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PubMed2025

Comparative phylogeographic patterns in three pan-Amazonian antwren lineages (Aves: Passeriformes: Thamnophilidae: Myrmotherula and Isleria).

We examined DNA sequences of 328 individuals of three lineages (species or species complexes) of Amazonian antwrens to evaluate their degree of geographical and historical concordance. All lineages (Myrmotherula longipennis, M. menetriesii, and the Isleria guttata-hauxwelli species complex) consist of small insectivorous birds that occupy understory or midstory of terra firme forest and are widely distributed across the Amazon Basin. Individuals of each of the three lineages grouped into genetic clades mainly separated by the Amazon and some major tributaries, although members of different clades of both M. menetriesii and I. hauxwelli were documented in the Madeira-Tapajós interfluvium. Branching patterns differed among taxa, but all taxa were highly differentiated across the lower or upper Amazon. Despite the morphological, ecological, and phylogenetic similarities among lineages, and despite the fact that nearly all taxa are bounded by rivers, the effect of the other major rivers as biogeographic barriers was highly variable. The Marañón, Ucayali, Madeira, Tapajós, Xingu, Napo, Negro, and Branco all separated main clades in one or two lineages but not in the others. Levels of genetic differentiation along the Teles Pires were substantially higher than those across the Tapajós in M. menetriesii and I. hauxwelli, consistent with a proposed historical change of river course for the Tapajós. Genetic units in this study were comparable for the most part to taxonomic units delineated by analyses of vocal and morphological variation, and identical, with one exception, to units defined solely by vocal variation in a companion paper (Isler et al. 2025). These results, in conjunction with those of Isler et al. (2025), provide additional instances of the variability of responses to the historical dynamism of Amazonia, in this case in closely related and ecologically similar species; highlight the consistency of genetic differentiation with vocal differentiation in additional species of Neotropical suboscine birds; support the importance of Amazonian rivers in creating conditions that result in the differentiation of independent evolutionary lineages; and demonstrate that species richness in two of the lineages studied (M. longipennis and M. menetriesii) was previously underestimated.

Passeriformes↗
PubMed2025

Phylogenomics Unveils the Complex Evolution of Retroviruses in Birds.

The rise of birds represents one of the major evolutionary transitions in the history of life. Yet, much remains obscure about the origins and diversification of viruses in birds. Endogenous retroviruses (ERVs), relics of past retroviral infections, provide molecular fossils for interrogating the evolution and ecology of retroviruses. Here, we perform phylogenomic mining of ERVs within the genomes of 758 bird species and identify more than 470,000 ERVs, revealing a highly diverse and complex retrovirus repertoire in birds. These ERVs greatly expand the diversity of retroviruses in birds, indicating that exogenous retroviruses characterized in birds to date are highly underestimated. The evolution of retroviruses in birds is shaped by both coevolution and cross-species transmission. Tens of retrovirus lineages originated during the early evolution of birds, four of which contribute to more than 90% of complete ERVs in birds. We also observe recent ERV activity across the bird phylogeny (particularly in Passeriformes). Moreover, we find that ERVs can mediate genome rearrangements, potentially facilitating the genome evolution of birds. Many bird retroviruses recruited genes of cellular provenience, which might drive the evolution of the genome complexity of retroviruses. Together, these results unveil a diverse and complex retrovirosphere in birds and provide insights into the intricate evolution of retrovirus-bird interaction.

Animals↗
PubMed1977

Host feeding patterns of Connecticut mosquitoes (Diptera: Culicidae).

Blood-engorged Coquillettidia perturbans, Psorophora ferox, Culex, Culiseta, and Aedes mosquitoes were collected principally by sweep net from salt marsh and woodland habitats in Connecticut. Of the 570 mosquitoes tested, precipitin tests identified the origins of 517 blood meals and revealed distinct host feeding patterns. Aedes mosquitoes fed chiefly on mammals; A. abserratus, A. cantator, and A. vexans showed selectivity for cattle and (or) horses. A. cantator also obtained blood from avian hosts and, in some instances, showed mixed passerine-mammal blood meals. These findings increase the vector potential of this salt marsh mosquito for eastern equine encephalomyelitis virus. Feedings on deer by A. abserratus suggest potential involvement of this mosquito in the transmission of certain subtypes of California encephalitis. Culex-pipiens, C. restuans, Culiseta melanura, and Cs. morsitans dyari acquired blood almost exclusively from passeriform birds.

Aedes↗
PubMed2025

First surveillance study of avian orthoavulavirus type 1 in wild birds in Morocco: Insights and implications for future monitoring.

