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PubMed2025

Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes.

Centromeres are an important part of chromosomes which direct chromosome segregation during cell division. Their modifications can therefore explain the unusual mitotic and meiotic behaviour of certain chromosomes, such as the germline-restricted chromosome (GRC) of songbirds. This chromosome is eliminated from somatic cells during early embryogenesis and later also from male germ cells during spermatogenesis. Although the mechanism of elimination is not yet known, it is possible that it involves a modification of the centromeric sequence on the GRC, resulting in problems with the attachment of this chromosome to the mitotic or meiotic spindle and its lagging during anaphase, which eventually leads to its elimination from the nucleus. However, the repetitive nature and rapid evolution of centromeres make their identification and comparative analysis across species and chromosomes challenging. Here, we used a combination of cytogenetic and genomic approaches to identify the centromeric sequences of two closely related songbird species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia). We found a 436-bp satellite repeat present in the centromeric regions of all regular chromosomes (i.e., autosomes and sex chromosomes), making it a strong candidate for the centromeric repeat. This centromeric repeat was highly similar between the two nightingale species. Interestingly, hybridization of the probe to this satellite repeat on meiotic spreads suggested that this repeat is missing on the GRC. Our results indicate that the change of the centromeric sequence may underlie the unusual inheritance and programmed DNA elimination of the GRC in songbirds.

Animals↗
PubMed1978

A new auditory area of the songbird forebrain: a connection between auditory and song control centers.

Single unit microelectrode recordings followed by electrolytic lesions which mark the recording sites demonstrate that there is an auditory region of the songbird forebrain that is distinct from and superficial to field L, the primary auditory region of the telencephalon. The location of the superficial auditory area and its large cells suggest identification with HVc, the large-celled telencephalic nucleus which controls song in the canary.

Acoustic Stimulation↗
PubMed1976

Sexual dimorphism in vocal control areas of the songbird brain.

In canaries and zebra finches, three vocal control areas in the brain are strikingly larger in males than in females. A fourth, area X of the lobus parolfactorius, is well developed in males of both species, less well developed in femal canaries, and absent or not recognizable in femal zebra finches. These size differences correlate well with differences in singing behavior. Males of both species learn song by reference to auditory information, and females do not normally sing. Exogenous testosterone induces singing in female canaries but not in female zebra finches. This is believed to be the first report of such gross sexual dimorphism in a vertebrate brain.

Animals↗
PubMed1992

[The aerobic bacterial flora of songbird nests].

In the area around Ober- and Unterschleissheim, a medium term decrease in the singing bird population appears to be happening. Therefore, material from nesting-boxes (used for nesting or sleeping) was examined for bacterial contamination. Mainly gram positive bacteria were isolated which were considered to belong to the normal flora. The occurrence of Streptomyces spp. is described in the nesting material of Passeres probably for the first time. Enterobacteriaceae represent only a fraction of the total isolates, but are demonstrated relatively frequently in the nests of the Nuthatch (Sitta europaea) and nests of other non-identified bird spp., so that colonization of the intestinal tract with Enterobacteriaceae cannot be excluded. Surprisingly, bacteria of the aquatic habitats such as Alcaligenes, Bordetella, Aeromonas, Non-Cholera (NC)-Vibrio were isolated, although in small amounts. The occurrence of NC-Vibrio has not yet been described in singing birds. Nests with high numbers of gram negative rods were successful in most instances, therefore, there was no proof that aerobic bacteria are responsible for the decrease in the population.

Animals↗
PubMed1977

Role of auditory feedback in canary song development.

As in other songbirds, early deafening had drastic effects on the song of the roller canary, a cardueline finch, resulting in a song that was much simpler and more variable than the normal. The repertoire of the syllable types, of which the song is made, was reduced from 30 to a mean of 5.0. Loud white noise was successfully used as a reversible method of cutting off auditory feedback from vocal behavior. Although suffering permanent elevation of hearing thresholds, birds reared in noise to 200 days, singing at first like deaf birds, subsequently increased their syllable repertoires significantly. Birds reared in noise to weaning at 40 days, again partly deaf, achieved a normal repertoire size when stimulated with a singing adult. Without such stimulation the repertoire was significantly reduced, showing that canary song is not fully innate, as had been thought. Although abnormal, the song of deaf canaries retained more species-specific features than did the song of emberizine sparrows when the songs developed without auditory feedback. The results are interpreted in terms of a sensory template theory.

