Recombinase-aid amplification combined with lateral flow detection assay for sex identification of the great white pelican (Pelecanus onocrotalus).

Sex identification in avian species is essential for biodiversity conservation and ecological studies. However, the sex of nearly half of the birds could not be identified based on their external appearance. It is difficult to visually identify sex to monitor the ecology and conservation of wild populations. In this study, we designed primer pairs for large white pelican using recombinase-based isothermal amplification combined with a lateral flow dipstick (RAA-LFD) assay for chromo-helicase-DNA binding protein (CHD) genes mapped to W chromosomes and an ultra-conserved element (UCE) located on chromosome 6, respectively. Our result showed that the raaW4-RAA-LFD can detect up to 0.1 ng of genomic DNA (gDNA) templates of female pelicans in 30 min at 39 ℃ and accurately distinguish female from male without any cross reactivity. RaaUCE2-RAA-LFD can amplify both male and female pelicans with a detection limit of 25 pg. To further evaluate the assay, 15 white pelicans of unknown sex were tested using the RAA-LFD assay and conventional polymerase chain reaction (PCR). The results of the raaW4-RAA-LFD assay were consistent with those of the conventional PCR. The developed RAA-LFD assay is equipped with field-deployable instruments and offers a field platform for rapid and reliable sex identification in pelicans.

A Deep Learning Framework for Real-Time Bird Detection and Its Implications for Reducing Bird Strike Incidents.

Bird strikes are a substantial aviation safety issue that can result in serious harm to aircraft components and even passenger deaths. In response to this increased tendency, the implementation of new and more efficient detection and prevention technologies becomes urgent. The paper presents a novel deep learning model which is developed to detect and alleviate bird strike issues in airport conditions boosting aircraft safety. Based on an extensive database of bird images having different species and flight patterns, the research adopts sophisticated image augmentation techniques which generate multiple scenarios of aircraft operation ensuring that the model is robust under different conditions. The methodology evolved around the building of a spatiotemporal convolutional neural network which employs spatial attention structures together with dynamic temporal processing to precisely recognize flying birds. One of the most important features of this research is the architecture of its dual-focus model which consists of two components, the attention-based temporal analysis network and the convolutional neural network with spatial awareness. The model's architecture can identify specific features nested in a crowded and shifting backdrop, thereby lowering false positives and improving detection accuracy. The mechanisms of attention of this model itself enhance the model's focus by identifying vital features of bird flight patterns that are crucial. The results are that the proposed model achieves better performance in terms of accuracy and real time responses than the existing bird detection systems. The ablation study demonstrates the indispensable roles of each component, confirming their synergistic effect on improving detection performance. The research substantiates the model's applicability as a part of airport bird strike surveillance system, providing an alternative to the prevention strategy. This work benefits from the unique deep learning feature application, which leads to a large-scale and reliable tool for dealing with the bird strike problem.

Sod farms drive habitat selection of a migratory grassland shorebird during a critical stopover period.

Migratory shorebirds are one of the fastest declining groups of North American avifauna. Yet, relatively little is known about how these species select habitat during migration. We explored the habitat selection of Buff-breasted Sandpipers (Calidris subruficollis) during spring and fall migration through the Texas Coastal Plain, a major stopover region for this species. Using tracking data from 118 birds compiled over 4 years, we found Buff-breasted Sandpipers selected intensively managed crops such as sod and short-stature crop fields, but generally avoided rangeland and areas near trees and shrubs. This work supports prior studies that also indicate the importance of short-stature vegetation for this species. Use of sod and corn varied by season, with birds preferring sod in spring, and avoiding corn when it is tall, but selecting for corn in fall after harvest. This dependence on cropland in the Texas Coastal Plain is contrary to habitat use observed in other parts of their non-breeding range, where rangelands are used extensively. The species' almost complete reliance on a highly specialized crop, sod, at this critical stopover site raises concerns about potential exposure to contaminants as well as questions about whether current management practices are providing suitable conditions for migratory grassland birds.

Quantification of wildlife visits to pig farms via camera traps in Japan.

