The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird.

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

Video evidence that cuckoos farm their hosts by ejecting nestlings.

When host nests are scarce, avian brood parasites would benefit from behaviours that increase the availability of suitable nests. Several studies reported ejection of host nestlings from nests by brood parasites; however, whether brood parasites do so to induce the host to re-nest and thus increase opportunities for future parasitism (i.e. 'farming' behaviour) remains unclear. Here, we report observational evidence of farming behaviour by a common cuckoo Cuculus canorus female in a Daurian redstart Phoenicurus auroreus population: (1) the cuckoo destroyed a host nest by ejecting all nestlings, (2) the host then produced a new nest and (3) the cuckoo successfully parasitized the replacement nest. We suggest that farming behaviour may be more common, but often goes undetected because it requires intense nest monitoring.

Removal of older males increases extra-pair siring success of yearling males.

In animals, reproductive performance typically improves over time early in life. Several ultimate and proximate mechanisms may contribute to such an age-related improvement and these mechanisms can act in a relative or in an absolute sense. Low performance of young individuals may be the consequence of a comparison or competition with older individuals (relative), or it may be due to specific traits of young individuals and be unrelated to the presence of older competitors (absolute). Here, we perform a test to disentangle whether the effect of age class (yearling or older) on male extra-pair siring success is relative or absolute. Male age is the most consistent predictor of male extra-pair siring success across bird species, yet the mechanisms underlying this pattern are not well understood. Low extra-pair siring success of yearling males may be a consequence of the presence of older ("adult") males (hypothesis 1), because adult males are more successful in intra- and intersexual interactions or because females prefer to copulate with adult males when available (relative preference). Alternatively, low extra-pair siring success of yearlings may be independent of the presence of adult males (hypothesis 2), for example, if yearling males on average invest less in extra-pair behavior or if females avoid them as extra-pair mates, independent of the availability of older males (absolute preference). To distinguish between these 2 hypotheses, we experimentally manipulated the age structure of a nest-box-breeding population of blue tits (Cyanistes caeruleus) by removing almost all adult males, and compared patterns of extra-pair paternity in the experimental year with those from the preceding 15 "control" years. Removal of adult males resulted in a substantial increase in the extra-pair siring success of yearling males compared to the "control" years, but did not affect the population-level frequency of extra-pair paternity or its spatial patterns. Our results provide clear evidence that extra-pair siring success of yearlings can increase and that it depends on the presence of older males in the population, indicating a relative effect of age on reproductive performance. These results suggest that older males outcompete yearling males in direct or indirect interactions, in sperm competition or as a result of differences in attractiveness to females.

Mutual mate guarding with limited sexual conflict in a sex-role-reversed shorebird.

Mate guarding is typically considered a male strategy to protect paternity. However, under some circumstances, females might also benefit from guarding their mate. Female mate guarding might be particularly important in socially polyandrous species in which females compete for access to care-giving males. Because males also benefit from being near their partner to avoid paternity loss, pair members may have a mutual interest in mate guarding in polyandrous species. We studied the time spent together and movements that lead to separation, as behavioral measures of mate guarding, in the classically polyandrous red phalarope (Phalaropus fulicarius). We equipped 64 breeding pairs with miniaturized telemetry loggers with GPS to assess variation in mate-guarding intensity in relation to breeding phenology and season, nest attendance, and the occurrence of extrapair paternity. We show that red phalarope pairs were almost continuously together in the days before clutch initiation with no sex bias in separation movements, indicating mutual contribution to mate guarding. Our results suggest that in red phalaropes, both pair members guard their mate, with limited sexual conflict arising through biases in the operational sex ratio and a trade-off with male nest attendance. We found no clear relationship between mate-guarding intensity and the occurrence of extrapair paternity. In this non-territorial socially polyandrous species, mutual mate guarding might be the process underlying the evolution of a brief but strong social pair bond, with no other purpose than producing a clutch for a care-giving male.

Genotyping blastoderms of avian eggs.