BACKGROUND: Wild birds, particularly migratory species, can act as natural reservoirs and vectors of avian orthoavulavirus type 1 (AOAV-1) or Newcastle disease virus (NDV), contributing to its spread across regions and potentially threatening domestic poultry populations. AOAV-1, also known as NDV, is a major pathogen affecting avian species and poses a global threat to poultry production. It belongs to the Paramyxoviridae family and is an RNA virus encoding six key proteins, including the fusion (F) protein, which determines pathogenicity. AOAV-1 is classified into three pathotypes based on virulence: velogenic (highly pathogenic), mesogenic (moderately pathogenic), and lentogenic (mild or asymptomatic). In Morocco, AOAV-1 is endemic in poultry production systems, as evidenced by recent studies reporting a 52.1% seroprevalence and active viral RNA detection in backyard chickens in the Khemisset and Skhirat-Temara provinces; however, effective vaccination strategies have contributed to controlling the clinical signs and widespread dissemination of the virus. AIM: The main objective of this study was to investigate the presence of AOAV-1 in wild bird populations across Morocco, providing insights into possible transmission of infection affecting domestic poultry. METHODS: From November 2016 to April 2022, a total of 1984 samples were collected from 840 individual birds, encompassing 79 species, 25 families, and 12 orders. The majority of the samples belonged to Charadriiformes, Anseriformes, Pelecaniformes, and Passeriformes. Sampling was conducted at 17 wetlands and six additional locations throughout Morocco. Viral detection was performed using real-time reverse transcriptase PCR (RT-qPCR) targeting Matrix (M) and RNA polymerase (L) genes to confirm the presence of AOAV-1. RESULTS: Although the study spanned 6 years and included a large number of samples from bird orders considered primary AOAV-1 reservoirs, all samples tested negative for NDV RNA using both M and L gene targets. CONCLUSION: This study represents the first effort in Morocco to monitor wild birds for AOAV-1. The samples analyzed were initially collected for avian influenza surveillance, which shares epidemiological similarities with Newcastle's disease. However, to improve future surveillance efforts, sample collection should be optimized to target scenarios with the highest probability of virus detection.

Animals↗
PubMed2025

Exploring the associations between preen oil bacterial, chemical and proteomic profiles of passerines.

Preen gland bacteria are thought to be the key producers of preen oil components such as chemosignalling molecules including volatile organic compounds (VOCs) and antimicrobial compounds including peptides and antimicrobial VOCs. However, data on the preen oil bacteriome and chemical composition are limited to a small subset of bird species, and the presence of antimicrobial peptides is largely unexplored. Here, we performed an exploratory study to characterize, for the first time, the preen oil chemical and proteomic profiles and to explore the possible contribution of the bacteriome to the production of preen oil VOCs and antimicrobial peptides (bacteriocins) in eight passerine species, each represented by a single individual. Preen oil bacteriome, chemical and proteomic profiles varied among birds. The bacterial profiles were dominated by the genera Streptococcus, Lactococcus, Corynebacterium and Cutibacterium. The chemical profiles mainly consisted of alcohols, ketones and carboxylic acids. The biological functions primarily associated with the proteomic profiles were proteolysis and response to oxidative stress. Although we were unable to explore a direct association between the bacteriome and chemical profiles, the preen oil contained bacteriocin- and VOC-producing bacterial genera capable of producing detected microbially-derived VOCs (mVOCs), the relative abundance of which varied between birds. Riparian species showed the highest chemical diversity and high abundances of putative preen oil mVOC-producing bacteria, which could suggest habitat-specific adaptations. This exploratory study may significantly contribute to the formulation of hypotheses on the potential role of host ecological factors in the variation of preen oil bacterial, chemical and proteomic profiles in passerines.

Animals↗
PubMed2026

Accounting for recombination rate variation improves inference of barrier loci and reveals the role of both natural and sexual selection in an incipient bird radiation.

Examining genomic patterns of differentiation across lineage pairs at different stages of the speciation continuum, in combination with recombination maps, can help disentangle the effects of linked and divergent selection and identify lineage-specific targets of selection that may act as barrier loci during speciation. Here, we apply this framework to genomic data from African and Indian Ocean bird species of the genus Zosterops (Zosteropidae) to identify candidate barrier loci between ecologically, phenotypically, and genetically distinct Reunion gray white-eye (Zosterops borbonicus) parapatric geographic forms. Using analyses that account for recombination rate variation, we show that putative targets of divergent selection are primarily located on the Z chromosome, except in comparisons between geographic forms that differ in their ecologies. Functional annotation revealed that candidate barrier loci between forms with similar environmental niches are associated with genes involved in song formation and immune function, whereas those between forms with different environmental niches are associated with adaptation to altitude, morphology, and song behavior. Our results highlight the combined roles of natural and sexual selection in the evolution of reproductive barriers in this incipient species radiation.

