Cathartes melambrotus is the largest member of the genus Cathartes, and soars over the forested areas of Amazonia in search of carrion. The complete mitochondrial genome of C. melambrotus was reported in this study. The 19,232 base pair genome consisted of 16 protein coding genes, 25 tRNAs, two rRNAs, and two control regions. The mitochondrial genome contained the avian ancestral duplicated gene region, with the same rearrangements previously reported in Accipitriformes, Cathartiformes, and Stigiformes. With the publishing of the C. melambrotus genome all seven Cathartiformes species mitochondrial genomes are available and can be included in subsequent phylogenetic and genomic analyses.

We present a draft genome of the little bush moa ( Anomalopteryx didiformis )—one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand—using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.

Smell is one of the five senses we use to experience the world. It allows humans and other animals to find their food, avoid danger, and even recognize family members. Animals detect smells with olfactory receptors, special proteins that sit on the surface of the nose cells. These interact with odor molecules (small particles that have a smell) and send signals to the brain so the animal can perceive the smell. We know mammals have hundreds of olfactory receptors and can detect tens of thousands of smells, but what about birds? For decades, many people thought that birds did not use smell in their daily lives, but recent studies have shown that birds respond to smell. We show that many birds have a large number of olfactory receptors similar to mammals, strengthening the case for smell playing an important role in the life of birds.

ABSTRACT Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species—all traits associated with lower dispersal ability—were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated. LAY SUMMARY - What factors are common among bird species with cryptic diversity in Panama? What role do geography, ecology, phylogeographic history, and other factors play in generating bird diversity? - 19% of widely-sampled bird species form two or more distinct DNA barcode clades, suggesting widespread unrecognized diversity. - Traits associated with reduced dispersal ability, such as use of forest understory, high territoriality, low hand-wing index, and insectivory, were more common in taxa with cryptic diversity. Filogeografía comparada revela amplia diversidad críptica causada por la ecología en las aves de Panamá RESUMEN Especies extendidas frecuentemente tiene diversidad genética no reconocida, y investigando los factores asociados con esta variación críptica puede ayudarnos a entender las fuerzas que impulsan la diversificación. Aquí, identificamos especies crípticas potenciales basadas en un conjunto de datos de códigos de barras de ADN mitocondrial de 2,333 individuos de aves de Panama en 429 especies, representando 391 (59%) de las 659 especies de aves terrestres residentes del país, además de algunas aves acuáticas muestreada de manera oportunista. Adicionalmente, complementamos estos datos con secuencias mitocondriales disponibles públicamente de otros loci, tal como ND2 o citocroma b, obtenidos de los genomas mitocondriales completos de 20 taxones. Utilizando los números de identificación de código de barras (en ingles: BINs), un sistema taxonómico numérico que proporcina una estimación imparcial de la diversidad potencial a nivel de especie, encontramos especies crípticas putativas en 19% de las especies de aves terrestres, lo que destaca la diversidad oculta en la avifauna bien descrita de Panamá. Aunque algunos de estos eventos de divergencia conciden con características geográficas que probablemente aislaron las poblaciones, la mayoría (74%) de la divergencia en las tierras bajas se encuentra entre las poblaciones orientales y occidentales. El tiempo de esta divergencia no coincidió entre los taxones, sugiriendo que eventos históricos tales como la formación del Istmo de Panamá y los ciclos climáticos del pleistoceno, no fueron los principales impulsores de la especiación. En cambio, observamos asociaciones fuertes entre las características ecológicas y la divergencia mitocondriale: las especies del bosque, sotobosque, con una dieta insectívora, y con territorialidad fuerte mostraton múltiple BINs probables. Adicionalmente, el índice mano-ala, que está asociado a la capacidad de dispersión, fue significativamente menor en las especies con BINs multiples, sugiriendo que la capacidad de dispersión tiene un rol importamente en la generación de la diversidad de las aves neotropicales. Estos resultos demonstran la necesidad de que estudios evolutivos de las comunidades de aves tropicales consideren los factores ecológicos en conjunto con las explicaciones geográficos. Palabras clave: biodiversidad tropical, biogeografía, códigos de barras, dispersión, especies crípticas

