title: Bird evolution: testing the Metaves clade with six new mitochondrial genomes.
abstract: BACKGROUND
  Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade.
  
  
  RESULTS
  Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the beta-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved.
  
  
  CONCLUSIONS
  Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.
authors.affiliation: Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand. m.morgan-richards@massey.ac.nz
authors.forename: Mary
authors.initials: M
authors.lastname: Morgan-Richards
authors.forename: Steve A
authors.initials: SA
authors.lastname: Trewick
authors.forename: Anna
authors.initials: A
authors.lastname: Bartosch-Härlid
authors.forename: Olga
authors.initials: O
authors.lastname: Kardailsky
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Phillips
authors.forename: Patricia A
authors.initials: PA
authors.lastname: McLenachan
authors.forename: David
authors.initials: D
authors.lastname: Penny
mesh_terms: D000818:Animals; D001717:Birds / Q000145:classification* / Q000235:genetics; D019143:Evolution, Molecular; D005340:Fibrinogen / Q000235:genetics; D054629:Genome, Mitochondrial; D054643:INDEL Mutation; D007438:Introns; D016013:Likelihood Functions; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D005340:Fibrinogen