Natural sounds, and bird song in particular, play a key role in building and maintaining our connection with nature, but widespread declines in bird populations mean that the acoustic properties of natural soundscapes may be changing. Using data-driven reconstructions of soundscapes in lieu of historical recordings, here we quantify changes in soundscape characteristics at more than 200,000 sites across North America and Europe. We integrate citizen science bird monitoring data with recordings of individual species to reveal a pervasive loss of acoustic diversity and intensity of soundscapes across both continents over the past 25 years, driven by changes in species richness and abundance. These results suggest that one of the fundamental pathways through which humans engage with nature is in chronic decline, with potentially widespread implications for human health and well-being.
- MeSH
- Acoustics * MeSH
- Biodiversity MeSH
- Humans MeSH
- Population Dynamics MeSH
- Birds classification physiology MeSH
- Seasons MeSH
- Vocalization, Animal classification physiology MeSH
- Conservation of Natural Resources MeSH
- Animals MeSH
- Sound MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Europe MeSH
- North America MeSH
Two key cytosolic receptors belonging to the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) family sense the viral RNA-derived danger signals: RIG-I and melanoma differentiation-associated protein 5 (MDA5). Their activation establishes an antiviral state by downstream signaling that ultimately activates interferon-stimulated genes (ISGs). While in rare cases RIG-I gene loss has been detected in mammalian and avian species, most notably in the chicken, MDA5 pseudogenization has only been detected once in mammals. We have screened over a hundred publicly available avian genome sequences and describe an independent disruption of MDA5 in two unrelated avian lineages, the storks (Ciconiiformes) and the rallids (Gruiformes). The results of our RELAX analysis confirmed the absence of negative selection in the MDA5 pseudogene. In contrast to our prediction, we have shown, using multiple dN/dS-based approaches, that the MDA5 loss does not appear to have resulted in any compensatory evolution in the RIG-I gene, which may partially share its ligand-binding specificity. Together, our results indicate that the MDA5 pseudogenization may have important functional effects on immune responsiveness in these two avian clades.
- MeSH
- DEAD Box Protein 58 chemistry genetics immunology MeSH
- Gene Deletion * MeSH
- Phylogeny MeSH
- Humans MeSH
- Models, Molecular MeSH
- Immunity, Innate MeSH
- Pseudogenes MeSH
- Avian Proteins chemistry genetics immunology MeSH
- Birds classification genetics immunology MeSH
- Amino Acid Sequence MeSH
- Sequence Alignment MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% across fish lineages. This raises the question as to what extent does the chromosome size drive GC% as posited by the currently accepted explanation based on the recombination rate. We ascribe the differences found across fishes to varying GC% of repetitive sequences. Generally, our results suggest that the GC% of repeats and proportion of repeats are independent of the chromosome size. This leaves an open space for another mechanism driving the GC evolution in vertebrates.
- MeSH
- Chromosomes genetics MeSH
- Cytogenetics * MeSH
- Genome genetics MeSH
- Evolution, Molecular * MeSH
- Vertebrates classification genetics MeSH
- Birds classification genetics MeSH
- Recombination, Genetic genetics MeSH
- Repetitive Sequences, Nucleic Acid MeSH
- Fishes classification genetics MeSH
- Base Composition genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Keywords
- záchranné stanice,
- MeSH
- Columbidae MeSH
- Animal Welfare statistics & numerical data MeSH
- Birds * classification MeSH
- Rescue Work * methods statistics & numerical data MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Geographicals
- Czech Republic MeSH
Many animals emit vocal sounds which, independently from the sounds' function, contain some individually distinctive signature. Thus the automatic recognition of individuals by sound is a potentially powerful tool for zoology and ecology research and practical monitoring. Here, we present a general automatic identification method that can work across multiple animal species with various levels of complexity in their communication systems. We further introduce new analysis techniques based on dataset manipulations that can evaluate the robustness and generality of a classifier. By using these techniques, we confirmed the presence of experimental confounds in situations resembling those from past studies. We introduce data manipulations that can reduce the impact of these confounds, compatible with any classifier. We suggest that assessment of confounds should become a standard part of future studies to ensure they do not report over-optimistic results. We provide annotated recordings used for analyses along with this study and we call for dataset sharing to be a common practice to enhance the development of methods and comparisons of results.