Infectious diseases in livestock not only cause significant economic losses but also affect food security. Although wildlife may be involved in these infectious diseases by serving as reservoirs, research has primarily focused on livestock and related species. Moreover, while these species represent a potential threat in wildlife-borne infectious diseases, comprehensive surveys of the presence of various species are limited. In this study, we aimed to quantitatively investigate the occurrence of various mammals and birds at three pig farms in Japan. We conducted camera trap surveys from October 15, 2020, to March 24, 2022, and determined the relative abundance index inside and outside the sanitary control zone. Wild boar (Sus scrofa), sika deer (Cervus nippon), and Japanese serow (Capricornis crispus) were photographed only outside the sanitary control zone. In contrast, small and medium-sized mammals, such as feral cats (Felis catus), raccoons (Procyon lotor), and rodent species (Muridae), and birds, such as the rufous oriental turtle dove (Streptopelia orientalis) and crows of the genus Corvus, were photographed both inside and outside the sanitary control zone. This comprehensive quantitative evidence suggests that various mammals and birds may be in indirect contact with livestock, highlighting the need to improve biosecurity at livestock farms. Moreover, while fences are effective against large mammals, they are inefficient against small to medium-sized mammals and birds. Therefore, the results of this study provide important insights into enhancing biosecurity on livestock farms by strengthening physical fencing, disinfecting clothing and equipment, and complying with standards of hygiene management.

Small energy benefits of in-wake flying in long-duration migratory flights.

During long-distance migrations, some bird species make use of in-wake flying, which should allow them to profit from the upwash produced by another bird. While indirect evidence supports energy saving as the primary benefit of in-wake flying, measurements are still missing. We equipped migrating northern bald ibises (Geronticus eremita) with high-precision global navigation satellite system data loggers to track their position in the flock. We estimated birds' energy expenditure through different proxies, namely dynamic body acceleration (DBA), heart rate and effective wingbeat frequency. During active flapping flight, DBA estimates dropped off when in-wake compared with when not-in-wake. In addition, effective wingbeat frequency decreased, suggesting an increased use of intermittent gliding flight during in-wake periods. Heart rate varied greatly among individuals, with a clear decrease during gliding-corroborating its energy-saving function. Furthermore, we found consistent proof for decreased heart rate during in-wake flying, by up to 4.2%. Hence, we have shown that flying in the wake of another individual reduces birds' DBA, heart rate and effective wingbeat frequency, which could reflect reduced energy requirement.

GoEnrich: creating high quality genomic DNA resources from limited voucher specimen tissues or museum specimens of at-risk species for conservation-friendly use in the validation of environmental DNA assays.

OBJECTIVE: Environmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible. Natural history museum collections could serve as a valuable and ethical voucher specimen resource for eDNA assay validation. The present study demonstrates the effectiveness of whole genome amplification (WGA) in providing enough gDNA to assemble high quality mitogenomes from which robust targeted eDNA assays can be designed. RESULTS: Using fresh and historical museum tissue samples from six species spanning fish, birds, and mammals, we successfully developed a WGA method with an average yield of 380 to 1,268 ng gDNA per 20 µL reaction. This gDNA was used for whole genome shotgun sequencing and subsequent assembly of high quality mitogenomes using mtGrasp. These mitogenomes were then used to develop six new robust, targeted quantitative real time polymerase chain reaction-based eDNA assays and 200 ng WGA-enriched yielded satisfactory Cq values and near 100% detection frequencies for all assays tested. This approach offers a cost-effective and non-invasive alternative, streamlining eDNA research processes and aiding in conservation efforts.

Fins, feathers, fingers, and finding an explanation for the puzzle of ephemeral rewards.

This article discusses the ephemeral reward task and how it is not always a clear and concise choice. This is demonstrated through some animal studies involving birds and primates. This article also shows that when compared to human studies, that there are positive correlations between the BART and optimal choice in the ephemeral reward task, meaning that those who took more risks also were more inclined to be optimal. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability.