Animals↗
PubMed2026

Digest: Speciation involves both barriers and bridges in the tropical Andes.

Mountains are important centers of biodiversity and studies of speciation. In particular, the north-south linear orientation of the Andes allows examination of how geographic isolation, elevation, and latitude influence divergence in closely related species such as Myioborus warblers (Parulidae), the focal taxa of this study. Traditional models of Andean speciation have emphasized allopatric divergence due to geographic barriers, but thanks to the limited sampling of hybrid zones and lack of genome-wide datasets in tropical taxa, we may have underestimated of the role of gene flow in shaping patterns of divergence in the region. Using ddRAD-seq genomic data, Céspedes Arias et al. (2026) demonstrated that geographic isolation and hybridization both contribute to the generation and maintenance of Andean warbler lineages. Their results revealed how complex patterns of genetic divergence, introgression, and isolation-by-distance contribute to the historical buildup of biodiversity in the Andes, challenging strictly isolationist models of mountain evolution.

Animals↗
PubMed2026

The First Highly Contiguous Genome Assembly for the Western Bluebird (Sialia mexicana).

The western bluebird (Sialia mexicana) is a secondary cavity-nesting thrush that has experienced historical population declines, local extirpations, and more recent recoveries associated with nest box programs. Despite these regional successes, recent eBird estimates suggest continued range-wide declines and substantial geographic variation in population trajectories, making this species a useful system for future studies of demographic change, connectivity, and conservation genomics. However, genomic resources for western bluebirds remain limited, and no reference genome currently exists for any species in the genus Sialia. Here, we present the first high-quality de novo reference genome for S. mexicana. Using PacBio HiFi long-read sequencing from an adult female, we generated a highly contiguous, phased 1.3 Gb nuclear assembly with a contig N50 of 24.8 Mb and high BUSCO completeness of 98.3%. We annotated the nuclear genome using transcriptomic and protein evidence, identifying 16,656 protein-coding genes and 26,060 transcripts/protein isoforms. We also assembled a complete ∼16 kb mitochondrial genome from Illumina short-read data. This reference genome provides a foundational resource for future studies of population structure, genetic diversity, connectivity, demographic history, and adaptation in western bluebirds and related taxa.

Animals↗
PubMed2025

Birds of a feather flock together: social context exacerbates the effects of light pollution on circadian disruption.

Artificial light at night (ALAN), a growing pervasive pollutant, disrupts physiological and behavioural rhythms across organisms. Social interactions play a significant role in shaping individual and group biological rhythms, but they are often overlooked in the context of environmental stressors, such as ALAN. We explore how dim ALAN affects zebra finches (Taeniopygia guttata) in social and isolated environments, examining behavioural, physiological and molecular rhythms. We found that social birds under ALAN had an earlier activity onset and greater disruption in hypothalamic and liver circadian gene expression than control or isolated counterparts under ALAN. Additionally, we found that activity onset correlated negatively with hypothalamic bmal1 and cry1 expression in birds exposed to ALAN. Within ALAN-exposed birds, there was a larger disassociation between central and peripheral clock gene expression for social birds than in isolated birds. However, rhythmic melatonin concentrations did not differ among treatment groups. We show that social interactions may exacerbate the effects of ALAN, which highlights the impact of social interactions on circadian regulation at a molecular level and a critical need to consider social contexts in biological studies.

Animals↗
PubMed2026

Comparisons Between Large-Scale Genomic Variants and SNPs in Driving Population Divergence and Local Adaptation.

