Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina

Abstract

Molecular estimates of phylogenetic relationships rely heavily on multiple sequence alignment construction. There has been little consensus, however, on how to properly address issues pertaining to the alignment of variable regions. Here, we construct alignments from four commonly sequenced molecular markers (16S, 18S, 28S and cytochrome c oxidase subunit I) for the Nudibranchia using three different methodologies: (i) strict mathematical algorithm; (ii) exclusion of variable or divergent regions and (iii) manually curated, and examine how different alignment construction methods can affect phylogenetic signal and phylogenetic estimates for the suborder Doridina. Phylogenetic informativeness (PI) profiles suggest that the molecular markers tested lack the power to resolve relationships at the base of the Doridina, while being more robust at family-level classifications. This supports the lack of consistent resolution between the 19 families within the Doridina across all three alignments. Most of the 19 families were recovered as monophyletic, and instances of non-monophyletic families were consistently recovered between analyses. We conclude that the alignment of variable regions has some effect on phylogenetic estimates of the Doridina, but these effects can vary depending on the size and scope of the phylogenetic query and PI of molecular markers.

Micro‐computed tomography of spicule networks in three genera of dorid sea‐slugs (Gastropoda: Nudipleura: Doridina) shows patterns of phylogenetic significance

“…Spicule network form characters were fairly consistent among the clades found by Hallas et al. () and Johnson (), especially in the Dorididae + Discodoridiae (Figure ). Species in the Cadlinidae + Dendrodorididae + Phylidiidae posses either a trabecular or orthogonal network, but the latter may simply be a more organized version of a trabecular network (Penney, ).…”

“…Character state distribution for mantle and foot networks. The phylogeny is from Hallas et al., . Species not used in that phylogeny but for which character state information was available are included: those from an included genus have the specific epithet in parentheses, those with the family represented have the entire name in parenthesis.…”

“…The phylogeny of Hallas et al. () is one of the most recent to question the monophyly of the Cryptobranchia and focused on the Onchodorididae. Onchidoris spp.…”

“…We combined data from this study and any previous study that described network form in enough detail to code characters (Alba‐Tercedor & Sánchez‐Tocino, ; Garcia, Garcia, & Cervera, ; Moles, Wägele, Uhl, & Avila, ; Sánchez‐Tocino et al., ) with characters from Okenia rosacea (Weiss et al., MS in prep.). Characters and taxa were entered into Mesquite 3.40 (Maddison & Maddison, ), and the tree was built to match the most recent molecular phylogeny available (Hallas et al., ). Species for which character state information was available but that were not used in that phylogeny are also included; in the figures, those that are congeners of an included species have the specific epithet in parentheses, although those only from the same family as an included species have their entire name in parenthesis.…”

“…First, dorids have traditionally been divided into four suborders (Bouchet et al., ) with most defence and feeding studies carried out on the Cryptobranchia (Cimino & Gavagnin, ), a group which can withdraw their gill into a specialized pocket. However, recent work has questioned the monophyly of the Cryptobranchia (Hallas, Chichvarkhin, & Gosliner, ; Hallas & Gosliner, ; Martynov & Schrödl, ). Second, the genus Cadlina has been found to be closely related to Aldisa (Johnson, ), breaking the previously thought relationship between Cadlina and the chromodorids, the latter of which have the best‐described chemical defences (Cimino & Gavagnin, ).…”