Two aspects along the continuum of pigeon evolution: A South-Pacific radiation and the relationship of pigeons within Neoaves Gillian C. Gibb * , David Penny Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11222 Palmerston North 4442, New Zealand article info Article history: Received 3 December 2009 Revised 24 March 2010 Accepted 12 April 2010 Available online 23 April 2010 Keywords: Ptilinopus Ducula Hemiphaga Columbiformes Sandgrouse Mitochondrial genomes Phylogeny abstract Phylogenetics explores the continuum of shallower to deeper genetic divergences between taxa. Along this continuum increasing lengths of DNA sequence can be used to answer deeper and deeper questions about biological relationships. We use shorter, and then longer mitochondrial DNA sequences to address two aspects of pigeon evolution. Firstly, we examine the phylogenetic relationships of the eight genera within the South Pacific Ducula–Ptilinopus radiation, and examine how this radiation fits into pigeons generally. Within Ducula, taxa are closely related, whereas Ptilinopus is very diverse, and paraphyletic. One third of all pigeon species are within the Ducula–Ptilinopus radiation, however all are very similar ecologically. Secondly, we study the deeper phylogenetic question regarding the relationship of pigeons to other birds. To this end, we report the complete mitochondrial genome of Hemiphaga novaeseelandiae, a member of the Ducula–Ptilinopus radiation. We use this mitochondrial genome, along with additional sandgrouse (Pterocles namaqua) mitochondrial genes to assess various candidates for the closest relative of pigeons. Of parrots, shorebirds, and sandgrouse, we find highest support for the sandgrouse–pigeon grouping. Furthermore in these analyses the pigeon and sandgrouse group closer to the falcons than any other included taxon. The finding that pigeons and sandgrouse may be more closely related to falcons than to previous candidates such as shorebirds or parrots invites further investigation. Ó 2010 Elsevier Inc. All rights reserved. 1. Introduction This study uses mitochondrial DNA sequences to address two main questions about pigeon phylogeny. Firstly, we evaluate the phylogenetic radiation of pigeons in the Asia/Pacific region, domi- nated by the speciose genera Ducula (imperial pigeons) and Ptilin- opus (fruit doves). Secondly, we examine more closely the question of where pigeons fit within Neoaves. We particularly investigate the many candidates that have been purported to be closest rela- tives of pigeons. This study is part of a broad investigation of ques- tions of avian phylogeny (Gibb et al., 2007; Pratt et al., 2009). 1.1. A South East Asian/Pacific radiation of pigeons Ducula and Ptilinopus, together with six other near-monotypic genera (Hemiphaga, Lopholaimus, Gymnophaps, Cryptophaps, Alec- troenas, and Drepanoptila), form a radiation of pigeons and doves that stretches from the Himalayas to Polynesia (Gibbs et al., 2001; Johnson, 2004). This Ducula–Ptilinopus radiation includes al- most one third of all pigeon species (99 out of 312 species, Gibbs et al., 2001), and all of this radiation are arboreal and frugivorous. Almost all are island dwellers with only nine of the 99 species breeding in mainland Asia or Australia. Both Ducula and Ptilinopus have been successful in dispersing across the Pacific, with most islands having one or more species of each genus before human contact (Steadman, 1997). Although many pigeon species have become locally or totally extinct since the arrival of humans (Steadman, 2006), at least one (Ducula pacif- ica) appears to have successfully expanded its range through the Pacific since human colonization (Steadman, 1997). There have been a few recent molecular studies of pigeons. None of these studies have included more than four Ducula or Pti- linopus species, and some only included one species per genus. Of these studies, Shapiro et al. (2002) considered particularly the rela- tionships of the extinct dodo (Raphus cucullatus) and solitaire (Pezophaps solitaria) to other pigeons. Johnson (2004) used short mitochondrial (mt) and nuclear sequences to examine the utility and evolution of indels in pigeon phylogeny. Pereira et al. (2007) used longer nuclear and mt sequences from just one exemplar per genus to study biogeography and times of divergence. Because of this approach, in Pereira et al., 2007 analysis, the huge radiation of Ducula and Ptilinopus can appear insignificant when compared to the six monotypic lineages that surround them. Thus, a better phylogeny for Ducula and Ptilinopus is required to understand their evolutionary history. 1055-7903/$ - see front matter Ó 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2010.04.016 * Corresponding author. Fax: +64 6 350 5626. E-mail addresses: g.c.gibb@massey.ac.nz (G.C. Gibb), d.penny@massey.ac.nz (D. Penny). Molecular Phylogenetics and Evolution 56 (2010) 698–706 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev