Biology subjects

Carneiro, M.

Publications and source records attributed to Carneiro, M..

12 recordsLinked to original sources

bioRxiv2026

ARTIFICIAL SELECTION DIVERSIFIES BIRDSONG THROUGH POLYGENIC CHANGES ACROSS SENSORY AND MOTOR SYSTEMS

Vocal learning, or the ability to acquire and produce contextualized sounds through social interaction, underlies human speech yet has evolved in a few animal lineages, including songbirds. In songbirds, learned song is produced by a dedicated neural circuit and depends on auditory feedback for its acquisition and maintenance. Roughly four centuries of artificial selection on the domestic canary (Serinus canaria) have produced song breeds whose vocalizations diverge as much as those of distinct species, offering a rare intraspecific system in which to identify the genetic and neural changes underlying vocal divergence. Here we show that selection for song reshaped the canary song control system. Compared with breeds selected for plumage or body form, song breeds show increased neural progenitor proliferation and breed-specific changes in neuronal recruitment, sensorimotor brain region volume, and auditory sensitivity. Genome-wide analyses reveal a polygenic architecture underlying song divergence, enriched for transcriptional regulation and synaptic transmission genes. Among these, we find a coding variant in ADGRV1, the gene mutated in human Usher syndrome type 2C, associated with low-frequency singing and elevated auditory thresholds in canary. Disrupting ADGRV1 in zebrafish alters hair cell dynamics, linking adgrv1 mutation to a peripheral sensory mechanism. These findings demonstrate that learned vocal behavior can diversify rapidly through changes spanning sensory, neurogenic, and motor systems, with hearing itself as a substrate for selection.

evolutionary biology↗

bioRxiv2026

The genome sequence of Pavonine herpesvirus 1, a novel Mardivirus infecting peafowl

Avian alphaherpesviruses of the genus Mardivirus include several economically important pathogens, such as the tumour-causing Mareks disease virus (MDV-1) of chickens. However, the diversity of related viruses in wild and non-model avian hosts remains poorly characterised. Here, we describe the genome of Pavonine herpesvirus 1 (PaHv1), a novel Mardivirus infecting peafowl (Pavo spp.). Through de novo assembly of reads generated from whole-genome sequencing of 370 captive peafowl, we generated a single viral genomic scaffold of 134,149 bp in length and an estimated total genome size of [~]146 kbp following reconstruction of terminal repeat regions. PaHv1 exhibits canonical Mardivirus UL-IRL-IRS-US genomic architecture and encodes 169 open reading frames, of which 82 have clear orthologs in other Mardivirus species. Comparative genomic analyses revealed strong syntenic concordance between PaHv1, MDV-1, MDV-2 and Meleagrid alphaherpesvirus 1 (HVT), but with notable absences of the Meq oncogene, viral interleukin-8 (vIL8), and a truncated pp38 gene - genes known to underpin oncogenicity and virulence in MDV-1. Phylogenetic analysis places PaHv1 firmly within the Mardivirus genus as a sister to the poultry-associated MDV-1 and MDV-2 viruses, but distinct from a previously described Phasianid herpesvirus with a partial DNA terminase sequence. PaHv1 was detected predominantly in feather-derived samples, consistent with replication or persistence in the feather follicle epithelium. Taken together, these findings identify PaHv1 as a novel, likely non-oncogenic Mardivirus, expanding our understanding of herpesvirus diversity, evolution and host association in galliform birds. ImportanceHerpesviruses cause several economically important diseases in domesticated birds, including Mareks disease, duck plague and infectious laryngotracheitis. Despite this, our understanding of herpesviruses infecting wild and semi-wild birds remains limited. Here, we present the genome of Pavonine herpesvirus 1 (PaHv1), a virus in the Mardivirus genus which infects peafowl. Based on comparative genomics with other Mardivirus species, we note the absence of several genes important for the high virulence of Mareks Disease Virus, such as the Meq oncogene, viral interleukin-8 and a truncated pp38. This, taken together with absence of clinical disease in preliminary observations, suggests that PaHv1 causes either a subclinical infection or one with mild symptoms. Our work expands the known evolutionary breadth of avian herpesviruses in the Mardivirus genus. In addition, PaHv1 may provide a useful starting point for the development of novel vaccine vectors for pathogenic herpesvirus infections.

