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.

Experimental study of the effect of preen oil against feather bacteria in passerine birds.

Avian plumage harbors various pathogens such as feather-degrading bacteria, which have the potential to reduce host fitness. A growing body of evidence suggests that the secretion of the uropygial gland of birds-preen oil-acts as one of the first lines of defence against harmful bacteria. However, previous studies on the antimicrobial impact of preen oil have yielded controversial results. The impact of preen oil on bacterial densities of feathers was experimentally investigated in two passerine species: great tits Parus major and pied flycatchers Ficedula hypoleuca. More specifically, we tested whether the antibacterial effect of the preen oil secreted by the same individual differs from that of the preen oil originating from the gland of other species. In the laboratory, ventral feathers were treated with preen oil from (1) an individual's own gland, (2) from the gland of another passerine species, or (3) from the gland of a phylogenetically distant bird species. We detected a significant antibacterial effect of preen oil on bacteria that were attached to feathers, though the effect did not depend on whether the oil originated from the individual's own gland or from the gland of another bird species. However, treatment with preen oil suppressed the density of bacteria more in the pied flycatcher than in the great tit. This is the first study providing experimental evidence that preen oil represents an important antimicrobial mechanism against those plumage bacteria that are attached to feathers.

Host dispersal shapes the population structure of a tick-borne bacterial pathogen.

Birds are hosts for several zoonotic pathogens. Because of their high mobility, especially of longdistance migrants, birds can disperse these pathogens, affecting their distribution and phylogeography. We focused on Borrelia burgdorferi sensu lato, which includes the causative agents of Lyme borreliosis, as an example for tick-borne pathogens, to address the role of birds as propagation hosts of zoonotic agents at a large geographical scale. We collected ticks from passerine birds in 11 European countries. B. burgdorferi s.l. prevalence in Ixodes spp. was 37% and increased with latitude. The fieldfare Turdus pilaris and the blackbird T. merula carried ticks with the highest Borrelia prevalence (92 and 58%, respectively), whereas robin Erithacus rubecula ticks were the least infected (3.8%). Borrelia garinii was the most prevalent genospecies (61%), followed by B. valaisiana (24%), B. afzelii (9%), B. turdi (5%) and B. lusitaniae (0.5%). A novel Borrelia genospecies "Candidatus Borrelia aligera" was also detected. Multilocus sequence typing (MLST) analysis of B. garinii isolates together with the global collection of B. garinii genotypes obtained from the Borrelia MLST public database revealed that: (a) there was little overlap among genotypes from different continents, (b) there was no geographical structuring within Europe, and (c) there was no evident association pattern detectable among B. garinii genotypes from ticks feeding on birds, questing ticks or human isolates. These findings strengthen the hypothesis that the population structure and evolutionary biology of tick-borne pathogens are shaped by their host associations and the movement patterns of these hosts.

Corvids exhibit dynamic risk assessment during escape.

It is widely accepted that stationary prey are able to carefully assess the risk levels associated with an approaching predator to make informative decisions on when to escape. However, little is known about subsequent decision-making process. We set out to compare whether escape durations of three species of corvids differ depending on how a human observer (in the role of a predator) behaves after the escape has begun. When birds were being followed during escape, escape durations were the longest, escape trajectory was modified the most during escape, and a larger proportion of individuals changed from terrestrial to aerial escape strategy compared to observations where birds were not followed. Mean horizontal escape angle of ca 120° was also a potential indication that monitoring the threat is taken into account when deciding on the escape trajectory. While there were some differences between the behaviour of these three closely related species, the general patterns supported the notion that birds dynamically assess risk during escape to find an optimal balance between getting caught and spending too much time and energy on escaping. Further research using different predator-prey combinations or making comparisons between habitats could help understand the generality of our results.

Maternal Care in Free-Ranging Arboreal Grey-Cheeked Mangabeys (Lophocebus albigena johnstoni) in Kibale National Park, Uganda.

