Enterococcus faecalis provides protection during scavenging in carrion crow ( Corvus corone).

The gut microbiota significantly influences host physiology and provides essential ecosystem services. While diet can affect the composition of the gut microbiota, the gut microbiota can also help the host adapt to specific dietary habits. The carrion crow ( Corvus corone), an urban facultative scavenger bird, hosts an abundance of pathogens due to its scavenging behavior. Despite this, carrion crows infrequently exhibit illness, a phenomenon related to their unique physiological adaptability. At present, however, the role of the gut microbiota remains incompletely understood. In this study, we performed a comparative analysis using 16S rRNA amplicon sequencing technology to assess colonic content in carrion crows and 16 other bird species with different diets in Beijing, China. Our findings revealed that the dominant gut microbiota in carrion crows was primarily composed of Proteobacteria (75.51%) and Firmicutes (22.37%). Significant differences were observed in the relative abundance of Enterococcus faecalis among groups, highlighting its potential as a biomarker of facultative scavenging behavior in carrion crows. Subsequently, E. faecalis isolated from carrion crows was transplanted into model mice to explore the protective effects of this bacterial community against Salmonella enterica infection. Results showed that E. faecalis down-regulated the expression of pro-inflammatory cytokines tumor necrosis factor alpha (TNF-α), interferon gamma (IFN-γ), and interleukin 6 (IL-6), prevented S. enterica colonization, and regulated the composition of gut microbiota in mice, thereby modulating the host's immune regulatory capacity. Therefore, E. faecalis exerts immunoregulatory and anti-pathogenic functions in carrion crows engaged in scavenging behavior, offering a representative case of how the gut microbiota contributes to the protection of hosts with specialized diets.

The roles of non-structural carbohydrates in fruiting: a review focusing on mango (Mangifera indica).

Reproductive development of fruiting trees, including mango (Mangifera indica L.), is limited by non-structural carbohydrates. Competition for sugars increases with cropping, and consequently, vegetative growth and replenishment of starch reserves may reduce with high yields, resulting in interannual production variability. While the effect of crop load on photosynthesis and the distribution of starch within the mango tree has been studied, the contribution of starch and sugars to different phases of reproductive development requires attention. This review focuses on mango and examines the roles of non-structural carbohydrates in fruiting trees to clarify the repercussions of crop load on reproductive development. Starch buffers the plant's carbon availability to regulate supply with demand, while sugars provide a direct resource for carbon translocation. Sugar signalling and interactions with phytohormones play a crucial role in flowering, fruit set, growth, ripening and retention, as well as regulating starch, sugar and secondary metabolites in fruit. The balance between the leaf and fruit biomass affects the availability and contributions of starch and sugars to fruiting. Crop load impacts photosynthesis and interactions between sources and sinks. As a result, the onset and rate of reproductive processes are affected, with repercussions for fruit size, composition, and the inter-annual bearing pattern.

Synthesizing avian dreams.

During sleep, sporadically, it is possible to find neural patterns of activity in areas of the avian brain that are activated during the generation of the song. It has recently been found that in the vocal muscles of a sleeping bird, it is possible to detect activity patterns during these silent replays. In this work, we employ a dynamical systems model for song production in suboscine birds in order to translate the vocal muscles activity during sleep into synthetic songs. Besides allowing us to translate muscle activity into behavior, we argue that this approach poses the biomechanics as a unique window into the avian brain, with biophysical models as its probe.

Range and climate niche shifts in European and North American breeding birds.

Species respond dynamically to climate change and exhibit time lags. Consequently, species may not occupy their full climatic niche during range shifting. Here, we assessed climate niche tracking during recent range shifts of European and United States (US) birds. Using data from two European bird atlases and from the North American Breeding Bird Survey between the 1980s and 2010s, we analysed range overlap and climate niche overlap based on kernel density estimation. Phylogenetic multiple regression was used to assess the effect of species morphological, ecological and biogeographic traits on range and niche metrics. European birds shifted their ranges north and north-eastwards, US birds westwards. Range unfilling was lower than expected by null models, and niche expansion was more common than niche unfilling. Also, climate niche tracking was generally lower in US birds and poorly explained by species traits. Overall, our results suggest that dispersal limitations were minor in range shifting birds in Europe and the USA while delayed extinctions from unfavourable areas seem more important. Regional differences could be related to differences in land use history and monitoring schemes. Comparative analyses of range and niche shifts provide a useful screening approach for identifying the importance of transient dynamics and time-lagged responses to climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Eimeria atricillae n. sp. (Apicomplexa: Eimeriidae) from the laughing gull Leucophaeus atricilla (Linnaeus) (Aves: Charadriiformes: Laridae) in Port Isabel, Texas.

