Phylogenetic supermatrix analysis of obtectomeran Lepidoptera: Total evidence from 7 genes and 1796 species

A phylogenetic supermatrix analysis of the hyper-diverse Lepidopteran group, Obtectomera was conducted. In total, 1796 species were sampled for six protein-coding nuclear genes and one mitochondrial gene. Unpublished sequences from Regier et al. (2008) were combined with all sequences available from GenBank. A semi-automated pipeline was designed to construct the supermatrix. Multiple sequence alignments were conducted separately for each gene, and the seven data sets were concatenated into a single data matrix. Multiple sequences of the same species were fused using IUPAC/IUB ambiguity codes and made into a single consensus sequence representing that particular species. Maximum likelihood analyses were conducted using parallel Grid computing and processors on the University of Maryland Altus 3400 Server. Results were generally in concordance with a preliminary molecular analysis with lesser taxon and gene sampling. However, unlike prior molecular analyses, results from the present study recovered a monophyletic Obtectomera, a result which has traditionally been supported by morphology.