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Home , Adelidae, Amphiesmenoptera, Anthelidae, Bombycidae, Brahmaeidae, Carposinidae

A Supermatrix Perspective on the Amphiesmenoptera Phylogeny Bret M. Boyd2,3 & Gordon Burleigh1,3 1Department of Biology, College of Liberal Arts and Sciences; 2Genetics Institute; and 3Florida Museum of Natural History: University of Florida, Gainesville, Florida

Results and Conclusions: ef1a ITS ND5 NADH SU1 RpS5 RpS2 18SrRNA GAPDH rRNA CAD cytb MDH 28SrRNA COI Wingless 28SrRNA Stratiomyidae YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO Abstract: The Amphiesmenoptera are a highly diverse of Methods: YES NO NO YES YES YES NO NO NO YES YES YES NO YES YES NO •Our data matrix and contains 5344 Amphiesmenoptera taxa Chathamiidae YES NO NO NO NO NO NO NO YES NO NO NO YES YES NO NO Oeconesidae YES NO NO NO NO NO NO NO YES NO NO NO YES NO NO NO endopterygote that includes ( and .Downloaded core nucleotide sequence data from Helicophidae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO (5020 from Lepidoptera and 324 from Trichoptera) and 265 outgroup taxa. YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO ) and Trichoptera (). We built a comprehensive www.ncbi.nlm.nih.gov YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO •Our data matrix contained thirteen clusters representing elongation factor 1 alpha, YES NO NO YES NO NO YES NO NO YES YES NO NO YES NO NO YES NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO phylogenetic framework of Amphiesmenotpera that reflects both .Clustered sequences using an all-by-all blastn Kokiriidae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO ITS, NDS, NADH subunit 1, ribosomal protein s5, ribosomal protein s2, 18SrRNA, Geometridae YES NO NO YES YES NO NO YES NO NO NO YES YES YES YES NO . YES NO NO NO NO NO NO NO NO YES NO NO NO YES NO NO the rapidly growing sequence data and the computational advances Aligned sequences within single linkage clusters using Muscle GADPH (glyceraldehyde-3-phosphate dehydrogenase), rRNA, CAD YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO that allow for large-scale phylogenetic analyses. We first assembled .Manually edited alignments and removed problematic sequences YES NO NO NO NO NO NO NO NO NO NO NO NO YES YES NO (carbamoylphosphate synthetase), cytochrome b, MDH (Malate Dehydrogenase), YES NO NO NO NO NO NO NO NO NO NO NO YES YES YES NO Arctiidae YES NO NO NO NO NO NO NO NO NO YES NO YES YES YES NO all potentially phylogenetic informative sequence data from .Built phylogenetic trees for each cluster (loci) using RAxML 28SrRNA, COI, wingless, and 28SrRNA. YES NO NO NO NO NO NO NO NO NO NO NO NO YES YES NO YES NO YES YES YES YES YES YES NO YES YES YES NO YES YES NO Amphiesmenotpera and selected outgroups in GenBank. After .Removed any questionable sequences from single locus trees YES NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO •Two primitive mandibulate families formed the base of the Papilionidae YES NO YES YES YES NO YES YES NO YES YES YES YES YES YES NO YES NO YES YES YES YES YES YES NO YES YES YES NO YES YES NO pruning questionable or anomalous sequences and editing the .Selected clusters that included 100 or more taxa YES NO YES YES NO NO YES NO NO NO YES NO YES YES YES NO Amphiesmenopteran clade Lymantriidae YES NO NO NO NO NO YES YES NO NO NO NO NO YES YES NO alignments, homologous sequence clusters with more than 100 taxa .Constructed supermatrix by concatenating alignments from YES NO NO NO NO NO NO NO NO NO NO NO YES YES NO NO •Trichoptera forms a clade within Lepidoptera YES NO NO NO NO NO YES NO NO NO NO NO YES YES YES NO Conoesucidae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO were concatenated into a single phylogenetic “supermatrix” that selected clusters Fragilariophycidae YES NO NO NO NO NO NO NO NO NO NO NO NO YES YES NO •Superfamilies and are supported as polyphyletic YES NO NO YES YES YES YES YES NO YES NO YES YES YES YES NO . YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO contained 5609 taxa, representing by far the largest possible Built phylogenetic tree from supermatrix using RAxML •More work is needed to understand the relationships between Lepidoptera and YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO YES YES YES YES NO NO NO YES NO YES YES YES NO YES YES NO Amphiesmenoptera data set. Maximum likelihood phylogenetic .Conducted bootstrap replicates using RAxML and Fast Tree YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Trichoptera Helicopsychidae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Molannidae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO analyses on the supermatrix revealed a credible phylogenetic •More work is needed to understand the relationships among Ditrysian Lepidoptera YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Dipseudopsidae YES NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO hypothesis that raises intriguing evolutionary questions and suggests YES NO NO YES NO NO NO NO NO YES NO NO NO YES NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO Hedylidae YES NO NO YES YES YES NO YES NO YES NO YES NO YES YES NO directions for future data collection. The supermatrix phylogenetic Hesperiidae YES NO YES YES NO NO NO NO NO NO YES NO NO YES YES NO YES NO NO NO NO NO YES NO NO NO NO NO NO YES NO NO Sericostomatidae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO hypothesis provides not only a starting point for large scale Beraeidae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Philorheithridae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO evolutionary and ecological analyses of the hyper-diverse Acknowledgements: We would like to thank YES NO YES NO NO NO YES NO NO NO YES NO NO YES NO NO YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO Amphiesmenoptera clade, but will hopefully be a resource to Marc Branham, Andy Warren, Delano Lewis, YES NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO Lemoniidae YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO promote and guide future phylogenetic studies within Jacqueline Miller, and Debbie Mathews for their YES NO NO NO NO NO YES NO NO NO NO NO NO YES YES YES Calocidae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Odontoceridae YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Amphiesmenotpera. research assistance and David Reed, Marta YES NO NO NO YES NO YES YES NO NO YES YES NO YES NO NO YES NO NO NO NO NO YES NO NO NO NO NO YES NO