title: Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation.
abstract: Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context.
  
  
  
  We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves.
  
  
  
  Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.
authors: Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
authors: André E R
authors: AE
authors: Soares
authors: Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.|Revive & Restore, The Long Now Foundation, San Francisco, CA, 94123, USA.
authors: Ben J
authors: BJ
authors: Novak
authors: Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
authors: James
authors: J
authors: Haile
authors: Environmental Futures Research Institute, Griffith University, 170 Kessels Road QLD 4111, Nathan, Australia.
authors: Tim H
authors: TH
authors: Heupink
authors: Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
authors: Jon
authors: J
authors: Fjeldså
authors: Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
authors: M Thomas P
authors: MT
authors: Gilbert
authors: McMaster Ancient DNA Centre, Departments of Anthropology and Biology, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 L9, Canada.
authors: Hendrik
authors: H
authors: Poinar
authors: Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA.|Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
authors: George M
authors: GM
authors: Church
authors: Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA. bashapir@ucsc.edu.
authors: Beth
authors: B
authors: Shapiro
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D005075:Biological Evolution; D010856:Columbidae / Q000145:classification / Q000235:genetics*; D053476:Extinction, Biological; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D017422:Sequence Analysis, DNA
keywords: Ancient DNA; Columbidae; Passenger pigeon; Pezophaps solitaria; Raphus cucullatus; time calibrated phylogeny