Genomic variations, such as indels (2-49 bp) and structural variants (SVs, ≥50 bp), are larger-scale mutations than single nucleotide polymorphisms (SNPs) and can substantially impact evolutionary processes, including speciation, adaptation, and phenotypes. Despite their functional importance, integrative population genetic analyses that jointly consider genome-wide SNPs, indels, and SVs remain under-explored. The ground tit (Pseudopodoces humilis), an endemic species to the Qinghai-Tibet Plateau (QTP), exhibits divergence across distinct glacial refugia, accompanied by habitat and morphological divergence, making it an excellent example for investigating how different types of genomic variants contribute to population divergence and local adaptation. Here, by retrieving 81 whole-genome sequence data, over 13 million SNPs, 2 million indels, and 22,101 SVs were identified. Variants were unevenly distributed across the genome, characterized by distinct hotspot regions. Indels and SVs revealed four genetic clusters consistent with previous SNP-based results, thereby validating the reliability of our variant datasets. FST and genotype-environment association (GEA) analyses independently revealed numerous candidate indels and SVs; each showed minimal overlap with previously identified SNPs, and were enriched in similar functional pathways such as signal transduction, skeletal muscle development, water transport, DNA repair, reproduction, nervous system development, and immunity. Collectively, our results demonstrated that indels and SVs could capture additional signatures besides SNPs. Furthermore, similar but distinct gene functions among different types of genomic variants collectively and complementarily drive genomic divergence across environmental gradients in such a high-elevation endemic species, underscoring its evolutionary relevance in local adaptation.

indels↗
PubMed2025

Combined Evidence Reveals the Origin of a Rapid Range Expansion Despite Retained Genetic Diversity and a Weak Founder Effect.

Many species are currently experiencing range shifts in response to changing environmental conditions with potentially serious genetic consequences. Repeated founder events and strong genetic drift are expected to erode genetic variation at the range front, reducing adaptive potential and slowing or even halting the expansion. However, the severity of these consequences for common and highly mobile species undergoing environment-driven range shifts (c.f. invasions) is less clear. Here, we combined historical observations and contemporary movement data of the common reed warbler (Acrocephalus scirpaceus) with genomic evidence from across its European breeding range to (1) infer the origin and (2) quantify the genetic consequences of a recent and rapid northward range expansion. Although there were no reductions in levels of nucleotide diversity or allelic richness, nor a signal of founder effect in the directionality index (ψ), our combined dataset approach was able to infer an expansion origin from the southwest. Furthermore, we found that private allelic richness retained a slight but significant linear decline along the colonisation route. These results suggest that high dispersal capabilities can allow even philopatric species to avoid the loss of genetic diversity during rapid range expansions. Nevertheless, if multiple lines of evidence enable identification of an expansion pathway, we may still detect genetic signals of expansion.

Founder Effect↗
PubMed2025

A colorful legacy of hybridization in wood-warblers includes frequent sharing of carotenoid genes among species and genera.

Introgression between species has the potential to shape evolutionary trajectories in important ways, but uncovering complex introgression dynamics has only recently been made possible by advances in genomics. Warblers of the avian family Parulidae exemplify rapid diversification and sexual trait divergence, and we endeavored to study historical introgression in the family. We sequenced multiple genomes of nearly every species, constructed a phylogeny for the family, and investigated gene flow across the genome and at genes known for controlling feather color. We found that DNA haplotypes including the gene BCO2, which encodes an enzyme that degrades yellow carotenoids, have spread among genera multiple times-from Vermivora to Geothlypis and from Leiothlypis to multiple Cardellina and Setophaga species. Patterns of inheritance in the latter case point to introgression that occurred 0.5 to 2 million years ago, and the shared haplotype among recipient species is less than 100 nucleotides long. Separately, we found evidence of introgression from red Cardellina species to both of the two red Myioborus species at BDH1L and from one red Myioborus species to the other at CYP2J19; both are key genes in the pathway that converts yellow carotenoids to red ketocarotenoids. Our results show that introgression is a common mechanism for the evolution of colorful plumage in parulid warblers and hint at complex histories of gene flow behind some of the Western Hemisphere's most colorful birds.

Animals↗