Computational protocol: Consensus and Confusion in Molluscan Trees: Evaluating Morphological and Molecular Phylogenies

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Protocol publication

[…] The supertrees presented here were not constructed to provide yet another hypothesis of molluscan relationships, but rather to algorithmically evaluate the relationships present in the disparate topologies proposed over the last 86 years () (). Similar to the TOPD analysis discussed above, the supertree approach provided a method that allowed the summarization of tree topologies with unequal taxonomic representation, which precluded tree comparisons using more traditional consensus methods where all taxa are shared amongst the trees. However, supertree reconstruction assumptions, methods, and performance are not uncontroversial (, , , ), and we therefore used several different methods in an attempt to avoid possible artifacts.Four programs were used to construct supertrees:;1) Clann 3.0 (Creevey and McInerney 2005), (2) Rainbow 0.3 (), (3) RF-Supertrees 2.0 (), and (4) PhySIC_IST (). These programs provided different algorithms and approaches for the construction of supertrees, including: (1) matrix representation using parsimony analysis (mrp), (2) matrix representation using flipping (mrf), (3) most similar supertree method (dfit), (4) maximum split fit (sfit), (5) average consensus (avcon), (6) maximum quartet fit (qfit), (7) Robinson–Foulds distance (RF), and (8) phylogenetic signal with induction and noncontradiction (PHYsic_IST). With these programs we ultimately constructed eight molluscan supertrees from two partitions (morphological and molecular) using seven analytical methods (). Additional program parameters and settings for each analysis are included in .Our attempt to construct supertrees using the conservative consensus approach of PHYsic_IST only produced a four-taxon tree from the molecular partition source trees ([Cephalopoda, Caudofoveata), (Gastropoda, Bivalvia]) The inability of the PHYsic_IST analysis to place the remaining four groups was likely due to the absence of these taxa from many of the source trees and the conservative nature of this method (). In contrast, analysis of the morphological partition produced a larger seven taxon tree: ((Polyplacophora, (Monoplacophora, Cephalopoda, (Scaphopoda, Bivalvia))), (Caudofoveata, Solenogastres))). However, this tree was lacking Gastropoda, which was likely excluded because of its highly variable placement in the source trees. These trees were not further considered because of the lack of taxa compared with the complete supertrees generated by the more liberal optimization methods. However, the PHYsic_IST morphological tree did recover Scaphopoda + Bivalvia and Caudofoveata + Solenogastres (Aplacophora) clades, which were also recovered by the majority of the more liberal optimization analyses of the morphological trees (see below).Symmetric distance differences between supertrees were calculated using PAUP 4b10 (). The TreeSetVis Package (Amenta and Klinger 2002) for the Mesquite system for phylogenetic computing () was used to visualize the distributions of the source trees and supertrees in a tree space defined by the distribution of 5000 random eight-taxon molluscan trees (). The visualization process uses multidimensional scaling (MDS) of the Robinson–Foulds tree-to-tree distances amongst the trees to position them in tree space (). […]

Pipeline specifications

Software tools Clann, PhySIC_IST, PAUP*, Mesquite
Application Phylogenetics