A sex chromosome polymorphism maintains divergent plumage phenotypes between extensively hybridizing yellowhammers (Emberiza citrinella) and pine buntings (E. leucocephalos).

Under allopatric speciation, populations of a species become isolated by a geographic barrier and develop reproductive isolation through genetic differentiation. When populations meet in secondary contact, the strength of evolved reproductive barriers determines the extent of hybridization and whether the populations will continue to diverge or merge together. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are avian sister species that diverged in allopatry on either side of Eurasia during the Pleistocene glaciations. Though they differ greatly in plumage and form distinct genetic clusters in allopatry, these taxa show negligible mitochondrial DNA differentiation and hybridize extensively where they overlap in central Siberia, lending uncertainty to the state of reproductive isolation in the system. To assess the strength of reproductive barriers between taxa, we examined genomic differentiation across the system. We found that extensive admixture has occurred in sympatry, indicating that reproductive barriers between taxa are weak. We also identified a putative Z chromosome inversion region that underlies plumage variation in the system, with the 'pine bunting' haplotype showing dominance over the 'yellowhammer' haplotype. Our results suggest that yellowhammers and pine buntings are currently at a crossroads and that evolutionary forces may push this system towards either continued differentiation or population merging. However, even if these taxa merge, recombination suppression between putative chromosome Z inversion haplotypes may maintain divergent plumage phenotypes within the system. In this way, our findings highlight the important role hybridization plays in increasing the genetic and phenotypic variation as well as the evolvability of a system.

Satellitome analysis on the pale-breasted thrush Turdus leucomelas (Passeriformes; Turdidae) uncovers the putative co-evolution of sex chromosomes and satellite DNAs.

Do all birds' sex chromosomes follow the same canonical one-way direction of evolution? We combined cytogenetic and genomic approaches to analyze the process of the W chromosomal differentiation in two selected Passeriform species, named the Pale-breasted Thrush Turdus leucomelas and the Rufous-bellied thrush T. rufiventris. We characterized the full catalog of satellite DNAs (satellitome) of T. leucomelas, and the 10 TleSatDNA classes obtained together with 16 microsatellite motifs were in situ mapped in both species. Additionally, using Comparative Genomic Hybridization (CGH) assays, we investigated their intragenomic variations. The W chromosomes of both species did not accumulate higher amounts of both heterochromatin and repetitive sequences. However, while T. leucomelas showed a heterochromatin-poor W chromosome with a very complex evolutionary history, T. rufiventris showed a small and partially heterochromatic W chromosome that represents a differentiated version of its original autosomal complement (Z chromosome). The combined approach of CGH and sequential satDNA mapping suggest the occurrence of a former W-autosomal translocation event in T. leucomelas, which had an impact on the W chromosome in terms of sequence gains and losses. At the same time, an autosome, which is present in both males and females in a polymorphic state, lost sequences and integrated previously W-specific ones. This putative W-autosomal translocation, however, did not result in the emergence of a multiple-sex chromosome system. Instead, the generation of a neo-W chromosome suggests an unexpected evolutionary trajectory that deviates from the standard canonical model of sex chromosome evolution.

Genetic patterns reveal geographic drivers of divergence in silvereyes (Zosterops lateralis).

Identifying mechanisms that drive population divergence under varying geographic and ecological scenarios can inform our understanding of evolution and speciation. In particular, analysis of genetic data from island populations with known colonisation timelines allows us to identify potential source populations of diverging island subspecies and current relationships among populations. Silvereyes (Zosterops lateralis) are a small passerine that have served as a valuable study system to investigate evolutionary patterns on both large and small geographic scales. We examined genetic relatedness and diversity of two silvereye subspecies, the mainland Z. l. cornwalli and island Z. l. chlorocephalus, and used 18 077 single nucleotide polymorphisms (SNPs), to compare locations across southeast Queensland, Australia. Although silvereyes are prolific island colonisers our findings revealed population divergence over relatively small spatial scales was strongly influenced by geographic isolation mediated by water barriers. Strong genetic connectivity was displayed between mainland sites, but minimal inter-island connectivity was shown despite comparable sampling distances. Genetic diversity analysis showed little difference in heterozygosity between island and mainland populations, but lower inbreeding scores among the island populations. Our study confirmed the range of the Z. l. chlorocephalus subspecies throughout the southern Great Barrier Reef. Our results show that water barriers and not geographic distance per se are important in driving incipient divergence in island populations. This helps to explain the relatively high number of phenotypically differentiated, but often geographically proximate, island silvereye subspecies compared to a lower number of phenotypically less well-defined Australian continental subspecies.

