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In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes., Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome.

Aim: To investigate the structure and rate of gene flow among populations of habitat‐specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction.Location: Peruvian and Argentine Andes.Taxon: Two subspecies of torrent duck (Merganetta armata).Methods: We sampled 156 individuals in Peru (M. a. leucogenis; Chillón River, n = 57 and Pachachaca River, n = 49) and Argentina (M. a. armata; Arroyo Grande River, n = 33 and Malargüe River, n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine‐scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, n = 10 and Argentina, n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z‐linked double‐digest restriction‐associated DNA sequences.Results: Haplotype and nucleotide diversities were higher in Peru than Argentinaacross all markers. Peruvian and Argentine subspecies showed concordant species‐level differences (ΦST mtDNA= 0.82;ΦST autosomal = 0.30;ΦST Z chromosome = 0.45),including no shared mtDNA haplotypes. Demographic parameters estimated formtDNA using IM and IMa2 analyses, and for autosomal markers using ∂a∂i (isolation‐with‐migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal ∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply divergedlineages. The populations were well‐differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country.Main conclusions: We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure. Fil: Alza, Luis. University of Alaska; Estados Unidos. University of Miami. Department of Biology; Estados Unidos. División de Ornitología. Centro de Ornitología y Diversidad; Perú Fil: Lavretsky, Philip. University of Texas at El Paso; Estados Unidos Fil: Peters, Jeffrey L.. Wright State University; Estados Unidos Fil: Cerón, Gerardo. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche. Departamento de Zoología. Laboratorio de Parasitología; Argentina Fil: Smith, Matthew. University of Alaska; Estados Unidos Fil: Kopuchian, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Centro de Ecología Aplicada del Litoral. Universidad Nacional del Nordeste. Centro de Ecología Aplicada del Litoral; Argentina. Museo Argentino de Ciencias Naturales, División Ornitología,; Argentina Fil: Astié, Andrea Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina Fil: McCracken, Kevin G.. División de Ornitología. Centro de Ornitología y Diversidad; Perú. University of Miami. Department of Biology; Estados Unidos. University of Miami; Estados Unidos. University of Alaska; Estados Unidos

Local adaptation frequently occurs across populations as a result of migration-selection balance between divergent selective pressures and gene flow associated with life in heterogeneous landscapes. Studying the effects of selection and gene flow on the adaptation process can be achieved in systemsthat have recently colonized extremeenvironments. This study utilizes an endemic South American duck species, the speckled teal (Anas flavirostris),which has both high- and low-altitude populations. High-altitude speckled teal (A. f. oxyptera) are locally adapted to the Andean environment and mostly allopatric from low-altitude birds (A. f. flavirostris);however, there is occasional geneflowacross altitudinal gradients. In this study,we used next-generation sequencing to explore genetic patterns associated with high-altitude adaptation in speckled teal populations, as well as the extent to which the balance between selection and migration have affected genetic architecture. We identified a set of loci with allele frequencies strongly correlated with altitude, including those involved in the insulin-like signaling pathway, bone morphogenesis, oxidative phosphorylation, responders to hypoxia-induced DNAdamage, and feedback loops to the hypoxia-inducible factor pathway. These same outlier loci were found to have depressed gene flow estimates, as well as being highly concentrated on the Z-chromosome. Our results suggest a multifactorial response to life at high altitudes through an array of interconnected pathways that are likely under positive selection and whose genetic components seem to be providing an effective genomic barrier to interbreeding, potentially functioning as an avenue for population divergence and speciation

