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Introgression between species has the potential to shape evolutionary trajectories in important ways, but uncovering complex introgression dynamics has only recently been made possible by advances in genomics. Warblers of the avian family Parulidae exemplify rapid diversification and sexual trait divergence, and we endeavored to study historical introgression in the family. We sequenced multiple genomes of nearly every species, constructed a phylogeny for the family, and investigated gene flow across the genome and at genes known for controlling feather color. We found that DNA haplotypes including the gene BCO2, which encodes an enzyme that degrades yellow carotenoids, have spread among genera multiple times-from Vermivora to Geothlypis and from Leiothlypis to multiple Cardellina and Setophaga species. Patterns of inheritance in the latter case point to introgression that occurred 0.5 to 2 million years ago, and the shared haplotype among recipient species is less than 100 nucleotides long. Separately, we found evidence of introgression from red Cardellina species to both of the two red Myioborus species at BDH1L and from one red Myioborus species to the other at CYP2J19; both are key genes in the pathway that converts yellow carotenoids to red ketocarotenoids. Our results show that introgression is a common mechanism for the evolution of colorful plumage in parulid warblers and hint at complex histories of gene flow behind some of the Western Hemisphere's most colorful birds.

Hybrid birds discovered outside of known hybrid zones have often presented an identification challenge but also a source of insight into evolutionary processes. With the advance of modern genetics, the tools are now available to definitively identify hybrids for which genetic samples are available and, in many cases, determine the identity and the sex of each parent species as well as F1 versus backcross status. Typically, hybrids formed outside of hybrid zones are rare; however, one apparently common hybrid New World warbler (family Parulidae) is the cross between Mourning Warblers (Geothlypis philadelphia) and Common Yellowthroats (G. trichas), which has been reported at least 14 times between 1955 and 2025, though never confirmed genetically. Here we describe the results of genetic and plumage analyses identifying a putative G. philadelphia × G. trichas hybrid captured in July 2017 in New York, USA. We used genotype likelihoods derived from whole-genome sequencing data of the putative hybrid and several species in Geothlypis and Oporornis to confirm the bird's identity as an F1 hybrid between G. philadelphia and G. trichas. We sequenced one mitochondrial gene and used publicly available sequences of related species to identify the maternal parent as G. philadelphia. Based on this evidence and previous reports, we propose that male G. trichas × female G. philadelphia is the more common direction—and potentially the only one possible—of this hybrid pairing. Finally, we describe the color characteristics of the hybrid compared to its parental species and discuss potential implications for research into the genetic control of plumage color. Las aves híbridas encontradas fuera de zonas de hibridación han representado un reto de identificación aunque también una fuente de entendimiento de procesos evolutivos. Con el avance de la genética moderna, hoy en día tenemos herramientas disponibles para identificar definitivamente híbridos de los cuales hay muestras genéticas y, en muchos casos, determinar la identidad y el sexo de cada una de las especies parentales así como su estatus F1 versus retrocruzas. Típicamente, los híbridos obtenidos fuera de zonas de hibridación son raros; sin embargo, un parúlido aparentemente común es la cruza entre Geothlypis philadelphia y G. trichas que se ha registrado al menos 14 veces entre 1955 y 2025, aunque nunca confirmado genéticamente. Aquí describimos los resultados de análisis genéticos y del plumaje para identificar un híbrido putativo de G. philadelphia × G. trichas capturado en julio de 2017 en Nueva York, EUA. Usamos la probabilidad genotípica derivada de los datos del genoma completo del híbrido putativo y de varias especies de Geothlypis y Oporornis para confirmar la identidad de esta ave como un F1 híbrido entre G. philadelphia y G. trichas. Secuenciamos un gen mitocondrial y usamos secuencias públicamente disponibles de varias especies cercanamente emparentadas para identificar a la madre como G. philadelphia. Basados en esta evidencia, proponemos que macho G. trichas × hembra G. philadelphia es la dirección más común—y potencialmente la única posible—de este emparejamiento híbrido. Finalmente, describimos las características de color del híbrido comparados con la especie parental y discutimos las implicaciones potenciales para investigar el control genético del color del plumaje. PALABRAS CLAVE Chipes; hibridación; Parulidae; secuencia de genoma completo; subunidad I citocromo c oxidasa

Introgression between species has the potential to shape evolutionary trajectories in important ways, but uncovering complex introgression dynamics has only recently been made possible by advances in genomics. Warblers of the avian family Parulidae exemplify rapid diversification and sexual trait divergence, and we endeavored to study historical introgression in the family. We sequenced multiple genomes of nearly every species, constructed a phylogeny for the family, and investigated gene flow across the genome and at genes known for controlling feather color. We found that DNA haplotypes including the gene BCO2, which encodes an enzyme that degrades yellow carotenoids, have spread among genera multiple times-from Vermivora to Geothlypis and from Leiothlypis to multiple Cardellina and Setophaga species. Patterns of inheritance in the latter case point to introgression that occurred 0.5 to 2 million years ago, and the shared haplotype among recipient species is less than 100 nucleotides long. Separately, we found evidence of introgression from red Cardellina species to both of the two red Myioborus species at BDH1L and from one red Myioborus species to the other at CYP2J19; both are key genes in the pathway that converts yellow carotenoids to red ketocarotenoids. Our results show that introgression is a common mechanism for the evolution of colorful plumage in parulid warblers and hint at complex histories of gene flow behind some of the Western Hemisphere's most colorful birds.