Undeveloped eggs occur frequently in birds and are often considered infertile, and discarded. However, the majority of undeveloped eggs may in fact have been fertilised and embryos might have died at an early stage. Such eggs contain valuable information, for example about offspring sex and paternity, and level of inbreeding. Obtaining such information may also give insight into the patterns and causes of early embryo mortality. Here we describe a simple technique for removing embryo cells from the blastoderm to obtain DNA to genotype the offspring and unequivocally ascertain fertilisation status, while retaining the overlying perivitelline layer (PVL) for sperm counts over the entire membrane. We tested this method on freshly collected eggs (high-quality material), as well as on eggs from abandoned clutches and unhatched eggs (potentially deteriorated material) of blue tits (Cyanistes caeruleus). We sampled a total of 707 eggs from a wild population of blue tits, extracted DNA from the eggs' blastoderm using a Qiagen kit, and genotyped the samples with 14 polymorphic microsatellite markers, plus one sexing marker. Overall, we successfully genotyped 97% of all eggs. Our study is the most extensive dataset of genotyped undeveloped eggs to date and demonstrates that one can reliably genotype undeveloped fertile eggs as well as retain the PVL for observations of sperm and embryo cells.

Sexual selection for extreme physical performance in a polygynous bird is associated with exceptional sex differences in oxygen carrying capacity.

In many animals, males compete for access to fertile females. The resulting sexual selection leads to sex differences in morphology and behaviour, but may also have consequences for physiology. Pectoral sandpipers are an arctic-breeding polygynous shorebird in which males perform elaborate displays around-the-clock and move over long distances to sample potential breeding sites, implying the need for physiological adaptations to cope with extreme endurance. We examined the oxygen carrying capacity of pectoral sandpipers, measured as the volume percentage of red blood cells in blood (haematocrit, Hct). We found a remarkable sex difference in Hct levels, with males having much higher values (58.9 ± 3.8 s.d.) than females (49.8 ± 5.3 s.d.). While Hct values of male pectoral sandpipers are notable for being among the highest recorded in birds, the sex difference we report is unprecedented and more than double that of any previously described. We also show that Hct values declined after arrival to the breeding grounds in females, but not in males, suggesting that males maintain an aerobic capacity during the mating period equivalent to that sustained during trans-hemispheric migration. We conclude that sexual selection for extreme physical performance in male pectoral sandpipers has led to exceptional sex differences in oxygen carrying capacity.

A dawn and dusk chorus will emerge if males sing in the absence of their mate.

The spring dawn and dusk chorus of birds is a widespread phenomenon, yet its origin remains puzzling. We propose that a dawn and dusk chorus will inevitably arise if two criteria are met: (1) females leave their roost later in the morning and go to roost earlier in the evening than their mate, and (2) males sing more when separated from their mate. Previous studies on blue tits (Cyanistes caeruleus) support the first criterion. We here report that males sing at a higher rate whenever they are separated from their mate and that song rate increases with the duration of female absence. These findings can explain the existence of the dawn and dusk chorus in blue tits, and they can explain why the dawn chorus is more pronounced than the dusk chorus, as is typically observed. An exhaustive literature search provides support for both criteria of the 'absent mate' hypothesis in several passerine birds. We found no evidence contradicting the hypothesis. The new hypothesis is not inconsistent with many of the existing hypotheses about dawn singing, but may be a more general explanation for the occurrence of a dawn and dusk chorus. We describe how the 'absent mate' hypothesis leads to testable predictions about daily and seasonal variation in song output.

Evolutionary predictors of the specific colors of birds.

