Explore the vast range of titles available.

The complex patterns on bird eggs, characterized by their replicability, distinctiveness, and intricacy, play significant roles in avian biology, including camouflage, protection from brood parasites, protecting embryos, nest identification, strengthening eggshells, and female sexual selection. The genus Lanius , known for its distinctive pigmentation patterns, shows considerable variability within species, making it an intriguing but poorly understood group. We applied Explainable AI (XAI) methods to uncover pigmentation patterns that represent species-wide identification signatures. To do this, we used Convolutional Neural Networks (CNNs) to classify shrike eggs and explore potential correlations between egg identification and eggshell patterns. Our CNN model achieved over 95% accuracy in predicting species, but identifying specific discriminative features proved difficult, as the model only highlighted general trends. This method could help organize collections and verify species affiliation in global ornithological collections, which often face challenges such as missing or illegible labels. CNNs can enhance species identification and improve the accuracy of ornithological studies. Despite some challenges, the potential applications of this research in avian biology and museum collections are promising. It offers new insights into the role of eggshell patterns in avian evolutionary strategies. This approach not only enriches our understanding of egg pigmentation but also contributes to advancements in studies spanning from ecology to biomedical research.

Biomineral-associated proteins, such as those found in bone, teeth, and eggshell, have become instrumental for studying ancient life, as they often survive far longer than DNA. Harnessing advancements in avian genomics, we annotate bone and eggshell protein sequences for 112 Anatidae (ducks, geese and swans) species, a biologically complex group of birds that are central to many archaeological and ecological questions. While palaeoproteomics conventionally assumes that protein sequences vary only between-species or above, our research demonstrates widespread evidence for single amino acid polymorphisms (SAPs) occurring within-species, particularly within avian eggshell proteins. Furthermore, we construct a phylogenetic tree from 13 proteins that aligns with mtDNA-based phylogenies, while revealing highly variable topologies for individual protein trees, underscoring the need for caution when using fragmented proteins for taxonomic identification and determining evolutionary relationships. However, with comprehensive taxonomic coverage of Anatidae proteins, clear taxonomic patterns enable reliable identification of bone and eggshell. We demonstrate this application to archaeological material from Teotihuacan, Mexico, and Shubayqa, Jordan. We highlight that extensive curated protein datasets accompanied by rigorous standards for assessing SAPs as taxonomic biomarkers are fundamental for correct taxonomic identification, setting benchmarks for palaeoproteomic applications in archaeology, ecology, and evolutionary biology. Here, the authors present eggshell protein sequences for 112 ducks, geese, and swans, species important to archaeological and ecological investigations. They then use these palaeoproteomic benchmarks to identify archaeological material from Mexico and Jordan.

Birds host diverse bacterial assemblages, which play a critical role in individual health, but which can also lead to disease or mortality. It is therefore important for developing embryos to acquire appropriate bacterial communities from maternal (vertical transmission) and environmental (horizontal transmission) sources. Eggshell bacterial assemblages are acquired before and after oviposition, and are shaped by external factors, including habitat, nesting material and parental incubation. Understanding the source of eggshell bacteria is important, because eggshell penetration of horizontally-transmitted bacteria can affect embryonic health. Most research on eggshell-associated bacteria has occurred on ‘dry-nesting’ terrestrial birds. However, little is known on bacterial acquisition in waterbirds, particularly in nests where eggs are in direct contact with water. Moist environments favour bacterial growth and wet-nesting species are therefore expected to have higher bacterial loads. To date, no study has focussed on contrasting the abundance and diversity of eggshell bacterial assemblages in wet- and dry-nesting species. We used both bacterial culture and genetic techniques (automated ribosomal intergenic spacer analysis) to document the bacterial load and assemblage structure of eggshell-associated bacteria in both wet- and dry-nesting wetland-associated bird species. Bacterial loads were several orders of magnitude greater on eggs of wet-nesting species and bacterial assemblages tended to cluster by nesting strategy. These findings suggest a possible association of eggshell-associated bacteria with nesting strategies in these species. Further research is, however, required to confirm these patterns, incorporating more comprehensive sampling and utilising more advanced genetic approaches. Overall, our findings highlight a promising direction for future research into the association between nesting in moist environments and eggshell-associated bacteria, as well as the potential for antimicrobial adaptations that may characterise the eggshells of these species.

