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DNA sequences: RAD-seq GenBank accessions SRR17125662- SRR17125721, RRBS-seq GenBank accessions SRR17145241-SRR17145300; NCBI project PRJNA786007. Scripts: Github repository https://github.com/AudeCaizergues/Epigenetics_and_the_city.; International audience; Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability are central questions in evolutionary biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a substantial role in rapid adaptation. In the context of rampant urbanization, joint examinations of genomic and epigenomic mechanisms are still lacking. Here, we investigated genomic (SNP) and epigenomic (CpG methylation) responses to urban life in a passerine bird, the Great tit (Parus major). To test whether urban evolution is predictable (i.e. parallel) or involves mostly nonparallel molecular processes among cities, we analysed both SNP and CpG methylation variations across three distinct pairs of city and forest Great tit populations in Europe. Our analyses reveal a polygenic response to urban life, with both many genes putatively under weak divergent selection and multiple differentially methylated regions (DMRs) between forest and city great tits. DMRs mainly overlapped transcription start sites and promotor regions, suggesting their importance in modulating gene expression. Both genomic and epigenomic outliers were found in genomic regions enriched for genes with biological functions related to the nervous system, immunity, or behavioural, hormonal and stress responses. Interestingly, comparisons across the three pairs of city-forest populations suggested little parallelism in both genetic and epigenetic responses. Our results confirm, at both the genetic and epigenetic levels, hypotheses of polygenic and largely nonparallel mechanisms of rapid adaptation in novel environments such as urbanized areas.

The genetic structure of animal populations has considerable behavioural, ecological and evolutionary implications and may arise from various demographic traits. Here, we use observational field data and molecular genetics to determine the genetic structure of an invasive population of monk parakeets, Myiopsitta monachus, at a range of spatial scales, and investigate the demographic processes that generate the observed structure. Monk parakeets construct large nests that can house several pairs occupying separate chambers; these nests are often aggregated within nesting trees. We determined patterns of relatedness within compound nests, within nesting trees and between trees. Spatial autocorrelation analyses of pairwise genetic relatedness revealed fine-scale genetic structure with relatives of both sexes spatially clustered within, but not beyond, nesting trees. In addition, males were more related to males sharing their compound nests than to other males occupying the same nesting tree. By contrast, males and females within compound nests were not significantly more closely related than elsewhere in the same tree, and we found no evidence for inbreeding. Adults showed high breeding site fidelity between years despite considerable disturbance of nest sites. Natal dispersal was female-biased, but dispersal distances were relatively short with some natal philopatry observed in both sexes. Sibling coalitions, typically of males, were observed amongst both philopatric and dispersing birds. Our results show significant clustering of kin within compound nests and nesting trees resulting from limited and coordinated natal dispersal, with subsequent breeding site fidelity. The resulting genetic structure has implications for social behaviour in this unusual parrot species.

Background The monk parakeet Myiopsitta monachus (Boddaert), native to South America, is an invasive species in several European countries, causing crop damage and potential negative impacts on wildlife. Only Spain and Great Britain have regulations to control monk parakeets, thus fast growth and spread of populations are likely to occur on a wide scale. The aims of this research are to update information on the distribution and population size of monk parakeets in Europe, assess whether differences in population growth or spread rate exist between populations, and provide recommendations to decision-makers. Results Our study estimates that there are 23 758 monk parakeets in the wild, across 179 municipalities in eight European Union (EU) countries; 84% of these municipalities hold between 1 and 100 monk parakeets. All countries with a representative historical record are experiencing exponential growth of monk parakeets. Mediterranean countries are experiencing higher exponential growth, spread rate and faster colonization of new municipalities than Atlantic countries. Conclusions We recommend that EU Mediterranean countries consider declaration of the monk parakeet as invasive alien species of regional concern, and develop coordinated efforts to monitor and manage the species, taking advantage of the low population sizes in most municipalities. © 2019 Society of Chemical Industry.