Animal coloration is one of the most conspicuous aspects of human-perceived organismal diversity, yet also one of the least understood. In particular, explaining why species have specific colors (e.g., blue vs. red) has proven elusive. Here, we quantify for nearly all bird species, the proportion of the body covered by each of 12 human-visible color categories, and test whether existing theory can predict the direction of color evolution. The most common colors are black, white, gray and brown, while the rarest are green, blue, purple, and red. Males have more blue, purple, red, or black, whereas females have more yellow, brown, or gray. Sexual dichromatism is partly due to sexual selection favoring ornamental colors in males but not in females. However, sexual selection also correlated positively with brown in both sexes. Strong social selection favors red and black, colors used in agonistic signaling, with the strongest effects in females. Reduced predation risk selects against cryptic colors (e.g., brown) and favors specific ornamental colors (e.g., black). Nocturnality is mainly associated with brown. The effects of habitat use support the sensory drive theory for camouflage and signaling. Darker colors are more common in species living in wet and cold climates, matching ecogeographical rules. Our study unambiguously supports existing theories of color evolution across an entire class of vertebrates, but much variation remains unexplained.

Skyglow relieves a crepuscular bird from visual constraints on being active.

Artificial light at night significantly alters the predictability of the natural light cycles that most animals use as an essential Zeitgeber for daily activity. Direct light has well-documented local impacts on activity patterns of diurnal and nocturnal organisms. However, artificial light at night also contributes to an indirect illumination of the night sky, called skyglow, which is rapidly increasing. The consequences of this wide-spread form of artificial night light on the behaviour of animals remain poorly understood, with only a few studies performed under controlled (laboratory) conditions. Using animal-borne activity loggers, we investigated daily and seasonal flight activity of a free-living crepuscular bird species in response to nocturnal light conditions at sites differing dramatically in exposure to skyglow. We find that flight activity of European Nightjars (Caprimulgus europaeus) during moonless periods of the night is four times higher in Belgium (high skyglow exposure) than in sub-tropical Africa and two times higher than in Mongolia (near-pristine skies). Moreover, clouds darken the sky under natural conditions, but skyglow can strongly increase local sky brightness on overcast nights. As a result, we find that nightjars' response to cloud cover is reversed between Belgium and sub-tropical Africa and between Belgium and Mongolia. This supports the hypothesis that cloudy nights reduce individual flight activity in a pristine environment, but increase it when the sky is artificially lit. Our study shows that in the absence of direct light pollution, anthropogenic changes in sky brightness relieve nightjars from visual constraints on being active. Individuals adapt daily activities to artificial night-sky brightness, allowing them more time to fly than conspecifics living under natural light cycles. This modification of the nocturnal timescape likely affects behavioural processes of most crepuscular and nocturnal species, but its implications for population dynamics and interspecific interactions remain to be investigated.

Age trajectories in extra-pair siring success suggest an effect of maturation or early-life experience.

Across birds, male age is the most consistent predictor of extra-pair siring success, yet little is known about age effects on paternity over the lifetime of individuals. Here, we use data from a 13-year study of a population of blue tits (Cyanistes caeruleus) to investigate how extra-pair siring success changes with age within individuals. Our results indicate that extra-pair siring success does not continuously increase with male age. Instead, siring success was related to male age in a threshold fashion, whereby yearling males were less likely to gain paternity than older males. This effect was independent of the age of the social partner, but influenced by the age of the extra-pair female: success of yearlings at siring extra-pair young (EPY) with older females was even lower. Among males that sired at least one EPY, the number of extra-pair mates and the proportion of EPY sired were unrelated to male age. We found no evidence for an influence of selective disappearance on extra-pair reproduction. Senescence, if anything, only occurs at ages blue tits rarely reach. A literature review indicates that an effect of male age on extra-pair siring success may be limited to the switch from yearling to older in many species. Thus, the generally observed age effect on male extra-pair siring success may be linked to age class rather than continuous ageing. This suggests that lack of experience or not fully completed maturation are important drivers of age patterns in extra-pair paternity.

Experimentally advancing morning emergence time does not increase extra-pair siring success in blue tit males.