Human infection with avian influenza A H7N9 virus emerged in eastern China in February, 2013, and has been associated with exposure to poultry. We report the clinical and microbiological features of patients infected with influenza A H7N9 virus and compare genomic features of the human virus with those of the virus in market poultry in Zhejiang, China. Between March 7 and April 8, 2013, we included hospital inpatients if they had new-onset respiratory symptoms, unexplained radiographic infiltrate, and laboratory-confirmed H7N9 virus infection. We recorded histories and results of haematological, biochemical, radiological, and microbiological investigations. We took throat and sputum samples, used RT-PCR to detect M, H7, and N9 genes, and cultured samples in Madin-Darby canine kidney cells. We tested for co-infections and monitored serum concentrations of six cytokines and chemokines. We collected cloacal swabs from 86 birds from epidemiologically linked wet markets and inoculated embryonated chicken eggs with the samples. We identified and subtyped isolates by RT-PCR sequencing. RNA extraction, complementary DNA synthesis, and PCR sequencing were done for one human and one chicken isolate. We characterised and phylogenetically analysed the eight gene segments of the viruses in the patient's and the chicken's isolates, and constructed phylogenetic trees of H, N, PB2, and NS genes. We identified four patients (mean age 56 years), all of whom had contact with poultry 3–8 days before disease onset. They presented with fever and rapidly progressive pneumonia that did not respond to antibiotics. Patients were leucopenic and lymphopenic, and had impaired liver or renal function, substantially increased serum cytokine or chemokine concentrations, and disseminated intravascular coagulation with disease progression. Two patients died. Sputum specimens were more likely to test positive for the H7N9 virus than were samples from throat swabs. The viral isolate from the patient was closely similar to that from an epidemiologically linked market chicken. All viral gene segments were of avian origin. The H7 of the isolated viruses was closest to that of the H7N3 virus from domestic ducks in Zhejiang, whereas the N9 was closest to that of the wild bird H7N9 virus in South Korea. We noted Gln226Leu and Gly186Val substitutions in human virus H7 (associated with increased affinity for α-2,6-linked sialic acid receptors) and the PB2 Asp701Asn mutation (associated with mammalian adaptation). Ser31Asn mutation, which is associated with adamantane resistance, was noted in viral M2. Cross species poultry-to-person transmission of this new reassortant H7N9 virus is associated with severe pneumonia and multiorgan dysfunction in human beings. Monitoring of the viral evolution and further study of disease pathogenesis will improve disease management, epidemic control, and pandemic preparedness. Larry Chi-Kin Yung, National Key Program for Infectious Diseases of China.

Birds are the only living amniotes with coloured eggs 1 – 4 , which have long been considered to be an avian innovation 1 , 3 . A recent study has demonstrated the presence of both red-brown protoporphyrin IX and blue-green biliverdin 5 —the pigments responsible for all the variation in avian egg colour—in fossilized eggshell of a nonavian dinosaur 6 . This raises the fundamental question of whether modern birds inherited egg colour from their nonavian dinosaur ancestors, or whether egg colour evolved independently multiple times. Here we present a phylogenetic assessment of egg colour in nonavian dinosaurs. We applied high-resolution Raman microspectroscopy to eggshells that represent all of the major clades of dinosaurs, and found that egg colour pigments were preserved in all eumaniraptorans: egg colour had a single evolutionary origin in nonavian theropod dinosaurs. The absence of colour in ornithischian and sauropod eggs represents a true signal rather than a taphonomic artefact. Pigment surface maps revealed that nonavian eumaniraptoran eggs were spotted and speckled, and colour pattern diversity in these eggs approaches that in extant birds, which indicates that reproductive behaviours in nonavian dinosaurs were far more complex than previously known 3 . Depth profiles demonstrated identical mechanisms of pigment deposition in nonavian and avian dinosaur eggs. Birds were not the first amniotes to produce coloured eggs: as with many other characteristics 7 , 8 this is an attribute that evolved deep within the dinosaur tree and long before the spectacular radiation of modern birds. A phylogenetic assessment based on Raman microspectroscopy of pigment traces in fossilized eggshells from all major dinosaur clades reveals that eggshell coloration and pigment pattern originated in nonavian theropod dinosaurs.

Expansion of anthropogenic noise and night lighting across our planet 1 , 2 is of increasing conservation concern 3 – 6 . Despite growing knowledge of physiological and behavioural responses to these stimuli from single-species and local-scale studies, whether these pollutants affect fitness is less clear, as is how and why species vary in their sensitivity to these anthropic stressors. Here we leverage a large citizen science dataset paired with high-resolution noise and light data from across the contiguous United States to assess how these stimuli affect reproductive success in 142 bird species. We find responses to both sensory pollutants linked to the functional traits and habitat affiliations of species. For example, overall nest success was negatively correlated with noise among birds in closed environments. Species-specific changes in reproductive timing and hatching success in response to noise exposure were explained by vocalization frequency, nesting location and diet. Additionally, increased light-gathering ability of species’ eyes was associated with stronger advancements in reproductive timing in response to light exposure, potentially creating phenological mismatches 7 . Unexpectedly, better light-gathering ability was linked to reduced clutch failure and increased overall nest success in response to light exposure, raising important questions about how responses to sensory pollutants counteract or exacerbate responses to other aspects of global change, such as climate warming. These findings demonstrate that anthropogenic noise and light can substantially affect breeding bird phenology and fitness, and underscore the need to consider sensory pollutants alongside traditional dimensions of the environment that typically inform biodiversity conservation. Human-generated noise and night lighting affect breeding habits and fitness in birds, implying that sensory pollutants must be considered alongside other environmental factors in assessing biodiversity conservation.