BACKGROUND: As feeding by humans is one of the main food resources to pigeons (Columba livia), there is general agreement that public education that aims to reduce the food base may be the most feasible way to reduce pigeon abundance. However, except for the classic example of Basel, the method has rarely been tested or implemented. We provide results from a 1 year study in the city of Barcelona where we tested the effect of public education on pigeon population abundance and composition. RESULTS: The quantity of food provided by people to pigeons was significantly reduced during the study. Feral pigeon density was reduced by 40% in the two experimental districts, but no variation was detected in the control district. Detailed analyses in one of the districts showed that the reduction was mainly related to the reduction in food availability but not to culling. Pigeons captured at the end of the experiment were larger than at the start of the study, but body condition was reduced. CONCLUSION: Results show the effectiveness of public information to manage feral pigeon populations in a large city, and that control operations can exert important selection pressure on the population, leading to changes in population composition. © 2016 Society of Chemical Industry

Determination of fitness differentials between individuals adopting different migratory and dispersal strategies is basic to understand the evolution of migration. In the Eurasian siskin Carduelis spinus, both resident and transient birds forage within the same wintering area, providing the rare opportunity to compare their foraging behaviour in the same area and habitat. The aim of this study was to test the predictions associated to the different hypothesized costs of transience by studying the vigilance and foraging behaviour of wild wintering siskins foraging at three bird tables with different predation risk and interference competition levels. Transient siskins showed longer scan durations than residents, either because of site unfamiliarity or subordination (i.e. prior-occupancy effect). However, residents and transients did not differ in aggression rates, contrary to the dear-enemy effect. Transient siskins did not show a higher allocation of time to vigilance, contrary to the hypothesis of compensation vigilance to reduce predation risk by dispersing animals. Moreover, transients increased pecking rate with increasing predation risk, showed lower scan rates, longer foraging bouts and, in males, presented marginally higher proportions far from cover. Altogether these results strongly support the hypothesis that transients incur a predation cost due to a less efficient vigilance and foraging system.

Divergent selection stemming from environmental variation may induce local adaptation and ecological speciation whereas gene flow might have a homogenizing effect. Gene flow among populations using different environments can be reduced by geographical distance (isolation-by-distance) or by divergent selection stemming from resource use (isolation-by-ecology). We tested for and encountered phenotypic and genetic divergence among Spanish crossbills utilizing different species of co-occurring pine trees as their food resource. Morphological, vocal and mtDNA divergence were not correlated with geographical distance, but they were correlated with differences in resource use. Resource diversity has now been found to repeatedly predict crossbill diversity. However, when resource use is not 100% differentiated, additional characters (morphological, vocal, genetic) must be used to uncover and validate hidden population structure. In general, this confirms that ecology drives adaptive divergence and limits neutral gene flow as the first steps towards ecological speciation, unprevented by a high potential for gene flow.

Yearling birds generally display duller colours than adults. This may be due to selection favouring birds with more intensely coloured plumage or to an increase in colour after the first complete moult. Most research to date on the topic has been carried out on species with structural plumage coloration or with carotenoid-based coloration that is produced by the unmodified deposition of pigments. However, no study has been carried out on species whose carotenoids are metabolically modified before deposition. In this study, we assess age-related changes in the carotenoid-based coloration of European Serins, a species that metabolically processes carotenoids before they can be deposited into feathers. Birds were captured over consecutive years and we carried out both cross-sectional and longitudinal analysis. Adults had significantly greater values of lightness and chroma than yearling birds. However, there were no changes in plumage colour when analysing the same individuals captured in subsequent seasons. Plumage lightness and chroma of adult males after moult were related to body mass, suggesting a role of body condition on plumage coloration. Our results suggest that changes in plumage coloration with age in European Serins are due to a selection process that favours more intensely coloured individuals.