genomics↗

bioRxiv2026

Modulation of Avian Iridescence via Malanogenesis

The iridescent colors of birds originate in nanoscale feather structures that interact with light. Although the physical principles governing avian iridescence are well-established, the molecular mechanisms assembling these nanostructures into photonic materials remain unknown. Here, we integrated genomic, cellular, and optical approaches to investigate the molecular basis of iridescent color formation in birds. We leveraged mutations that arose in the domesticated Indian peafowl and natural color variation in wild birds. In peafowl, we identified eight genes underlying gains, losses, and shifts of iridescence, whereas in two wild species, we used single-cell transcriptomics to profile asymmetric feathers in which iridescent and non-iridescent barbules develop on opposite sides of the same feather. We found that all peafowl mutations mapped to melanogenesis genes, showing that variation in this pathway can modify diverse geometric features of feather photonic nanostructures. Mutations altering melanin composition collapsed multilayered photonic systems and yielded non-iridescent tissues, whereas changes in melanosome abundance, elongation, or deposition timing generated multilayer architectures with variable periodicity and color. We further show in peafowl that transitions from non-iridescent to iridescent plumage were associated with single-nucleotide mutations in a melanogenesis gene, suggesting that, in species already capable of forming multilayered nanostructures, iridescence can be gained by relatively small genetic changes. Single-cell transcriptomes from wild species also supported extensive melanocyte-centered regulatory rewiring associated with iridescence, including changes in melanosome maturation, trafficking, and intercellular signaling. Together, these results show that the nanoscale order underlying iridescence is developmentally plastic and highly responsive to the melanogenic environment. Significance StatementBird feathers can produce brilliant, shifting colors, but how these colors form during development has remained poorly understood. By comparing the genomes of color variants of domesticated peafowl and transcriptomes during feather development in wild birds, and combining these with chemical and optical analyses, we show that mutations in genes associated with melanogenesis can profoundly alter the amount, shape, and arrangement of the melanin granules inside feathers that interact with light and produce iridescence. These changes can switch feather appearance between dull and iridescent, or generate entirely new colors by restructuring how those granules are layered at the microscopic scale. Our results reveal a direct and flexible link between pigment production and the physical structures that generate iridescence in birds.

evolutionary biology↗

bioRxiv2025

MHC-I diversity enables rapid adaptation during viral pandemic in wild rabbit populations

Emerging diseases can have devastating consequences for wild species, with long-term effects depending on the ability of the host to evolve resistance. Here, we show that major histocompatibility complex (MHC) genes provided standing genetic variation that enabled rabbits to mount a rapid evolutionary response to the myxoma virus pandemic that began in the 1950s. Using historical and modern specimens starting in 1865 and spanning the pandemic, we found strong parallel shifts in MHC-I allele frequencies across Australia, Britain and France, alongside population-specific signals. These evolutionary shifts appear to have altered antigen presentation to T cells. Our results provide evidence that MHC-I is under strong selection in natural populations during a pandemic, and that the high polymorphism of MHC may have contributed to the evolutionary rescue of these populations.

evolutionary biology↗

bioRxiv2025

Sexual signal reliability in male zebra finches: Food intake explains the impact of immune activation on carotenoid-based coloration

Theory predicts that traits evolving as animal signals must transmit reliable information about the bearers quality. Two hypotheses are often invoked to explain how carotenoid-based colorations function as reliable individual quality signals. The first hypothesis suggests that carotenoid allocation trade-offs between signaling and survival-related functions maintain signal reliability. Only high-quality individuals could resolve these trade-offs without incurring a fitness loss. Such signals are plastic, and the signaler can strategically manage their expression level to increase fitness returns. The second hypothesis posits that certain carotenoid-based signals are strongly constrained in their expression, not allowing strategic manipulations or cheating. We challenged captive male zebra finches (Taeniopygia guttata) with simulated infections by injecting lipopolysaccharides (LPS) derived from Escherichia coli and assessed organ masses, body temperature, and carotenoid levels in several tissues. Compared to controls, LPS-treated birds reduced the bill redness, a sexual signal. However, this reduction was largely explained by decreased food intake caused by LPS. Bill redness negatively correlated with body temperature and spleen mass but positively correlated with blood, spleen and subcutaneous fat carotenoid levels. Overall, our findings suggest that carotenoid-based bill coloration predominantly reflects the recent physiological condition of individuals and resource allocation trade-offs rather than directly signaling individual quality.

evolutionary biology↗

bioRxiv2025

Inversions Dominate Evolution in the Highly Admixed European Sardine (Sardina pilchardus)

