Today’s Science sees the publication of a phylogenomic study of 196 bird species, which has some rather marked differences to the traditional phylogenies of bird species. Abstract says -
Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ~32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors.
Abstract is here. Much news coverage will be forthcoming, I suspect, and I’ll link to some of these as they come through.
Update: GrrlScientist has covers the paper excellently (although, not enough phylogenetic details for my liking 
