Search Results (28)

Autism spectrum disorder (ASD) encompasses a range of neurodevelopmental conditions characterized by impairments in social abilities and communication. Studying appropriate animal models can enhance our understanding of the neural mechanisms underlying these conditions, potentially leading to improved treatment and intervention strategies. Modeling impairments in linguistic development and vocal communication caused by autism had been a challenging goal for a long time. Prenatal valproic acid (VPA) treatment has been successfully used to induce ASD-like behavioral symptoms in several vertebrate species including birds. Applying VPA-treatment on songbirds, therefore, offers a promising research paradigm to model ASD. In this study, we investigated the effect of embryonic VPA treatment on song learning in the highly social zebra finch (Taeniopygia guttata). Fertilized eggs were injected with either 0.45 µmol VPA or a saline solution on day 9 of incubation, and hatchlings were allowed to stay with their parents until day 35 post-hatching to facilitate song learning from the father. Once male offsprings reached adulthood, their songs were recorded and compared to those of their fathers. VPA-exposed males exhibited significantly greater similarity to their fathers’ songs compared to control males (74% vs. 31%, respectively), suggesting a reduced ability to modify and develop their own vocal patterns as subadults. Additionally, they showed higher entropy in their songs compared to controls (−1.4 vs. −1.7), indicating more disorganized vocalizations. These findings suggest that prenatal VPA exposure disrupts typical song learning and vocal development in zebra finches, likely by affecting neural mechanisms involved in vocal learning and crystallization of the songs. Our study suggests VPA treatment in songbirds provides a useful tool to model and investigate linguistic developmental disorders related to ASD in humans. Full article

Birds are inherently social creatures that rely on pairing to enhance their well-being. Since many bird species lack obvious physical differences between females and males, sex identification is essential for ensuring their welfare. Additionally, early determination of the sexes of birds is crucial for their breeders, especially considering that most companion birds do not display clear sexual characteristics. Molecular genetic sexing has been demonstrated to be the most reliable method for determining the sexes of monomorphic birds. The objective of the present study was to demonstrate rapid, effective, and precise identification of sex in birds through quantitative real-time PCR (qPCR) using samples obtained via a minimally invasive technique (oral swabs). This qPCR method assesses variations in gene copy numbers within conserved Z-specific genes such as CHRNA6, DDX4, VPS13A, LPAR1, and TMEM161B, which are absent from the W chromosome. A total of 34 samples were included in this study from the following 17 bird species: domestic pigeon (Columba livia domestica), domestic chicken (Gallus gallus domesticus), domestic goose (Anser anser f domesticus), domestic duck (Anas platyrhynchos domesticus), Mute swan (Cygnus olor), Budgerigar (Melopsittacus undulatus), Lovebird (Agapornis roseicollis), Cockatiel (Nymphicus hollandicus), Red-rumped parrot (Psephotus haematonotus), Rose-ringed parakeet (Psittacula krameri), African grey parrot (Psittacus erithacus), domestic Canary (Serinus canaria forma domestica), Goldfinch (Carduelis carduelis major), Gouldian Finch (Chloebia gouldiae), Red Siskin (Carduelis cucullata), Australian Zebra Finch (Taeniopygia castanotis), and Common buzzard (Buteo buteo). The results proved that the CHRNA6, DDX4, VPS13A, LPAR1, and TMEM161B genes can reveal the sexes in the Neognath birds tested. Full article

Background/Objectives: Transcriptome assembly and functional annotation are essential in understanding gene expression and biological function. Nevertheless, many existing pipelines lack the flexibility to integrate both short- and long-read sequencing data or fail to provide a complete, customizable workflow for transcriptome analysis, particularly for non-model organisms. Methods: We present TrAnnoScope, a transcriptome analysis pipeline designed to process Illumina short-read and PacBio long-read data. The pipeline provides a complete, customizable workflow to generate high-quality, full-length (FL) transcripts with broad functional annotation. Its modular design allows users to adapt specific analysis steps for other sequencing platforms or data types. The pipeline encompasses steps from quality control to functional annotation, employing tools and established databases such as SwissProt, Pfam, Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and Eukaryotic Orthologous Groups (KOG). As a case study, TrAnnoScope was applied to RNA-Seq and Iso-Seq data from zebra finch brain, ovary, and testis tissue. Results: The zebra finch transcriptome generated by TrAnnoScope from the brain, ovary, and testis tissue demonstrated strong alignment with the reference genome (99.63%), and it was found that 93.95% of the matched protein sequences in the zebra finch proteome were captured as nearly complete. Functional annotation provided matches to known protein databases and assigned relevant functional terms to the majority of the transcripts. Conclusions: TrAnnoScope successfully integrates short and long sequencing technologies to generate transcriptomes with minimal user input. Its modularity and ease of use make it a valuable tool for researchers analyzing complex datasets, particularly for non-model organisms. Full article

