Climatic fluctuations during the Quaternary period governed the demography of species and contributed to population differentiation and ultimately speciation. Studies of these past processes have ...previously been hindered by a lack of means and genetic data to model changes in effective population size (Nₑ) through time. However, based on diploid genome sequences of high quality, the recently developed pairwise sequentially Markovian coalescent (PSMC) can estimate trajectories of changes in Nₑ over considerable time periods. We applied this approach to resequencing data from nearly 200 genomes of four species and several populations of the Ficedula species complex of black‐and‐white flycatchers. Nₑ curves of Atlas, collared, pied and semicollared flycatcher converged 1–2 million years ago (Ma) at an Nₑ of ≈ 200 000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate Nₑ trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100–200 thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in Nₑ differed among species, and for pied flycatcher, the temporal dynamics of Nₑ differed between Spanish birds and central/northern European populations. This cautions against extrapolation of demographic inference between lineages and calls for adequate sampling to provide representative pictures of the coalescence process in different species or populations. We also empirically evaluate criteria for proper inference of demographic histories using PSMC and arrive at recommendations of using sequencing data with a mean genome coverage of ≥18X, a per‐site filter of ≥10 reads and no more than 25% of missing data.
Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to ...develop a high‐density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best‐order map contained 4215 markers, with a total distance of 3132 cM and a mean genetic distance between markers of 0.12 cM. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second‐generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super‐scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cM/Mb and correlated closely with chromosome size, from 2 cM/Mb for chromosomes >100 Mb to >10 cM/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cM was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.
Boldness, defined as the behavioural response of individuals when facing a risky situation, is a major personality trait and often phenotypically correlates with other behavioural traits, in ...particular aggressiveness, exploration behaviour and neophobia. Yet, whether such links result from among-individual correlations, i.e. form behavioural syndromes sensu stricto, is often ignored and whether such syndromes may yield individual fitness benefits, and thus be selected for, remains poorly explored. We measured boldness as the nest defence behaviour against a dummy nest predator in a natural population of a small passerine bird, the collared flycatcher, Ficedula albicollis, and investigated the existence of a behavioural syndrome between boldness and two other behavioural traits, aggressiveness (measured as the agonistic response to competitors) and neophobia (measured as the behavioural response to a novel object in a known environment). Then we assessed the links between this potential syndrome and reproductive success, measured as fledging and recruitment success. Boldness score differed between the sexes and depended on whether the partner was present during the test. Nevertheless, it was repeatable, showing that boldness can be considered as a personality trait in our population. We found a positive among-individual correlation between boldness and aggressiveness, showing the existence of a behavioural syndrome between both personality traits. This syndrome was related to reproductive success: the number of fledged young (but not recruitment probability) increased with one integrative value of the boldness–aggressiveness syndrome. Conversely, boldness score was not correlated with neophobia. Our results thus clearly reveal a behavioural syndrome between boldness and aggressiveness with possible consequences for reproductive success in the study population, and therefore raise the question of the evolutionary implications of such a behavioural syndrome.
•Boldness is an important personality trait often correlated with other traits.•We measured boldness in a nest defence context in collared flycatchers.•Boldness was repeatable but not heritable in the study population.•We found a behavioural syndrome between boldness and aggressiveness but not neophobia.•A measure of this behavioural syndrome was related to the number of fledged young.
The use of social information for making decisions is common but can be constrained by behavioural traits via, for example, the ability to gather information. Such constrained information use has ...been described in foraging habitat selection; yet it remains unexplored in the breeding habitat selection context, despite potentially strong fitness consequences. We experimentally tested whether three behavioural traits (aggressiveness, boldness and neophobia) affected the use of heterospecific social information for nest site selection in wild collared flycatchers
. Flycatchers have previously been found to copy or reject an artificial apparent preference of tits (their main competitors) for a nest site feature: they preferred nest-boxes with the same or a different feature, depending on tit early reproductive investment. Here, we confirmed this result and showed that shy individuals and less aggressive old males (i.e. 2 years old or older) copied tit apparent preference, while more aggressive old males rejected the tit preference. Aggressiveness and boldness may allow males to access more information sources or affect males' interactions with dominant tits when selecting a nest site. Our study highlights the links between variation in behaviours and social information use for breeding habitat selection and calls for further work to explore underlying mechanisms.
Abstract The bioacoustic analyses of animal sounds result in an enormous amount of digitized acoustic data, and we need effective automatic processing to extract the information content of the ...recordings. Our research focuses on the song of Collared Flycatcher (Ficedula albicollis) and we are interested in the evolution of acoustic signals. During the last 20 years, we obtained hundreds of hours of recordings of bird songs collected in natural environment, and there is a permanent need for the automatic process of recordings. In this study, we chose an open-source, deep-learning image detection system to (1) find the species-specific songs of the Collared Flycatcher on the recordings and (2) to detect the small, discrete elements so-called syllables within the song. For these tasks, we first transformed the acoustic data into spectrogram images, then we trained two deep-learning models separately on our manually segmented database. The resulted models detect the songs with an intersection of union higher than 0.8 and the syllables higher than 0.7. This technique anticipates an order of magnitude less human effort in the acoustic processing than the manual method used before. Thanks to the new technique, we are able to address new biological questions that need large amount of acoustic data.