Organismal behavior, with its tremendous complexity and diversity, is generated by numerous physiological systems acting in coordination. Understanding how these systems evolve to support differences in behavior within and among species is a longstanding goal in biology that has captured the imagination of researchers who work on a multitude of taxa, including humans. Of particular importance are the physiological determinants of behavioral evolution, which are sometimes overlooked because we lack a robust conceptual framework to study mechanisms underlying adaptation and diversification of behavior. Here, we discuss a framework for such an analysis that applies a "systems view" to our understanding of behavioral control. This approach involves linking separate models that consider behavior and physiology as their own networks into a singular vertically integrated behavioral control system. In doing so, hormones commonly stand out as the links, or edges, among nodes within this system. To ground our discussion, we focus on studies of manakins (Pipridae), a family of Neotropical birds. These species have numerous physiological and endocrine specializations that support their elaborate reproductive displays. As a result, manakins provide a useful example to help imagine and visualize the way systems concepts can inform our appreciation of behavioral evolution. In particular, manakins help clarify how connectedness among physiological systems-which is maintained through endocrine signaling-potentiate and/or constrain the evolution of complex behavior to yield behavioral differences across taxa. Ultimately, we hope this review will continue to stimulate thought, discussion, and the emergence of research focused on integrated phenotypes in behavioral ecology and endocrinology.

Hybridization often occurs at the parapatric range interface between closely related species, but fitness outcomes vary: hybrid offspring exhibit diverse rates of viability and reproduction compared with their parental species. The mobile hybrid zone between two chickadee congeners (Poecile atricapillus × Poecile carolinensis) has been well studied behaviorally and genetically, but the viability of hybrids and the underlying mechanisms contributing to hybrid fitness have remained unclear. To better characterize the fitness costs of hybridization in this system, we analyzed 21 years of data from four sites, including more than 1,400 breeding attempts by the two species, to show that rates of hatching success changed substantially as the zone of hybridization moved across the landscape. Admixture-associated declines in hatching success correlated with reduced proportions of heterogametic (female) offspring, as predicted by Haldane’s rule. Our data support an underlying mechanism implicating genetic admixture of the homogametic (male) parent as the primary determinant of offspring sex ratio, via incompatibilities on the hemizygous Z chromosome. Our long-term study is the first to directly measure changes in fitness costs as a vertebrate hybrid zone moves, and it shows that changes in these costs are a way to track the distribution of a hybrid zone across the landscape.

Identifying the molecular process of complex trait evolution is a core goal of biology. However, pinpointing the specific context and timing of trait-associated changes within the molecular evolutionary history of an organism remains an elusive goal. We study this topic by exploring the molecular basis of elaborate courtship evolution, which represents an extraordinary example of trait innovation. Within the behaviorally diverse radiation of Central and South American manakin birds, species from two separate lineages beat their wings together using specialized "superfast" muscles to generate a "snap" that helps attract mates. Here, we develop an empirical approach to analyze phylogenetic lineage-specific shifts in gene expression in the key snap-performing muscle and then integrate these findings with comparative transcriptomic sequence analysis. We find that rapid wing displays are associated with changes to a wide range of molecular processes that underlie extreme muscle performance, including changes to calcium trafficking, myocyte homeostasis and metabolism, and hormone action. We furthermore show that these changes occur gradually in a layered manner across the species history, wherein which ancestral genetic changes to many of these molecular systems are built upon by later species-specific shifts that likely finalized the process of display performance adaptation. Our study demonstrates the potential for combining phylogenetic modeling of tissue-specific gene expression shifts with phylogenetic analysis of lineage-specific sequence changes to reveal holistic evolutionary histories of complex traits.