Inversions can play key roles in the genetic architecture of adaptation, but the scale of their effects across different species remains poorly understood. Here, we use whole- genome sequencing to investigate the influence of inversions on the population genomics of the r-selected European sardine (Sardina pilchardus). Allele frequency differences from millions of SNPs across 34 populations spanning the species range were analyzed. Genomic scans identified several extreme outlier regions overlapping chromosome-scale inversions, collectively representing over half the genome. Our findings suggest these inversions are associated with locally adapted life history strategies. First, SNPs within outlier regions containing inversions exhibited striking allele frequency differences between Atlantic and Mediterranean sardines, which differ in key adaptive life history traits. In the Atlantic, inversion allele frequencies varied latitudinally, while in the Mediterranean, they shifted longitudinally, aligning with temperature and oceanographic features that influence sardine life history strategies. Moreover, adjacent populations in contrasting environments displayed pronounced allele frequency differences in inversions. These spatial patterns of allele frequencies sharply contrasted with those based on neutral loci, indicating they are driven by selection. After rigorously filtering SNPs affected by selection and inversions, sardine populations showed high admixture across their range but significant population structure and isolation by distance, especially in the Mediterranean. This study demonstrates that inversions can shape genome-wide patterns of genetic diversity and population structure in highly admixed r-selected marine species. These findings also offer crucial insights for stock delimitation and management of this commercially valuable species in the face of climate change.

genomics↗

bioRxiv2024

Mechanisms underlying the loss of migratory behaviour in a long-lived bird

Human-induced environmental changes are shifting the migration patterns of birds worldwide. Species are adjusting migration timings, shortening and diversifying migratory routes, or even completely disrupting migration and transitioning towards residency. Whilst the ultimate causes driving changes in migratory patterns are well established, the underlying mechanisms by which migratory species adapt to environmental change remain unclear. Here, we studied the mechanisms driving the recent and rapid loss of migratory behaviour in Iberian white storks Ciconia ciconia, a long-lived and previously fully migratory species through the African-Eurasian flyway. We combined 25 years of census data, GPS-tracking data from 213 individuals (80 adults and 133 first-year juveniles) followed for multiple years, and whole-genome sequencing, to disentangle whether within- (phenotypic flexibility) or between- (developmental plasticity or microevolution, through selection) individual shifts in migratory behaviour over time can explain the observed population-level changes towards residency. Between 1995 and 2020, the proportion of individuals no longer migrating and remaining in Southern Europe year-round increased dramatically, from 18% to 68-83%. We demonstrate that this behavioural shift is likely explained by developmental plasticity. Within first-year birds, 98% crossed the Strait of Gibraltar towards their African wintering grounds, in Morocco or Sub-Saharan Africa. However, the majority shifted towards a non-migratory strategy as they aged - the proportion of migrants decreased to 67% and 33%, on their second and third year of life, respectively - suggesting that migratory behaviour is determined during ontogeny. Supporting these findings, only 19% of GPS-tracked adults migrated. Moreover, we did not find evidence of phenotypic flexibility, as adults were highly consistent in migratory behaviour over multiple years (only 3 individuals changed strategy between years, out of 113 yearly transitions), nor of selection acting on genetic variation, since genomes of migrants and residents are essentially undifferentiated. Our results suggest that through developmental plasticity, traits that are plastic during specific windows of development, become fixed during adulthood. Thus, inter-generational shifts in the frequency of migratory and non-migratory young individuals could drive population changes in migratory behaviour. This can provide a fast mechanism for long-lived migratory birds to respond to rapid human-driven environmental changes.

evolutionary biology↗

bioRxiv2023

Mutation in SLC45A2 leads to loss of melanin in parrot feathers

Bird plumage coloration is a complex and multi-factorial process that involves both genetic and environmental factors. Diverse pigment groups contribute to plumage variation in different birds. In parrots, the predominant green color results from the combination of two different primary colors-yellow and blue. Psittacofulvin, a pigment uniquely found in parrots, is responsible for the yellow coloration, while blue is suggested to be the result of light scattering by feather nanostructures and melanin granules. So far, genetic control of melanin-mediated blue coloration has been elusive. In this study, we demonstrated that feather from the yellow mutant rose-ringed parakeet displays loss of melanosome granules in spongy layer of feather barb. Using whole genome sequencing, we found that mutation in SLC45A2, an important solute carrier protein in melanin synthetic pathway, is responsible for the sex-linked yellow phenotype in rose-ringed parakeet. Intriguingly, one of the mutations, P53L found in yellow P. krameri is already reported as P58A/S in the human albinism database, known to be associated with human OCA4. We further showed that mutations in SLC45A2 gene affect melanin production also in other members of Psittaculidae family such as alexandrine, and plum-headed parakeets. Additionally, we demonstrate that the mutations associated with the sex-linked yellow phenotype, localized within the transmembrane domains of the SLC45A2 protein, affect the protein localization pattern. This is the first evidence of plumage color variation involving SLC45A2 in parrots and confirmation of associated mutations in the transmembrane domains of the protein that affect its localization. Article SummaryThe vibrant green tone of parrot plumage emerges from a blend of yellow and blue. While yellow comes from a unique pigment psittacofulvin, the genetics of blue structural color has puzzled scientists. Through novel genetic study, here we identified mutations in SLC45A2 gene, causing loss of melanin in feathers that contributes to the blue structural color. This insight opens a new chapter in understanding avian coloration and the complex interplay of feather microstructure and genetics in natures palette.