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.

Odorant receptors (ORs) form one of the largest gene families in vertebrates; most mammals have hundreds of intact OR genes. Although birds display diverse breeding and foraging behaviors, they were long assumed to rely minimally on olfaction. Here we show that, similar to mammals, bird genomes often encode hundreds - and in some species, thousands - of intact ORs. We further present evidence that most avian ORs within the bird-specific gamma-c subfamily have undergone extensive gene conversion. We show that avian ORs are expressed in olfactory sensory neurons and respond to defined odorants. Notably, we identify ligands for avian ORs, revealing both unique functions within the gamma-c clade and functional conservation with a deeply divergent mammalian OR. These findings uncover unexpected parallels between mammals and birds in olfactory system organization while revealing a distinctive evolutionary feature: widespread gene conversion shaping the majority of avian ORs.

Domestic cats have been transported around the world by humans for thousands of years and released into the wild. Cats are generalist predators and hunt instinctively. On islands with few native predators, cats have had devastating consequences on native wildlife. Though negative impacts of cats on native wildlife has been predicted for mainland areas, most previous research relied on measuring cat predation using homeowner questionnaires and inferring impacts. Few studies to date have examined the association between free-ranging cats and survival of their prey on a regional scale. In addition, basic information regarding how cats respond to variables like urbanization and human demographics is scarce and also tends to rely on questionnaires. I addressed these shortcomings by surveying for cats and then modeling cat abundance, its influencing variables, and the relationship between cat abundance and apparent annual survival of seven breeding bird species along an urban-rural gradient in the Washington, D.C. region. Cat abundance was highest in suburban areas, suggesting that the ecological drivers of cat abundance across the urban-rural gradient is more complex than simply reflecting human population density. Cat abundance was also highest in areas with lower levels of high school education. Patterns of bird survival differed by species, with one species exhibiting a negative relationship with cat abundance. This study represents one of the first characterizations of domestic cat abundance over a regional area using outdoor cat censusing techniques and the first to use survival modeling to study the impacts of cats on birds on a regional scale.

Genomic data can provide valuable insights into the evolutionary history of rapidly diversifying groups and the genetic basis of phenotypic differences among lineages. We used whole-genome sequencing of the warbler genus Myioborus to investigate dynamics of its recent diversification in Neotropical mountains. We found that mitochondrial and UCE phylogenies are mostly, but not fully, concordant, and we found phylogenetic support for a pattern of north-to-south and low-to-high elevation colonization in the genus. Within the ornatus–melanocephalus complex, which showed topological incongruence between our phylogenies, we found that genetic structure generally coincides with geographic variation in plumage, although three subspecies with striking plumage differences exhibit low mitochondrial divergence. The hybridizing taxa M. o. chrysops and M. m. bairdi show very shallow genomic differentiation, with marked peaks of divergence. Most of these are shared with other parulid warbler pairs, pointing to broad genomic features, like recombination rate, as the processes shaping these regions. However, other highly differentiated regions were unique to Myioborus, including one containing the gene CCDC91, which is associated with melanin-based plumage differences in several other birds. Lastly, we found higher levels of differentiation on the Z chromosome relative to autosomes, including two putative chromosomal inversions. Together, these results highlight the interplay of deep ancestral divergence, recent hybridization, and shared genomic architecture in shaping the evolution of phenotypic and genomic diversity within Myioborus.

Odorant receptors (ORs) form one of the largest gene families in vertebrates1,2; most mammals have hundreds of intact OR genes1. Although birds display diverse breeding and foraging behaviors, they were long assumed to rely minimally on olfaction3–5. Recent behavioral work in birds has shown important roles for olfaction6–9. Here, we show that bird ORs are numerous and function in the olfactory system. As part of the Vertebrate Genomes Project Phase I10, we found far greater numbers of ORs in long read bird genomes than short-read Illumina-based assemblies, including the nocturnal kiwi (Apteryx mantellii), which possesses the largest number of ORs known. We show that avian ORs are generally expressed in olfactory sensory neurons. We find that chicken ORs within bird-specific gamma-c subfamily respond to defined odorants. We further reveal a distinctive evolutionary feature: widespread gene conversion shaping this gamma-c subfamily. Our results reevaluate the historical view that olfaction is largely irrelevant to birds and highlight the importance of this sensory modality in avian life history.

Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed asymmetrically ∼50 km across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989 - 1994) and contemporary (2017 - 2020) transect samples to survey both morphological and genetic variation. Genome-wide SNP data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.