Under allopatric speciation, populations of a species become isolated by a geographic barrier and develop reproductive isolation through genetic differentiation. When populations meet in secondary contact, the strength of evolved reproductive barriers determines the extent of hybridization and whether the populations will continue to diverge or merge together. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are avian sister species that diverged in allopatry on either side of Eurasia during the Pleistocene glaciations. Though they differ greatly in plumage and form distinct genetic clusters in allopatry, these taxa show negligible mitochondrial DNA differentiation and hybridize extensively where they overlap in central Siberia, lending uncertainty to the state of reproductive isolation in the system. To assess the strength of reproductive barriers between taxa, we examined genomic differentiation across the system. We found that extensive admixture has occurred in sympatry, indicating that reproductive barriers between taxa are weak. We also identified a putative Z chromosome inversion region that underlies plumage variation in the system, with the \'pine bunting\' haplotype showing dominance over the \'yellowhammer\' haplotype. Our results suggest that yellowhammers and pine buntings are currently at a crossroads and that evolutionary forces may push this system towards either continued differentiation or population merging. However, even if these taxa merge, recombination suppression between putative chromosome Z inversion haplotypes may maintain divergent plumage phenotypes within the system. In this way, our findings highlight the important role hybridization plays in increasing the genetic and phenotypic variation as well as the evolvability of a system.

Trade represents a significant threat to many wild species and is often clandestine and poorly monitored. Information on which species are most prevalent in trade and potentially threatened by it therefore remains fragmentary. We used 7 global data sets on birds in trade to identify species or groups of species at particular risk and assessed the extent to which they were congruent in terms of the species recorded in trade. We used the frequency with which species were recorded in the data sets as the basis for a trade prevalence score that was applied to all bird species globally. Literature searches and questionnaire surveys were used to develop a list of species known to be heavily traded to validate the trade prevalence score. The score was modeled to identify significant predictors of trade. Although the data sets sampled different parts of the broad trade spectrum, congruence among them was statistically strong in all comparisons. Furthermore, the frequency with which species were recorded within data sets was positively correlated with their occurrence across data sets, indicating that the trade prevalence score captured information on trade volume. The trade prevalence score discriminated well between species identified from semi-independent assessments as heavily or unsustainably traded and all other species. Globally, 45.1% of all bird species and 36.7% of globally threatened bird species had trade prevalence scores ≥1. Species listed in Appendices I or II of CITES, species with large geographical distributions, and nonpasserines tended to have high trade prevalence scores. Speciose orders with high mean trade prevalence scores included Falconiformes, Psittaciformes, Accipitriformes, Anseriformes, Bucerotiformes, and Strigiformes. Despite their low mean prevalence score, Passeriformes accounted for the highest overall number of traded species of any order but had low representation in CITES appendices. Geographical hotspots where large numbers of traded species co-occur differed among passerines (Southeast Asia and Eurasia) and nonpasserines (central South America, sub-Saharan Africa, and India). This first attempt to quantify and map the relative prevalence in trade of all bird species globally can be used to identify species and groups of species that may be at particular risk of harm from trade and can inform conservation and policy interventions to reduce its adverse impacts.
Análisis de la prevalencia mundial de aves silvestres en el mercado Resumen El mercado representa una amenaza importante para muchas especies silvestres y a menudo es clandestino y mal vigilado. Por ello, la información sobre las especies más presentes en el mercado y bajo amenaza potencial todavía está fragmentada. Utilizamos siete conjuntos de datos mundiales sobre aves comercializadas para identificar especies o grupos de especies bajo riesgo especial y evaluamos hasta qué punto eran congruentes en cuanto a las especies registradas en el comercio. Utilizamos la frecuencia con la que las especies se registraban en los conjuntos de datos como base para una puntuación de prevalencia del comercio que se aplicó a todas las especies de aves a nivel mundial. Para validar la puntuación de prevalencia del comercio, realizamos búsquedas bibliográficas y cuestionarios para elaborar una lista de especies que se sabe son objeto de comercio intenso. Modelamos la puntuación para identificar los predictores significativos del mercado. Aunque los conjuntos de datos muestrearon partes distintas del amplio espectro del mercado, la congruencia entre ellos fue estadísticamente robusta en todas las comparaciones. Además, la frecuencia con la que se registraron las especies dentro de los conjuntos de datos se correlacionó positivamente con su presencia en todos los conjuntos de datos, lo que indica que la puntuación de prevalencia del mercado captó información sobre el volumen de este. La puntuación de prevalencia del mercado distinguió entre las especies identificadas a partir de evaluaciones semiindependientes como objeto de comercio intenso o insostenible y todas las demás especies. A nivel mundial, el 45.1% de todas las especies de aves y el 36.7% de las especies de aves amenazadas mundialmente tenían puntuaciones de prevalencia del mercado ≥1. Las especies incluidas en los Apéndices I o II de CITES, las especies con una amplia distribución geográfica y los no paseriformes tendieron a tener puntuaciones elevadas de prevalencia del mercado. Los órdenes de especies con puntuaciones medias de prevalencia del mercado elevadas fueron Falconiformes, Psittaciformes, Accipitriformes, Anseriformes, Bucerotiformes y Strigiformes. A pesar de su baja puntuación media de prevalencia, los Passeriformes representaron el mayor número total de especies comercializadas de todos los órdenes, pero tuvieron una baja representación en los apéndices de CITES. Los puntos calientes geográficos en los que coexisten un gran número de especies comercializadas difieren entre los paseriformes (Sudeste Asiático y Eurasia) y los no paseriformes (centro de Sudamérica, África subsahariana e India). Este primer intento de cuantificar y cartografiar la prevalencia relativa en el comercio de todas las especies de aves a escala mundial puede utilizarse para identificar especies y grupos de especies que pueden correr un riesgo especial de sufrir daños a causa del comercio y puede servir de base para intervenciones políticas y de conservación destinadas a reducir sus efectos adversos.