Maternal styles have been intensively studied in a variety of terrestrial species of primates, but far less in arboreal species. However, to have a balanced view of the evolution of maternal care, it is necessary to investigate this behaviour in the context of habitat. Here, we investigate whether the mother's parity, age and dominance rank, as well as the infant's age and sex, influence maternal care and mother-infant proximity in arboreal grey-cheeked mangabeys (Lophocebus albigena). We observed 13 mother-infant dyads in four free-ranging groups for 6 months. Our main finding is that maternal care is a dynamic process affected by a mix of mothers' and infants' characteristics. We found that first-time mothers spent more time watching their infants than multiparous mothers, who carried, groomed and protected their infants more often. We also found that low-ranking mothers prevented their infants from leaving them more often than did high-ranking mothers. Moreover, mothers adjusted their care as infants became older. They groomed and protected female infants more than male infants, behaviours common in female-bonded species. Our study shows the ever-changing dynamics of maternal care related to infant age and highlights the role of the mother's parity and rank in this process.

Phenological sensitivity to climate change is higher in resident than in migrant bird populations among European cavity breeders.

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 and flycatchers of on average 0.94 days per decade over the current study period. Interestingly, this divergence was stronger at lower latitudes where the interval between tit and flycatcher phenology is smaller and winter conditions can be considered more favorable for resident birds. This could indicate that phenological adjustment to climate change by flycatchers is increasingly hampered by competition with resident species. Indeed, we found that tit laying date had an additional effect on flycatcher laying date after controlling for temperature, and this effect was strongest in areas with the shortest interval between both species groups. Combined, our results suggest that the differential effect of climate change on species groups with overlapping breeding ecology affects the phenological interval between them, potentially affecting interspecific interactions.

Metabolic rate associates with, but does not generate covariation between, behaviours in western stutter-trilling crickets, Gryllus integer.

The causes and consequences of among-individual variation and covariation in behaviours are of substantial interest to behavioural ecology, but the proximate mechanisms underpinning this (co)variation are still unclear. Previous research suggests metabolic rate as a potential proximate mechanism to explain behavioural covariation. We measured the resting metabolic rate (RMR), boldness and exploration in western stutter-trilling crickets, Gryllus integer, selected differentially for short and fast development over two generations. After applying mixed-effects models to reveal the sign of the covariation, we applied structural equation models to an individual-level covariance matrix to examine whether the RMR generates covariation between the measured behaviours. All traits showed among-individual variation and covariation: RMR and boldness were positively correlated, RMR and exploration were negatively correlated, and boldness and exploration were negatively correlated. However, the RMR was not a causal factor generating covariation between boldness and exploration. Instead, the covariation between all three traits was explained by another, unmeasured mechanism. The selection lines differed from each other in all measured traits and significantly affected the covariance matrix structure between the traits, suggesting that there is a genetic component in the trait integration. Our results emphasize that interpretations made solely from the correlation matrix might be misleading.

Interspecific variation in the relationship between clutch size, laying date and intensity of urbanization in four species of hole-nesting birds.

The increase in size of human populations in urban and agricultural areas has resulted in considerable habitat conversion globally. Such anthropogenic areas have specific environmental characteristics, which influence the physiology, life history, and population dynamics of plants and animals. For example, the date of bud burst is advanced in urban compared to nearby natural areas. In some birds, breeding success is determined by synchrony between timing of breeding and peak food abundance. Pertinently, caterpillars are an important food source for the nestlings of many bird species, and their abundance is influenced by environmental factors such as temperature and date of bud burst. Higher temperatures and advanced date of bud burst in urban areas could advance peak caterpillar abundance and thus affect breeding phenology of birds. In order to test whether laying date advance and clutch sizes decrease with the intensity of urbanization, we analyzed the timing of breeding and clutch size in relation to intensity of urbanization as a measure of human impact in 199 nest box plots across Europe, North Africa, and the Middle East (i.e., the Western Palearctic) for four species of hole-nesters: blue tits (Cyanistes caeruleus), great tits (Parus major), collared flycatchers (Ficedula albicollis), and pied flycatchers (Ficedula hypoleuca). Meanwhile, we estimated the intensity of urbanization as the density of buildings surrounding study plots measured on orthophotographs. For the four study species, the intensity of urbanization was not correlated with laying date. Clutch size in blue and great tits does not seem affected by the intensity of urbanization, while in collared and pied flycatchers it decreased with increasing intensity of urbanization. This is the first large-scale study showing a species-specific major correlation between intensity of urbanization and the ecology of breeding. The underlying mechanisms for the relationships between life history and urbanization remain to be determined. We propose that effects of food abundance or quality, temperature, noise, pollution, or disturbance by humans may on their own or in combination affect laying date and/or clutch size.