A new coccidian species, Eimeria atricillae n. sp. (Apicomplexa: Eimeriidae) collected from the laughing gull Leucophaeus atricilla, is reported from Port Isabel, Texas, USA. Sporulated oöcysts of the new species are spherical to subspherical, 16.0-18.1 × 14.4-16.6 (17.1 × 15.4) µm, with a length/width (L/W) ratio of 1.0-1.1; polar granules are present, but micropyle and oöcyst residuum are absent. Sporocysts are ovoid, 9.1-9.7 × 6.1-7.1 (9.4 × 6.6) µm, with a L/W ratio of 1.3-1.5; Stieda body present, but sub-Stieda and para-Stieda bodies are absent; sporocyst residuum diffuse.

Deep learning workflow to support in-flight processing of digital aerial imagery for wildlife population surveys.

Deep learning shows promise for automating detection and classification of wildlife from digital aerial imagery to support cost-efficient remote sensing solutions for wildlife population monitoring. To support in-flight orthorectification and machine learning processing to detect and classify wildlife from imagery in near real-time, we evaluated deep learning methods that address hardware limitations and the need for processing efficiencies to support the envisioned in-flight workflow. We developed an annotated dataset for a suite of marine birds from high-resolution digital aerial imagery collected over open water environments to train the models. The proposed 3-stage workflow for automated, in-flight data processing includes: 1) image filtering based on the probability of any bird occurrence, 2) bird instance detection, and 3) bird instance classification. For image filtering, we compared the performance of a binary classifier with Mask Region-based Convolutional Neural Network (Mask R-CNN) as a means of sub-setting large volumes of imagery based on the probability of at least one bird occurrence in an image. On both the validation and test datasets, the binary classifier achieved higher performance than Mask R-CNN for predicting bird occurrence at the image-level. We recommend the binary classifier over Mask R-CNN for workflow first-stage filtering. For bird instance detection, we leveraged Mask R-CNN as our detection framework and proposed an iterative refinement method to bootstrap our predicted detections from loose ground-truth annotations. We also discuss future work to address the taxonomic classification phase of the envisioned workflow.

ETV2 induces endothelial, but not hematopoietic, lineage specification in birds.

Cardiovascular system develops from the lateral plate mesoderm. Its three primary cell lineages (hematopoietic, endothelial, and muscular) are specified by the sequential actions of conserved transcriptional factors. ETV2, a master regulator of mammalian hemangioblast development, however, is absent in the chicken genome and acts downstream of NPAS4L in zebrafish. Here, we investigated the epistatic relationship between NPAS4L and ETV2 in avian hemangioblast development. We showed that ETV2 is deleted in all 363 avian genomes analyzed. Mouse ETV2 induced LMO2, but not NPAS4L or SCL, expression in chicken mesoderm. Squamate (lizards, geckos, and snakes) genomes contain both NPAS4L and ETV2 In Madagascar ground gecko, both genes were expressed in developing hemangioblasts. Gecko ETV2 induced only LMO2 in chicken mesoderm. We propose that both NPAS4L and ETV2 were present in ancestral amniote, with ETV2 acting downstream of NPAS4L in endothelial lineage specification. ETV2 may have acted as a pioneer factor by promoting chromatin accessibility of endothelial-specific genes and, in parallel with NPAS4L loss in ancestral mammals, has gained similar function in regulating blood-specific genes.

Dynamics of evolutionary succession and coordination between opposite adaptations in cuckoo hosts under antagonistic coevolution.