Third-generation (long-read-based) sequencing technologies are reshaping our understanding of genome structure and function. One of the most persistent challenges in genome biology has been confidently reconstructing radiations of complex gene families. Olfactory receptors (ORs) represent just such a gene family with upward of thousands of receptors in some mammalian taxa. Whereas in birds olfaction was historically an overlooked sensory modality, new studies have revealed an important role for smell. Chromosome-level assemblies for birds allow a new opportunity to characterize patterns of OR diversity among major bird lineages. Previous studies of short-read-based (second-generation) genome assemblies have associated OR gene family size with avian ecology, but such conclusions could be premature especially when new assembly methods reshape our understanding of avian OR evolution. Here we provide a fundamental characterization of OR repertoires in five recent genome assemblies, including the most recent assembly of golden-collared manakin (Manacus vitellinus). We find that short read-based assemblies systematically undercount the avian-specific gamma-c OR subfamily, a subfamily that comprises over 65% of avian OR diversity. Therefore, in contrast to previous studies, we find a high diversity of gamma-c ORs across the avian tree of life. Building on these findings, ongoing sequencing efforts and improved genome assemblies will clarify the relationship between OR diversity and avian ecology.

English common names are widely used in ornithological research, birding, media and by the general public and, unlike other taxa, often receive considerably greater use than scientific names. Across the world, many of these names were coined from 18th and 19th century European perspectives and are symbolic of a time when this was the only worldview considered in science. Here, we highlight formal efforts by ornithological societies around the world to change common names of birds to better reflect the diverse perspectives of scientists in the 21st century. We focus on particular case studies from regions with a history of colonialism, including South Africa and North America, as well as the successful implementation of Indigenous bird names in New Zealand. In addition to detailing independent and repeated efforts by different ornithological communities to address culturally inappropriate English common names, we discuss dissention and debate in North America regarding these changes. The continued use of problematic common names must change if we wish to create a more diverse and inclusive discipline.

The Hardy-Weinberg principle (HWP) is an application of the binomial expansion theorem that is foundational to the field of population genetics. Because of the important history of the HWP in answering how variation is preserved during evolution, and the ability of Hardy-Weinberg equilibrium (HWE) to detect natural and sexual selection acting on a trait, the HWP is a staple of the introductory biology undergraduate curriculum in the United States. Introductory courses often cover a wide range of topics in ecology and evolution, and it is important that students have enough time during the semester to grasp the foundations of population genetics. At the same time, information needs to be presented clearly to ensure that the student gains a correct understanding of the HWP. This article discusses the importance of the HWP to undergraduate education in biology and describes misconceptions from the instructor's perspective. These misconceptions are pervasive and risk undermining a proper understanding of the HWP. We provide examples adapted from university- and AP-level standardized tests.

How does a naive, young animal decide from which adults to learn behavior? Obligate brood parasitic birds, including brown-headed cowbirds (Molothrus ater), face a particular challenge in learning species-specific behaviors; they lay their eggs in the nest of another species, and juveniles are raised without exposure to adult conspecifics. Nevertheless, male cowbirds need to learn a conspecific song to attract appropriate mates, and female cowbirds need to learn to identify conspecific males for mating. Traditionally, it was thought that parasitic bird species rely purely on instinctual species recognition [1-4], but an alternative is that a species-specific trait serves as a "password" [5], a non-learned cue for naive animals that guides decisions regarding from whom to learn. Here, we tested the hypothesis that the adult "chatter call" enhances the learning of specific songs in juvenile cowbirds. We exposed acoustically naive juvenile male and female cowbirds to songs paired with chatter calls and found that the chatter call enhanced song production learning in males and induced a neurogenomic profile of song familiarity in females, even for heterospecific songs. Thus, a combination of experience-independent and -dependent mechanisms converges to explain how young cowbirds emerge from another species' nest yet learn behaviors from conspecifics. Identifying whether such password-based mechanisms relate to perceptual and behavioral learning in non-parasitic taxa will contribute to our general understanding of the development of social recognition systems.

