Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.

Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation ("differentiation islands") widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (d(xy) and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.

Cross-fostering eggs reveals that female collared flycatchers adjust clutch sex ratios according to parental ability to invest in offspring.

Across animal taxa, reproductive success is generally more variable and more strongly dependent upon body condition for males than for females; in such cases, parents able to produce offspring in above-average condition are predicted to produce sons, whereas parents unable to produce offspring in good condition should produce daughters. We tested this hypothesis in the collared flycatcher (Ficedula albicollis) by cross-fostering eggs among nests and using the condition of foster young that parents raised to fledging as a functional measure of their ability to produce fit offspring. As predicted, females raising heavier-than-average foster fledglings with their social mate initially produced male-biased primary sex ratios, whereas those raising lighter-than-average foster fledglings produced female-biased primary sex ratios. Females also produced male-biased clutches when mated to males with large secondary sexual characters (wing patches), and tended to produce male-biased clutches earlier within breeding seasons relative to females breeding later. However, females did not adjust the sex of individuals within their clutches; sex was distributed randomly with respect to egg size, laying order and paternity. Future research investigating the proximate mechanisms linking ecological contexts and the quality of offspring parents are able to produce with primary sex-ratio variation could provide fundamental insight into the evolution of context-dependent sex-ratio adjustment.

Geographic patterns of genetic differentiation and plumage colour variation are different in the pied flycatcher (Ficedula hypoleuca).

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

Multiphase progenetic development shaped the brain of flying archosaurs.

The growing availability of virtual cranial endocasts of extinct and extant vertebrates has fueled the quest for endocranial characters that discriminate between phylogenetic groups and resolve their neural significances. We used geometric morphometrics to compare a phylogenetically and ecologically comprehensive data set of archosaurian endocasts along the deep evolutionary history of modern birds and found that this lineage experienced progressive elevation of encephalisation through several chapters of increased endocranial doming that we demonstrate to result from progenetic developments. Elevated encephalisation associated with progressive size reduction within Maniraptoriformes was secondarily exapted for flight by stem avialans. Within Mesozoic Avialae, endocranial doming increased in at least some Ornithurae, yet remained relatively modest in early Neornithes. During the Paleogene, volant non-neoavian birds retained ancestral levels of endocast doming where a broad neoavian niche diversification experienced heterochronic brain shape radiation, as did non-volant Palaeognathae. We infer comparable developments underlying the establishment of pterosaurian brain shapes.

Identification of differentially expressed proteins in Ficedula flycatchers.

This is the first report on the large-scale identification and comparison of proteins in non-model organisms, Ficedula flycatchers. It highlights the potential of proteomics approaches in both non-sequenced and non-model organisms for identification of differentially expressed proteins. Not surprisingly, more than 55% of the proteins failed to be identified even though the MS spectra were of high quality. Nevertheless, the protein information obtained in this study will serve as a valuable resource for continued research.

Wing bone geometry reveals active flight in Archaeopteryx.

Archaeopteryx is an iconic fossil taxon with feathered wings from the Late Jurassic of Germany that occupies a crucial position for understanding the early evolution of avian flight. After over 150 years of study, its mosaic anatomy unifying characters of both non-flying dinosaurs and flying birds has remained challenging to interpret in a locomotory context. Here, we compare new data from three Archaeopteryx specimens obtained through phase-contrast synchrotron microtomography to a representative sample of archosaurs employing a diverse array of locomotory strategies. Our analyses reveal that the architecture of Archaeopteryx's wing bones consistently exhibits a combination of cross-sectional geometric properties uniquely shared with volant birds, particularly those occasionally utilising short-distance flapping. We therefore interpret that Archaeopteryx actively employed wing flapping to take to the air through a more anterodorsally posteroventrally oriented flight stroke than used by modern birds. This unexpected outcome implies that avian powered flight must have originated before the latest Jurassic.

Evolutionary analysis of the female-specific avian W chromosome.

The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear-cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution.

Experimental evidence for species-specific habitat preferences in two flycatcher species in their hybrid zone.