The breeding phenology of Collared Flycatchers was studied over an 11-year period (2006‒2011 and 2013‒2017) in oak-maple-lime stands located in the Northern-East of Ukraine (in the National Park ...Homilshanski Lisy). In most years, egg laying began in the first and second ten-day periods of May. The earliest recorded first-egg date (368 broods) was 23 April, while the latest was 5 May. These dates varied from year to year. The relationship between the first-egg date and the date of daily average temperature transition through + 10 °C suggests that birds bred earlier due to warmer local temperatures. The clutch size was negatively correlated with the date of the average air temperature transition through + 5 °C. The earliest hatching date was 15 May, and the latest was 25 May. Fledging typically began in the first half of June. The breeding season’s length ranged from 30 to 42 days, and the breeding cycle was positively correlated with the transition of the average daily temperature through +5 °C. To determine which factors explained the first egg date and clutch size, Generalized Linear Models (GLMs) were conducted. GLMs suggest a correlation between the first-egg date and the sum of effective temperatures (∑T150), arrival date temperature, migration route temperature, and average temperature of the third decade of April. Clutch size is determined by the sum of effective temperature accumulation (∑130) and migration route temperature. Reproductive success is negatively correlated with the average of 30 daily temperatures until the median date.
White plumage areas are widespread among birds but the mechanisms generating individual differences in white feather reflectance are poorly known. Additionally, the proximate mechanisms of ...within‐season feather colour changes in general are also poorly known. Here we explored within‐individual changes in macrostructure and reflectance of the white wing‐patch of female Collared Flycatchers Ficedula albicollis using data from three stages within a breeding season. Changes in brightness and UV chroma were related to changes in the neatness and size of reflective surfaces, respectively. This suggests that white feather reflectance traits may act as indicators of feather intactness and preening activity.
Dispersal is a key life history trait impacting ecological and evolutionary processes. Yet, the fitness consequences of dispersal remain poorly investigated. Using a displacement experiment of 616 ...individuals in a patchy population of collared flycatchers, Ficedula albicollis, we investigated behavioural responses to forced movement in terms of settlement, subsequent breeding performance and return rate. Newly arrived birds were caught and displaced between patches or released back in the patch of capture. We analysed (1) the probability of successful settlement within the study area, (2) for displaced birds, the probability of accepting the forced movement rather than returning to the patch of capture, (3) components of reproductive performance and (4) return rate in subsequent years according to experimental treatment. The probability of settling within the study area tended to be lower for displaced than control birds and was lower for immigrants than local birds. This suggests that displacement induced long-distance dispersal movements or nonbreeding, which could reflect costs of unfamiliarity with the environment. Nondispersers (individuals caught early in the breeding season in the same patch as their previous one) were more likely to return to their patch of capture, probably because of higher benefits of familiarity. Once individuals had settled, their breeding performance did not vary markedly between treatments, although displaced individuals that did not return to their patch of capture raised lighter young than other individuals. This could indicate a lower phenotypic quality of these individuals or, again, a cost of breeding in an unfamiliar environment. Finally, individuals that settled (and nondispersers) were more likely to return to the study area in subsequent years than individuals that disappeared (and immigrants/dispersers, respectively). Together, these results suggest that, in addition to the costs of transience, dispersal (here forced) may entail costs linked to settlement in an unfamiliar habitat.
•Experimentally displaced birds were less likely to settle and breed than controls.•Immigrants were also less likely to settle than local birds.•Once settled, displaced birds raised lighter young than other individuals.•Dispersal may entail costs linked to settlement in an unfamiliar habit.
Relatively little is known about the character of gene expression evolution as species diverge. It is for instance unclear if gene expression generally evolves in a clock‐like manner (by stabilizing ...selection or neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression, we sequenced and compared the transcriptomes of multiple organs from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), two species which diverged less than one million years ago. Ordination analysis separated samples by organ rather than by species. Organs differed in their degrees of expression variance within species and expression divergence between species. Variance was negatively correlated with expression breadth and protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between‐species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression PST approach, we identified genes differentially expressed between species and found 16 genes uniquely expressed in one of the species. For one of these, DPP7, uniquely expressed in collared flycatcher, the absence of expression in pied flycatcher could be associated with a ≈20‐kb deletion including 11 of 13 exons. This study of a young vertebrate speciation model system expands our knowledge of how gene expression evolves as natural populations become reproductively isolated.
Nest site selection significantly affects fitness, so adaptations for assessment of the qualities of available sites are expected. The assessment may be based on personal or social information, the ...latter referring to the observed location and performance of both conspecific and heterospecific individuals. Contrary to large-scale breeding habitat selection, small-scale nest site selection within habitat patches is insufficiently understood. We analyzed nest site selection in the migratory Collared Flycatcher
Ficedula albicollis
in relation to present and past cues provided by conspecifics and by resident tits within habitat patches by using long-term data. Collared Flycatchers preferred nest boxes that were occupied by conspecifics in the previous year. This preference was strongest in breeding pairs where both individuals bred in the same forest patch in the previous year. The results also suggest preference for nest boxes close to boxes where conspecifics had a high breeding success in the previous year, and for nest boxes which are presently surrounded by a high number of breeding Great Tits
Parus major
. The results indicate social information use in nest site selection at a small spatial scale, where Collared Flycatchers use conspecific cues with a time lag of one year and heterospecific cues instantly.
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