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Seasonal migration is a taxonomically widespread behaviour that integrates across many traits. The European blackcap exhibits enormous variation in migration and is renowned for research on its evolution and genetic basis. We assembled a reference genome for blackcaps and obtained whole genome resequencing data from individuals across its breeding range. Analyses of population structure and demography suggested divergence began ~30,000 ya, with evidence for one admixture event between migrant and resident continent birds ~5000 ya. The propensity to migrate, orientation and distance of migration all map to a small number of genomic regions that do not overlap with results from other species, suggesting that there are multiple ways to generate variation in migration. Strongly associated single nucleotide polymorphisms (SNPs) were located in regulatory regions of candidate genes that may serve as major regulators of the migratory syndrome. Evidence for selection on shared variation was documented, providing a mechanism by which rapid changes may evolve.

Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs. Bioinformatic analysis of this large dataset quantified the association of DNA methylation with the underlying genomic DNA sequence throughout vertebrate evolution. We observed a broadly conserved link with two major transitions—once in the first vertebrates and again with the emergence of reptiles. Cross-species comparisons focusing on individual organs supported a deeply conserved association of DNA methylation with tissue type, and cross-mapping analysis of DNA methylation at gene promoters revealed evolutionary changes for orthologous genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.

Ticks are blood‐feeding parasites which act as major vectors for various pathogenic microorganisms affecting both animal and human health. Hard ticks are known to move passively (i.e. ‘hitchhike') on migratory birds as they transit between breeding and non‐breeding grounds. This potentially leads to exchange and establishment of non‐endemic tick species in novel environments. However, it is not yet clear if all migratory bird taxa play an equal role in movement of specific tick species, especially outside of medically important tick taxa. To clarify these interactions, we performed a systematic literature review regarding primary data of ticks moving on migratory birds within the African–Western Palearctic flyways. In total, 35 studies were found which showed 123 bird species from 37 families and 12 orders connected to potential movement of 30 tick species representing six genera (Amblyomma, Dermacentor, Haemaphysalis, Hyalomma, Ixodes, Rhipicephalus). Most tick species did not show high abundance for any bird species, or, if they did, only on very few. Only Ixodes ricinus and Hyalomma marginatum were estimated to be carried at above average burdens by multiple bird species. This could indicate an increased likelihood of these species to be moved during migration. Specific tick species or whole genera were only found in certain migratory seasons as expected based on their geographic distributions. Even so, species found in both migratory seasons did not differ in their estimated abundances on birds between seasons. This result could suggest that tick abundance on migrating birds is not always a direct result of geographic distribution and may suggest an understudied importance of stopover sites towards potential tick introduction or turnover. Taken together, the results presented here provide guiding information for future analyses integrating individual level variation into the current understanding of tick movement with migratory birds.

Transposable elements (TEs) are mobile genetic elements that can move around the genome, and as such are a source of genomic variability. Based on their characteristics we can annotate TEs within the host genome and classify them into specific TE types and families. The increasing number of available high-quality genome references in recent years provides an excellent resource that will enhance the understanding of the role of recently active TEs on genetic variation and phenotypic evolution. Here we showcase the use of a high-quality TE annotation to understand the distinct effect of recent and ancient TE insertions on the evolution of genomic variation, within our study species the Eurasian blackcap ( Sylvia atricapilla ). We investigate how these distinct TE categories are distributed along the genome and evaluate how their coverage across the genome is correlated with four genomic features: recombination rate, gene coverage, CpG island coverage and GC content. We found within the recent TE insertions an accumulation of LTRs previously not seen in birds. While the coverage of recent TE insertions was negatively correlated with both GC content and recombination rate, the correlation with recombination rate disappeared and turned positive for GC content when considering ancient TE insertions.

Timing is essential for survival and reproduction of organisms across the tree of life. The core circadian clock gene Clk is involved in the regulation of annual timing events and shows highly conserved sequence homology across vertebrates except for one variable region of poly-glutamine repeats. Clk genotype varies in some species with latitude, seasonal timing and migration. However, findings are inconsistent, difficult to disentangle from environmental responses, and biased towards high latitudes. Here we combine field data with a common-garden experiment to study associations of Clk polymorphism with latitude, migration and annual-cycle timing within the stonechat species complex across its trans-equatorial distribution range. Our dataset includes 950 records from 717 individuals from nine populations with diverse migratory strategies. Gene diversity was lowest in resident African and Canary Island populations and increased with latitude, independently of migration distance. Repeat length and annual-cycle timing was linked in a population-specific way. Specifically, equatorial African stonechats showed delayed timing with longer repeat length for all annual-cycle stages. Our data suggest that at low latitudes with nearly constant photoperiod, Clk genotype might orchestrate a range of consistent, individual chronotypes. In contrast, the influence of Clk on annual-cycle timing at higher latitudes might be mediated by its interactions with genes involved in (circadian) photoperiodic pathways.