Higher efficiency in large-scale and long-term biodiversity monitoring can be obtained through the use of Essential Biodiversity Variables, among which species population sizes provide key data for conservation programs. Relevant estimations and assessment of actual population sizes are critical for species conservation, especially in the current context of global biodiversity erosion. However, knowledge on population size varies greatly, depending on species conservation status and ranges. While the most threatened or restricted-range species generally benefit from exhaustive counts and surveys, monitoring common and widespread species population size tends to be neglected or is simply more challenging to achieve. In such a context, citizen science (CS) is a powerful tool for the long-term monitoring of common species through the engagement of various volunteers, permitting data acquisition on the long term and over large spatial scales. Despite this substantially increased sampling effort, detectability issues imply that even common species may remain unnoticed at suitable sites. The use of structured CS schemes, including repeated visits, enables to model the detection process, permitting reliable inferences of population size estimates. Here, we relied on a large French structured CS scheme (EPOC-ODF) comprising 27,156 complete checklists over 3,873 sites collected during the 2021-2023 breeding seasons to estimate the population size of 63 common bird species using hierarchical distance sampling (HDS). These population size estimates were compared to the previous expert-based French breeding bird atlas estimations, which did not account for detectability issues. We found that population size estimates from the former French breeding bird atlas were lower than those estimated using HDS for 65% of species. Such a prevalence of lower estimations is likely due to more conservative estimates inferred from semi-quantitative expert-based assessments used for the previous atlas. We also found that species with long-range songs such as the Common Cuckoo (Cuculus canorus), Eurasian Hoopoe (Upupa epops) or the Eurasian Blackbird (Turdus merula) had, in contrast, higher estimated population sizes in the previous atlas than in our HDS models. Our study highlights the need to rely on sound statistical methodology to ensure reliable ecological inferences with adequate uncertainty estimation and advocates for a higher reliance on structured CS in support of long-term biodiversity monitoring.

Blending census and paleolimnological data allows for tracking the establishment and growth of a major gannet colony over several centuries.

Seabird colonies with long-term monitoring records, i.e., > 50 years, are rare. The population data for northern gannets (Morus bassanus) in Cape St. Mary's (CSM) Ecological Reserve (Newfoundland and Labrador, Canada) is robust, extending back to 1883 when the colony was presumed established. We inferred the colony's historical population shifts by measuring ornithogenic proxies in a dated sediment record collected from a nearby pond. Our record extended to the early eighteenth century, but the proxy data only began to show significant signs of seabird presence between ca. 1832 and 1910, aligning with the period gannets were first observed at CSM. Through the twentieth century, we observed significant increases in δ15N, P, Zn, Cd, and chlorophyll a, coeval with a shift in the dominant diatom species, indicating rapid colony growth. The proxies were overall highest in ca. 2005, corresponding to the reported historical maximum of the gannet colony in 2009. Our results validate that paleo-reconstructions using ornithogenic proxies can accurately reflect population trends and provide a stronger understanding of the colony's establishment and growth. This study highlights the value of applying paleolimnological methods in seabird population studies to frame the history of a colony's dynamics and inform conservation efforts.

Coordination of parental performance is breeding phase-dependent in the Dovekie (Alle alle), a pelagic Arctic seabird.

Currently, parental care is becoming increasingly perceived as male and female cooperation, instead of being primarily shaped by sexual conflict. Most studies examining cooperating performance consider coordination of parental activities, and doing so focuses on a short time-window including only one stage of breeding (i.e., incubation or chick rearing period). Here, we considered the cooperation of breeding partners, investigating the coordination of parental care in a long-lived seabird species with long and extensive biparental care, the Dovekie (or Little Auk), Alle alle, and looked at the issue throughout the breeding season. Previous studies on this species revealed coordinated chick provisioning, but parental coordination during incubation remains unstudied. Using video recordings collected over the course of two breeding seasons, we tested whether coordination was subject to small-scale changes within each stage and whether there was a relationship between coordination levels across the two stages. We found that the level of parental coordination is overall high and increases during the incubation period but decreases through the chick rearing phases. There were some inter-annual differences in the coordination level both at the incubation and chick rearing stages. We also found some dependency between the coordination during the incubation and chick rearing periods. All these results suggest that coordination is not a fixed behavior but breeding-phase dependent. The present study thus provides insights into how parental care and parents' cooperation is shaped by brood needs and conditions. It also highlights a relationship between coordination levels during chick rearing and incubation periods, suggesting some extent of temporal dependence in coordination of parental performance within the breeding season.