Acute embryonic exposure to corticosterone alters physiology, behaviour and growth in nestlings of a wild passerine.

Maternally-derived glucocorticoids can modify the normal development of young animals. To date, little is known about maternal effects that are mediated by acute embryonic exposure to glucocorticoids. In birds, elevated maternal transmission of corticosterone (CORT) to egg albumen is mainly dependent on acute stress. In this study, we increased CORT levels in the egg albumen of a wild passerine, the great tit (Parus major), breeding in favourable deciduous and less suitable coniferous habitat. Subsequently we measured the somatic growth, baseline and acute glucocorticoid responses, immunity and behaviour of prenatally manipulated offspring with respect to control siblings. We found that prenatally CORT-exposed nestlings had lower baseline CORT levels, a more rapid decline in CORT during recovery from a standardized stressor, and a reduced heterophil/lymphocyte ratio compared with controls. Although stress-induced total CORT levels remained unchanged, free CORT levels were significantly lower and the levels of corticosteroid binding globulins (CBG) significantly higher in experimental offspring. Prenatally CORT-exposed offspring begged longer after hatching than controls. Stress-induced behavioural activity of fledglings did not differ between treatments, while its association with baseline CORT levels was significant in the control group only. The body mass and tarsus length of fledglings was positively affected by manipulation in unfavourable coniferous habitat only. We conclude that maternal effects related to elevated levels of albumen CORT modify diverse aspects of offspring phenotype and potentially increase offspring performance in resource poor environments. Moreover, our results indicate that maternal glucocorticoids may suppress the effect of hormones on behavioural responses.

Call rates of mothers change with maternal experience and with infant characteristics in free-ranging gray-cheeked mangabeys.

Studies have shown that becoming a mother triggers important social changes within females, according to both social experience and infant characteristics, showing different maternal concerns. But how this impacts call usage has been far less studied. Based on 6 months of observations of five free-ranging groups of gray-cheeked mangabeys, we investigated variations in the production of three call types (contact, excitement, and alarm calls) in 29 females of different ages, dominance ranks, and infant rearing experiences: 15 females with infants of different ages and sexes, and 14 females without infants. We found that in females with infants-both maternal and infant characteristics influenced call production in a call type-dependent way. Females produced contact calls at a higher rate during the first month of infant age and after weaning when infants start to move away. Mothers of daughters produced more contact calls than mothers of sons. More excitement calls were recorded for first-time and young mothers and for females with young infants, while alarm call rates were not influenced by any of these factors. Increased mother-infant spatial separation enhanced only contact and excitement call rates. Finally, we found that females with infants vocalized much more than females without infants. Our results contribute to the current debate about the social factors responsible for the flexibility of call usage in nonhuman primates and open new lines for research on mothering behavior in forest-dwelling species. Am. J. Primatol. 78:983-991, 2016. © 2016 Wiley Periodicals, Inc.

Manipulation of parental effort affects plumage bacterial load in a wild passerine.

It has been suggested that plumage microorganisms play an important role in shaping the life histories of wild birds. Some bacteria may act as pathogens or cause damage to feathers, and thereby reduce individual fitness. Intense parental care in birds can result in a reduction of self-maintenance and preening behavior in parents and therefore might affect the dynamics of microbiota living on their feathers. However, experimental evidence of this relationship is virtually absent. We manipulated the parental effort of wild breeding pied flycatcher (Ficedula hypoleuca) females by modifying their brood size or temporarily removing male partners. We expected that experimentally decreasing or increasing parental effort would affect feather sanitation in females and therefore also bacterial density on their plumage. In accordance with this hypothesis, manipulation affected the density of free-living bacteria: females with reduced broods had the lowest number of free-living bacteria on their feathers, while females left without male partners had the highest. However, manipulation did not have a significant effect on the densities of attached bacteria. Our results provide experimental evidence that a trade-off between self-maintenance and parental effort affects plumage bacterial densities in birds.

Urbanized birds have superior establishment success in novel environments.