Behavioural integration associated with the fusion of two flocks is analyzed in captive siskins (Curduelrs sptncts) by quantifying changes in social behaviour with time since joining. In general there was an increase in the incidence of tolerant behaviour, supplanting attacks and hopping withdrawals with time since fusion of the flocks. However, the number of displays and flights showed the opposite, negative, trend. Taking dominance status into account, the greatest change in behaviour with time since joining is an increase in tolerance by dominants of new flock companions. Factorial analysis of correspondences was used to study how different birds changed their behaviour with time since joining a flock. This analysis showed that the introduction of new birds did not disrupt relationships with familiar birds, and that residents are dominant in interactions with the incoming new flock companions. The analysis also demonstrated that relationships within the new flock had stabilized 20 days after the flocks had joined. The characteristics of the socially integrated group of siskins are quite similar to those described by ROI-IWER & EWALD (1981) in their shepherds hypothesis: dominants tolerate thew subordinates feeding in close proximity, offering them a profitable feeding area, but also supplant them to obtain food; both dominants and subordinates benefit from being in a flock. As a consequence, constant changes of membership in flocks is costly not only because birds lose dominance status, but also the advantages of clear dominant and subordinate roles.

Nest size is commonly believed to be naturally selected,and to covary with requirements of developing eggs andnestlings (Collias & Collias 1984). In many altricial birdspecies, it is an important component of parental effort,as parents devote an important amount of energy andtime to nest building, but by doing so they expose them-selves and their offspring to a substantial predation risk(Martin et al. 2000). In this paper, we studied nest-sizevariation in a Great Tit Parus major population in rela-tion to breeding factors and parental carotenoid-basedplumage characteristics. The Great Tit is a secondary-cavity nesting species and females are solely responsiblefor building the nest (Gosler 1993). Sexual signalling viacarotenoid-based plumage coloration is known to occurin this species (Hill & McGraw 2006). We found thatplumage chroma of female and especially male GreatTits was positively related to nest size, suggesting greaterfemale investment in nest building when mated to malesin good condition.Nest-building behaviour and ultimately the nest itselfare often associated with courtship and pair formation(Collias & Collias 1984, Soler et al. 1998a). Further,nest-building behaviour may be involved in post-matingsexual communication between partners (Soler et al.1998a). In this way, individuals may increase their nest-building effort to signal their quality, or willingness toinvest in the current reproductive event (e.g. Soler et al.2001). Likewise, they may respond to their partner’scharacteristics in a similar way, to promote their invest-ment. However, knowledge of the use of the nest as apost-mating sexual display is limited, and most empiricalevidence comes from species where males are responsi-ble for nest building (Moreno et al. 1994, Hoi et al.1996, Soler et al. 1998b, 2001).Plumage coloration is known to be a sexually selectedcharacter signalling individual quality, and is ofteninvolved in pair formation and courtship (Hill &McGraw 2006). In particular, carotenoid-based plumagecoloration has been the focus of numerous recent stud-ies, and as carotenoids can only be obtained through thediet, they can be reliable indicators of the bearer’s feed-ing efficiency (Senar & Escobar 2002, Senar et al. 2008),body condition (Saks et al. 2003a, 2003b, Ferns & Hins-ley 2008) and survival (Horak et al. 2001). Thus, carot-enoid-based plumage coloration can reflect individualparenting ability (Senar et al. 2002, Doutrelant et al.2008), and consequently could be expected to affect sev-eral components of parental investment and resourceallocation (Clutton-Brock & Godfray 1991). In this way,nest-size variation may be related to parental quality,which in turn may be reflected by the parents’ plumagecoloration.METHODSThe study was performed in a forest area (c.4km

Siskins Carduelis spinus show great variation in the acquisition of adult plumage, so that yearling birds can be classified as either “delayed” (i.e. still showing yearling plumage) or “advanced” (i.e. with an adult plumaged appearance). The extent of moult in males is related to the size of their black bib, which in turn is highly correlated with their social dominance rank. Autumn male body mass is higher in advanced than in delayed moult birds, but by winter the relationship is reversed, suggesting a trade-off between investment in moult and subsequent body condition. Results were similar in Spain and Britain. A possible cost of advancing moult is suggested by an analysis of aggressive interactions at bird feeding tables which showed that adult males discriminate between delayed and advanced birds, directing most aggression towards adult-looking yearling males. The results suggest that the variation in the extent of postjuvenile moult is not only related to energetic constraints but has other important behavioural and ecological implications.

