Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome

As a case study for single-nucleotide polymorphism (SNP) identification in species for which little or no sequence information is available, we investigated several approaches to identifying SNPs in two passerine bird species: pied and collared flycatchers (Ficedula hypoleuca and F. albicollis). All approaches were successful in identifying sequence polymorphism and over 50 candidate SNPs per species were identified from approximately 9.1 kb of sequence. In addition, 17 sites were identified in which the frequency of alternative bases differed by > 50% between species (termed interspecific SNPs). Interestingly, polymorphism of microsatellite/intron loci in the source species appeared to be a positive predictor of nucleotide diversity in homologous flycatcher sequences. The overall nucleotide diversity of flycatchers was 2.3-2.7 x 10(-3), which is approximately 3-6 times higher than observed in recent studies of human SNPs. Higher nucleotide diversity in the avian genome could be due to the relatively older age of flycatcher populations, compared with humans, and/or a higher long-term effective population size.     

Sympatric divergence and clinal variation in multiple coloration traits of Ficedula flycatchers

Geographic variation in phenotypes plays a key role in fundamental evolutionary processes such as local adaptation, population differentiation and speciation, but the selective forces behind it are rarely known. We found support for the hypothesis that geographic variation in plumage traits of the pied flycatcher Ficedula hypoleuca is explained by character displacement with the collared flycatcher Ficedula albicollis in the contact zone. The plumage traits of the pied flycatcher differed strongly from the more conspicuous collared flycatcher in a sympatric area but increased in conspicuousness with increasing distance to there. Phenotypic differentiation (P_ST) was higher than that in neutral genetic markers (F_ST), and the effect of geographic distance remained when statistically controlling for neutral genetic differentiation. This suggests that a cline created by character displacement and gene flow explains phenotypic variation across the distribution of this species. The different plumage traits of the pied flycatcher are strongly to moderately correlated, indicating that they evolve non‐independently from each other. The flycatchers provide an example of plumage patterns diverging in two species that differ in several aspects of appearance. The divergence in sympatry and convergence in allopatry in these birds provide a possibility to study the evolutionary mechanisms behind the highly divergent avian plumage patterns.     

Development of stress response in nestling pied flycatchers

Birds respond to unpredictable events by secreting corticosterone, which induces various responses to cope with stressful situations. However, the evidence is still elusive whether altricial nestlings perceive and respond to external stressors. We investigated the development of adrenocortical stress response to handling-related stressor in nestlings of a small passerine bird, the pied flycatcher (Ficedula hypoleuca). Nestlings were held in isolation from their parents during the experiment to ensure that they indeed respond to handling, not to parental alarm calls. We found that both 9- and 13-day-old nestlings were able to elicit hormonal stress response. Although baseline as well as stress-induced corticosterone levels rose slightly with age, the magnitude of difference between the control and stress-induced levels remained similar in both age groups. However, comparison with adults showed that the stress response of nestlings prior to fledging was still incomplete and significantly lower than in adults. Overall, our results indicate that altricial nestlings do respond to acute stressors, but on the contrary to previous predictions the development of corticosterone stress response during growth period is not gradual and varies remarkably between different passerine species.     

Female Pied Flycatchers fail to respond to variations in nest humidity

We examined the possibility that a cavity-nesting passerine, the Pied Flycatcher (Ficedula hypoleuca), can modify the permeability of its eggs to water vapor facultatively in response to variations in nest humidity (P(N)). We found no significant relationship between the water-vapor conductance (G(E)) of flycatcher eggs and P(N). In addition, incubating female flycatchers failed to change their patterns of incubation when we modified P(N) experimentally. These data, coupled with large variations that occur in the G(E) of the eggs within individual clutches, suggest that Pied Flycatchers do not alter the structure of their eggs as they lay them and may not be aware of differences in P(N). It is more likely that G(E) is determined genetically and has been established by natural selection for eggs with high degrees of hatchability.     

Increased divergence but reduced variation on the Z chromosome relative to autosomes in Ficedula flycatchers: differential introgression or the faster-Z effect?

Recent multilocus studies of congeneric birds have shown a pattern of elevated interspecific divergence on the Z chromosome compared to the autosomes. In contrast, intraspecifically, birds exhibit less polymorphism on the Z chromosome relative to the autosomes. We show that the four black-and-white Ficedula flycatcher species show greater genetic divergence on the Z chromosome than on the autosomes, and that the ratios of intraspecific polymorphism at Z-linked versus autosomal markers are below the neutral expectation of 75%. In all species pairs, we found more fixed substitutions and fewer shared polymorphisms on the Z chromosome than on the autosomes. Finally, using isolation with migration (IMa) models we estimated gene flow among the four closely related flycatcher species. The results suggest that different pattern of evolution of Z chromosomes and autosomes is best explained by the faster-Z hypothesis, since the estimated long-term gene flow parameters were close to zero in all comparisons.     

Characterization of the first growth hormone gene sequence for a passerine bird--the pied flycatcher (Ficedula hypoleuca).

While the growth hormone (GH) gene has been characterized in a broad range of vertebrates, surprisingly little is known about this gene in birds. In order to extend knowledge of the GH gene in avian species and non-domestic species, the pied flycatcher (Ficedula hypoleuca) GH gene has been sequenced in this study. The overall average pairwise sequence divergence level was 0.08 among all available avian sequences and 0.27 among other taxa. However, the overall genetic organization of the gene is quite conserved. The similarity of the GH gene sequence of pied flycatchers with those of chicken and duck suggests that the rapid bursts of molecular evolution observed in mammalian and fish GH have not occurred during the divergence of passerine and non-passerine birds.     

