Champagne: Whole-genome phylogenomic character matrix method places Myomorpha basal in Rodentia

We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic events that, by rigorously picking orthologous genes and locating large, virtually homoplasy-free insertion and deletion events, delivers a character matrix that outperforms existing morphological and nucleotide-based matrices on both established phylogenies, and difficult-to-resolve nodes in the mammalian tree. Champagne harbors distinct theoretical advantages, and can easily be run on any clade of related species, of the many currently being sequenced. Champagne considerably improves the retention index in the parsimony analysis of a number of widely established topologies, observes incomplete lineage sorting (ILS) at the root of Paenungulata, finds little evidence for human-chimp-gorilla ILS, and most surprisingly, offers convincing evidence for a reconsideration of squirrel9s position in the rodent tree.