Phylogenomic Resolution of the Hemichordate and Echinoderm Clade

Abstract

Ambulacraria, comprising Hemichordata and Echinodermata, is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters. Unfortunately, relationships within Hemichordata and Echinodermata have remained unresolved, compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced transcriptomes for 14 hemichordates as well as 8 echinoderms and complemented these with existing data for a total of 33 ambulacrarian operational taxonomic units (OTUs). Examination of leaf stability values revealed rhabdopleurid pterobranchs and the enteropneust Stereobalanus canadensis were unstable in placement; therefore, analyses were also run without these taxa. Analyses of 185 genes resulted in reciprocal monophyly of Enteropneusta and Pterobranchia, placed the deep-sea family Torquaratoridae within Ptychoderidae, and confirmed the position of ophiuroid brittle stars as sister to asteroid sea stars (the Asterozoa hypothesis). These results are consistent with earlier perspectives concerning plesiomorphies of Ambulacraria, including pharyngeal gill slits, a single axocoel, and paired hydrocoels and somatocoels. The resolved ambulacrarian phylogeny will help clarify the early evolution of chordate characteristics and has implications for our understanding of major fossil groups, including graptolites and somasteroideans.

The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics

“…Later, Janies et al (2011) used combined Sanger sequencing data and morphology to show that Asterozoa and Echinozoa are methods-dependent when alignment and optimality criteria are varied. Recent transcriptomic studies with limited taxonomic and locus sampling have supported Asterozoa-Echinozoa (Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015) and were reviewed by Peterson and Eernisse (2016). These studies also strongly supported a monophyletic Asteroidea, consistent with prior morphological analyses including fossils (Blake et al, 2000;Shackleton, 2005) and molecular studies (Janies, 2001;Janies et al, 2011).…”

“…1 underscores the need for a wellsupported molecular phylogeny for asteroids, to permit the resolution of early divergence of asteroid orders as well as allow the placement of problematic and morphologically unusual taxa. Here, we used the recent demonstration, via molecular analyses of echinoderms (Janies, 2001;Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015) and our own broader analyses, that ophiuroids (brittlestars) are the sister group to asteroids and the outgroup of choice. However, recent transcriptomic analyses sampled asteroids poorly (Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015).…”

“…Here, we used the recent demonstration, via molecular analyses of echinoderms (Janies, 2001;Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015) and our own broader analyses, that ophiuroids (brittlestars) are the sister group to asteroids and the outgroup of choice. However, recent transcriptomic analyses sampled asteroids poorly (Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015). Specifically, O'Hara et al (2014) and Telford et al (2014) each sampled two asteroids, Simakov et al (2015) sampled one asteroid and Cannon et al (2014) sampled four asteroids.…”

“…However, recent transcriptomic analyses sampled asteroids poorly (Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015). Specifically, O'Hara et al (2014) and Telford et al (2014) each sampled two asteroids, Simakov et al (2015) sampled one asteroid and Cannon et al (2014) sampled four asteroids. Reich et al (2015) sampled 11 asteroids, but only four families that represented four orders were studied.…”

The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest

“…2c). Of the secreted proteins, 48 are enzymes, of which 83.3% (40) are hydrolyases, including plancitoxin-1, a type II DNase present in COTS venom 17 . In addition, 37 proteins are related to known secreted signalling and structural proteins, including 15 ependymin-related proteins (EPDRs), five lectins and four proteins related to deleted in malignant brain tumours 1.…”