Altruism and natural selection in a variable environment.

Hamilton's rule provides the cornerstone for our understanding of the evolution of all forms of social behavior, from altruism to spite, across all organisms, from viruses to humans. In contrast to the standard prediction from Hamilton's rule, recent studies have suggested that altruistic helping can be favored even if it does not benefit relatives, as long as it decreases the environmentally induced variance of their reproductive success ("altruistic bet-hedging"). However, previous predictions both rely on an approximation and focus on variance-reducing helping behaviors. We derived a version of Hamilton's rule that fully captures environmental variability. This shows that decreasing (or increasing) the variance in the absolute reproductive success of relatives does not have a consistent effect-it can either favor or disfavor the evolution of helping. We then empirically quantified the effect of helping on the variance in reproductive success across 15 species of cooperatively breeding birds. We found that a) helping did not consistently decrease the variance of reproductive success and often increased it, and b) the mean benefits of helping across environments consistently outweighed other variability components of reproductive success. Altogether, our theoretical and empirical results suggest that the effects of helping on the variability components of reproductive success have not played a consistent or strong role in favoring helping.

USE OF THE ZOOLOGICAL INFORMATION MANAGEMENT SYSTEM (ZIMS) DATABASE (2003-2023) FOR EVALUATION OF PRACTITIONER-SELECTED MELOXICAM DOSES AND THE RELATIONSHIP TO AVIAN TAXONOMY.

Meloxicam, a commonly used NSAID, has wide variation in pharmacokinetics between different avian species. The present study hypothesized that meloxicam dosage regimens were similar within, but differ between, groups of avian species with similar feeding habits, habitats, or migratory behaviors. Utilizing the international Zoological Information Management System (ZIMS), drug usage extracts were compiled for meloxicam across eleven major orders of birds. The orders were selected based on their prevalence in zoological collections, wildlife rehabilitation centers, the pet trade, and production environments. Each species with a record available in drug usage extracts was classified into broad categories of main habitat, diet, and migratory status. Significant patterns associated with habitat, diet, or migratory status were not identified statistically. An inverse relationship was identified statistically between the practitioner mg/kg dose and body weight in kg in birds that weigh approximately 20 kg or greater. This study includes practitioner-reported summary data of current doses used in the veterinary field to treat many different avian species. Adverse effects of meloxicam were recorded in <5% of individuals evaluated at the species level in this study.

One Health: Urban birds peck up resistant pathogens.

A spatial-genomic analysis reveals that bird species living closer to humans have higher diversity of the pathogen Campylobacter and its antimicrobial resistance genes. This suggests that urbanization could promote pathogen transmission among wild animals and, potentially, humans.

Prevalence and genotypes of Chlamydia psittaci in pet birds of Hong Kong.

Psittacosis, or parrot fever, is a zoonotic disease caused by Chlamydia species associated with birds. One of the causative agents of the disease is Chlamydia psittaci, which is commonly carried by psittacine and other bird species, can be highly pathogenic and virulent to humans. In Hong Kong, a city with high population density, psittacosis is a notifiable disease with over 60% of cases in the last decade resulting in hospitalization. However, the sources of transmission of C. psittaci and its prevalence in pet birds in Hong Kong are currently unknown. To evaluate the risks of psittacosis transmission through pet birds, we tested the presence of C. psittaci and determined its genotypes in samples obtained from 516 captive birds from households, pet shops, and a veterinary hospital in Hong Kong. Results revealed that five samples (0.97%), collected from budgerigars and cockatiels, were C. psittaci-positive, while four (80%) of them were obtained from pet shops. Our phylogenetic analysis revealed that all identified strains belonged to Genotype A and showed high similarity to other sequences of this genotype obtained from various geographical locations and host species, including mammals. Our findings provide evidence for the presence of Chlamydia psittaci and shed light on its sources in captive birds in Hong Kong. They highlight the potential zoonotic risks associated with this pathogen, which can affect both humans and wild birds.