Hybrid zones are often found in areas where the environmental characteristics of native habitat of both parental species meet. One of the plausible mechanisms that maintain species distinctiveness, or limit hybridization, is the existence of local species-specific preferences for the natal habitat type. We evaluated this hypothesis for two passerine bird species, the pied Ficedula hypoleuca and collared flycatcher F. albicollis, in their narrow hybrid zone in Central Europe. Both species have quite distinct habitat distributions, and they have also been reported to differ in their foraging niches. In a series of aviary experiments, we demonstrated that both species show distinct preferences for trees from their native area. The pied flycatcher preferred coniferous vegetation, while the collared flycatcher favored deciduous vegetation. In addition, both species differed in foraging substrate preferences. The pied flycatcher preferred to forage in the lower strata on the ground than the canopy, whereas the collared flycatcher foraged more at the canopy level. Both males and females of each species were highly consistent in their preference patterns. Due to the widespread nature of hybrid zones as places with transitional habitat features and the well-known habitat tight associations of various animal taxa with particular habitat types, we propose that habitat preferences might be an important and common mechanism that enhances the formation of conspecific pairs.

Sex chromosome-linked species recognition and evolution of reproductive isolation in flycatchers.

Interbreeding between species (hybridization) typically produces unfit offspring. Reduced hybridization should therefore be favored by natural selection. However, this is difficult to accomplish because hybridization also sets the stage for genetic recombination to dissociate species-specific traits from the preferences for them. Here we show that this association is maintained by physical linkage (on the same chromosome) in two hybridizing Ficedula flycatchers. By analyzing the mating patterns of female hybrids and cross-fostered offspring, we demonstrate that species recognition is inherited on the Z chromosome, which is also the known location of species-specific male plumage traits and genes causing low hybrid fitness. Limited recombination on the Z chromosome maintains associations of Z-linked genes despite hybridization, suggesting that the sex chromosomes may be a hotspot for adaptive speciation.

Sources and timing of calcium intake during reproduction in flycatchers.

Calcium availability may limit the reproductive output of birds and snail shells are considered to be the main source of calcium in many passerine species. This study of collared ( Ficedula albicollis) and pied ( F. hypoleuca) flycatchers evaluates calcium intake of a natural diet in Central Europe, and sex differences in the utilization of experimentally supplemented sources of calcium during the entire breeding period in aviary birds. The study provides the first evidence that successful reproduction of these species depends on the availability of woodlice (Isopoda) and millipedes (Diplopoda). Each of these two components provided about 3 times more calcium than the snail shells contained in a natural nestling diet. The breeding performance of aviary birds was poor when only snail shells and the fragments of eggshells were provided in food, i.e., irregular laying, smaller clutches, eggshell defects (25 of 53 eggs), and eggs dried-up during incubation. In contrast, no defective eggshell or dried-up eggs were found and the overall breeding performance increased 2-3 times when woodlice were added to the food. Females increased their intake of woodlice during both the pre-laying and laying periods, and both sexes did so during the nestling period. Both sexes took more woodlice in the evening than in the morning, independent of the nesting stage. Intake by females was low until 4 days before laying the first egg, then increased to the highest level, dropping immediately after laying the last egg. Intake of woodlice by both sexes increased steadily from hatching until the nestling age of about 10-12 days decreasing thereafter, which corresponds with the period of rapid skeletal growth. In contrast, the intake of mealworms increased until the nestling age of 13-14 days leveling off thereafter which corresponds with the growth curve of nestling body mass.

Egg size and offspring performance in the collared flycatcher ( Ficedula albicollis): a within-clutch approach.

Adaptive within-clutch allocation of resources by laying females is an important focus of evolutionary studies. However, the critical assumption of these studies, namely that within-clutch egg-size deviations affect offspring performance, has been properly tested only rarely. In this study, we investigated effects of within-clutch deviations in egg size on nestling survival, weight, fledgling condition, structural size and offspring recruitment to the breeding population in the collared flycatcher ( Ficedula albicollis). Besides egg-size effects, we also followed effects of hatching asynchrony, laying sequence, offspring sex and paternity. There was no influence of egg size on nestling survival, tarsus length, condition or recruitment. Initially significant effect on nestling mass disappeared as nestlings approached fledging. Thus, there seems to be limited potential for a laying female to exploit within-clutch egg-size variation adaptively in the collared flycatcher, which agrees with the majority of earlier studies on other bird species. Instead, we suggest that within-clutch egg-size variation originates from the effects of proximate constraints on laying females. If true, adaptive explanations for within-clutch patterns in egg size should be invoked with caution.