Heat shock proteins (HSPs) are essential to cellular protection against heat stress. However, the causes of inter-individual variation in HSP regulation remain unclear. This study aimed to test the impact of early-life conditions on the HSP response to heat in zebra finches. In this arid-adapted bird, incubating parents emit “heat-calls” at high temperatures, which adaptively alter offspring’s phenotypes. Embryos were exposed to heat-calls or control-calls, and at 13 days post-hatch nestlings were separated into two different experiments to test responses to either chronic nest temperature (“in-nest” experiment) or an acute “heat-challenge”. Blood samples were collected to measure levels of heat shock cognate 70, heat shock protein 90α, corticosterone and the heterophil-to-lymphocyte (H/L) ratio. In the in-nest experiment, both HSPs were upregulated in response to increasing nest temperatures only in control-calls nestlings (HSC70: p = 0.010, HSP90α: p = 0.050), which also had a marginally higher H/L ratio overall than heat-call birds (p = 0.066). These results point to a higher heat sensitivity in control-call nestlings. Furthermore, comparing across experiments, only the H/L ratio differed, being higher in heat-challenged than in in-nest nestlings (p = 0.009). Overall, this study shows for the first time that a prenatal acoustic signal of heat affects the nestling HSP response to postnatal temperature. Full article

Among eukaryotes, there are many examples of partial genome elimination during ontogenesis. A striking example of this phenomenon is the loss of entire avian chromosomes during meiosis, called a germline-restricted chromosome (GRC). The GRC is absent in somatic tissues but present in germ cells. It has been established that a prophase I male GRC is usually represented by a univalent surrounded by heterochromatin. In the present study, an immunocytochemical analysis of zebra finch spermatocytes was performed to focus on some details of this chromosome’s organization. For the first time, it was shown that a prophase I GRC contains the HORMAD1 protein, which participates in the formation of a full axial element. This GRC axial element has signs of a delay of core protein loading, probably owing to peculiarities of meiotic silencing of chromatin. The presence of repressive marks (H3K9me3 and H3K27me3) and the lack of RNA polymerase II, typically associated with active transcription, indicate transcriptional inactivation in the GRC body, despite the known activity of some genes of the GRC. Nevertheless, RPA and RAD51 proteins were found at some GRC sites, indicating the formation and repair of double-strand breaks on this chromosome. Our results provide new insights into the meiotic behavior and structure of a GRC. Full article

The environmental risk assessment (ERA) of plant protection products (PPPs) is commonly conducted for a number of standard laboratory species, though its scope includes all species, especially those that are vulnerable or endangered. This begs the question of how the eco-physiological and life history traits of those data-rich species compare to those of less documented species. This paper investigates the utility of a database of such traits, the Add-my-Pet collection of Dynamic Energy Budget theory, for the ERA of North American birds. We identified 72 bird species in the collection that have a federal listing status or are otherwise of interest for the ERA of PPPs and compared their eco-physiological and life history traits in relation to body size, feeding guild, and taxonomic identity to those of 446 terrestrial Holarctic birds, as well as those of standard lab species, notably the northern bobwhite, mallard, and zebra finch. The properties of standard lab species generally align with those of a similar taxonomy and size, with the notable exception of the relatively high reproductive capacity of the northern bobwhite and mallard due to the unique properties of laboratory study data. In addition, taxonomy appears to be a better predictor of eco-physiological traits than feeding guild. We conclude that, to identify representative species for the ERA of PPPs, more traits need to be included, such as those directly linked to the likelihood of exposure and those related to reproductive behavior. Full article