The common eider, Somateria mollissima mollissima (Chordata; Aves; Anseriformes; Anatidae), is a large sea duck with a circumpolar distribution. We here describe a chromosome-level genome assembly from an individual female. The haplotype-resolved assembly contains one pseudo-haplotype spanning 1205 megabases (with both Z and W sex chromosomes) and one pseudo-haplotype spanning 1080 megabases. Most of these two assemblies (91.13% and 93.18%, respectively) are scaffolded into 32 autosomal chromosomal pseudomolecules plus Z and W for pseudo-haplotype one. The BUSCO completeness scores are 94.0% and 89.9%, respectively, and gene annotations of the assemblies identified 17,479 and 16,315 protein coding genes. Annotation of repetitive sequences classify 17.84 % and 14.62 % of pseudo-haplotype one and two, respectively, as repeats. The genome of the common eider will be a useful resource for the widely distributed northern species in light of climate change and anthropogenic threats.

As DNA sequencing technology continues to rapidly improve, studies investigating the microbial communities of host organisms (i.e., microbiota) are becoming not only more popular but also more financially accessible. Across many taxa, microbiomes can have important impacts on organismal health and fitness. To evaluate the microbial community composition of a particular microbiome, microbial DNA must be successfully extracted. Fecal samples are often easy to collect and are a good source of gut microbial DNA. Additionally, interest in the avian preen gland microbiome is rapidly growing, due to the importance of preen oil for many aspects of avian life. Microbial DNA extractions from avian fecal and preen oil samples present multiple challenges, however. Here, we describe a modified PrepMan Ultra Sample Preparation Reagent microbial DNA extraction method that is less expensive than other commonly used methodologies and is highly effective for both fecal and preen oil samples collected from a broad range of avian species. We expect our method will facilitate microbial DNA extractions from multiple avian microbiome reservoirs, which have previously proved difficult and expensive. Our method therefore increases the feasibility of future studies of avian host microbiomes.

The taxonomic status of many species of the family Cyclocoelidae is still unclear. Two species of cyclocoelids, Harrahium obscurum and Morishitium dollfusi, were collected from the air sacs of birds (Turdus merula and Tringa ochropus) inhabiting the Middle Volga region (European Russia). Here, we provide the first detailed morphological description of these cyclocoelids and combine it with the first molecular phylogenetic analysis of Cyclocoelidae from birds in Russia based on partial sequences of their 28s rDNA and coI mtDNA genes. Specimens of both flatworm species from different host individuals differ slightly in body shape and size, which probably reflects host-induced intraspecific variability. For the first time, we have shown that a stable morphological character such as the length of the vitelline fields in the studied digeneans is variable at the species level and cannot be used in their morphological diagnosis.

As global heating and other anthropogenic influences alter tropical marine environments, it is unclear how marine bird populations will be impacted and whether their current roles in tropical marine ecosystems will change. Although marine birds roost and breed on tropical islands in large numbers, the direct trophic interactions between these birds and their prey across the tropics are poorly documented. We present a first framework for evaluating the dependence on and contributions of marine birds to tropical coral reef ecosystems and use it to examine the evidence for different kinds of interaction, focusing primarily on avian diets. We found 34 publications between 1967 and 2023 that presented a total of 111 data sets with enough detail for quantitative dietary analysis of tropical marine birds. Only two bird species out of 37 (5.4%) had diets of >50% coral reef fishes and only one, the Pacific Reef Egret, appeared to depend almost entirely on reef-based production. Marine birds are also prey for other marine organisms, but insufficient data are available for quantitative analysis. Evidence for indirect effects of birds in tropical marine environments is stronger than for direct dependence on coral reefs, particularly in relation to nutrient concentration and the fertilisation impacts of guano on corals. Dispersal of propagules (e.g. seeds, spores, invertebrate eggs) by bathing, drinking, resting or foraging birds is under-studied and poorly documented. Although the degradation of coral reefs appears unlikely to have a significant direct impact on food availability for most marine bird populations, indirect effects involving marine birds may be disrupted by global environmental change.