Eciton burchellii is a Neotropical army ant that influences the ecology of many associated animal species, including their prey and species that attend the ant's foraging raids. At least 29 bird species are obligate specialists on foraging at army ant raid fronts, and additional species across diverse avian orders follow army ant raids in a facultative manner. These facultative ant-following birds include species of raptors in Accipitriformes, Strigiformes, and Falconiformes. The most frequently documented raptors that follow raids are forest-falcons in the genus Micrastur. Micrastur falcons add a unique type of predation to raids, catching larger arthropod species that would otherwise likely escape the ants, and also prey on small fleeing vertebrates, such as lizards and other ant-following bird species. Here we present an observation of a Collared Forest-falcon (Micrastur semitorquatus) attending an E. b. parvispinum raid and flying toward a Ruddy Woodcreeper (Dendrocincla homochroa) at the raid front, as well as capturing a fleeing snake from the raid front. To our knowledge, this is the first report of a snake falling prey to a raptor at an army ant raid front.

Yellow-shafted Flickers (Colaptes auratus auratus subspecies group of the Northern Flicker) occasionally have orange to red flight feathers in eastern North America far from the hybrid zone with the Red-shafted Flicker (C.a. cafer subspecies group). Blocks of feathers of anomalous color tend to show bilateral symmetry and may differ from one year to the next in the same bird. It has been suggested that hybridization with cafer must be the source of the red color and that selection for that color could explain the high incidence of red or orange shafts in eastern flickers in some localities. Complex, though largely unproven, physiological mechanisms have been hypothesized to explain the variegated look. We evaluated a simpler, dietary explanation for the variation: that the pigment rhodoxanthin acquired exogenously at the time of feather molt comes to rest alongside the carotenoids normally present in these feathers. An exogenous source of rhodoxanthin exists in the berries of nonnative bush honeysuckles (Lonicera spp.) now naturalized in eastern North America and the American Midwest. We confirm the presence of rhodoxanthin and a probable metabolite, rather than the 4-keto-carotenoids found in the Red-shafted Flicker, in the red flight feathers of 2 Yellow-shafted Flickers from eastern North America. In these individuals, dietary rhodoxanthin appeared to interfere with the production of lutein, the main carotenoid in auratus. A fairly abrupt appearance of red color in earlier-molted primaries (usually p4 or p5) followed by its gradual fading in subsequent primaries in a large series of aberrantly colored flickers from eastern North America and the American Midwest supports a dietary explanation. We use data on the timing of replacement of primaries in the Northern Flicker at Manomet in Plymouth, eastern Massachusetts, to infer that these aberrantly colored Yellow-shafted Flickers on average acquired the unusual red pigment in early August.

Sleep homeostasis, which refers to the maintenance of sleep amount or depth following sleep deprivation, indicates that sleep and sleep-like states serve fundamental functions that cannot be bypassed [1]. Homeostasis of sleep-like behavior is observed during C. elegans lethargus, a 2-3 hr behavioral quiescent period that occurs during larval state transitions [2]. Here, we report a role for DAF-16/FOXO, a transcription factor that is active under conditions of stress [3], in the response to deprivation of lethargus quiescence. Forced locomotion during lethargus results in nuclear translocation of DAF-16. The formation of dauer larvae, a developmental state promoted by daf-16, is increased in response to quiescence deprivation. daf-16 mutants show an impaired homeostatic response to deprivation of lethargus quiescence and are hypersensitive to the lethal effects of forced locomotion during lethargus. DAF-16 expression in muscle cells, but not in neurons, is sufficient to restore a homeostatic response to deprivation of quiescence, pointing to a role for muscle in sleep homeostasis. These findings are relevant to clinical observations of altered metabolic signaling in response to sleep deprivation and suggest that these signaling pathways may act in nonneuronal tissue to regulate sleep behaviors.