For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.

Nest boxes are a popular management tool to increase nest site availability for hole-nesting birds, but biological consequences of this technique in different habitats are poorly studied. In our study area in southwestern Estonia, nest boxes for small passerines were set up in deciduous and coniferous woods. Great tits Parus major preferred the food-rich deciduous habitat for breeding, as judged by higher nest-box occupation, earlier egg-laying and larger clutches and eggs. However, in coniferous habitat more and heavier young fledged per nest, and the return rate of both fledglings and adults was higher. We propose two mutually non-exclusive explanations, both related to the maladaptive outcome of the provision of nest boxes: (i) in the preferred habitat, nest boxes caused a supra-optimal breeding density leading to an ecological trap; (ii) boxes drastically improved the non-preferred habitat, but birds were unable to exploit the breeding habitat fully. One should be careful in providing large numbers of artificial nest sites in preferred habitats. Sometimes it would be more preferable to improve less favourable habitats by removing critical constraints.

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Microorganisms have been shown to play an important role in shaping the life histories of animals, and it has recently been suggested that feather-degrading bacteria influence the trade-off between parental effort and self-preening behavior in birds. We studied a wild breeding population of great tits (Parus major) to explore habitat-, seasonal-, and sex-related variation in feather-degrading and free-living bacteria inhabiting the birds' yellow ventral feathers and to investigate associations with body condition. The density and species richness of bacterial assemblages was studied using flow cytometry and ribosomal intergenic spacer analysis. The density of studied bacteria declined between the nest-building period and the first brood. The number of bacterial phylotypes per bird was higher in coniferous habitat, while bacterial densities were higher in deciduous habitat. Free-living bacterial density was positively correlated with female mass; conversely, there was a negative correlation between attached bacterial density and female mass during the period of peak reproductive effort. Bacterial species richness was sex dependent, with more diverse bacterial assemblages present on males than females. Thus, this study revealed that bacterial assemblages on the feathers of breeding birds are affected both by life history and ecological factors and are related to body condition.