UNASSIGNED: Cancer is a disease that affects nearly all multicellular life, including the broad and diverse taxa of Aves. While little is known about the factors that contribute to cancer risk across Aves, life history trade-offs may explain some of this variability in cancer prevalence. We predict birds with high investment in reproduction may have a higher likelihood of developing cancer. In this study, we tested whether life history traits are associated with cancer prevalence in 108 species of birds.
UNASSIGNED: We obtained life history data from published databases and cancer data from 5,729 necropsies from 108 species of birds across 24 taxonomic orders from 25 different zoological facilities. We performed phylogenetically controlled regression analyses between adult body mass, lifespan, incubation length, clutch size, sexually dimorphic traits, and both neoplasia and malignancy prevalence. We also compared the neoplasia and malignancy prevalence of female and male birds.
UNASSIGNED: Providing support for a life history trade-off between somatic maintenance and reproduction, we found a positive relationship between clutch size and cancer prevalence across Aves. There was no significant association with body mass, lifespan, incubation length, sexual dimorphism, and cancer.
UNASSIGNED: Life history theory presents an important framework for understanding differences in cancer defenses across various species. These results suggest a trade-off between reproduction and somatic maintenance, where Aves with small clutch sizes get less cancer.

Myoglobin (Mb) mediates oxygen diffusion and storage in muscle tissue and thus is important for the energy utilization and activity of animals. Birds generally have a high body temperature, and most species also possess the capability of powered flight. Both of these require high levels of aerobic metabolism. Within endothermic mammals, bats also independently evolved flight. Although the functional evolution of myoglobins in deep-diving amniote vertebrates has been well-studied, the functional evolution of myoglobin since the origins of both birds and bats is unclear. Here, with Mb-coding sequences from >200 extant amniote species, we reconstructed ancestral sequences to estimate the functional properties of myoglobin through amniote evolution. A dramatic change in net surface charge on myoglobin occurred during the origin of Aves, which might have been driven by positively selected amino acid substitutions that occurred on the lineage leading to all birds. However, in bats, no change in net surface charge occurred and instead, the Mb genes show evidence of strong purifying selection. The increased net surface charge on bird myoglobins implies an adaptation to flight-related endothermic and higher body temperatures, possibly by reducing harmful protein aggregations. Different from the findings of net surface charge, myoglobins of extant birds show lower stability compared with other amniotes, which probably accelerates the rate of oxygen utilization in muscles. In bats and other mammals, higher stability of Mb may be an alternative pathway for adaptation to endothermy, indicating divergent evolution of myoglobin in birds and bats.

Inflammasomes are multiprotein complexes that form in response to ligands originating from pathogens as well as alterations of normal cell physiology caused by infection or tissue damage. These structures engage a robust inflammatory immune response that eradicates environmental microbes before they cause disease, and slow the growth of bona fide pathogens. Despite their undeniable utility in immunity, inflammasomes are radically reduced in birds. Perhaps most surprising is that, within all birds, NLRP3 is retained, while its signaling adapter ASC is lost, suggesting that NLRP3 signals via a novel unknown adapter. Crocodilian reptiles and turtles, which share a more recent common ancestor with birds, retain many of the lost inflammasome components, indicating that the deletion of inflammasomes occurred after birds diverged from crocodiles. Some bird lineages have even more extensive inflammasome loss, with songbirds continuing to pare down their inflammasomes until only NLRP3 and CARD8 remain. Remarkably, songbirds have lost caspase-1 but retain the downstream targets of caspase-1: IL-1β, IL-18, and the YVAD-linker encoding gasdermin A. This suggests that inflammasomes can signal through alternative proteases to activate cytokine maturation and pyroptosis in songbirds. These observations may reveal new contexts of activation that may be relevant to mammalian inflammasomes and may suggest new avenues of research to uncover the enigmatic nature of the poorly understood NLRP3 inflammasome.

The Americas hold the greatest bird diversity worldwide. Likewise, ectoparasite diversity is remarkable, including ticks of the Argasidae and Ixodidae families - commonly associated with birds. Considering that ticks have potential health implications for humans, animals, and ecosystems, we conducted a systematic review to evaluate the effects of bioclimatic, geographic variables, and bird species richness on tick infestation on wild birds across the Americas. We identified 72 articles that met our inclusion criteria and provided data on tick prevalence in wild birds. Using Generalized Additive Models, we assessed the effect of environmental factors, such as habitat type, climatic conditions, bird species richness, and geographic location, on tick infestation. Our findings show that most bird infestation case studies involved immature ticks, such as larvae or nymphs, while adult ticks represented only 13% of case studies. We found birds infested by ticks of the genera Amblyomma (68%), Ixodes (22%), Haemaphysalis (5%), Dermacentor (1%), and Rhipicephalus (0.8%) in twelve countries across the Americas. Our findings revealed that temperature variation and bird species richness were negatively associated with tick infestation, which also varied with geographic location, increasing in mid-latitudes but declining in extreme latitudes. Our results highlight the importance of understanding how environmental and bird community factors influence tick infestation in wild birds across the Americas and the dynamics of tick-borne diseases and their impact on biodiversity.