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 pied flycatcher is one of the most phenotypically variable bird species in Europe. The geographic variation in phenotypes has often been attributed to spatial variation in selection regimes that is associated with the presence or absence of the congeneric collared flycatcher. Spatial variation in phenotypes could however also be generated by spatially restricted gene flow and genetic drift. We examined the genetic population structure of pied flycatchers across the breeding range and applied the phenotypic Q(ST) (P(ST))-F(ST) approach to detect indirect signals of divergent selection on dorsal plumage colouration in pied flycatcher males. Allelic frequencies at neutral markers were found to significantly differ among populations breeding in central and southern Europe whereas northerly breeding pied flycatchers were found to be one apparently panmictic group of individuals. Pairwise differences between phenotypic (P(ST)) and neutral genetic distances (F(ST)) were positively correlated after removing the most differentiated Spanish and Swiss populations from the analysis, suggesting that genetic drift may have contributed to the observed phenotypic differentiation in some parts of the pied flycatcher breeding range. Differentiation in dorsal plumage colouration however greatly exceeded that observed at neutral genetic markers, which indicates that the observed pattern of phenotypic differentiation is unlikely to be solely maintained by restricted gene flow and genetic drift.

Contact CEH NORA team at noraceh@ceh.ac.ukThe NERC and CEH trademarks and logos ('the Trademarks') are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner. Although it is claimed that over 95% of scientists in evolution and ecology believe data should be 131 publicly archived [1], mandatory public data archiving (PDA) is raising many issues in the scientific 132 community as evidenced by debates on websites, in blogs and publications [2-10]. Here we focus on the 133 perspective from long-term individual-based studies of wild populations that often span several 134 decades. 135Short and long-term ecological studies differ in several important aspects. For example, in the former, 136 data tend to be collected over a short period of time for one or two papers and once published the data 137 in these papers become less valuable to the collector and can be more useful to others with different 138 perspectives or analytical skills. In contrast, in studies that have followed individuals over their lifetimes, 139 a lot of crucial information is assessed from derived metrics (e.g. survival, lifetime reproductive success) 140 that can only be estimated after many years of fieldwork. Therefore, much value can remain in the 141 primary data even after some of the initial questions are answered. 142Long-term studies are rare and have great scientific value since many important questions in ecology 143 and evolutionary biology can only be answered from the life histories of recognizable individuals [11]. A 144 detailed analysis of the importance of individual-based studies has been documented elsewhere [11], 145 but a few examples are given in Box 1. 146While group discussions and blog posts on PDA related issues have been flourishing, little is formally 147 known and published about the position and concerns of people collecting long-term data. To fill this 148 gap, a survey was conducted to learn their perspectives, and if current data requirements were 149 perceived as problematic, to identify potential alternative data-sharing policies that could be acceptable 150 to the journals, the scientific community and the Principal investigators. 151 152 The survey 153To obtain the opinions of scientists with individual-based longitudinal data, a worldwide survey was sent 154 to 146 PIs of long-term research projects. Responses were received from 73 PIs working on 59 bird 155 studies, 13 mammalian studies and 1 plant study. The 92 projects (some PIs have several projects) range 156 in duration from 5 to 68 years ( Figure 1), with 55 percent collecting data for more than 30 years. Thirty-157 five percent of researchers were required to archive data used in a publication by their current funding 158 agency and 19% by their institution. Eight researchers were required to deposit data by both; therefore 159 59% were not required to archive their data. There was diversity of opinion among PIs about data 160 archiving, but some strong points of consens...

Many organisms adjust their reproductive phenology in response to climate change, but phenological sensitivity to temperature may vary between species. For example, resident and migratory birds have vastly different annual cycles, which can cause differential temperature sensitivity at the breeding grounds, and may affect competitive dynamics. Currently, however, adjustment to climate change in resident and migratory birds have been studied separately or at relatively small geographical scales with varying time series durations and methodologies. Here, we studied differential effects of temperature on resident and migratory birds using the mean egg laying initiation dates from 10 European nest box schemes between 1991 and 2015 that had data on at least one resident tit species and at least one migratory flycatcher species. We found that both tits and flycatchers advanced laying in response to spring warming, but resident tit populations advanced more strongly in relation to temperature increases than migratory flycatchers. These different temperature responses have already led to a divergence in laying dates between tits --

The role of natural selection in shaping adaptive trait differentiation in natural populations has long been recognized. Determining its molecular basis, however, remains a challenge. Here, we search for signals of selection in candidate genes for colour and its perception in a passerine bird. Pied flycatcher plumage varies geographically in both its structural and pigment-based properties. Both characteristics appear to be shaped by selection. A single-locus outlier test revealed 2 of 14 loci to show significantly elevated signals of divergence. The first of these, the follistatin gene, is expressed in the developing feather bud and is found in pathways with genes that determine the structure of feathers and may thus be important in generating variation in structural colouration. The second is a gene potentially underlying the ability to detect this variation: SWS1 opsin. These two loci were most differentiated in two Spanish pied flycatcher populations, which are also among the populations that have the highest UV reflectance. The follistatin and SWS1 opsin genes thus provide strong candidates for future investigations on the molecular basis of adaptively significant traits and their co-evolution.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Despite basal metabolic rate (BMR) being one of the most commonly measured physiological traits and an important indicator of competitive ability, very little is known about its genetic basis and relation to other physiological traits. Here, we present the first attempt to estimate the multivariate basis of BMR using a natural population of pied flycatcher Ficedula hypoleuca breeding in the Tomsk Region, Western Siberia. We show relatively high and significant heritability of whole‐organism BMR, mass‐specific BMR and mass‐independent BMR (h 2 = 0.43, 0.55 and 0.52, respectively), which indicates the potential of these energetic traits to respond to direct selection. In contrast to some previous reports, we found that the genetic correlations between body mass and all three measures of BMR were not significantly different from zero. Independent evolution of body mass and BMR in this species should therefore be possible. Following a previous report, we also estimated the genetic correlations between the different BMR measures and show they are all close to unity, suggesting that they are, from a genetic point of view, a similar trait. Our results are in contrast with previous studies measuring the genetic basis of metabolic rates using aviary‐bred birds and highlight the importance of considering BMR in a natural setting.

The majority of our knowledge of avian energetics is based on studies of birds from temperate and high latitudes. Using the largest existing sample of wild-caught Old World tropical species, we showed that birds from Southern Vietnam had lower basal metabolic rate (BMR) than temperate species. The strongest dissimilarity between tropical and temperate species was the low scaling exponent in the allometric relation between BMR and body mass in tropical birds (the regression slope was 0.573). The passerine migrants to temperate and high latitudes had higher BMR than tropical sedentary passerines. Body mass alone accounted for 93% of the variation in BMR (body mass ranged from 5 to 252 g). Contrary to some other studies, we did not find evidence besides the above mentioned that phylogeny, taxonomy, behavior, or ecology have a significant influence on BMR variation among tropical birds.