Climate and land use/land cover changes increasing habitat overlap among endangered crested ibis and sympatric egret/heron species.

Climate and land use/land cover (LULC) changes have far-reaching effects on various biological processes in wildlife, particularly interspecific interactions. Unfortunately, interspecific interactions are often overlooked when assessing the impacts of environmental changes on endangered species. In this study, we examined niche similarities and habitat overlaps between wild Crested Ibis and sympatric Egret and Heron species (EHs) in Shaanxi, China, using Ecological niche models (ENMs). We aimed to forecast potential alterations in habitat overlaps due to climate and LULC changes. The results showed that although EHs possess a broader niche breadth compared to the Crested Ibis, they still share certain niche similarities, as indicated by Schoener's D and Hellinger's I values exceeding 0.5, respectively. Notably, despite varying degrees of habitat reduction, the shared habitat area of all six species expands with the changes in climate and LULC. We suggest that with the climate and LULC changes, the habitats of sympatric EHs are likely to suffer varying degrees of destruction, forcing them to seek refuge and migrate to the remaining wild Ibis habitat. This is primarily due to the effective conservation efforts in the Crested Ibis habitat in Yangxian County and neighboring areas. Consequently, due to the niche similarity, they will share and compete for limited habitat resources, including food and space. Therefore, we recommend that conservation efforts extend beyond protecting the Crested Ibis habitat. It is crucial to control human activities that contribute to LULC changes to safeguard the habitats of both Crested Ibis and other sympatric birds.

Parental feeding in the dinosaur Lufengosaurus revealed through multidisciplinary comparisons with altricial and precocious birds.

Previous studies arguing for parental care in dinosaurs have been primarily based on fossil accumulations of adults and hatchlings, perinatal and post-hatchlings in nests and nest areas, and evidence of brooding, the majority of which date to the Late Cretaceous. Similarly, the general body proportions of preserved embryonic skeletons of the much older Early Jurassic Massospondylus have been used to suggest that hatchlings were unable to forage for themselves. Here, we approach the question of parental care in dinosaurs by using a combined morphological, chemical, and biomechanical approach to compare early embryonic and hatchling bones of the Early Jurassic sauropodomorph Lufengosaurus with those of extant avian taxa with known levels of parental care. We compare femora, the main weight-bearing limb bone, at various embryonic and post-embryonic stages in a precocious and an altricial extant avian dinosaur with those of embryonic and hatchling Lufengosaurus, and find that the rate and degree of bone development in Lufengosaurus is closer to that of the highly altricial Columba (pigeon) than the precocious Gallus (chicken), providing strong support for the hypothesis that Lufengosaurus was fully altricial. We suggest that the limb bones of Lufengosaurus hatchlings were not strong enough to forage for themselves and would likely need parental feeding.

Assessing citizen science data quality for bird monitoring in the Iberian Peninsula.

Citizen science data on biodiversity has experienced significant growth, largely driven by advancements in technology that facilitate data sharing. In recent years, mobile applications have provided a substantial boost to both the collection and sharing of this data. While this accessible information is undoubtedly valuable, we must consider the numerous biases present in this data when used for high-quality research. In this study, we analyse citizen science data for the birds of the Iberian Peninsula, comprising over 23 million unique records after filtering for duplicates (i.e., instances where the same observation was uploaded more than once). Using a 10 × 10 km square grid, we present information on well-surveyed cells (completeness) as well as temporal, taxonomic, geographical, and land use coverages. We found that the completeness of information is generally high, with better coverage around densely populated areas such as major cities and coastal regions, as well as popular birding destinations, which are frequently visited. The Mediterranean ecoregion and wetlands exhibit the highest levels of surveying. Furthermore, we observed an increase in temporal coverage since the 1980s and broad taxonomic coverage across all bird orders in the Iberian region. Our results underscore the utility of citizen science for many locations, as expressed in 10 × 10 km cells. However, they also highlight the inadequate data completeness across part of the territory, particularly in forested or sparsely inhabited areas. These findings not only identify cells suitable for bird diversity or conservation studies but also indicate areas where citizen-driven bird recording efforts should be encouraged.