The role of chemical communication in the social relationships of birds is receiving growing attention, but our knowledge is still scarce compared to that of other taxa. Previous evidence suggests that chemical cues emitted by birds may carry information about their characteristics, which may be useful in the context of sexual selection. However, experimental studies are needed to investigate the role of bird chemical cues in signalling the quality of potential partners. We performed an experimental study aimed at disentangling whether the female Zebra Finches (Taeniopygia guttata), use chemical cues to assess the body condition of potential partners. We offered focal females (N = 28) the scent of two males differing in body condition (body mass/tarsus length ratio) (N = 28 scent donor males). Our results showed that females can assess the body condition of potential partners using olfaction. However, contrary to what should be expected in a mate choice context, females avoided the scent of males with greater body condition. Our results, therefore, suggest that, despite performing the study during the breeding period, social interactions may be mediating the avoidance of the scent of the male in better condition in this gregarious species, probably to avoid a conspecific competitor with better body condition. Full article

Zebra finches are a model animal used in the study of audition. They are adept at recognizing zebra finch songs, and the neural pathway involved in song recognition is well studied. Here, this example is used to illustrate the estimation of mutual information between stimuli and responses using a Kozachenko–Leonenko estimator. The challenge in calculating mutual information for spike trains is that there are no obvious coordinates for the data. The Kozachenko–Leonenko estimator does not require coordinates; it relies only on the distance between data points. In the case of bird songs, estimating the mutual information demonstrates that the information content of spiking does not diminish as the song progresses. Full article

Passeriformes birds are widely recognized for their remarkable diversity, with over 5700 species described so far. Like most bird species, they possess a karyotype characteristic of modern birds, which includes a bimodal karyotype consisting of a few pairs of macrochromosomes and many pairs of microchromosomes. Although the karyotype is typically 2n = 80, the diploid number can atypically vary greatly, ranging from 56 to approximately 100 chromosomes. In this study, we aimed to understand the extent of conservation of the karyotype’s organizational structure within four species of this group using Bacterial Artificial Chromosomes via Fluorescence In Situ Hybridization (BAC-FISH) with microchromosome probes from Chicken (Gallus gallus) or Zebra Finch (Taeniopygia guttata) per microchromosomes (GGA10-28, except GGA16). By examining the chromosome complement of four passerine species—the Streaked Flycatcher (Myiodynastes maculatus), Shiny Cowbird (Molothrus bonariensis), Southern House Wren (Troglodytes aedon), and Double-collared Seedeater (Sporophila caerulescens)—we discovered a new chromosome number for Southern House Wren. Through FISH experiments, we were able to observe the same pattern of microchromosome organization as in the common ancestor of birds. As a result, we propose a new diploid number for Southern House Wren and confirm the conservation status of microchromosome organization, which may confer evolutionary advantages to this group. Full article

Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome-level genome assemblies cannot be made from long-extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro- and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species. The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft-shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine–Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes. Full article

We evaluate if the iconic Australian Zebra Finch (Taeniopygia guttata) has a unique physiology or if its metabolic, thermal and hygric physiology are similar to other Australian poephiline finches, by comparing it with three other species, the arid-habitat Painted Finch (Emblema pictum) and the mesic-habitat Double-barred (Taeniopygia bichenovii) and Red-browed (Neochmia temporalis) Finches. All physiological variables responded to ambient temperature as expected. There were no species differences for any of the standard physiological variables, consistent with the hypotheses that birds are pre-adapted to arid habitats, the recent development of Australian deserts has limited opportunity for physiological adaptation, and all four species share similar behavioural and ecological traits. Nevertheless, the ambient temperature where metabolic water production equals evaporative water loss (point of relative water economy) was highest for the Zebra (19.1 °C), lower for Double-barred (16.4 °C) and Painted (15.2 °C) and lowest for Red-Browed (4.1 °C) Finches, corresponding with their general patterns of habitat aridity. The point of relative water economy may be a sensitive index for assessing a species’ tolerance of aridity because it integrates individual physiological variables. We conclude that the Zebra Finch is not a physiological outlier amongst Australian finches, but is at the end of a continuum of aridity tolerance for the four study species. Full article

