DOI: 10.5061/dryad.b4m2c
title: Data from: Consensus and confusion in Molluscan trees: evaluating morphological and molecular phylogenies

description: Mollusks are the most morphologically disparate living animal phylum, they
 have diversified into all habitats, and have a deep fossil record.
 Monophyly and identity of their eight living classes is undisputed, but
 relationships between these groups and patterns of their early radiation
 have remained elusive. Arguments about traditional morphological phylogeny
 focus on a small number of topological concepts but often without regard
 to proximity of the individual classes. In contrast, molecular studies
 have proposed a number of radically different, inherently contradictory,
 and controversial sister relationships. Here, we assembled a dataset of 42
 unique published trees describing molluscan interrelationships. We used
 these data to ask several questions about the state of resolution of
 molluscan phylogeny compared to a null model of the variation possible in
 random trees constructed from a monophyletic assemblage of eight
 terminals. Although 27 different unique trees have been proposed from
 morphological inference, the majority of these are not statistically
 different from each other. Within the available molecular topologies, only
 four studies to date have included the deep-sea class Monoplacophora; but
 36.4% of all trees are not significantly different. We also present
 supertrees derived from 2 data partitions and 3 methods, including all
 available molecular molluscan phylogenies, which will form the basis for
 future hypothesis testing. 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 published topologies. Based on the totality of available
 evidence, certain patterns of relatedness among constituent taxa become
 clear. The internodal distance is consistently short between a few taxon
 pairs, particularly supporting the relatedness of Monoplacophora and the
 chitons, Polyplacophora. Other taxon pairs are rarely or never found in
 close proximity, such as the vermiform Caudofoveata and Bivalvia. Our
 results have specific utility for guiding constructive research planning
 in order to better test relationships in Mollusca as well as other
 problematic groups. Taxa with consistently proximate relationships should
 be the focus of a combined approach in a concerted assessment of potential
 genetic and anatomical homology, while unequivocally distant taxa will
 make the most constructive choices for exemplar selection in higher-level
 phylogenomic analyses.
description: Supplementary Table
 1Tree
 file containing all trees used in analyses.SL_SuppTable_s1_treefile.nexSupplementary Figure 1Percentage of trees wherein a given taxon pair are separated by two nodes or fewer (e.g. sister-taxa are separated by 1 node). Zero-values indicate that a given pair are always more than 2 nodes apart, in our dataset of 42 trees including morphological (blue, n=27) and molecular (green, n=15) datasets.suppl-figure1_nodedistances.epsSupplementary Figure 2Multidimensional scaling plot of 5000 randomly-generated trees including 8 molluscan classes, and our dataset of 42 trees from the literature (morphological, blue circles; molecular, red circles). Trees plotted outside of the randomly generated trees represent source trees with fewer than 8 classes in their topology.suppl-figure2_TreViz_SourceTrees.epsSupplementary Tables 2-4TABLE S2. Tree notation, scores, permutation tail probability tests, source tree fit, and related data for each of the molecular supertrees analyses. TABLE S3. Tree notation, scores, permutation tail probability tests, source tree fit, and related data for each of the morphological supertrees analyses. TABLE S4. Symmetric distances between supertrees. Partition: Morph = morphology, Molec = molecular.SL_SuppTables_S2-S4.docx