Nestling sex and behaviour determine the host preference of insect vectors in avian nests.

Sexual differences in pathogen prevalence in wildlife often arise from varying susceptibility influenced by factors such as sex hormones and exposure to pathogens. In the case of vector-borne pathogens, host selection by insect vectors determines the exposure of hosts to infections, largely affecting the transmission of these infectious diseases. We identify the blood-feeding patterns of insect vectors in Blue Tit (Cyanistes caeruleus) nestlings in a 3-year study. Blood from both nestlings and insect vectors (Culicoides spp. and Simuliidae) captured inside nest-boxes were used to molecularly determine the sex of the host. We then compared the sex-ratios of the nestlings that had been bitten and those of the complete brood in each nest. We found that males were bitten more frequently than females in 2021, when males weighed less in comparison to other years. Additionally, we molecularly identified bitten nestlings individually by genotyping the DNA of blood obtained from both, the vector's abdomen and nestlings of each brood in 2022. Nestlings more frequently bitten by vectors were males, weighed less and were closest to the nest entrance. To our knowledge this is the first study identifying the nestling selection by insect vectors in bird nests under natural conditions. These results contribute to understanding the mechanisms of host selection by insect vectors, shedding light on pathogen transmission and offering insights into the observed sex-biased infections in wildlife populations.

A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta).

Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation in recombination rate is widespread despite recombination often being essential for progression of meiosis. One such variation is heterochiasmy, where recombination rates differ between sexes. Heterochiasmy has been observed across broad taxonomic groups, yet it remains an evolutionary enigma. We used Lep-MAP3, a pedigree-based software that is efficient in handling large datasets, to generate linkage maps for the hihi or stitchbird (Notiomystis cincta), utilising information from >36 K SNPs and 36 families. We constructed 29 linkage maps, including for the previously unscaffolded Z chromosome. The hihi is an endangered passerine endemic to Aotearoa New Zealand that is sexually dimorphic and exhibits high levels of sexual conflict, including sperm competition. Patterns in recombination in the hihi are consistent with those in other birds, including higher recombination rates in micro-chromosomes. Heterochiasmy in the hihi is male-biased, in line with predictions of the Haldane-Huxley rule, with the male linkage map being 15% longer. Micro-chromosomes exhibit heterochiasmy to a greater extent, contrary to that reported in other birds. At the intra-chromosomal level, heterochiasmy is higher nearer to chromosome ends and in gene-rich regions. Regions of extreme heterochiasmy are enriched for genes implicated in cell structure. This study adds an important contribution in assessing evolutionary theories of heterochiasmy and provides a framework for future studies investigating fine-scale heterochiasmy.

Inter-organ differences in redox imbalance and apoptosis depict metabolic resilience in migratory redheaded buntings.

Migration, a bird's metabolic apex, depends primarily on the liver and muscle for fuel mobilization and endurance flight. In migratory redheaded buntings, adaptive increase in mitochondrial membrane (MM) proton gradient to drive ATP synthesis, measured by MM potential (MMP+) and reactive oxygen species (ROS) response, have been well characterized in the blood but not in the muscle or liver. We assessed MMP+, ROS, and apoptosis in the liver and pectoralis muscle of photosensitive nonmigratory (nMig.) male redheaded buntings photoinduced to migratory (Mig.) states. Relative expression levels of genes associated with energy (ACADM, PEPCK, GOT2, GLUT1, and CS), ROS modulation (SIRT1), mitochondrial free-radical scavengers (SOD1, PRX4, NOS2, GPX1, and GPX4), anti-apoptotic genes (NF-κß), apoptotic (CASP7), and tissue damage using histology, during migration were assessed. The MMP+ decreased and the ROS concentration increased, due to the metabolic load on liver and pectoralis muscle tissues during Mig. However, percentage of apoptotic cells increased in liver but decreased in muscle, which is of functional significance to migratory passerines. During Mig., in muscle, SIRT1 increased, while an increase in anti-apoptotic NF-κß aided immune pathway-mediated antioxidant activity and guarded against muscle oxidative damage during migration. Inter-organ differences in metabolism add to our current understanding of metabolic flexibility that supports successful migration in buntings.

Nest site correlates with nest type and body size in Troglodytidae passerines.

