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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. IMPORTANCE 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.

Background Rapid morphological change is emerging as a consequence of climate change in many systems. It is intuitive to hypothesize that temporal morphological trends are driven by the same selective pressures that have established well-known ecogeographic patterns over spatial environmental gradients (e.g., Bergman’s and Allen’s rules). However, mechanistic understanding of contemporary morphological shifts is lacking. Results We combine morphological data and whole genome sequencing from a four-decade dataset in the migratory bird hermit thrush ( Catharus guttatus ) to test whether morphological shifts over time are accompanied by genetic change. Using genome-wide association, we identify alleles associated with body size, bill length, and wing length. Shifts in morphology and concordant shifts in morphology-associated alleles over time would support a genetic basis for the observed changes in morphology over recent decades, potentially an adaptive response to climate change. In our data, bill size decreases were paralleled by genetic shifts in bill size-associated alleles. On the other hand, alleles associated with body size showed no shift in frequency over time. Conclusions Together, our results show mixed support for evolutionary explanations of morphological response to climate change. Temporal shifts in alleles associated with bill size support the hypothesis that selection is driving temporal morphological trends. The lack of evidence for genetic shifts in body size alleles could be explained by a large role of plasticity or technical limitations associated with the likely polygenic architecture of body size, or both. Disentangling the mechanisms responsible for observed morphological response to changing environments will be vital for predicting future organismal and population responses to climate change.

Gut microbiota interact with host biology in numerous important ways. The forces shaping the composition, diversity, and function of the microbiota vary within and between species. Avian microbiota often correlate more strongly with sampling location specific environmental variables than with host‐associated factors such as age, but robust, range‐wide sampling is rare. To better understand the connection between geographic distance and the microbiota, fecal samples were collected from non‐migratory Canada goose populations across the United States. We expected that geographically closer populations would be exposed to more similar environmental microbes and would therefore have more similar gut microbiota. We hypothesized that intrinsic host‐associated factors would have a weak correlation to gut microbial composition and geographic distance would have a stronger correlation. We found that some components of Canada goose microbiota are present in a majority of the geese, including four bacterial phyla, five families, and three genera. However, there were significant differences in microbial alpha diversity based on state of origin as well as significant positive correlations between geography and beta diversity. Supervised machine learning models were able to predict the state and flyway of origin of a fecal sample based on bacterial composition alone. Distance−decay analysis showed a significant positive relationship between geographic distance and beta diversity. Our work provides novel insights into the microbiota of the Canada goose and supports the hypothesis that avian microbiota are influenced by the host's environment. This work also suggests that there is a minimum geographic distance, likely associated with sufficient variation in habitat, climate, and local food sources, that must be reached before significant differences in the microbiota between two populations can be detected.

Large comparative datasets of avian functional traits have been used to address a wide range of questions in ecology and evolution. To date, this work has been constrained by the limited availability of skeletal trait datasets that include extensive inter- and intra-specific sampling. We use computer vision to identify and measure bones from photographs of museum skeletal specimens to assemble an extensive dataset of functionally important skeletal elements in birds. The dataset spans 2,057 species of birds (Aves: Passeriformes) and includes measurements of 12 skeletal elements from 14,419 individuals. In addition to the trait values directly measured from photographs, we leverage the multi-dimensional nature of our dataset and known phylogenetic relationships of the species to impute missing data under an evolutionary model. To facilitate use of the dataset, the taxonomy has been reconciled with an existing comprehensive avian phylogeny and an additional dataset of external functional traits for all birds.

Geographic turnover in community composition is created and maintained by eco-evolutionary forces that limit the ranges of species. One such force may be antagonistic interactions among hosts and parasites, but its general importance is unknown. Understanding the processes that underpin turnover requires distinguishing the contributions of key abiotic and biotic drivers over a range of spatial and temporal scales. Here, we address these challenges using flexible, nonlinear models to identify the factors that underlie richness (alpha diversity) and turnover (beta diversity) patterns of interacting host and parasite communities in a global biodiversity hot spot. We sampled 18 communities in the Peruvian Andes, encompassing ∼1,350 bird species and ∼400 hemosporidian parasite lineages, and spanning broad ranges of elevation, climate, primary productivity, and species richness. Turnover in both parasite and host communities was most strongly predicted by variation in precipitation, but secondary predictors differed between parasites and hosts, and between contemporary and phylogenetic timescales. Host communities shaped parasite diversity patterns, but there was little evidence for reciprocal effects. The results for parasite communities contradicted the prevailing view that biotic interactions filter communities at local scales while environmental filtering and dispersal barriers shape regional communities. Rather, subtle differences in precipitation had strong, fine-scale effects on parasite turnover while host–community effects only manifested at broad scales. We used these models to map bird and parasite turnover onto the ecological gradients of the Andean landscape, illustrating beta-diversity hot spots and their mechanistic underpinnings.

To holistically understand the biology of animals, we must unravel the complexities and specificities of host-microbe interactions across animal taxa. Birds represent enigmatic and scientifically compelling hosts in which to understand these interactions. Here, we present a brief summary of a series of conversations among avian microbiome researchers regarding methodological challenges facing the avian microbiome field, where most research to date has focused on bacterial communities of the gut. Collectively, we acknowledged a commonly shared but underreported issue facing the avian microbiome field: that of difficulty in obtaining high-quality and high-yield microbial DNA from avian fecal samples. We discuss some of the potential reasons underlying low DNA yields, such as inhibitory compounds and rapid DNA degradation, and provide recommendations for how researchers in the avian microbiome field might cope with these methodological challenges. Collective and dedicated efforts to address these challenges will be required for a robust understanding of host-microbe interactions in avian systems.

Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a salient issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the English-language common names of bird species, a group of 85 professional ornithologists and non-professional contributors classified unique descriptors in the common names of all recognized species of birds. In the AvianLexiconAtlas database produced by this work, each species’ common name is assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references, human names, or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contain specialized or historic terminology unknown to many of the data collectors, and we include these terms in a glossary and gazetteer alongside the dataset. The AvianLexiconAtlas can be used as a quantitative resource to assess the state of terminology in English-language common names of birds. Future research using the database can shed light on historical approaches to nomenclature and how people engage with species through their names.

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.

Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a particular issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the common names of bird species and their frequency of use, we used a crowdsourcing approach and recruited 85 professional ornithologists and non-professional participants to classify unique descriptors in the English-language common names of all recognized bird species from around the world. Each species' common name was assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contained specialized or historic terminology unknown to many of the data collectors, and this was documented in a glossary and gazetteer alongside the dataset. As the first comprehensive assessment of the state of terminology in English-language common names of birds, the AvianLexiconAtlas database sheds light on historical approaches to nomenclature and provides insight into how the general public currently engages with species through their names.Competing Interest StatementThe authors have declared no competing interest.Footnotes* The title, abstract, introduction, and conclusion have been updated to present the new dataset, glossary, and gazetteer produced during this research as a research database, now called the AvianLexiconAtlas. Researchers from across academic fields can use the resources in this database to study the history of English-language bird names from a quantitative perspective. In the text we clarify the utility of this database as a resource, but have not changed any of the methods, analyses, figures, or supplemental files.* https://github.com/ajshultz/AvianLexiconAtlas