title: A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies).
abstract: BACKGROUND
  Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies.
  
  
  RESULTS
  483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity.
  
  
  CONCLUSIONS
  Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.
authors.affiliation: Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, USA. regier@umd.edu
authors.forename: Jerome C
authors.initials: JC
authors.lastname: Regier
authors.forename: Charles
authors.initials: C
authors.lastname: Mitter
authors.forename: Andreas
authors.initials: A
authors.lastname: Zwick
authors.forename: Adam L
authors.initials: AL
authors.lastname: Bazinet
authors.forename: Michael P
authors.initials: MP
authors.lastname: Cummings
authors.forename: Akito Y
authors.initials: AY
authors.lastname: Kawahara
authors.forename: Jae-Cheon
authors.initials: JC
authors.lastname: Sohn
authors.forename: Derrick J
authors.initials: DJ
authors.lastname: Zwickl
authors.forename: Soowon
authors.initials: S
authors.lastname: Cho
authors.forename: Donald R
authors.initials: DR
authors.lastname: Davis
authors.forename: Joaquin
authors.initials: J
authors.lastname: Baixeras
authors.forename: John
authors.initials: J
authors.lastname: Brown
authors.forename: Cynthia
authors.initials: C
authors.lastname: Parr
authors.forename: Susan
authors.initials: S
authors.lastname: Weller
authors.forename: David C
authors.initials: DC
authors.lastname: Lees
authors.forename: Kim T
authors.initials: KT
authors.lastname: Mitter
mesh_terms: D000818:Animals; D002080:Butterflies / Q000145:classification / Q000235:genetics*; D009036:Moths / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
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