Adaptations are driven by specific natural selection pressures throughout biological evolution. However, these cannot inherently align with future shifts in selection dynamics, thus manifesting in opposing directions. We performed field experiments on cuckoo hosts to investigate the coexistence and conflict between two evolutionarily successive but opposing behavioral adaptations-egg retrieval and rejection. Our findings provide key insights. (1) Egg rejection against brood parasites in hosts reshapes egg retrieval to flexible reactions-retrieval, ignoring, or outright rejection of foreign eggs outside the nest cup, departing from instinctual retrieval. (2) Parasitism pressure and egg mimicry by parasites remarkably alter the proportions of the three host reactions. Host species with higher parasitism pressure exhibit frequent and rapid rejection of non-mimetic foreign eggs and reduced ignoring or retrieval responses. Conversely, heightened egg mimicry enhances retrieval behaviors while diminishing ignoring responses. (3) Cuckoos employ consistent mechanisms for rejecting foreign eggs inside or outside the nest cup. Direct rejection of eggs outside the nest cup shows that rejection precedes retrieval, indicating prioritization of specific adaptation over instinct. (4) Cuckoo hosts navigate the conflict between the intentions and motivations associated with egg rejection and retrieval by ignoring foreign eggs, a specific outcome of the rejection-retrieval tradeoff.

Effects of Maturation on Antibacterial Properties of Vietnamese Mango (Mangifera indica) Leaves.

This study, for the first time, has investigated the relationships between alterations of mangiferin contents in mango leaves at different maturity stages and their antibacterial properties. Leaves were classified into six different maturity stages based on their color: (1) young dark reddish brown, (2) young yellow, (3) young light green, (4) mature green, (5) old dark green, and (6) old yellow leaves. Ethanol extracts were then examined against Gram-positive and Gram-negative bacteria, applying broth dilution and agar well diffusion methods. In addition, we also measured the mangiferin contents in leaves at different stages for the purpose of evaluating how the changes in this phytochemistry value affects their activities against bacteria. The results showed that extracts from leaves at young ages had better antibacterial properties than those from old leaves, as evidenced by the lower minimum inhibitory concentrations and larger inhibitory zones. In addition, we also found that the contents of mangiferin were significantly decreased followed the maturation process. These results suggest that mango leaves at young stages, especially dark reddish brown and young yellow leaves, are preferable for application in bacterial infections and other therapies related to mangiferin's constituents.

Hammerhead-type FXR agonists induce an enhancer RNA Fincor that ameliorates nonalcoholic steatohepatitis in mice.

The nuclear receptor, farnesoid X receptor (FXR/NR1H4), is increasingly recognized as a promising drug target for metabolic diseases, including nonalcoholic steatohepatitis (NASH). Protein-coding genes regulated by FXR are well known, but whether FXR also acts through regulation of long non-coding RNAs (lncRNAs), which vastly outnumber protein-coding genes, remains unknown. Utilizing RNA-seq and global run-on sequencing (GRO-seq) analyses in mouse liver, we found that FXR activation affects the expression of many RNA transcripts from chromatin regions bearing enhancer features. Among these we discovered a previously unannotated liver-enriched enhancer-derived lncRNA (eRNA), termed FXR-induced non-coding RNA (Fincor). We show that Fincor is specifically induced by the hammerhead-type FXR agonists, including GW4064 and tropifexor. CRISPR/Cas9-mediated liver-specific knockdown of Fincor in dietary NASH mice reduced the beneficial effects of tropifexor, an FXR agonist currently in clinical trials for NASH and primary biliary cholangitis (PBC), indicating that amelioration of liver fibrosis and inflammation in NASH treatment by tropifexor is mediated in part by Fincor. Overall, our findings highlight that pharmacological activation of FXR by hammerhead-type agonists induces a novel eRNA, Fincor, contributing to the amelioration of NASH in mice. Fincor may represent a new drug target for addressing metabolic disorders, including NASH.