- MeSH
- Models, Biological MeSH
- Species Specificity MeSH
- Individuality * MeSH
- Birds classification MeSH
- Vocalization, Animal classification MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- MeSH
- Anseriformes classification MeSH
- Raptors injuries MeSH
- Ecology methods organization & administration legislation & jurisprudence MeSH
- Geese injuries MeSH
- Ducks classification injuries MeSH
- Columbiformes injuries MeSH
- Hospitals, Animal organization & administration trends MeSH
- Endangered Species * MeSH
- Birds classification injuries MeSH
- Statistics as Topic MeSH
- Veterinary Medicine * methods organization & administration MeSH
- Conservation of Natural Resources * economics methods legislation & jurisprudence MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
Here, we present a comprehensive analysis of the H5N8/H5N5 highly pathogenic avian influenza (HPAI) virus strains detected in the Czech Republic during an outbreak in 2017. Network analysis of the H5 Hemagglutinin (HA) from 99% of the outbreak localities suggested that the diversity of the Czech H5N8/H5N5 viruses was influenced by two basic forces: local microevolution and independent incursions. The geographical occurrence of the central node H5 HA sequences revealed three eco-regions, which apparently played an important role in the origin and further spread of the local H5N8/HPAI variants across the country. A plausible explanation for the observed pattern of diversity is also provided.
- MeSH
- Disease Outbreaks MeSH
- Phylogeny MeSH
- Genetic Variation MeSH
- Hemagglutinin Glycoproteins, Influenza Virus genetics MeSH
- Evolution, Molecular * MeSH
- Influenza in Birds epidemiology virology MeSH
- Birds classification virology MeSH
- Virulence MeSH
- Influenza A Virus, H5N8 Subtype classification genetics isolation & purification pathogenicity MeSH
- Influenza A virus classification genetics isolation & purification pathogenicity MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic epidemiology MeSH
Bacterial communities within avian nests are considered an important determinant of egg viability, potentially selecting for traits that confer embryos with protection against trans-shell infection. A high bacterial density on the eggshell increases hatching failure, whether this effect could be due to changes in bacterial community or just a general increase in bacterial density. We explored this idea using intra- and interspecific comparisons of the relationship between hatching success and eggshell bacteria characterized by culture and molecular techniques (fingerprinting and high-throughput sequencing). We collected information for 152 nests belonging to 17 bird species. Hatching failures occurred more frequently in nests with higher density of aerobic mesophilic bacteria on their eggshells. Bacterial community was also related to hatching success, but only when minority bacterial operational taxonomic units were considered. These findings support the hypothesis that bacterial density is a selective agent of embryo viability, and hence a proxy of hatching failure only within species. Although different avian species hold different bacterial densities or assemblages on their eggs, the association between bacteria and hatching success was similar for different species. This result suggests that interspecific differences in antibacterial defenses are responsible for keeping the hatching success at similar levels in different species.
- MeSH
- Bacteria classification genetics growth & development isolation & purification MeSH
- Biodiversity MeSH
- Phenotype MeSH
- Ovum growth & development microbiology MeSH
- Birds classification growth & development microbiology physiology MeSH
- Egg Shell microbiology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The evolutionary distinctiveness (ED) score is a measure of phylogenetic isolation that quantifies the evolutionary uniqueness of a species. Here, we compared the ED score of parasitic and non-parasitic cuckoo species world-wide, to understand whether parental care or parasitism represents the largest amount of phylogenetic uniqueness. Next, we focused only on 46 cuckoo species characterized by brood parasitism with a known number of host species, and we explored the associations among ED score, number of host species and breeding range size for these species. We assessed these associations using phylogenetic generalized least squares (PGLS) models, taking into account the phylogenetic signal. Parasitic cuckoo species were not more unique in terms of ED than non-parasitic species. However, we found a significant negative association between the evolutionary uniqueness and host range and a positive correlation between the number of host species and range size of parasitic cuckoos, probably suggesting a passive sampling of hosts by parasitic species as the breeding range broadens. The findings of this study showed that more generalist brood parasites occupied very different positions in a phylogenetic tree, suggesting that they have evolved independently within the Cuculiformes order. Finally, we demonstrated that specialist cuckoo species also represent the most evolutionarily unique species in the order of Cuculiformes.
We studied the abundance of the common cuckoo Cuculus canorus L. little cuckoo Cuculus poliocephalus L. and Asian cuckoo Cuculus saturatus L. and avian top predators as indicators of bird species richness (surrogate of biodiversity) in disturbed environments caused by radioactive contamination in Chernobyl, Ukraine and Fukushima, Japan, comparing their efficiency as indicators of local biodiversity hotspots. Bird species richness and birds abundance were quantified in each sample site during the breeding seasons between 2006 and 2015 and the level of background radiation was measured at every site. The correlation between number of cuckoos, top predators, land use composition and level of background radiation with bird species richness as response variable were examined using Generalized Linear Mixed Models. The strength of correlation between species richness and abundance and the covariates obtained from the model outputs were used as measure of the efficiency of each predictor, as well as the AIC of each model. Background radiation was negatively correlated with bird species richness and bird abundance in both countries, while number of top predators and cuckoos were both positively correlated with bird species richness and abundance. However, model with number of cuckoos was more performant than model with number of avian top predators. These differences in performance supports the hypothesis that cuckoos are a largely superior bioindicator than top predators.
- MeSH
- Biodiversity * MeSH
- Environmental Monitoring methods MeSH
- Birds classification physiology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