Extra-pair paternity occurs frequently in socially monogamous birds, but there is substantial variation in extra-pair siring success among males. Several studies have shown that siring success relates to the timing of morning activity, with the earliest active males being more successful, suggesting that early activity is important for acquiring extra-pair copulations. However, these studies are correlational, and it, therefore, remains unclear whether the relationship between timing and extra-pair siring success is causal. An alternative explanation is that successful extra-pair sires tend to be active earlier (e.g., because they are of high quality or in good condition), but that early activity in itself does not increase siring success. We experimentally advanced the emergence time of male blue tits by exposing them to light about half an hour before their natural emergence time. Although males that were exposed to the light treatment emerged from their roost substantially earlier than males that were exposed to a control treatment, light-treated males were not more likely to sire extra-pair offspring. Furthermore, whereas control males showed the expected relation between emergence time and siring success (although not statistically significant), there was no relation between emergence time and extra-pair siring success among light-treated males. Our results suggest that the timing of emergence from the roost is not an important factor underlying extra-pair siring success.

Sexual transmission may drive pair similarity of the cloacal microbiome in a polyandrous species.

All animals host a microbial community within and on their reproductive organs, known as the reproductive microbiome. In free-living birds, studies on the sexual transmission of bacteria have typically focused on a few pathogens instead of the bacterial community as a whole, despite a potential link to reproductive function. Theory predicts higher sexual transmission of the reproductive microbiome in females via the males' ejaculates and higher rates of transmission in promiscuous systems. We studied the cloacal microbiome of breeding individuals of a socially polyandrous, sex-role-reversed shorebird, the red phalarope (Phalaropus fulicarius). We expected (i) higher microbial diversity in females compared to males; (ii) low compositional differentiation between sexes; (iii) lower variation in composition between individuals (i.e. microbiome dispersion) in females than in males; (iv) convergence in composition as the breeding season progresses as a consequence of sexual transmission and/or shared habitat use; and (v) higher similarity in microbial composition between social pair members than between two random opposite-sex individuals. We found no or small between-sex differences in cloacal microbiome diversity/richness and composition. Dispersion of predicted functional pathways was lower in females than in males. As predicted, microbiome dispersion decreased with sampling date relative to clutch initiation of the social pair. Microbiome composition was significantly more similar among social pair members than among two random opposite-sex individuals. Pair membership explained 21.5% of the variation in taxonomic composition and 10.1% of functional profiles, whereas temporal and sex effects explained only 0.6%-1.6%. Consistent with evidence of functional convergence of reproductive microbiomes within pairs, some select taxa and predicted functional pathways were less variable between social pair members than between random opposite-sex individuals. As predicted if sexual transmission of the reproductive microbiome is high, sex differences in microbiome composition were weak in a socially polyandrous system with frequent copulations. Moreover, high within-pair similarity in microbiome composition, particularly for a few taxa spanning the spectrum of the beneficial-pathogenic axis, demonstrates the link between mating behaviour and the reproductive microbiome. Our study is consistent with the hypothesis that sexual transmission plays an important role in driving reproductive microbiome ecology and evolution.

Micro Germline-Restricted Chromosome in Blue Tits: Evidence for Meiotic Functions.

The germline-restricted chromosome (GRC) is likely present in all songbird species but differs widely in size and gene content. This extra chromosome has been described as either a microchromosome with only limited basic gene content or a macrochromosome with enriched gene functions related to female gonad and embryo development. Here, we assembled, annotated, and characterized the first micro-GRC in the blue tit (Cyanistes caeruleus) using high-fidelity long-read sequencing data. Although some genes on the blue tit GRC show signals of pseudogenization, others potentially have important functions, either currently or in the past. We highlight the GRC gene paralog BMP15, which is among the highest expressed GRC genes both in blue tits and in zebra finches (Taeniopygia guttata) and is known to play a role in oocyte and follicular maturation in other vertebrates. The GRC genes of the blue tit are further enriched for functions related to the synaptonemal complex. We found a similar functional enrichment when analyzing published data on GRC genes from two nightingale species (Luscinia spp.). We hypothesize that these genes play a role in maintaining standard maternal inheritance or in recombining maternal and paternal GRCs during potential episodes of biparental inheritance.

Weak antagonistic fitness effects can maintain an inversion polymorphism.