NO NO YES NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO Wayne, and Wilfred Vermeris for their support Sialidae YES NO NO NO NO NO YES NO YES NO NO NO NO YES NO NO YES NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO Introduction: The superorder Amphiesmenotpera has been and interest in our project. YES NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO YES NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO YES NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO supported by , morphological, rRNA sequence data. YES NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO Lepidoptera and Trichoptera are supported as sister that Literature Cited: YES NO NO NO NO NO NO NO NO NO YES NO NO YES YES NO Carthaeidae YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO YES YES NO NO NO YES NO YES NO YES YES NO shared an Amphiesmentopera ancestor during the Mesozoic Grimaldi, D., and Engle, M. S. 2005. The NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Phryganopsychidae NO NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO (Grimaldi and Engle 2005, Henning 1981, Kristensen et al. 2007, . Cambridge University Calamoceratidae NO NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO Apataniidae NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Uenoidae NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Kristensen and Skalski 1999). Lepidoptera is a hyperdiverse Press, Cambridge. 755pp. Phryganeidae NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Hydrosalpingidae NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO with 500,000 potential and Trichoptera is smaller with Petrothrincidae NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Hennig, W. 1981. Phylogeny. John Wiley Anomalopsychidae NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Atriplectididae NO NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO 50,000 potential species (Grimaldi and Engle 2005, Kristensen et al. and Sons, Chinchester. 514pp. NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO Brachycentridae NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Tasimiidae NO NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO 2007). Previous phylogenetic studies within Amphiesmenotpera Kristensen, N. P., Scoble, M. J., and Karsholt, O. NO NO NO NO NO NO YES NO NO NO NO NO NO YES NO NO Plectrotarsidae NO NO NO NO NO NO YES NO YES NO NO NO YES NO NO NO have inferred backbone relationships based on a small number of 2007. Lepidoptera phylogeny and systematics: NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO Agathiphagidae NO NO NO NO NO NO YES NO NO NO NO NO YES YES NO NO representative taxa and have focused within either the Lepidoptera the state of inventorying moth and Mnesarchaeidae NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO or Trichoptera clades (Mutanen et al. 2010 ). We utilized all diversity. Zootaxa 1668:699-747. NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO Heterobathmiidae NO NO NO NO NO NO YES NO NO NO NO NO YES YES NO NO informative publically available data to assemble a more Kristensen, N. P., Skalski, A. W. 1999. NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO YES YES NO NO comprehensive phylogeny across all Amphiesmenotpera. Due to the Psychidae NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO Phylogeny and palaeontology. In Handbuch der Tischeriidae NO NO NO NO NO NO YES NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO YES YES NO NO patchy available data, we used a supermatrix approach to infer a Zoologie, a Natural History of the Phyla of the NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO YES NO NO NO YES NO YES YES NO NO comprehensive phylogenetic hypothesis. While the results derived Kingdom, Vol IV, Arthropoda: Insecta, NO NO NO NO NO NO YES NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO YES NO NO NO from this study are not conclusive, our methods provide an Part 35, Lepidoptera, Moths and Butterflies, Vol. NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO Himantopteridae NO NO NO NO NO NO YES NO NO NO NO NO YES NO NO NO Somabrachyidae NO NO NO NO NO NO YES NO NO NO NO NO YES NO NO NO unprecedented preliminary exploration of species-level relationships I: Evolution, Systematics, and Biogeography. NO NO NO NO NO NO YES NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO throughout the clade. This approach can help elucidate potential Edited Kristensen, N. P.. Walter de Gruyter, Pisuliidae NO NO NO NO NO NO YES NO YES NO NO NO YES YES NO NO Limnocentropodidae NO NO NO NO NO NO NO NO YES NO NO NO YES NO NO NO Barbarachthonidae NO NO NO NO NO NO NO NO YES NO NO NO YES YES NO NO polyphyly of paraphyly of currently accepted clades that may not be Berlin. Goeridae NO NO NO NO NO NO NO NO YES NO NO NO YES YES NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO YES NO NO evident from phylogenetic hypotheses that include only a small NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO Mutanen, M., Wahlberg, N., Kaila, L. 2010. NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO YES NO NO number of representative taxa. Members of the Amphiesmenotpera Comprehensive gene and taxon coverage Chironomidae NO NO NO NO NO NO NO NO NO NO YES NO NO YES NO NO Yponomeutidae NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO are of economic importance (crop pests and water quality indicator elucidates radiation patterns in moths and Argyresthiidae NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO species), flagship species in conservation efforts, and the focus butterflies. Proceeding of the Royal Society: NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO evolutionary and ecological studies. We hope that our supermatrix Biological Sciences doi:10.1098/rspb.2010.0392 NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO Xyloryctidae NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO based phylogeny will promote and guide more comprehensive NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO Corydalidae NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO Xylomyidae NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO phylogenetic studies to better understand this highly diverse and NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO NO important clade of insects. Figure 1: Phylogenetic reconstruction of Amphiesmenoptera using supermatrix generated in this study. Figure 2: Insect families and gene clusters represented in supermatrix