A preliminary study on effects of storage time and repeated freezing-thawing on the stability of avian serum amyloid A.

Within the field of clinical research, reports on the stability of avian serum amyloid A (SAA) under varying storage conditions are currently scarce. In this study, avian plasma samples were evaluated for SAA, a major acute-phase protein in birds, to assess how varying storage periods and repeated freeze-thaw cycles impact the stability of SAA in the frozen samples. Seven plasma samples from two species and six plasma samples from three species stored at ‒20 °C were used to evaluate the time and temperature effects accordingly. A chicken-specific SAA ELISA kit was used for the measurements. Statistical analysis was performed using SPSS, and the Kruskal-Wallis test and Spearman's correlation coefficient were applied, with statistical significance set at P < 0.05. The SAA concentrations measured daily for 30 days showed no statistically significant differences over time. Freezing-thawing was repeated five times, and a significant negative relationship was confirmed over the cycles (r=‒0.8857, P < 0.05). Although no significance was observed between a decreased concentration and the number of cycles, a decrease in the concentration of > 10% was observed after the fourth cycle in four out of six samples. However, one to three freeze-thaw cycles did not result in a significant decline. Taken together, the results indicate that a negative correlation existed between the mean concentration and multiple freeze-thaw cycles, indicating that these should be avoided where possible.

A rapid-response soft end effector inspired by the hummingbird beak.

Biology is a wellspring of inspiration in engineering design. This paper delves into the application of elastic instabilities-commonly used in biological systems to facilitate swift movement-as a power-amplification mechanism for soft robots. Specifically, inspired by the nonlinear mechanics of the hummingbird beak-and shedding further light on it-we design, build and test a novel, rapid-response, soft end effector. The hummingbird beak embodies the capacity for swift movement, achieving closure in less than [Formula: see text]. Previous work demonstrated that rapid movement is achieved through snap-through deformations, induced by muscular actuation of the beak's root. Using nonlinear finite element simulations coupled with continuation algorithms, we unveil a representative portion of the equilibrium manifold of the beak-inspired structure. The exploration involves the application of a sequence of rotations as exerted by the hummingbird muscles. Specific emphasis is placed on pinpointing and tailoring the position along the manifold of the saddle-node bifurcation at which the onset of elastic instability triggers dynamic snap-through. We show the critical importance of the intermediate rotation input in the sequence, as it results in the accumulation of elastic energy that is then explosively released as kinetic energy upon snap-through. Informed by our numerical studies, we conduct experimental testing on a prototype end effector fabricated using a compliant material (thermoplastic polyurethane). The experimental results support the trends observed in the numerical simulations and demonstrate the effectiveness of the bio-inspired design. Specifically, we measure the energy transferred by the soft end effector to a pendulum, varying the input levels in the sequence of prescribed rotations. Additionally, we demonstrate a potential robotic application in scenarios demanding explosive action. From a mechanics perspective, our work sheds light on how pre-stress fields can enable swift movement in soft robotic systems with the potential to facilitate high input-to-output energy efficiency.

Amazonian rivers are leaky barriers to gene flow in forest understory birds.

Ever since Alfred Russel Wallace's nineteenth-century observation that related terrestrial species are often separated on opposing riverbanks, major Amazonian rivers have been recognized as key drivers of speciation. However, rivers are dynamic entities whose widths and courses may vary through time. It thus remains unknown how effective rivers are at reducing gene flow and promoting speciation over long timescales. We fit demographic models to genomic sequences to reconstruct the history of gene flow in three pairs of avian taxa fully separated by different Amazonian rivers, and whose geographic ranges do not make contact in headwater regions where rivers may cease to be barriers. Models with gene flow were best fit but still supported an initial period without any gene flow, which ranged from 187 000 to over 959 000 years, suggesting that rivers are capable of initiating speciation through long stretches of allopatric divergence. Allopatry was followed by either bursts or prolonged episodes of gene flow that retarded genomic differentiation but did not fully homogenize populations. Our results support Amazonian rivers as key barriers that promoted speciation and the build-up of species richness, but they also suggest that river barriers are often leaky, with genomic divergence accumulating slowly owing to episodes of substantial gene flow.