New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias

Abstract

BackgroundWithin the complex metazoan phylogeny, the relationships of the three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses of 196 genes from 58 bilaterian taxa, paying particular attention to the influence of compositional heterogeneity.ResultsThe phylogenetic analyses strongly support the monophyly of Lophophorata and a sister-group relationship between Ectoprocta and Phoronida. Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic. Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata.ConclusionOur results indicate that the support for Polyzoa, Brachiozoa and Kryptrochozoa gathered so far is likely an artifact caused by compositional bias. The monophyly of Lophophorata implies that the horseshoe-shaped mesosomal lophophore, the tentacular feeding apparatus of ectoprocts, phoronids and brachiopods is, indeed, a synapomorphy of the lophophorate lineages. The same may apply to radial cleavage. However, among phoronids also spiral cleavage is known. This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates. The sister group relationship of ectoprocts and phoronids is in accordance with the interpretation of the eversion of a ventral invagination at the beginning of metamorphosis as a common derived feature of these taxa.

Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads

“…Given that nemerteans possess few morphological features compared with other lophotrochozoans, the phylogenetic position of Nemertea within Lophotrochozoa is highly controversial 2,3,[12][13][14][15] . Some phylogenomic studies place Nemertea as sister to Phoronida and Brachiopoda [3][4][5] (Fig. 1a).…”

“…For example, whether Ectoprocta belongs to the historical superphylum Lophophorata has been contentious [2][3][4][5][12][13][14][15] ( Supplementary Fig. 15).…”

“…According to the narrow definition, Lophotrochozoa is a subgroup of spiralians and most lophotrochozoans possess either lophophore or trochophore larvae during the planktonic stage. Lophotrochozoans sensu stricto include annelids (for example, leeches and polychaete worms), molluscs (for example, snails and octopuses), nemerteans (ribbon worms), phoronids (horseshoe worms), ectoprocts (bryozoans, otherwise known as moss animals) and brachiopods (lamp shells), although many phylogenetic relationships within the group remain unresolved [3][4][5] . Molecular phylogenetics suggests that nemerteans and phoronids are closely related 3 , yet these two phyla have divergent body plans and exhibit no morphological synapomorphic traits.…”

Evolution, divergence and loss of the Nodal signalling pathway: new data and a synthesis across the Bilateria

“…The sister-group relationship between chaetognaths and the remaining bilaterians has been under debate for decades. Chaetognaths have been related to deuterostomes (Ghirardelli 1981;Brusca and Brusca 2002), ecdysozoans (Littlewood et al, 1998;Zrzavy et al, 1998;Peterson and Eernisse 2001), spiralians (Matus et al, 2006) and as sister taxon to Spiralia + Ecdysozoa (Giribet et al, 2000;Helfenbein and Boore 2004;Marletaz et al, 2006;Nesnidal et al, 2013). However, new molecular and morphological evidence has supported their phylogenetic position as an independent lineage in the protostomes beside ecdysozoans and spiralians (Dunn et al, 2008).…”

From trochophore to pilidium and back again - a larva’s journey

“…Anatomical, ultrastructural and phylogenetic evidence suggests that they are related to the coelomate Lophotrochozoa/Spiralia (Turbeville and Ruppert 1985;Turbeville 1986Turbeville , 1991Turbeville et al, 1992;Giribet et al, 2000;Peterson and Eernissee 2001;Struck and Fisse 2008), with, somewhat puzzlingly, increasing phylogenomic support for a sister relationship with the Lophophorate phyla (phoronids, brachiopods, and ectoprocts) (e.g. Dunn et al, 2008;Bourlat et al, 2008;Hejnol et al, 2009;Nesnidal et al, 2013), rather than the groups that actually exhibit spiral cleavage (e.g. annelids and mollusks).…”