Non-alcoholic steatohepatitis, also known as NASH, is a severe condition whereby fat deposits around the liver lead to inflammation, swelling, scarring and lasting damage to the organ. Despite being one of the leading causes of liver-related deaths worldwide, the disease has no approved treatment. A protein known as Farnesoid X receptor (or FXR) is increasingly being recognized as a promising drug target for non-alcoholic steatohepatitis. Once activated, FXR helps to regulate the activity of DNA regions which are coding for proteins important for liver health. However, less is known about how FXR may act on non-coding regions, the DNA sequences that do not generate proteins but can be transcribed into RNA molecules with important biological roles. In response, Chen et al. investigated whether FXR activation of non-coding RNAs could be linked to the clinical benefits of hammerhead FXR agonists, a type of synthetic compounds that activates this receptor. To do so, genetic analyses of mouse livers were performed to identify non-coding RNAs generated when FXR was activated by the agonist. These experiments revealed that agonist-activated FXR induced a range of non-coding RNAs transcribed from DNA sequences known as enhancers, which help to regulate gene expression. In particular, hammerhead FXR agonists led to the production of a liver-specific enhancer RNA called Fincor. Additional experiments using tropifexor, a hammerhead FXR agonist currently into clinical trials, showed that this investigational new drug had reduced benefits in a mouse model of non-alcoholic steatohepatitis with low Fincor levels. This suggested that this enhancer RNA may play a key role in mediating the clinical benefits of hammerhead FXR agonists, encouraging further research into its role and therapeutic value.

The importance of migratory drop-off for island colonization in birds.

Seasonal migration is an underappreciated driver of animal diversification. Changes in migratory behaviour may favour the establishment of sedentary founder populations and promote speciation if there is sufficient reproductive isolation between sedentary and migratory populations. From a systematic literature review, we here quantify the role of migratory drop-off-the loss of migratory behaviour-in promoting speciation in birds on islands. We identify at least 157 independent colonization events likely initiated by migratory species that led to speciation, including 44 cases among recently extinct species. By comparing, for all islands, the proportion of island endemic species that derived from migratory drop-off with the proportion of migratory species among potential colonizers, we showed that seasonal migration has a larger effect on island endemic richness than direct dispersal. We also found that the role of migration in island colonization increases with the geographic isolation of islands. Furthermore, the success of speciation events depends in part on species biogeographic and ecological factors, here positively associated with greater range size and larger flock sizes. These results highlight the importance of shifts in migratory behaviour in the speciation process and calls for greater consideration of migratory drop-off in the biogeographic distribution of birds.

Unconventional life history in a migratory shorebird: desegregating reproduction and migration.

Conventional life-history theory predicts that energy-demanding events such as reproduction and migration must be temporally segregated to avoid resource limitation. Here, we provide, to our knowledge, the first direct evidence of 'itinerant breeding' in a migratory bird, an incredibly rare breeding strategy (less than 0.1% of extant bird species) that involves the temporal overlap of migratory and reproductive periods of the annual cycle. Based on GPS-tracking of over 200 female American woodcock, most female woodcock (greater than 80%) nested more than once (some up to six times) with short re-nest intervals, and females moved northwards on average 800 km between first and second nests, and then smaller distances (ca 200+ km) between subsequent nesting attempts. Reliance on ephemeral habitat for breeding, ground-nesting and key aspects of life history that reduce both the costs of reproduction and migration probably explain the prevalence of this rare phenotype in woodcock and why itinerant breeding so rarely occurs in other bird species.

Individual variation in life-history timing: synchronous presence, asynchronous events and phenological compensation in a wild mammal.

Many animals and plants have species-typical annual cycles, but individuals vary in their timing of life-history events. Individual variation in fur replacement (moult) timing is poorly understood in mammals due to the challenge of repeated observations and longitudinal sampling. We examined factors that influence variation in moult duration and timing among elephant seals (Mirounga angustirostris). We quantified the onset and progression of fur loss in 1178 individuals. We found that an exceptionally rapid visible moult (7 days, the shortest of any mammals or birds), and a wide range of moult start dates (spanning 6-10× the event duration) facilitated high asynchrony across individuals (only 20% of individuals in the population moulting at the same time). Some of the variation was due to reproductive state, as reproductively mature females that skipped a breeding season moulted a week earlier than reproductive females. Moreover, individual variation in timing and duration within age-sex categories far outweighed (76-80%) variation among age-sex categories. Individuals arriving at the end of the moult season spent 50% less time on the beach, which allowed them to catch up in their annual cycles and reduce population-level variance during breeding. These findings underscore the importance of individual variation in annual cycles.

