Comparative genomics reveal symbiont-host evolution of deep-sea tubeworms (Siboglinidae, Annelida) and wood-boring bivalves (Xylophagaidae, Mollusca)
Type of DegreePhD Dissertation
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Chemosynthetic communities are patchily distributed in deep-sea ecosystems, including hydrothermal vents, methane seeps and whale, wood, and algal falls. Unlike abyssal seafloor communities that suffer from food limitation due to lack of the input of detrital organic particles produced from the overlying water column, reducing sediments provide inorganic chemicals, such as sulfide or methane, to fuel chemoautotrophic endosymbionts, and in turn provide nutrition for hosts. Chemosynthetic habitats often support specialize communities that are attractive a wide-range of other marine species, thus facilitating adaptive radiation and evolutionary novelty. Although a wide variety of invertebrate taxa have evolved chemosynthetic symbioses independently, evolutionary relationships of hosts and symbionts, specific symbiont-host associations, dispersal potential, recruitment sources, reproductive modes of most chemosynthetic marine invertebrates are still largely unknown. Therefore, the objective of this dissertation is to explore evolutionary history and symbiont-host associations on deep-sea dominant fauna annelid Siboglinidae and wood-boring bivalve Xylophagaidae. Chapter 1 provides a brief introduction to the deep-sea chemosynthetic community with an emphasis on siboglinids and xylophgagiads, and outlines the specific aims of the dissertation. Chapter 2 presents a mitogenomic analysis to explore relationships among major lineages of Siboglinidae. Findings suggest that bone-eating Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. My collaborators and I also identified the size variation and repeat motifs of control regions within siboglinid mitochondrial genomes. Chapter 3 presents a subsequent analysis of siboglinid evolutionary relationship using a phylogenomic approach. Importantly, unlike previous studies, the alternative hypothesis that frenulates and Osedax are sister groups to one another was explicitly rejected by an approximately unbiased (AU) test. This result implies that Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts. My collaborators and I also compared the performances of different phylogenomic reconstruction methods on this empirical dataset. Although different methods showed largely congruent results, my collaborators and I found that a supermatrix method using data partitioning with site-homogenous models potentially outperformed a supermatrix method using the CAT-GTR model and multispecies-coalescence approaches when the amount of missing data varies in a dataset and when taxa susceptible to LBA are included in the analyses. Chapter 4 seeks to understand siboglinid symbiont association in hydrocarbon seeps and muddy sediments and compares them to symbiont genomes from hydrothermal vent regions using a comparative genomic approach. I found that metabolic capacity of seep-dwelling ones are largely similar to vent-living vestimentiferans. However, representative of frenulate endosymbionts, from Galatehalinum brachiosum, lack key enzymes associated with rTCA and can only use Calvin cycle for carbon fixation compared to vestimentiferan siboglinids. Therefore, symbionts with higher metabolic flexibility in carbon fixation are hypothesized to allow tubeworms to thrive in more reducing environments, such as seeps and vents. For my last dissertation data chapter, the host-symbiont evolution of the deep-sea wood-boring bivalve in Xylophgagaidae has been explored using several genomic tools. Mitogenomic analysis indicates that the Xylophaga lineage is a paraphyleyic group within Xylophagaid. 2b-RAD SNP analysis reveals that there is no population structure identified across ~500 km, indicating that individuals from same species of xylophagaid in the study region are most likely colonized from the same gene pool. Lastly, metagenomic analysis from Xylophaga gill tissue shows xylophaga symbiont genome is closely related to Teridinibacter species isolated from their close relatives shipworm Teredinidae. Multiple genes dedicated to processing complex polysaccharides associated with wood falls were identified in partial symbiont genome, suggesting that a similar functional role in these endosymbionts from both shallow and deep wood-boring bivalves.