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.

The design of artificial nestboxes for the study of secondary hole-nesting birds: a review of methodological inconsistencies and potential biases. Acta Ornithol. 45: 1-26.

Animal mitochondrial DNA is normally inherited clonally from a mother to all her offspring. Mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype within an individual, can be generated by relatively common somatic mutations within an individual, by heteroplasmy of the oocytes, or by paternal leakage of mitochondria during fertilization of an egg. This biparental inheritance has so far been reported only in mice, mussels, Drosophila, and humans. Here we present evidence that paternal leakage occurs in a bird, the great tit Parus major. The major and minor subspecies groups of the great tit mix in the middle Amur Valley in far-eastern Siberia, where we found a bird that possessed the very distinct haplotypes of the two groups. To our knowledge this is the first report of paternal leakage in birds.

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The great tit complex is divided into four groups, each containing several subspecies. Even though the groups are known to differ markedly on morphological, vocal and behavioural characters, some hybridization occurs in the regions where they meet. The great tit has often been referred to as an example of a ring species, although this has later been questioned. Here, we have studied the genetic structure and phylogenetic relationships of the subspecies groups to clarify the evolutionary history of the complex using control region sequences of the mitochondrial DNA. The subspecies groups were found to be monophyletic and clearly distinct in mitochondrial haplotypes, and therefore must have had long-independent evolutionary histories. This conflicts with the ring species assignment and supports the formation of secondary contact zones of previously temporarily isolated groups. According to the phylogenetic species concept, all the subspecies groups could be considered as separate species, but if the definition of the biological species concept is followed, none of the subspecies groups is a true species because hybridization still occurs.

Global climate change affects ecosystems via several trophic levels. We investigated changes in the timing of breeding in the willow tit (Poecile montanus) and timing of its caterpillar food resource in relation to warming springs in a boreal forest. We used generalized linear mixed effect models to study the importance of synchrony between the timing of breeding in willow tits and the caterpillar food availability on the breeding success, measured as nestling survival rate and mean nestling weight. Both the timing of breeding and the timing of the caterpillar peak advanced during the last decades, and were well explained by spring temperatures. Unlike in most passerine populations studied, synchrony has improved with rising spring temperatures. However, it had only a modest although statistically significant positive influence on breeding success. Spring temperatures do not seem to be used as cues for the timing of caterpillar food availability by willow tits. We conclude that responses to climatic warming seem to be population, species and habitat specific, necessitating research in a wide range of taxa in different climatic zones.

Summary 1.Basal metabolic rate (BMR) is the most widely used standard measurement of the cost of living. Despite the acknowledged phenotypic flexibility of BMR, little is known about the patterns of variation in wild animal populations. 2. We studied the sources of variation in BMR of great tit Parus major (L.) among individuals from two wild populations: Oulu (northern Finland) and Lund (southern Sweden) during six consecutive years. 3. By means of a multivariate approach, we found year, locality, date, previous week average minimum temperature, age, body mass, and the interaction between locality and year were the factors retained in the final model, together explaining 71·1% of the total variation in BMR. 4. Birds from Oulu ( n = 168) had a higher BMR than Lund birds ( n = 156), and their BMR varied more between years than that of Lund birds. The two populations reacted in the same way to the other sources of variation examined. 5. Great tits from both populations showed a positive relationship between BMR and body mass and a negative relationship between BMR and date, previous week average minimum temperature and age. 6. This study highlights the need to standardize BMR measurements when testing predictions about metabolic rates from individuals of wild populations.

Nests are structures built to support and protect eggs and/or offspring from predators, parasites, and adverse weather conditions. Nests are mainly constructed prior to egg laying, meaning that parent birds must make decisions about nest site choice and nest building behavior before the start of egg-laying. Parent birds should be selected to choose nest sites and to build optimally sized nests, yet our current understanding of clutch size-nest size relationships is limited to small-scale studies performed over short time periods. Here, we quantified the relationship between clutch size and nest size, using an exhaustive database of 116 slope estimates based on 17,472 nests of 21 species of hole and non-hole-nesting birds. There was a significant, positive relationship between clutch size and the base area of the nest box or the nest, and this relationship did not differ significantly between open nesting and hole-nesting species. The slope of the relationship showed significant intraspecific and interspecific heterogeneity among four species of secondary hole-nesting species, but also among all 116 slope estimates. The estimated relationship between clutch size and nest box base area in study sites with more than a single size of nest box was not significantly different from the relationship using studies with only a single size of nest box. The slope of the relationship between clutch size and nest base area in different species of birds was significantly negatively related to minimum base area, and less so to maximum base area in a given study. These findings are consistent with the hypothesis that bird species have a general reaction norm reflecting the relationship between nest size and clutch size. Further, they suggest that scientists may influence the clutch size decisions of hole-nesting birds through the provisioning of nest boxes of varying sizes.