The study of chromosomal inversion polymorphisms has received much recent attention, particularly in cases where inversions have drastic effects on phenotypes and fitness (e.g. lethality of homozygotes). Less attention has been paid to the question of the maintenance of inversion polymorphisms that show only weak effects. Here, we study the maintenance of such an inversion polymorphism that links 250 genes on chromosome Tgu11 in the zebra finch (Taeniopygia guttata). Based on data from over 6000 captive birds, we estimated the effects of this inversion on a wide range of fitness-related traits. We found that, compared with the ancestral allele A, the inverted allele D had small additive beneficial effects on male siring success and on female fecundity. These fitness-enhancing effects may explain the initial spread of the derived D allele (allele frequency 53%). However, individuals that were homozygous for D had a slightly lower survival rate, which may explain why the D allele has not spread to fixation. We used individual-based simulations to examine how an inversion polymorphism with such antagonistic fitness effects behaves over time. Our results indicate that polymorphisms become stabilized at an intermediate allele frequency if the inversion links an additively beneficial allele of small effect size to a recessive weakly deleterious mutation, overall resulting in weak net heterosis. Importantly, this conclusion remains valid over a wide range of selection coefficients against the homozygous DD (up to lethality), suggesting that the conditions needed to maintain the polymorphism may frequently be met. However, the simulations also suggest that in our zebra finch populations, the estimated recessive deleterious effect of the D allele (on survival in captivity) is not quite large enough to prevent fixation of the D allele in the long run. Estimates of fitness effects from free-living populations are needed to validate these results.

Extra-pair paternity and sexual dimorphism in birds.

Differences in the strength of sexual selection between males and females can lead to sexual dimorphism. Extra-pair paternity (EPP) can increase the variance in male reproductive success and hence the opportunity for sexual selection. Previous research on birds suggests that EPP drives the evolution of dimorphism in plumage colour and in body size. Because EPP increases the intensity of sexual selection in males, it should lead to increased dimorphism in species with larger or more colourful males, but decreased dimorphism in species with larger or more colourful females. We explored the covariation between EPP and sexual dimorphism in wing length and plumage colouration in 401 bird species, while controlling for other, potentially confounding variables. Wing length dimorphism was associated positively with the frequency of EPP, but also with social polygamy, sex bias in parental behaviour and body size and negatively with migration distance. The frequency of EPP was the only predictor of plumage colour dimorphism. In support of our prediction, high EPP levels were associated with sexual dichromatism, positively in species in which males are more colourful and negatively in those in which females are more colourful. Contrary to our prediction, high EPP rates were associated with increased wing length dimorphism in species with both male- and female-biased dimorphism. The results support a role for EPP in the evolution of both size and plumage colour dimorphism. The two forms of dimorphism were weakly correlated and predicted by different reproductive, social and life-history traits, suggesting an independent evolution.

Patterns of extra-territorial nest-box visits in a songbird suggest a role in extrapair mating.

Many animals make visits outside of their territory during the breeding period, but these are typically infrequent and difficult to observe. As a consequence, comprehensive data on extra-territorial movements at the population-level are scarce and the function of this behavior remains poorly understood. Using an automated nest-box visit tracking system in a wild blue tit population over six breeding seasons, we recorded all extra-territorial nest-box visits (n = 22 137) related to 1195 individual breeding attempts (761 unique individuals). Sixty-two percent of breeders made at least one extra-territorial visit between the onset of nest building and the day of fledging of their offspring, and individuals visited another nest-box on average on 11% of the days during this period. Visit behavior differed clearly between the sexes, with males making over three times as many extra-territorial forays as females. There was a strong overall seasonal decline in visit behavior, but this was sex dependent, with females showing a strong reduction in the number of extra-territorial visits before the onset of egg laying and males showing a strong and sudden reduction on the day their offspring hatched. The likelihood of visiting a particular nest-box declined sharply with the distance to that box, and blue tits almost exclusively visited direct neighbors. Individuals were more likely to have extrapair offspring with an individual whose box they visited, but they were not more likely to disperse to a box they had visited. Thus, our results are inconsistent with the hypothesis that extra-territorial nest-box visits serve to inform dispersal decisions, but suggest that such visits are linked to extrapair mating opportunities.

