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Data deposition to NCBI GenomesThis Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (>1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two scarlet macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the scarlet macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the scarlet macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.

Geophagy, the intentional ingestion of soil, is a widespread phenomenon whose function is still debated. Recent studies suggest that consumed soils adsorb dietary toxins and provide sodium. However, quantification of soil choice has been absent from most studies, prohibiting the direct comparison of soil use and characteristics.To determine correlates among bird use and soil characteristics, we analyze physical structure, mineral composition, and alkaloid adsorption (14 soil characteristics in total) for 22 soil samples from a riverbank 'clay lick' used by macaws and parrots (family Psittacidae) in Amazon lowland forests in the Tambopata region of southeastern Peru. We quantified bird preferences through photographic mapping. Mineral concentrations were determined using analyses designed to approximate the mineral availability in the vertebrate stomach. The sodium levels in the soil were much higher than in food plants consumed by parrots in this region. Both adsorption of quinine, the model alkaloid used, and sodium concentration correlated significantly with bird use. Sodium explained a much higher percentage of the variation in bird use than quinine adsorption. However, the analyses were complicated by the high degree of correlation among soil variables: clay percentage and sodium concentration were highly correlated with each other and with bird use, making it impossible to determine which of these may have the greater contribution to bird preference. The results suggest that the soils consumed provide an important source of dietary sodium and adsorb alkaloid toxins.Abstract in Spanish is available at http://www.blackwell-synergy.com/loi/btp.

We observed ten species of psittacids, three species of columbids, and two species of cracids consuming soil from banks of the lower Tambopata River in southeastern Peru. Our study used observations and soil analyses from eight exposed riverbank sections to test the predictions of three models to determine why birds consume clay: mechanical aid to digestion (grit), adsorption of dietary toxins, and mineral supplementation. We found that preferred soils were deficient in particles large enough to aid in the mechanical breakdown of food and help digestion. Percent clay content and cation exchange capacity (CEC), both predicted to correlate with adsorption of toxins, did not differ between used and unused sites as had been found in a similar study. Instead, preferred soils were more saline and had higher concentrations of exchangeable sodium. This suggests that the choice of soils at our site was based primarily on sodium content. Birds may be using the heavy, plastic texture of soils rich in clays and high in exchangeable sodium as a proximal cue for soil selection. Our findings suggest that avian soil selection decisions depend on the range of available soil characteristics.RESUMENObservamos diez especies de Psittasidos, trés especies de Columbidos, y dos especies de Cracidos consumiendo suelo de los bancos del bajo Rio Tambopata en el sureste del Perú. Nuestro estudio utiliza observaciones de aves y análisis de suelos de ocho secciones expuestas de los bancos de rio para probar las predicciones de tres modelos de porque las aves consumen arcilla: ayuda mecánica para la digestión (arena triturada), adsorción de toxinas en la dieta, y suplemento mineral. Encontramos que los suelos preferidos eran deficientes en particulas lo suficientemente grandes como para ayudar en la trituración mecánica del alimento y ayudar a la digestión. El porcentaje de contenido de arcilla y la capacidad de intercambio catiónico (CIC), ambos esperados para correlacionar con la adsorción de toxinas, no varió entre sitios usados y no usados como ha sido encontrado en un estudio similar. En cambio, los suelos preferidos fueron más salinos y con mayor concentracion de sodio intercambiable. Esto sugiere que la selección de suelos en nuestro sitio de estudio está basado principalmente en el contenido de sodio. Las aves pueden estar usando las texturas densas y plásticas de los suelos ricos en arcillas con alto contenido de sodio intercambiable como una señal próxima para la selección del suelo. Nuestros resultados sugieren que las decisiones de selección de suelos por las aves depende del rango de caracteristicas de suelos disponibles.

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Geophagy is widespread and well documented for mammals, but avian geophagy has only recently become the subject of serious scientific investigation. I analyzed data from 606 mornings of observations at a large avian geophagy site or "clay lick" in the southwestern Amazon Basin to examine the effects of weather on bird lick use. Birds used the clay lick on 94% of the mornings without precipitation or fog. Parrots dominated the site in both numbers of species (17) and individuals (>99%). Weather conditions were significantly correlated with total lick use: there was greater use on sunny mornings and less on rainy mornings. Fog and overnight rain were correlated with low lick use. Sun, rain, fog, and overnight rain were recorded on 47, 25, 20, and 8% of the mornings, respectively. I estimated that inclement weather caused an annual 29% reduction in geophagy for all bird species combined. When early morning rain prevented species from using the lick, they did not return later in the day nor did they compensate for rainy mornings by increasing lick use on subsequent days. The timing of lick use and the lack of compensation suggest that neutralization of toxins could be driving lick use in this system.