A multi-locus inference of the evolutionary diversification of extant flamingos (Phoenicopteridae)

0 Centre de Recherche de la Tour du Valat , Le Sambuc, Arles 13200 , France 1 Universite de Bourgogne, Equipe Ecologie Evolutive, UMR CNRS 6282 Biogeosciences , 6 bd. Gabriel, Dijon 21000 , France 2 Department of Biology and Marine Biology, University of North Carolina Wilmington , Wilmington, North Carolina , USA 3 Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics , Alfred-Kowalke-Str. 17, Berlin D-10315 , Germany Torres et al. - A multi-locus inference of the evolutionary diversification of extant flamingos (Phoenicopteridae) A multi-locus inference of the evolutionary diversification of extant flamingos (Phoenicopteridae) Chris R Torres1, Lisa M Ogawa1, Mark AF Gillingham2,3,4, Brittney Ferrari1 and Marcel van Tuinen1* Background: Modern flamingos (Phoenicopteridae) occupy a highly specialized ecology unique among birds and represent a potentially powerful model system for informing the mechanisms by which a lineage of birds adapts and radiates. However, despite a rich fossil record and well-studied feeding morphology, molecular investigations of the evolutionary progression among modern flamingos have been limited. Here, using three mitochondrial (mtDNA) markers, we present the first DNA sequence-based study of population genetic variation in the widely distributed Chilean Flamingo and, using two mtDNA and 10 nuclear (nDNA) markers, recover the species tree and divergence time estimates for the six extant species of flamingos. Phylogenetic analyses include likelihood and Bayesian frameworks and account for potential gene tree discordance. Analyses of divergence times are fossil calibrated at the divergence of Mirandornithes (flamingos + grebes) and the divergence of crown grebes. Results: mtDNA sequences confirmed the presence of a single metapopulation represented by two minimally varying mtDNA barcodes in Chilean flamingos. Likelihood and Bayesian methods recovered identical phylogenies with flamingos falling into shallow-keeled (comprising the Greater, American and Chilean Flamingos) and deep-keeled (comprising the Lesser, Andean and Jamess Flamingos) sub-clades. The initial divergence among flamingos occurred at or shortly after the Mio-Pliocene boundary (63 Ma) followed by quick consecutive divergences throughout the Plio-Pleistocene. There is significant incongruence between the ages recovered by the mtDNA and nDNA datasets, likely due to mutational saturation occurring in the mtDNA loci. Conclusion: The finding of a single metapopulation in the widespread Chilean Flamingo confirms similar findings in other widespread flamingo species. The robust species phylogeny is congruent with previous classifications of flamingos based on feeding morphology. Modern phoenicopterids likely originated in the New World with each sub-clade dispersing across the Atlantic at least once. Our divergence time estimates place flamingos among the youngest families of birds, counter to the classical notion of flamingos as among the oldest based on biogeography and the fossil record. Finally, we designate Phoeniconaias as a junior synonym of Phoenicoparrus and redefine the latter genus as containing all flamingos more closely related to Phoenicoparrus andinus than Phoenicopterus roseus. Open Access * Correspondence: 1Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA Full list of author information is available at the end of the article 2014 Torres et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Background Flamingos are a unique order (Phoenicopteriformes) of birds with a highly specialized ecology but their evolutionary history remains poorly understood and until recently has only been informed by the fossil record. Flamingos are traditionally perceived as among the oldest lineages of living birds with reports of flamingo-like birds appearing in the fossil record as early as the late Cretaceous (e.g. [1]). However, the earliest birds reliably placed as stem phoenicopteriforms (family Palaelodidae) first appear in the early Oligocene of Europe [2] and the earliest members of the crown family (Phoenicopteridae) appear during the OligoMiocene of the Old World [3-5], suggesting an age for the family on par with most other major familial divergences within Aves [6]. Notably, Harrisonavis croizeti, an apparently morphologically modern flamingo from the Oligo-Miocene of France, suggests the modern flamingo divergence occurred in the Old World as early as the late Paleogene [3]. Recent fossil and molecular work have shed new insight into phoenicopterid origins and cast doubt on the classical notion of flamingos as a particularly ancient lineage among the storks, herons and ibises (Ciconiiformes). Most notably, molecular [7-11] and morphological [12,13] studies have supported a sister relationship between flamingos and grebes (Podicipediformes) as the clade Mirandornithes [14]. However, despite these advances, the exact age and phylogeny of modern flamingos remains to be robustly tested and several questions about flamingo evolution are in need of further investigation: (1) how do the six extant species of flamingos relate to each other, (2) how long ago did these divergences occur, and (3) where did crown Phoenicopteridae originate? Sibley and Ahlquist [15] represents the only genetic study that addresses these questions. This study, based on differences in hybridization strength between genomic DNA of different species, documented a shallow age among five species and (the formerly classified) two subspecies (Phoenicopterus ruber ruber and P. ruber roseus) that likely form a single genus comprising two distinct sub-clades. This division is congruent with the organization by Jenkin [16] of flamingos into two groups reflecting mandibular morphology and feeding strategy: the Lesser, Andean and Jamess Flamingos (the so-called deep-keeled group) have bulbous bills in cross-section suited to filtration of smaller food items (e.g. blue-green algae and diatoms); the remaining species (shallowkeeled group) have more compact bills in cross-section suited to filtration of larger food items (e.g. mollusks and crustaceans). Further morphological variation within the two sub-clades is not completely known [17]. Intraspecific genomic variation in each flamingo species is also incompletely known but is an important consideration when investigating morphological and geographic origins of species with wide ranges. Recent population genetics studies have identi (...truncated)