Phylogeny of Lepidoptera: A genomics-inspired, community collaboration

The LepTree project is a genomics-inspired, community collaboration that aims to resolve higher-level relationships within Lepidoptera using up to 26 protein-coding, nuclear gene sequences. Current phylogenetic results for the lepidopteran taxon Apoditrysia (98% of all species) are presented and discussed from an analytical perspective. Issues to be addressed include the effectiveness of heuristic likelihood searches, the effect of nucleotide compositional heterogeneity and the benefits of restricting analysis to nonsynonymous versus total nucleotide data. A new approach to the coding of nonsynonymous data is showcased and shown to lead to significantly increased bootstrap support values for deeper nodes.