A region of suppressed recombination misleads neoavian phylogenomics.

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.

Significant shifts in latitudinal optima of North American birds.

Changes in climate can alter environmental conditions faster than most species can adapt. A prediction under a warming climate is that species will shift their distributions poleward through time. While many studies focus on range shifts, latitudinal shifts in species' optima can occur without detectable changes in their range. We quantified shifts in latitudinal optima for 209 North American bird species over the last 55 y. The latitudinal optimum (m) for each species in each year was estimated using a bespoke flexible non-linear zero-inflated model of abundance vs. latitude, and the annual shift in m through time was quantified. One-third (70) of the bird species showed a significant shift in their optimum. Overall, mean peak abundances of North American birds have shifted northward, on average, at a rate of 1.5 km per year (±0.58 SE), corresponding to a total distance moved of 82.5 km (±31.9 SE) over the last 55 y. Stronger poleward shifts at the continental scale were linked to key species' traits, including thermal optimum, habitat specialization, and territoriality. Shifts in the western region were larger and less variable than in the eastern region, and they were linked to species' thermal optimum, habitat density preference, and habitat specialization. Individual species' latitudinal shifts were most strongly linked to their estimated thermal optimum, clearly indicating a climate-driven response. Displacement of species from their historically optimal realized niches can have dramatic ecological consequences. Effective conservation must consider within-range abundance shifts. Areas currently deemed "optimal" are unlikely to remain so.

INFLUENCE OF GROOMING ON PERMANENT ARTHROPOD ASSOCIATES OF BIRDS: CATTLE EGRETS, LICE, AND MITES.

Birds have a diverse community of "permanent" arthropods that complete their entire life cycle on the body of the host. Because some of these arthropods are parasites that reduce host fitness, birds control them by grooming, which consists of preening with the beak and scratching with the feet. Although preening is the primary component of grooming, scratching is essential for controlling arthropods on the head and neck, which cannot be preened. Several unrelated groups of birds have evolved comb-like pectinate claws on the middle toenail of each foot. We tested the role of these claws in the control of arthropods by experimentally removing teeth from the claws of captive western cattle egrets (Bubulcus ibis) infested with chewing lice (Insecta: Phthiraptera), feather mites (Acari: Sarcoptiformes), and nasal mites (Acari: Mesostigmata). After a period of 4 mo, we compared the abundance of arthropods on experimental birds to that of control birds with intact teeth. We used video to quantify the grooming rates of the captive birds, which groomed twice as much as wild birds. Experimental and control birds did not differ significantly in grooming time. Both groups virtually eradicated the chewing lice, but not feather mites or nasal mites. We found no support for the hypothesis that pectinate claws increase the efficiency of arthropod control by grooming. Experiments with wild birds are needed to test the hypothesis further under conditions in which birds devote less time to grooming.

Long-term dataset for contaminants in fish, mussels, and bird eggs from the Baltic Sea.

Widespread persistent contaminants are a global environmental problem. In the Baltic Sea, wildlife contamination was first noticed in the 1960s, prompting the Swedish Environmental Protection Agency to establish a comprehensive Swedish National Monitoring Programme for Contaminants in Marine Biota (MCoM) in 1978 run by the Swedish Museum of Natural History. Eight species have been analysed, four fish species (Atlantic herring, Atlantic cod, European perch, viviparous eelpout), one bivalve species (blue mussel), and egg from three bird species (common guillemot, common tern, Eurasian oystercatcher). Here, we present a dataset containing MCoM data from its start until 2021. It includes 36 sets of time-series, each analysed for more than 100 contaminants. The longest time-series is for common guillemot and starts in 1968. We describe the structure of MCoM including historic changes to the number of stations, sample treatment, analytical methods, instruments, and laboratories. The MCoM data is available at the Bolin Centre repository and on GitHub through our R package mcomDb. The latter will be updated yearly with new MCoM records.

Worries about bird flu in U.S. cattle intensify.

Farm worker becomes infected as H5N1 appears to spread between dairy cows in five states.