Feathers are one of the defining characteristics of birds and serve a critical role in thermal insulation and physical protection against the environment. Feather structure is known to vary among individuals, and it has been suggested that populations exposed to different environmental conditions may exhibit different patterns in feather structure. We examined both down and contour feathers from two populations of male Torrent Ducks (Merganetta armata) from Lima, Peru, including one high-altitude population from the Chancay-Huaral River at approximately 3500 meters (m) elevation and one low-altitude population from the Chillón River at approximately 1500 m. Down feather structure differed significantly between the two populations. Ducks from the high-altitude population had longer, denser down compared with low-altitude individuals. Contour feather structure varied greatly among individuals but showed no significant difference between populations. These results suggest that the innermost, insulative layer of plumage (the down), may have developed in response to lower ambient temperatures at high elevations. The lack of observable differences in the contour feathers may be due to the general constraints of the waterproofing capability of this outer plumage layer.ResumenEl plumaje es una característica que define a las aves y cumple roles críticos en el aislamiento térmico y protección física del ambiente. Se sabe que la estructura de las plumas varía ente individuos, y se ha sugerido que poblaciones expuestas a diferentes condiciones ambientales pueden exhibir diferentes patrones en la estructura de las plumas. En este estudio se examinaron tanto el plumón como las plumas de contorno de machos adultos del Pato de los Torrentes (Merganetta armata) de dos poblaciones, una en el río Chancay-Huaral a 3,500 msnm y otra en el río Chillón a 1,500 msnm, ubicadas en Lima, Perú. La estructura de los plumones difiere significativamente entre las dos poblaciones. Los patos de la población a grandes elevaciones tienen plumones largos, y densos comparados con los individuos de las partes bajas. La estructura de las plumas de contorno varía ampliamente entre individuos pero no muestra diferencias significativas entre poblaciones. Estos resultados sugieren que las diferencias entre las capas interiores de aislamiento del plumaje (plumón), haberse desarrollado como respuesta en ambientes de bajas temperaturas a grandes elevaciones. En cambio la falta de detectables diferencias en las plumas de contorno puede ser debido a la constante selección en la capacidad impermeable de la capa de plumas exteriores.

High altitude flight in rarefied, extremely cold and hypoxic air is a very challenging activity. Only a few species of birds can achieve it. Hitherto, the structure of the lungs of such birds has not been studied. This is because of the rarity of such species and the challenges of preparing well-fixed lung tissue. Here, it was posited that in addition to the now proven physiological adaptations, high altitude flying birds will also have acquired pulmonary structural adaptations that enable them to obtain the large amounts of oxygen (O2) needed for flight at high elevation, an environment where O2 levels are very low. The Andean goose (Chloephaga melanoptera) normally resides at altitudes above 3000 meters and flies to elevations as high as 6000 meters where O2 becomes limiting. In this study, its lung was morphologically- and morphometrically investigated. It was found that structurally the lungs are exceptionally specialized for gas exchange. Atypically, the infundibulae are well-vascularized. The mass-specific volume of the lung (42.8 cm3.kg-1), the mass-specific respiratory surface area of the blood-gas (tissue) barrier (96.5 cm2.g-1) and the mass-specific volume of the pulmonary capillary blood (7.44 cm3.kg-1) were some of the highest values so far reported in birds. The pulmonary structural specializations have generated a mass-specific total (overall) pulmonary morphometric diffusing capacity of the lung for oxygen (DLo2) of 0.119 mlO2.sec-1.mbar-1.kg-1, a value that is among some of the highest ones in birds that have been studied. The adaptations of the lung of the Andean goose possibly produce the high O2 conductance needed to live and fly at high altitude.