Cryptochromes are ubiquitously expressed in various animal tissues including the retina. Some cryptochromes are involved in regulating circadian activity. Cryptochrome proteins have also been suggested to mediate the primary mechanism in light-dependent magnetic compass orientation in birds. Cryptochrome 1b (Cry1b) exhibits a unique carboxy terminus exclusively found in birds so far, which might be indicative for a specialised function. Cryptochrome 1a (Cry1a) is so far the only cryptochrome protein that has been localised to specific cell types within the retina of migratory birds. Here we show that Cry1b, an alternative splice variant of Cry1a, is also expressed in the retina of migratory birds, but it is primarily located in other cell types than Cry1a. This could suggest different functions for the two splice products. Using diagnostic bird-specific antibodies (that allow for a precise discrimination between both proteins), we show that Cry1b protein is found in the retinae of migratory European robins (Erithacus rubecula), migratory Northern Wheatears (Oenanthe oenanthe) and pigeons (Columba livia). In all three species, retinal Cry1b is localised in cell types which have been discussed as potentially well suited locations for magnetoreception: Cry1b is observed in the cytosol of ganglion cells, displaced ganglion cells, and in photoreceptor inner segments. The cytosolic rather than nucleic location of Cry1b in the retina reported here speaks against a circadian clock regulatory function of Cry1b and it allows for the possible involvement of Cry1b in a radical-pair-based magnetoreception mechanism.

The likelihood of a new migratory route emerging is presumably a function of 1) the associated fitness payoff and 2) the probability that the route arises in the first place. It has been suggested that diametrically opposed ‘reverse' migratory trajectories might be surprisingly common and, if such routes were heritable, it follows that they could underlie the rapid evolution of divergent migratory trajectories. Here, we used Eurasian blackcap (Sylvia atricapilla; ‘blackcap') ringing recoveries and geolocator trajectories to investigate whether a recently evolved northwards autumn migratory route – and accompanying rapid northerly wintering range expansion – could be explained by the reversal of each individual's population‐specific traditional southwards migratory direction. We found that northwards autumn migrants were recovered closer to the sites specified by an axis reversal than would be expected by chance, consistent with the rapid evolution of new migratory routes via bi‐axial variation in orientation. We suggest that the surprisingly high probability of axis reversal might explain why birds expand their wintering ranges rapidly and divergently, and propose that understanding how migratory direction is encoded is crucial when characterising the genetic component underlying migration.

Telomeres are regarded as key markers of cellular ageing and physiological state. Oxidative stress, which can accelerate telomere shortening, is thought to increase during energetically demanding processes such as bird migration. However, their study in the context of migratory behaviour is limited. Here we compared telomere length (TL) and mitochondrial DNA copy number (mitoDNAcn) between migratory and resident Eurasian blackbirds on the island of Helgoland, a migratory stopover site. Contrary to expectations, we found migrants had longer TLs despite similar mitochondrial densities. These findings reinforce the idea that migratory individuals may possess specific physiological adaptations, such as enhanced antioxidant defences, that help preserve telomere integrity. Overall, our results underscore the complex interactions between migratory behaviour and cellular maintenance and point to the need for broader comparative studies across species and migratory strategies.

Seasonal migration is a complex and variable behaviour with the potential to promote reproductive isolation. In Eurasian blackcaps ( Sylvia atricapilla ), a migratory divide in central Europe separating populations with southwest (SW) and southeast (SE) autumn routes may facilitate isolation, and individuals using new wintering areas in Britain show divergence from Mediterranean winterers. We tracked 100 blackcaps in the wild to characterize these strategies. Blackcaps to the west and east of the divide used predominantly SW and SE directions, respectively, but close to the contact zone many individuals took intermediate (S) routes. At 14.0° E, we documented a sharp transition from SW to SE migratory directions across only 27 (10–86) km, implying a strong selection gradient across the divide. Blackcaps wintering in Britain took northwesterly migration routes from continental European breeding grounds. They originated from a surprisingly extensive area, spanning 2000 km of the breeding range. British winterers bred in sympatry with SW-bound migrants but arrived 9.8 days earlier on the breeding grounds, suggesting some potential for assortative mating by timing. Overall, our data reveal complex variation in songbird migration and suggest that selection can maintain variation in migration direction across short distances while enabling the spread of a novel strategy across a wide range.

Avian long-distance migration requires refined programming to orchestrate the birds’ movements on annual temporal and continental spatial scales. Programming is particularly important as long-distance movements typically anticipate future environmental conditions. Hence, migration has long been of particular interest in chronobiology. Captivity studies using a proxy, the shift to nocturnality during migration seasons (i.e., migratory restlessness), have revealed circannual and circadian regulation, as well as an innate sense of direction. Thanks to rapid development of tracking technology, detailed information from free-flying birds, including annual-cycle data and actograms, now allows relating this mechanistic background to behaviour in the wild. Likewise, genomic approaches begin to unravel the many physiological pathways that contribute to migration. Despite these advances, it is still unclear how migration programmes are integrated with specific environmental conditions experienced during the journey. Such knowledge is imminently important as temporal environments undergo rapid anthropogenic modification. Migratory birds as a group are not dealing well with the changes, yet some species show remarkable adjustments at behavioural and genetic levels. Integrated research programmes and interdisciplinary collaborations are needed to understand the range of responses of migratory birds to environmental change, and more broadly, the functioning of timing programmes under natural conditions.