Many animals have adapted to the proximity of humans and thereby gained an advantage in a world increasingly affected by human activity. Numerous organisms have invaded novel areas and thereby increased their range. Here, we hypothesize that an ability to thrive in urban habitats is a key innovation that facilitates successful establishment and invasion. We test this hypothesis by relating the probability of establishment by birds on oceanic islands to the difference in breeding population density between urban and nearby rural habitats as a measure of urbanization in the ancestral range. This measure was the single-most important predictor of establishment success and the only statistically significant one, with additional effects of sexual dichromatism, number of releases and release effort, showing that the ability to cope with human proximity is a central component of successful establishment. Because most invasions occur as a consequence of human-assisted establishment, the ability to cope with human proximity will often be of central importance for successful establishment.

Resource availability as a proxy for terminal investment in a beetle.

Terminal investment hypothesis is a longstanding theoretical idea that organisms should increase their reproductive effort as their prospects for survival and reproduction decline. However, numerous attempts to test the terminal investment in reproduction have yielded contradictory results. This study reports an experimental confirmation of the terminal investment hypothesis. It was predicted that immune-challenged yellow mealworm beetles (Tenebrio molitor) are more likely to follow terminal investment strategy when their food resources are limited. Our results suggest the key role of food resources while making decisions to follow a terminal investment strategy. We found that male individuals invested in their sexual attractiveness at the expense of immune response and survival when food was not available. In contrast, the beetles did not decrease their lifespan and did not invest in the attractiveness of their sex odours under conditions of food ad libitum. Our results show the importance of food availability and quality in understanding the evolution of reproductive strategies.

Variation in clutch size in relation to nest size in birds.

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.

Large-scale geographical variation in eggshell metal and calcium content in a passerine bird (Ficedula hypoleuca).

Birds have been used as bioindicators of pollution, such as toxic metals. Levels of pollutants in eggs are especially interesting, as developing birds are more sensitive to detrimental effects of pollutants than adults. Only very few studies have monitored intraspecific, large-scale variation in metal pollution across a species' breeding range. We studied large-scale geographic variation in metal levels in the eggs of a small passerine, the pied flycatcher (Ficedula hypoleuca), sampled from 15 populations across Europe. We measured 10 eggshell elements (As, Cd, Cr, Cu, Ni, Pb, Zn, Se, Sr, and Ca) and several shell characteristics (mass, thickness, porosity, and color). We found significant variation among populations in eggshell metal levels for all metals except copper. Eggshell lead, zinc, and chromium levels decreased from central Europe to the north, in line with the gradient in pollution levels over Europe, thus suggesting that eggshell can be used as an indicator of pollution levels. Eggshell lead levels were also correlated with soil lead levels and pH. Most of the metals were not correlated with eggshell characteristics, with the exception of shell mass, or with breeding success, which may suggest that birds can cope well with the current background exposure levels across Europe.

Correlations between social context and fecal glucocorticoid metabolite concentrations in free-ranging female gray-cheeked mangabeys (Lophocebus albigena) in Kibale National Park, Uganda.

An elevated concentration of glucocorticoids is an indicator of stress, and chronically high glucocorticoid levels are often associated with poor health and reduced fertility. We explored conditions that might be stressors in the lives of adult female gray-cheeked mangabeys (Lophocebus albigena) by measuring fecal glucocorticoid metabolites (fGCM) concentrations. During a six-month study we collected 109 fecal samples from 28 adult females from five groups in Kibale National Park, Uganda. We examined fecal fGCM levels of individual females relative to their own reproductive status (cycling or not cycling) and that of other females and to the presence of newcomer (immigrant) males. We found elevated fGCM concentrations in females when other females in their groups were at the peak of sexual swelling, and when immigrant males joined the group.

Acute stress affects the corticosterone level in bird eggs: a case study with great tits (Parus major).

In vertebrates, stress experienced by mothers during the early stages of reproduction is an important source of epigenetic modifications in their offspring. Birds represent excellent models to test such effects as their maternal investment can be quantified in terms of egg quality. Recently, it has been demonstrated that corticosterone (CORT) can be transmitted from a female bird into its eggs. However, there is little published evidence about maternal effects that are mediated by acute stress. In this study, we demonstrated that female great tits Parus major facing an aerial predator during egg formation increased CORT concentration in eggs that were laid the morning after the treatment. By presenting a predator model to each experimental nest twice a day, we found that maternal stress influences corticosterone content in eggs during a time period from albumen production in the magnum until the initial phase of shell secretion, when additional water is added to the egg in the shell gland. We also found a positive correlation between the duration of parental alarm calls and CORT concentration in eggs. In conclusion, the response of female passerines to predatory cues brings about a maternal effect that may have negative consequences for offspring performance. We also suggest that the total duration of the behavioral response to a stressor is an important determinant of CORT levels in the albumen of bird eggs.