Fidelity to previous wintering areas (i.e. site fidelity) has important ecological and evolutionary implications. However, since the percentage of recaptures of ringed birds at the same wintering area in subsequent years does not allow the estimation of the proportion of birds alive that exhibit site fidelity, previous studies on different passerine species have failed to show the true extent of this site fidelity. Here we use a recent approach, based on the comparison of survival rate estimates from capture-recapture data at single field stations with recovery data from a much larger area. The idea is to determine the proportion of birds still alive that return to the area. The study was carried out on the Blackcap Sylvia atricapilla, comparing the capture-recapture data of two field stations (Pilas [SW] and Tiana [NE]) situated 1000 km apart in Spain with the complete winter recovery data of the Spanish Ringing Office. Totals of 1936 and 3976 Blackcaps were ringed at Pilas (1981–1986) and Tiana (1975–1986), respectively, and the numbers of recaptures in subsequent winters were 94 and 34. The pooled annual survival rate estimation based on the two sites is 0.40 (s.e. = 0.05). The annual survival rate estimated from the Spanish ringing recovery data was 0.48 (s.e. = 0.08), which is not significantly different. We can conclude, therefore, that migrant Blackcaps in Spain, if alive, tend to return year after year to the previous wintering site.

Although plumage coloration is recognized to convey valuable information about the bearer’s parental abilities, few studies have explored the relationship between coloration and nest defence. In this study in Great Tit Parus major, we analysed the relationship between nest defence and melanin- as well as carotenoid-based plumage coloration, after controlling for ecological variables known to influence nest defence. A principal components analysis was applied to classify birds according to how vigorously they defended the nest, and the intensity of nest defence was tested against plumage coloration. Males with a large black tie defended their nests more vigorously, but no such effect was found for yellow breast coloration. This suggests that melanin-based coloration in the Great Tit is associated with aggression, including both dominanceaggression and nest defence, whereas carotenoid-based coloration is not. The challenge in future studies will be to demonstrate whether females use this trait as an ornament to assess male quality and whether they trade off between the different ornaments a male may exhibit.

More ornamented individuals are supposed to signal their superior quality and health, however the development of larger ornaments or brighter plumages can affect their survival probabilities. The survival of male serins Serinus serinus in relation to the color characteristics of carotenoid-derived breast coloration was analyzed in a six-year capture — recapture study in northeastern Spain. A total of 210 males were individually marked generating 340 captures, between 1997 and 2003. The model with the best fit indicated a quadratic relationship between brightness of carotenoid-derived coloration and survival, independent of time and age of the birds, so that individuals with intermediate plumage brightness survived longer. Hence, results stress that plumage color in male serins is under stabilizing natural selection, with reduced survival both in drabber and brighter individuals. While lower condition of drabber individuals can explain their lower survival, brighter birds can suffer more from predation risk or from a higher investment of resources into mate attraction and/or reproduction.

Natural selection is demonstrated in most natural populations which suggests that populations are dispatched from their adaptive peaks as a result of selection on correlated characters, or conflicting selection between the sexes. We analysed patterns of survival selection in a population of serins (Serinus serinus) outside Barcelona over a period of 13 years. There was directional selection for increased wing length in males and females accompanied by strong disruptive selection on both tail and wing length in males and a selection against a positive correlation between the two characters in males. In females there was directional selection for increased bill width but decreased bill depth, which should be contrasted to the stabilizing selection acting on bill depth in males. There were conflicting selection on the characters within a sex and conflicting selection of the same characters between sexes, which constrain the rate of access to the nearest adaptive peak.