Nest characteristics are highly variable in the Passeriformes, but the macroevolutionary patterns observable for birds in general are not necessarily valid for specific families, suggesting that both global and within-family studies are needed. Here, we used phylogenetic comparative methods to address the evolutionary patterns of nest type, nest site and habitat in the Troglodytidae, a passerine group with diversified nest and habitat characteristics. The common ancestor of the Troglodytidae likely constructed enclosed nests within sheltered sites (cavity or crevice), but the radiation of the group was characterized by (i) shifts to exposed nest sites (vegetation) with retention of enclosed nests or (ii) retention of sheltered sites with nest simplification (cup nests). Nest site and nest type presented strong phylogenetic conservatism and evolved interdependently, while habitat was poorly correlated with nest evolution. A phylogenetic mixed modelling approach showed that sheltered nest sites were associated with small body size, likely to avoid competition with other animals for these places. With these results, we improve the understanding of nest character evolution in the Troglodytidae and reveal evolutionary aspects not observed so far for passerine birds.

Song determined by phylogeny and body mass in two differently constrained groups of birds: manakins and cardinals.

The songs of birds are complex signals that may have several functions and vary widely among species. Different ecological, behavioural and morphological factors, as well as phylogeny, have been associated as predictors of the evolution of song structure. However, the importance of differences in development, despite their relevance, has seldom been considered. Here, we analysed the evolution of song in two families of songbirds that differ in song development, manakins (suboscines) and cardinals (oscines), with their phylogeny, morphology, and ecology. Our results show that song characteristics had higher phylogenetic signal in cardinals than in manakins, suggesting higher evolutionary lability in the suboscines. Body mass was the main predictor of song parameters in manakins, and together with habitat type, had a major effect on cardinals' song structure. Precipitation and altitude were also associated with some song characteristics in cardinals. Our results bring unexpected insights into birdsong evolution, in which non-learners (manakins) revealed greater evolutionary lability than song learners (cardinals).

Extra-pair paternity in two passerine birds breeding in a gradient of urbanisation.

Urbanisation has been increasing worldwide in recent decades, driving environmental change and exerting novel selective pressures on wildlife. Phenotypic differences between urban and rural individuals have been widely documented in several taxa. However, the extent to which urbanisation impacts mating strategies is less known. Here, we investigated extra-pair paternity variation in great tits (Parus major) and blue tits (Cyanistes caeruleus) breeding in nestboxes set in a gradient of urbanisation in Warsaw, Poland, over three breeding seasons. Urbanisation was quantified as the amount of light pollution, noise pollution, impervious surface area (ISA) and tree cover within a 100-m radius around each nestbox. We obtained genotypes for 1213 great tits at 7344 SNP markers and for 1299 blue tits at 9366 SNP markers with a genotyping-by-sequencing method, and inferred extra-pair paternity by computing a genomewide relatedness matrix. We report higher extra-pair paternity in blue tits breeding in more urbanised areas, for example, with higher light pollution and ISA, and lower tree cover. However, no such trend was found in great tits. Late-stage survival of individual nestlings in both species was not associated with paternity or urbanisation proxies, thus we were not able to detect fitness benefits or drawbacks of being an extra-pair offspring in relation to urbanisation. Our results contribute to the growing body of knowledge reporting on the effects of urbanisation on avian ecology and behaviour, and confirm species-specific and population-specific patterns of extra-pair paternity variation.

Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies).

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.

Digest: Asymmetrical introgression of belly coloration across a manakin hybrid zone in Panama.

How does sexual selection impact introgression dynamics across a hybrid zone? Long et al. (2024) used historical (1989-1994) and contemporary (2017-2020) samples to quantify the stability of a Panamanian hybrid zone between golden-collared manakins (Manacus vitellinus) and white-collared manakins (M. candei). Their analyses revealed a spatially stable hybrid zone, except for one trait, belly plumage coloration, which has introgressed into the distribution of the white-collared manakin. This finding suggests possible sexual selection for this trait.

Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci?

When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million-ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.

Evolution of Chromosomal Inversions across an Avian Radiation.

Chromosomal inversions are structural mutations that can play a prominent role in adaptation and speciation. Inversions segregating across species boundaries (trans-species inversions) are often taken as evidence for ancient balancing selection or adaptive introgression, but can also be due to incomplete lineage sorting. Using whole-genome resequencing data from 18 populations of 11 recognized munia species in the genus Lonchura (N = 176 individuals), we identify four large para- and pericentric inversions ranging in size from 4 to 20 Mb. All four inversions cosegregate across multiple species and predate the numerous speciation events associated with the rapid radiation of this clade across the prehistoric Sahul (Australia, New Guinea) and Bismarck Archipelago. Using coalescent theory, we infer that trans-specificity is improbable for neutrally segregating variation despite substantial incomplete lineage sorting characterizing this young radiation. Instead, the maintenance of all three autosomal inversions (chr1, chr5, and chr6) is best explained by selection acting along ecogeographic clines not observed for the collinear parts of the genome. In addition, the sex chromosome inversion largely aligns with species boundaries and shows signatures of repeated positive selection for both alleles. This study provides evidence for trans-species inversion polymorphisms involved in both adaptation and speciation. It further highlights the importance of informing selection inference using a null model of neutral evolution derived from the collinear part of the genome.