High urban population density of birds reflects their timing of urbanization.

Living organisms generally occur at the highest population density in the most suitable habitat. Therefore, invasion of and adaptation to novel habitats imply a gradual increase in population density, from that at or below what was found in the ancestral habitat to a density that may reach higher levels in the novel habitat following adaptation to that habitat. We tested this prediction of invasion biology by analyzing data on population density of breeding birds in their ancestral rural habitats and in matched nearby urban habitats that have been colonized recently across a continental latitudinal gradient. We estimated population density in the two types of habitats using extensive point census bird counts, and we obtained information on the year of urbanization when population density in urban habitats reached levels higher than that of the ancestral rural habitat from published records and estimates by experienced ornithologists. Both the difference in population density between urban and rural habitats and the year of urbanization were significantly repeatable when analyzing multiple populations of the same species across Europe. Population density was on average 30 % higher in urban than in rural habitats, although density reached as much as 100-fold higher in urban habitats in some species. Invasive urban bird species that colonized urban environments over a long period achieved the largest increases in population density compared to their ancestral rural habitats. This was independent of whether species were anciently or recently urbanized, providing a unique cross-validation of timing of urban invasions. These results suggest that successful invasion of urban habitats was associated with gradual adaptation to these habitats as shown by a significant increase in population density in urban habitats over time.

Climate change, breeding date and nestling diet: how temperature differentially affects seasonal changes in pied flycatcher diet depending on habitat variation.

1. Climate warming has led to shifts in the seasonal timing of species. These shifts can differ across trophic levels, and as a result, predator phenology can get out of synchrony with prey phenology. This can have major consequences for predators such as population declines owing to low reproductive success. However, such trophic interactions are likely to differ between habitats, resulting in differential susceptibility of populations to increases in spring temperatures. A mismatch between breeding phenology and food abundance might be mitigated by dietary changes, but few studies have investigated this phenomenon. Here, we present data on nestling diets of nine different populations of pied flycatchers Ficedula hypoleuca, across their breeding range. This species has been shown to adjust its breeding phenology to local climate change, but sometimes insufficiently relative to the phenology of their presumed major prey: Lepidoptera larvae. In spring, such larvae have a pronounced peak in oak habitats, but to a much lesser extent in coniferous and other deciduous habitats. 2. We found strong seasonal declines in the proportions of caterpillars in the diet only for oak habitats, and not for the other forest types. The seasonal decline in oak habitats was most strongly observed in warmer years, indicating that potential mismatches were stronger in warmer years. However, in coniferous and other habitats, no such effect of spring temperature was found. 3. Chicks reached somewhat higher weights in broods provided with higher proportions of caterpillars, supporting the notion that caterpillars are an important food source and that the temporal match with the caterpillar peak may represent an important component of reproductive success. 4. We suggest that pied flycatchers breeding in oak habitats have greater need to adjust timing of breeding to rising spring temperatures, because of the strong seasonality in their food. Such between-habitat differences can have important consequences for population dynamics and should be taken into account in studies on phenotypic plasticity and adaptation to climate change.

Geographical variation in egg mass and egg content in a passerine bird.

Reproductive, phenotypic and life-history traits in many animal and plant taxa show geographic variation, indicating spatial variation in selection regimes. Maternal deposition to avian eggs, such as hormones, antibodies and antioxidants, critically affect development of the offspring, with long-lasting effects on the phenotype and fitness. Little is however known about large-scale geographical patterns of variation in maternal deposition to eggs. We studied geographical variation in egg components of a passerine bird, the pied flycatcher (Ficedula hypoleuca), by collecting samples from 16 populations and measuring egg and yolk mass, albumen lysozyme activity, yolk immunoglobulins, yolk androgens and yolk total carotenoids. We found significant variation among populations in most egg components, but ca. 90% of the variation was among individuals within populations. Population however explained 40% of the variation in carotenoid levels. In contrast to our hypothesis, we found geographical trends only in carotenoids, but not in any of the other egg components. Our results thus suggest high within-population variation and leave little scope for local adaptation and genetic differentiation in deposition of different egg components. The role of these maternally-derived resources in evolutionary change should be further investigated.