@ARTICLE{TreeBASE2Ref26728, author = {Joshua Mark Hallas and Anton Chichvarkhin and Terrence M. Gosliner}, title = {Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina}, year = {2017}, keywords = {sea slug, Nudibranchia, Doridina, PhyDesign, phylogenetics}, doi = {}, url = {http://dx.doi.org/10.1098/tsos/171095}, pmid = {}, journal = {Royal Society Open Science}, volume = {4}, number = {}, pages = {}, 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 1) for the Nudibranchia using three different methodologies: i) strict mathematical algorithm ii) exclusion of variable or divergent regions iii) manually curated, and examine how different alignment construction methods can affect phylogenetic signal and phylogenetic estimates for the suborder Doridina. Phylogenetic informativeness 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 nineteen families within the Doridina across all three alignments. However, most of the nineteen families were recovered as monophyletic, and instances of polyphyletic 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 phylogenetic informativeness of molecular markers.} }

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