Population structure in Mixornis tit-babblers across Sunda Shelf matches interfluvia of paleo-rivers.

Rivers constitute an important biogeographic divide in vast areas of tropical rainforest, such as the Amazon and Congo Basins. Southeast Asia's rainforests are currently fragmented across islands divided by sea, which has long obscured their extensive history of terrestrial connectivity as part of a vast (but now submerged) subcontinent - Sundaland - during most of the Quaternary. The role of paleo-rivers in determining population structure in Sundaic rainforests at a time when these forests were connected remains little understood. We examined the coloration of museum skins and used the genomic DNA of museum samples and freshly-collected blood tissue of a pair of Sundaic songbird species, the pin-striped and bold-striped tit-babblers (Mixornis gularis and M. bornensis, respectively), to assess the genetic affinity of populations on small Sundaic islands that have largely been ignored by modern research. Our genomic and morphological results place the populations from the Anambas and Natuna Islands firmly within M. gularis from the Malay Peninsula in western Sundaland, even though some of these islands are geographically much closer to Borneo, where M. bornensis resides. Our results reveal genetic structure consistent with the course of Sundaic paleo-rivers and the location of the interfluvia they formed, and add to a small but growing body of evidence that rivers would have been of equal biogeographic importance in Sundaland's former connected forest landscape as they are in Amazonia and the Congo Basin today.

The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird.

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone.

Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed ~50 km asymmetrically across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989-1994) and contemporary (2017-2020) transect samples to survey both morphological and genetic variation. Genome-wide single nucleotide polymorphism data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.

Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae).

The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.

Genes and gene networks underlying spatial cognition in food-caching chickadees.

Substantial progress has been made in understanding the genetic architecture of phenotypes involved in a variety of evolutionary processes. Behavioral genetics remains, however, among the least understood. We explore the genetic architecture of spatial cognitive abilities in a wild passerine bird, the mountain chickadee (Poecile gambeli). Mountain chickadees cache thousands of seeds in the fall and require specialized spatial memory to recover these caches throughout the winter. We previously showed that variation in spatial cognition has a direct effect on fitness and has a genetic basis. It remains unknown which specific genes and developmental pathways are particularly important for shaping spatial cognition. To further dissect the genetic basis of spatial cognitive abilities, we combine experimental quantification of spatial cognition in wild chickadees with whole-genome sequencing of 162 individuals, a new chromosome-scale reference genome, and species-specific gene annotation. We have identified a set of genes and developmental pathways that play a key role in creating variation in spatial cognition and found that the mechanism shaping cognitive variation is consistent with selection against mildly deleterious non-coding mutations. Although some candidate genes were organized into connected gene networks, about half do not have shared regulation, highlighting that multiple independent developmental or physiological mechanisms contribute to variation in spatial cognitive abilities. A large proportion of the candidate genes we found are associated with synaptic plasticity, an intriguing result that leads to the hypothesis that certain genetic variants create antagonism between behavioral plasticity and long-term memory, each providing distinct benefits depending on ecological context.

A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait.

The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations. Understanding the genetic mechanism underpinned feathered-foot development in wild birds is still in its infancy. Here, we assembled a chromosome-level genome of the Asian house martin (Delichon dasypus) using the long-read High Fidelity sequencing approach to initiate the search for genes associated with its feathered feet. We employed the whole-genome alignment of D. dasypus with other swallow species to identify high-SNP regions and chromosomal inversions in the D. dasypus genome. After filtering out variations unrelated to D. dasypus evolution, we found six genes related to feather development near the high-SNP regions. We also detected three feather development genes in chromosomal inversions between the Asian house martin and the barn swallow genomes. We discussed their association with the wingless/integrated (WNT), bone morphogenetic protein, and fibroblast growth factor pathways and their potential roles in feathered-foot development. Future studies are encouraged to utilize the D. dasypus genome to explore the evolutionary process of the feathered-foot trait in avian species. This endeavor will shed light on the evolutionary path of feathers in birds.

Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events.

Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.