs labelSequence networks of six protein-coding genes of Bathymodiolus bacterial symbionts labeling with OTUs.