Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods

Abstract

Deep‐sea tubeworms (Annelida, Siboglinidae) represent dominant species in deep‐sea chemosynthetic communities (e.g. hydrothermal vents and cold methane seeps) and occur in muddy sediments and organic falls. Siboglinids lack a functional digestive tract as adults, and they rely on endosymbiotic bacteria for energy, making them of evolutionary and physiological interest. Despite their importance, inferred evolutionary history of this group has been inconsistent among studies based on different molecular markers. In particular, placement of bone‐eating Osedax worms has been unclear in part because of their distinctive biology, including harbouring heterotrophic bacteria as endosymbionts, displaying extreme sexual dimorphism and exhibiting a distinct body plan. Here, we reconstructed siboglinid evolutionary history using 12 newly sequenced transcriptomes. We parsed data into three data sets that accommodated varying levels of missing data, and we evaluate effects of missing data on phylogenomic inference. Additionally, several multispecies‐coalescent approaches and Bayesian concordance analysis (BCA) were employed to allow for a comparison of results to a supermatrix approach. Every analysis conducted herein strongly supported Osedax being most closely related to the Vestimentifera and Sclerolinum clade, rather than Frenulata, as previously reported. 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. Furthermore, although different methods showed largely congruent results, we found that a supermatrix method using data partitioning with site‐homogenous models potentially outperformed a supermatrix method using the CAT‐GTR model and multispecies‐coalescent approaches when the amount of missing data varies in a data set and when taxa susceptible to LBA are included in the analyses.

An inordinate fondness for Osedax (Siboglinidae: Annelida): Fourteen new species of bone worms from California

“…Relationships within clade II, which represents most of the Osedax species with 'nudepalps', were also generally poorly supported. Despite use of the most appropriate outgroup, Monilifera (Fig.1), as evidenced from the phylogenomic results in Li et al (2016), further sequence data from other loci is clearly needed to resolve the internal phylogeny of Osedax. The current placement of Osedax deceptionensis, a nudepalp species, outside of clade II, has implications for the evolution of palps, the primary respiratory organ in Osedax.…”

Host–Symbiont Interactions in Deep-Sea Chemosymbiotic Vesicomyid Clams: Insights From Transcriptome Sequencing

“…Genomes or transcriptomes of several deep-sea tube worms and mussels have recently been sequenced (Li et al, 2015(Li et al, , 2017Sun et al, 2017). The results of both gene expression and positive selection provide a better understanding of the possible mechanisms of molecular adaptation behind developing and maintaining endosymbiosis as well as hostsymbiont relationships in the horizontal mode of transmission (Sun et al, 2017).…”

Annelid brain and nerve cord in siboglinidRiftia pachyptila

“…Relation among the siboglinid groups from a combination of recent phylogenetic trees: clade of frenulates resolved based on cladistic analysis [18], interrelationship of siboglinid clades based on phylogenetic and phylogenomic data [17,92]; annelid outgroups based on phylogenomic data [39]. Neural characters for homologization of cerebral elements of siboglinids and annelid sister groups are listed (1-8).…”

“…Organization of the brain of frenulates, sister group to all other siboglinids [2,92] are important for the analyisis of the ancestral state of the siboglinid brain. Although their brains were studied in less details, but it is known in the dorsal epidermis in Polybrachia annulata, Siboglinum caulleryi there is a dorsal commissure [19,20], and in Nereilinum murmanicum, S. modestum and S. subligatum there are two dorsal commissures [23].…”