Animals↗
PubMed2025

Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.

Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.

Animals↗
PubMed2026

Cooperative care influences genome-wide levels of DNA methylation in nestling chestnut-crowned babblers.

Carers in cooperatively breeding vertebrates increase food acquisition for offspring; however, they also impact the developmental social environment. One means of linking early-life environments, such as nutrition and social structure, with later-life phenotypes is DNA methylation. Here, using whole-genome methylation sequencing, we measured how additional carers influence DNA methylation in nestlings of the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps). A comparison of nestlings raised by their parents (two carers) and those raised by parents plus additional helpers ('three plus' carers; mean = 4.3 ± 1.4 s.d.) revealed that additional care is associated with genome-wide differences in DNA methylation. Overall, 570 cytosine-phosphate-guanine sites from the regulatory regions of 487 genes were differentially methylated, with 85% being more methylated in nestlings reared by groups. Specifially, sites associated with genes that are integral for metabolism, growth, the regulation and promotion of sociality, the ability to cope with stressors, and cell communication were differentially methylated between the groups. Furthermore, gene ontology-term analysis revealed that differentially methylated sites were over-represented in multiple pathways, including those important for protein binding, metabolism and cell-to-cell and environment-to-cell communication. Our results suggest that the effects of being reared by groups as opposed to pairs in cooperative breeders can extend beyond those typically attributed to nutritional benefits and that these effects are molecularly mediated. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.

Animals↗
PubMed2025

Two-Step Loss of GLUTs in the High-Metabolism Passerines.

Glucose transporters (GLUTs) play vital roles in cellular metabolism. Understanding their evolutionary dynamics in birds is essential for elucidating avian physiology and adaptation. However, the choice of gene detection method in gene family analysis may affect the conclusion. Here, we present a comprehensive investigation of methodologies and GLUT gene loss events in avian lineages, focusing on the loss of GLUT4 and GLUT8. To illustrate the effects of these methods, we first employed BUSCO-based homolog identification, calculated pairwise evolutionary distances between different species, and performed separate blastn and blastp searches to identify homologs in two groups of animals. Our analyses revealed a significant decline in blastn accuracy with increasing evolutionary distance, represented by relative divergence times. Through a more robust blastp-based gene detection pipeline, we provide evidence for the loss of GLUT genes in birds based on 58 vertebrate genomes, including 47 bird species. Our results support the reported early loss of GLUT4 in Aves. We also newly emphasize the absence of GLUT8 in passerines, potentially due to adaptation to high-sugar diets in their ancestors. These findings enhance our knowledge of avian metabolism and the evolution of GLUT genes.

Animals↗
PubMed2024

Repeated evolution on oceanic islands: comparative genomics reveals species-specific processes in birds.

Understanding the interplay between genetic drift, natural selection, gene flow, and demographic history in driving phenotypic and genomic differentiation of insular populations can help us gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study repeated evolution and identify shared patterns in their genomic landscapes of differentiation. We selected four species of passerine birds (Common Chaffinch Fringilla coelebs/canariensis, Red-billed Chough Pyrrhocorax pyrrhocorax, House Finch  Haemorhous mexicanus and Dark-eyed/island Junco Junco hyemalis/insularis) that have both mainland and insular populations. Changes in body size between island and mainland populations were consistent with the island rule. For each species, we sequenced whole genomes from mainland and insular individuals to infer their demographic history, characterize their genomic differentiation, and identify the factors shaping them. We estimated the relative (Fst) and absolute (dxy) differentiation, nucleotide diversity (π), Tajima's D, gene density and recombination rate. We also searched for selective sweeps and chromosomal inversions along the genome. All species shared a marked reduction in effective population size (Ne) upon island colonization. We found diverse patterns of differentiated genomic regions relative to the genome average in all four species, suggesting the role of selection in island-mainland differentiation, yet the lack of congruence in the location of these regions indicates that each species evolved differently in insular environments. Our results suggest that the genomic mechanisms involved in the divergence upon island colonization-such as chromosomal inversions, and historical factors like recurrent selection-differ in each species, despite the highly conserved structure of avian genomes and the similar selective factors involved. These differences are likely influenced by factors such as genetic drift, the polygenic nature of fitness traits and the action of case-specific selective pressures.

Animals↗