We report on the use and efficiency of an active mist-net method for capturing 3 subspecies of torrent ducks (Merganetta armata), a territorial and specialized South American waterfowl, in fast-moving rivers of the Andes Mountains. As an active process, the execution of this methodology required the presence of a well-trained, 3-person team. During the austral winter and spring between 2010 and 2014, we captured 372 torrent ducks in 410 capture events on 8 different rivers in Colombia (n = 1), Peru (n = 5), and Argentina (n = 2). Each captured torrent duck was banded and 32 opportunistic recaptures were obtained using the same methodology in the same territories. We deployed the mist-net across fast-moving deep rivers, along elevational gradients (680?4,200 m). Males were more easily captured than females, because of their greater tendency to fly. Our data validated this capture method for torrent ducks, as we succeeded in capturing individuals of the 3 subspecies in different habitats at different elevations and latitudes. To avoid animal mortality, we recommend application of this method only when 3 minimal conditions are met: 1) each field crew has at least 3 people; 2) all of the crew members have hand-radios to enable continuous communication, and 3) each crew member has received prior training (e.g., installation, inspection, manipulation and removal of the mist net, bird extraction, and familiarity with the behavior of the ducks). Fil: Alza, Luis. University Of Miami. Department Of Biology; Estados Unidos. University of Alaska Fairbanks. Institute of Arctic Biology. Department of Biology and Wildlife; Estados Unidos Fil: Bautista, Emil. Centro de Ornitología y Biodiversidad; Perú Fil: Smith, Matthew. University of Alaska Fairbanks. Institute of Arctic Biology. Department of Biology and Wildlife; Estados Unidos Fil: Gutierrez Pinto, Natalia. University Of Miami. Department Of Biology; Estados Unidos Fil: Astié, Andrea Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina Fil: McCracken, Kevin G.. University of Alaska Fairbanks. Institute of Arctic Biology. Department of Biology and Wildlife; Estados Unidos. University Of Miami. Department Of Biology; Estados Unidos

Aim The Malvinas/Falkland Islands (MFI) constitute the largest archipelago inthe southern Atlantic, and harbour endemic lineages that presumably evolvedafter sea-level rise, associated with glacial periods, isolated ancestral popula-tions. We investigate the role of the MFI in isolating populations from conti-nental counterparts of two highly vagile species: the sheldgeese Chloephagapicta and Chloephaga rubidiceps.Location Patagonia and the Malvinas/Falkland Islands.Methods We sampled C. picta and C. rubidiceps on the continent and MFI.Using a reduced-representation genomic approach, we quantified the geneticdifferentiation between insular and continental populations of both species,and used coalescent-based analyses to model their demography.Results The MFI harbour independently evolving lineages of C. picta andC. rubidiceps, which diverged from their continental counterparts during theMiddle-Late Pleistocene and have since experienced negligible gene flow.Main conclusions The c. 450 km that separate the archipelago from thecontinent are sufficient to isolate populations of these putatively highly vagilespecies. Ancestral lineages may have reached the MFI refugium during glacialcycles. Without conservation measures, the drastic decline of the morphologi-cally, behaviourally and ecologically distinct continental population ofC. rubidiceps,to< 1000 individuals, may lead to the extinction of an indepen-dently evolving taxon. Fil: Kopuchian, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Centro de Ecología Aplicada del Litoral. Universidad Nacional del Nordeste. Centro de Ecología Aplicada del Litoral; Argentina Fil: Campagna, Leonardo. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Di Giacomo, Adrian Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Centro de Ecología Aplicada del Litoral. Universidad Nacional del Nordeste. Centro de Ecología Aplicada del Litoral; Argentina Fil: Wilson, Robert E.. University Of Alaska; Estados Unidos Fil: Bulgarella, Mariana. University of Minnesota; Estados Unidos Fil: Petracci, Pablo. Universidad Nacional del Sur. Departamento de Biología, Bioquímica y Farmacia. Grupo de Estudios en Conservación y Manejo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Mazar Barnett, Juan. Asociación de Ornitología del Plata; Argentina Fil: Matus, Ricardo. Centro de Rehabilitación de aves Leñadura; Chile Fil: Blank, Olivia. Centro de Rehabilitación de aves Leñadura; Chile Fil: McCracken, Kevin G.. University Of Alaska; Estados Unidos