Understanding non-crown dinosaur reproduction is hindered by a paucity of directly associated adults with reproductive traces. Here we describe a new enantiornithine, Avimaia schweitzerae gen. et sp. nov., from the Lower Cretaceous Xiagou Formation with an unlaid egg two-dimensionally preserved within the abdominothoracic cavity. Ground-sections reveal abnormal eggshell proportions, and multiple eggshell layers best interpreted as a multi-layered egg resulting from prolonged oviductal retention. Fragments of the shell membrane and cuticle are both preserved. SEM reveals that the cuticle consists of nanostructures resembling those found in neornithine eggs adapted for infection-prone environments, which are hypothesized to represent the ancestral avian condition. The femur preserves small amounts of probable medullary bone, a tissue found today only in reproductively active female birds. To our knowledge, no other occurrence of Mesozoic medullary bone is associated with indications of reproductive activity, such as a preserved egg, making our identification unique, and strongly supported. The fossil record of the reproductive traits of early birds is limited. Here, Bailleul and colleagues describe the Cretaceous enantiornithine bird Avimaia schweitzerae , which preserves an unlaid egg in the abdominal cavity and putative medullary bone.

Egg size and structure reflect important constraints on the reproductive and life-history characteristics of vertebrates 1 . More than two-thirds of all extant amniotes lay eggs 2 . During the Mesozoic era (around 250 million to 65 million years ago), body sizes reached extremes; nevertheless, the largest known egg belongs to the only recently extinct elephant bird 3 , which was roughly 66 million years younger than the last nonavian dinosaurs and giant marine reptiles. Here we report a new type of egg discovered in nearshore marine deposits from the Late Cretaceous period (roughly 68 million years ago) of Antarctica. It exceeds all nonavian dinosaur eggs in volume and differs from them in structure. Although the elephant bird egg is slightly larger, its eggshell is roughly five times thicker and shows a substantial prismatic layer and complex pore structure 4 . By contrast, the new fossil, visibly collapsed and folded, presents a thin eggshell with a layered structure that lacks a prismatic layer and distinct pores, and is similar to that of most extant lizards and snakes (Lepidosauria) 5 . The identity of the animal that laid the egg is unknown, but these preserved morphologies are consistent with the skeletal remains of mosasaurs (large marine lepidosaurs) found nearby. They are not consistent with described morphologies of dinosaur eggs of a similar size class. Phylogenetic analyses of traits for 259 lepidosaur species plus outgroups suggest that the egg belonged to an individual that was at least 7 metres long, hypothesized to be a giant marine reptile, all clades of which have previously been proposed to show live birth 6 . Such a large egg with a relatively thin eggshell may reflect derived constraints associated with body shape, reproductive investment linked with gigantism, and lepidosaurian viviparity, in which a ‘vestigial’ egg is laid and hatches immediately 7 . A fossil egg unearthed from Cretaceous deposits in Antarctica is more than 20 cm long, exceeds all known nonavian eggs in volume, is soft-shelled, and was perhaps laid by a giant marine lizard such as a mosasaur.

Background Wulong geese ( Anser cygnoides orientalis ) are known for their excellent egg-laying performance. However, they show considerable population differences in egg-laying behavior. This study combined genome-wide selection signal analysis with transcriptome analysis (RNA-seq) to identify the genes related to high egg production in Wulong geese. Results A total of 132 selected genomic regions were screened using genome-wide selection signal analysis, and 130 genes related to high egg production were annotated in these regions. These selected genes were enriched in pathways related to egg production, including oocyte meiosis, the estrogen signaling pathway, the oxytocin signaling pathway, and progesterone-mediated oocyte maturation. Furthermore, a total of 890 differentially expressed genes (DEGs), including 340 up-regulated and 550 down-regulated genes, were identified by RNA-seq. Two genes — GCG and FAP — were common to the list of selected genes and DEGs. A non-synonymous single nucleotide polymorphism was identified in an exon of FAP . Conclusions Based on genome-wide selection signal analysis and transcriptome data, GCG and FAP were identified as candidate genes associated with high egg production in Wulong geese. These findings could promote the breeding of Wulong geese with high egg production abilities and provide a theoretical basis for exploring the mechanisms of reproductive regulation in poultry.