developmental biology↗

bioRxiv2021

Evidence of post-domestication hybridization and adaptive introgression in Western European grapevine varieties

Grapevine (Vitis vinifera L.) is one of the most significant crops in the world. Todays richness in grapevine diversity results from a complex domestication history over multiple historical periods. Here, we employed whole genome resequencing to elucidate different aspects of the recent evolutionary history of this crop. Our results support a model in which a central domestication event in grapevine was followed by post-domestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties, which show large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by geneflow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.

plant biology↗

bioRxiv2019

Genetic Basis Of De Novo Appearance Of Carotenoid Ornamentation In Bare-Parts Of Canaries

AO_SCPCAPBSTRACTC_SCPCAPUnlike wild and domestic canaries (Serinus canaria), or any of the three dozen species of finches in genus Serinus, the domestic urucum breed of canaries exhibits bright red bills and legs. This novel bare-part coloration offers a unique opportunity to understand how leg and bill coloration evolve in birds. To identify the causative locus, we resequenced the genome of urucum canaries and performed a range of analyses to search for genotype-to-phenotype associations across the genome. We identified a nonsynonymous mutation in the gene BCO2 (beta-carotene oxygenase 2, also known as BCDO2), an enzyme involved in the cleavage and breakdown of full-length carotenoids into short apocarotenoids. Protein structural models and in vitro functional assays indicate that the urucum mutation abrogates the carotenoid cleavage activity of BCO2. Consistent with the predicted loss of carotenoid cleavage activity, urucum canaries had increased levels of full-length carotenoid pigments in bill tissue and a significant reduction in levels of carotenoid cleavage products (apocarotenoids) in retinal tissue compared to other breeds of canaries. We hypothesize that carotenoid-based bare-part coloration might be readily gained, modified, or lost through simple switches in the enzymatic activity or regulation of BCO2 and this gene may be an important mediator in the evolution of bare-part coloration among bird species.

evolutionary biology↗

bioRxiv2018

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard, which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions, near genes associated with pterin (SPR) and carotenoid metabolism (BCO2), demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been co-opted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles and haplotype analysis revealed abundant trans-specific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.

evolutionary biology↗

bioRxiv2016

A computational method for detection of structural variants using Deviant Reads and read pair Orientation: DevRO

BackgroundNext generation sequencing (NGS) technology has made it possible to perform high-resolution screens for structural variants. Computational methods for detection of structural variants utilize paired-end mapping information, depth of coverage, split reads, or some combination of such data. The available methods are particularly designed to detect structural variants in single genomes or multiple genomes in a pairwise manner. The aim of this study was to develop a bioinformatics pipeline for detection of large structural variants using multiple pooled populations.\n\nResultsHere we describe the method \"DevRO\", developed to enable identification of structural variants using short insert paired-ends and long-range mate-pairs. DevRO uses paired-end mapping information from both types of libraries for identification of inversions, deletions and duplications followed by read depth information to screen for copy number variants. DevRO can detect structural variants in multiple populations without the need for pairwise comparisons. It uses a combined approach based on (i) paired-end mapping and (ii) depth of coverage that gives power to the study as compared to traditional methods that are based on either of these. DevRO is also designed to detect deletions in the reference assembly, which is an added functionality as compared to available methods.\n\nConclusionWe report a bioinformatics pipeline \"DevRO\" for detection of structural variants using paired-end mapping and depth of coverage methods tested on sequencing reads from multiple pooled rabbit populations. This method is useful when large numbers of populations have been re-sequenced as compared to traditional methods that can detect structural variants in a pairwise manner.

bioinformatics↗