(1) Background: The objective of this study was to uncover genomic causes of parental care. Since birds do not lactate and, therefore, do not show the gene expressional changes required for lactation, we investigate gene expression associated with parenting in caring and non-caring females in an avian species, the small passerine bird zebra finch (Taeniopygia guttata). Here, we compare expression patterns in the hypothalamic–septal region since, previously, we showed that this area is activated in parenting females. (2) Methods: Transcriptome sequencing was first applied in a dissected part of the zebra finch brain related to taking care of the nestlings as compared to a control group of social pairs without nestlings. (3) Results: We found genes differentially expressed between caring and non-caring females. When introducing a log2fold change threshold of 1.5, 13 annotated genes were significantly upregulated in breeding pairs, while 39 annotated genes were downregulated. Significant enrichments of dopamine and acetylcholine biosynthetic processes were identified among upregulated pathways, while pro-opiomelanocortin and thyroid hormone pathways were downregulated, suggesting the importance of these systems in parental care. Network analysis further suggested neuro-immunological changes in mothers. (4) Conclusions: The results confirm the roles of several hypothesized major pathways in parental care, whereas novel pathways are also proposed. Full article

An increase in artificial night lighting has blurred the boundaries of day and night and transformed the natural day-night environment with alteration in the temporal niche of the animals. Male zebra finches were exposed to a dim light at night (dLAN) protocol (Light: dLAN, 12L = 200 lux: 12dLAN = 5 lux) with controls on darkness at night (Light: dark, 12L = 200 lux: 12D = 0 lux) for six weeks. We assayed sleep-wake, daily behaviors, mood, and cognition, as well as changes in physiological parameters. Dim light at night increased sleep frequency, delayed sleep onset, advanced awakening latency, and caused a reduction in total sleep duration. dLAN birds did not associate (physical association) with novel object and birds spent significantly lesser time on perch with novel object as compared to LD. In colour learning task, night illuminated birds took more time to learn and made more error, compared to LD. dLAN significantly altered the 24-h daily behavioral rhythm (amplitude and acrophase) of feeding, drinking, preening, and perch-hopping behavior. In particular, birds extended their feeding hours in the nighttime under dLAN, with no difference in total food intake. Birds under dLAN increased fattening and hence significantly increased body mass. Our results show that dim light at night altered feeding rhythm, caused decrease in sleep behavior, and negatively affected learning and memory performance in male zebra finches. Full article

Comparative chromosome maps investigating sex chromosomal linkage groups in amniotes and microsatellite repeat motifs of a male house gecko lizard (Hemidactylus frenatus, HFR) and a flat-tailed house gecko lizard (H. platyurus, HPL) of unknown sex were examined using 75 bacterial artificial chromosomes (BACs) from chicken and zebra finch genomes. No massive accumulations of microsatellite repeat motifs were found in either of the gecko lizards, but 10 out of 13 BACs mapped on HPL chromosomes were associated with other amniote sex chromosomes. Hybridization of the same BACs onto multiple different chromosome pairs suggested transitions to sex chromosomes across amniotes. No BAC hybridization signals were found on HFR chromosomes. However, HFR diverged from HPL about 30 million years ago, possibly due to intrachromosomal rearrangements occurring in the HFR lineage. By contrast, heterochromatin likely reshuffled patterns between HPL and HFR, as observed from C-positive heterochromatin distribution. Six out of ten BACs showed partial homology with squamate reptile chromosome 2 (SR2) and snake Z and/or W sex chromosomes. The gecko lizard showed shared unrelated sex chromosomal linkages—the remnants of a super-sex chromosome. A large ancestral super-sex chromosome showed a correlation between SR2 and snake W sex chromosomes. Full article

Birdsong is a precisely timed animal behavior. The connectivity of song premotor neural networks has been proposed to underlie the temporal patterns of neuronal activity that control vocal muscle movements during singing. Although the connectivity of premotor nuclei via chemical synapses has been characterized, electrical synapses and their molecular identity remain unexplored. We show with in situ hybridizations that GJD2 mRNA, coding for the major channel-forming electrical synapse protein in mammals, connexin 36, is expressed in the two nuclei that control song production, HVC and RA from canaries and zebra finches. In canaries’ HVC, GJD2 mRNA is extensively expressed in GABAergic and only a fraction of glutamatergic cells. By contrast, in RA, GJD2 mRNA expression is widespread in glutamatergic and GABAergic neurons. Remarkably, GJD2 expression is similar in song nuclei and their respective embedding brain regions, revealing the widespread expression of GJD2 in the avian brain. Inspection of a single-cell sequencing database from zebra and Bengalese finches generalizes the distributions of electrical synapses across cell types and song nuclei that we found in HVC and RA from canaries, reveals a differential GJD2 mRNA expression in HVC glutamatergic subtypes and its transient increase along the neurogenic lineage. We propose that songbirds are a suitable model to investigate the contribution of electrical synapses to motor skill learning and production. Full article