Experimental evidence that cuckoos choose host nests following an egg matching strategy.

The arms race between brood parasites and their hosts provides a classic model to study coevolution. Hosts often reject the parasitic egg, and brood parasites should therefore select host nests in which the colour of the eggs best matches that of their own. Although this hypothesis has received some support, direct experimental evidence is still lacking. Here, we report on a study of Daurian redstarts, which show a distinct egg-colour dimorphism, with females laying either blue or pink eggs. Redstarts are often parasitized by common cuckoos, which lay light blue eggs. First, we showed that cuckoo eggs were more similar in spectral reflectance to the blue than to the pink redstart egg morph. Second, we report that the natural parasitism rate was higher in blue than in pink host clutches. Third, we performed a field experiment in which we presented a dummy clutch of each colour morph adjacent to active redstart nests. In this set-up, cuckoos almost always chose to parasitize a blue clutch. Our results demonstrate that cuckoos actively choose redstart nests in which the egg colour matches the colour of their own eggs. Our study thus provides direct experimental evidence in support of the egg matching hypothesis.

Brood parasitism risk drives birds to breed near humans.

Urbanization is transforming ecosystems at a global scale and at an increasing rate,1,2 and its profound consequences for wildlife have been well documented.3,4,5,6 Understanding how animals thrive in the urban environment and how this environment affects (co-)evolutionary processes remains an important challenge.7 Urban environments can provide resources such as food or nest sites (e.g., cavities)10,8,9 and also reduce exposure to predators.11,12 For some species, urban environments may also affect susceptibility to brood parasitism,13,14 but this has never been tested experimentally. Here, we use a combination of field observations and experimental manipulations to show that Daurian redstarts, Phoenicurus auroreus, a common host of the common cuckoo, Cuculus canorus, nest in proximity to humans to avoid brood parasitism. First, redstarts were more likely to be parasitized with increasing distance to the nearest building. Second, redstarts adjusted their nesting location in response to a seasonally predictable change in the risk of brood parasitism. Third, experimentally simulating the presence of cuckoos during a period when they are naturally absent increased the likelihood that redstarts nested indoors or closer to human settlements. These findings suggest that redstarts actively choose to place their nest in the vicinity of a human residence as a defense against cuckoos. Our study exemplifies how animals take advantage of the urban environment by using it as a novel line of defense against detrimental interspecific interactions.

Temperature synchronizes temporal variation in laying dates across European hole-nesting passerines.

Identifying the environmental drivers of variation in fitness-related traits is a central objective in ecology and evolutionary biology. Temporal fluctuations of these environmental drivers are often synchronized at large spatial scales. Yet, whether synchronous environmental conditions can generate spatial synchrony in fitness-related trait values (i.e., correlated temporal trait fluctuations across populations) is poorly understood. Using data from long-term monitored populations of blue tits (Cyanistes caeruleus, n = 31), great tits (Parus major, n = 35), and pied flycatchers (Ficedula hypoleuca, n = 20) across Europe, we assessed the influence of two local climatic variables (mean temperature and mean precipitation in February-May) on spatial synchrony in three fitness-related traits: laying date, clutch size, and fledgling number. We found a high degree of spatial synchrony in laying date but a lower degree in clutch size and fledgling number for each species. Temperature strongly influenced spatial synchrony in laying date for resident blue tits and great tits but not for migratory pied flycatchers. This is a relevant finding in the context of environmental impacts on populations because spatial synchrony in fitness-related trait values among populations may influence fluctuations in vital rates or population abundances. If environmentally induced spatial synchrony in fitness-related traits increases the spatial synchrony in vital rates or population abundances, this will ultimately increase the risk of extinction for populations and species. Assessing how environmental conditions influence spatiotemporal variation in trait values improves our mechanistic understanding of environmental impacts on populations.