Five species of migratory thrushes (Turdidae) occupy a transcontinental distribution across northern North America. They have largely overlapping breeding ranges, relatively similar ecological niches, and mutualistic relationships with northern woodland communities as insectivores and seed-dispersing frugivores. As an assemblage of ecologically similar species, and given other vertebrate studies, we predicted a shared pattern of genetic divergence among these species between their eastern and western populations, and also that the timing of the coalescent events might be similar and coincident with historical glacial events. To determine how these five lineages effectively established transcontinental distributions, we used mitochondrial cytochrome b sequences to assess genetic structure and lineage coalescence from populations on each side of the continent. Two general patterns occur. Hermit and Swainson’s thrushes (Catharus guttatus and C. ustulatus) have relatively deep divergences between eastern and western phylogroups, probably reflecting shared historic vicariance. The Veery (C. fuscescens), Gray-cheeked Thrush (C. minimus), and American Robin (Turdus migratorius) have relatively shallow divergences between eastern and western populations. However, coalescent and approximate Bayesian computational analyses indicated that among all species as many as five transcontinental divergence events occurred. Divergence within both Hermit and Swainson’s thrushes resembled the divergence between Gray-cheeked Thrushes and Veeries and probably occurred during a similar time period. Despite these species’ ecological similarities, the assemblage exhibits heterogeneity at the species level in how they came to occupy transcontinental northern North America but two general continental patterns at an among-species organizational level, likely related to lineage age.

Hybridization is common between species of animals, particularly in waterfowl (Anatidae). One factor shown to promote hybridization is restricted mate choice, which can occur when 2 species occur in sympatry but one is rare. According to the Hubbs principle, or "desperation hypothesis," the rarer species is more likely to mate with heterospecifics. We report the second of 2 independent examples of hybridization between 2 species of ducks inhabiting island ecosystems in the Subantarctic and South Atlantic Ocean. Yellow-billed pintails (Anas georgica) and speckled teal (Anas flavirostris) are abundant in continental South America, where they are sympatric and coexist in mixed flocks. But on South Georgia, an isolated island in the Subantarctic, the pintail population of approximately 6000 pairs outnumbers a small breeding population of speckled teal 300∶1. Using 6 genetic loci (mtDNA and 5 nuclear introns) and Bayesian assignment tests coupled with coalescent analyses, we identified hybrid-origin speckled teal alleles in 2 pintails on South Georgia. While it is unclear whether introgression has also occurred into the speckled teal population, our data suggest that this hybridization was not a recent event, but occurred some time ago. We also failed to identify unequivocal evidence of introgression in a much larger sample of pintails and speckled teal from Argentina using a 3-population "Isolation-with-Migration" coalescent analysis. Combined with parallel findings of hybridization between these same 2 duck species in the Falkland Islands, where population ratios are reversed and pintails are outnumbered by speckled teal 1:10, our results provide further support for the desperation hypothesis, which predicts that scarcity in one population and abundance of another will often lead to hybridization. While the South Georgia pintail population appears to be thriving, it's possible that low density of conspecific mates and inverse density dependence (Allee effect) may be one factor limiting the reproductive output of the speckled teal population, and this situation may persist unless speckled teal increase in abundance on South Georgia.

Species-level DNA phylogenies frequently suffer from two shortcomings--gene trees usually are constructed from a single locus, and often species are represented by only one individual. To evaluate the effect of these two shortcomings, we tested phylogenetic hypotheses within the wigeons and allies, a clade of Anas ducks (Anatidae) composed of five species. We sequenced two nuclear introns from the Z-chromosome-linked chromo-helicase binding protein gene (CHD1Zb and CHD1Za) and the mitochondrial DNA (mtDNA) control region for multiple individuals sampled from widespread geographic locations. We compared these phylogenies to previously published phylogenies constructed from morphology and protein coding regions of mtDNA. Relative to other nuclear introns, CHD showed remarkable phylogenetic utility. Of the 26 CHD1Zb alleles identified, only one was shared between two species, and the combined CHD datasets revealed that four of the five species were consistent with monophyly. Several species shared mtDNA haplotypes, which probably was a result of interspecific hybridization. Overall, the nuclear CHD tree and the mtDNA tree were more congruent with coding regions of mtDNA than they were with morphology.