Translocation as a novel approach to study effects of a new breeding habitat on reproductive output in wild birds

Environmental conditions under which species reproduce have major consequences on breeding success and subsequent fitness. Therefore breeding habitat choice is ultimately important. Studies rarely address the potential fitness pay-offs of alternative natural breeding habitats by experimental translocation. Here we present a new tool to study fitness consequences of free living birds in different habitats. We translocated a migratory passerine, the pied flycatcher (Ficedula hypoleuca), to a novel site, where pairs were subjected to a short stay (2-4 days) in a nest box-equipped aviary before being released. We show that it is technically possible to retain birds in the new area for breeding, allowing the study of reproductive consequences of dispersal under natural conditions. The translocation resulted in an extension of the interval between arrival and egg laying of four days, highlighting the importance of having an adequate control group. Clutch size and nestling parameters did not differ significantly between translocated and unmanipulated females, which suggests that the procedure did not affect birds in their reproductive performance later on. This method could be applied broadly in evolutionary and ecological research, e.g., to study the potential fitness benefits and costs for dispersing to more northern latitudes as a way of adapting to climate change.     

Arrival and onset of breeding of three passerine birds in eastern Finland tracks climatic variation and phenology of insects

Anthropogenic climate change poses a challenge to the annual cycles of migratory birds. It has become urgent to understand whether migratory birds are able to advance their spring phenology when the climate is warming and whether they are able to adjust these phenological phases to the spring phenology in their breeding areas. In this work, we studied long‐term trends in first arrival and onset of breeding for three passerine birds in eastern Finland; the pied flycatcher Ficedula hypoleuca, the common redstart Phoenicurus phoenicurus and the great tit Parus major. The pied flycatcher and the common redstart are long‐distance migrants while the great tit is a partial migrant in Finland. We asked what environmental variables best explain the first arrival or onset of breeding, if there is evidence of ‘thermal delay’ (long‐term increase in the accumulated temperatures) at arrival or onset of breeding and if the interannual variation in the onset of breeding correlates with variation in spring phenology of local insects. We found that the pied flycatcher and the common redstart had advanced their first arrival (explained by increased temperatures at the migration route), but we found no long‐term change in the onset of breeding (explained by local temperatures). Also, the onset of breeding of the great tit is tracking local temperatures. We found no or only weak evidence of thermal delay at arrival or onset of breeding for any of the species. The onsets of breeding for the pied flycatcher and the great tit are also closely tracking the spring phenology of the local insects. The stable or increasing population sizes of all three species in Finland could be a result from their ability to effectively track climatic and environmental variation.     

Does weather affect biting fly abundance in avian nests?

Environmental factors may strongly affect avian‐biting fly interactions in different ways because insects are heterothermic organisms that depend greatly on environmental variables to activate their metabolism and behaviour. We studied the effects of weather on both blackfly (Simuliidae) and biting midge Culicoides (Ceratopogonidae) abundance in nests of three passerine species: blue tits Cyanistes caeruleus, great tits Parus major and pied flycatchers Ficedula hypoleuca, breeding in the same area. We controlled for different host‐related factors (hatching date, brood size and host species). Blackfly abundance was negatively related to minimum temperature. In addition, blackfly and biting midge abundances were negatively affected by wind speed measured at 07.00 h, but blackfly abundance was positively associated to wind speed at 18.00 h. We found higher blackfly and biting midge abundances in nests with larger broods breeding later in the season, and significantly higher biting midge abundance in pied flycatcher nests as compared to tit nests. These results represent, to our knowledge, the first report of both environmental and host‐related effects on haematophagous fly abundance in the nests of wild hole‐nesting birds.     

HALDANE'S RULE AND SEX BIASSED GENE FLOW BETWEEN TWO HYBRIDIZING FLYCATCHER SPECIES (FICEDULA ALBICOLLIS AND F. HYPOLEUCA,AVES: MUSCICAPIDAE)

The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) hybridize where their geographic ranges overlap. Restriction fragment comparison of 5% of the mitochondrial genome showed a sequence divergence of 10% between these flycatcher species. This degree of sequence divergence between a closely related pair of bird species is unusually high and contrasts with the low level of divergence between F. albicollis and F. hypoleuca in nuclear genes (Nei's D = 0.0006) revealed by enzyme electrophoresis. The low nuclear differentiation is explained by sex biassed gene flow and introgression in nuclear genes (via fertile male hybrids), while the high mitochondrial DNA sequence divergence is preserved by sterility of female hybrids, which prevents mitochondrial introgression. This pattern is in accordance with Haldane's rule and is supported by field data on hybrid fertility. The high mtDNA differentiation could be explained by transfer of mitochondrial DNA from a third species during a past period of hybridization.     

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.     

Female collared flycatchers adjust yolk testosterone to male age, but not to attractiveness

The differential allocation hypothesis predicts that femalesinvest more resources into reproduction when mating with attractivemales. In oviparous animals this can include prefertilizationdecisions such as the production of larger eggs and the depositionof hormones, such as the steroid testosterone, into yolks. Onthe other hand, a compensatory hypothesis posits that femalesallocate more resources into the eggs when mated with malesof inferior quality. In the present study, we show that free-livingfemales of the collared flycatcher (Ficedula albicollis), asmall passerine bird, do not produce larger eggs or depositmore testosterone into eggs when mating with attractive malesreflected by a large forehead patch size, which is contraryto the prediction of the differential allocation hypothesis.However, we found higher yolk testosterone concentrations ineggs laid for young than older males. Because in young malesgenetic quality, parental experience, or willingness to investinto paternal care is likely to be low, high yolk testosteronelevel in their clutches may indicate that their females followa compensatory tactic. They may elicit more paternal care fromyoung, inexperienced males by hormonally increasing nestlingbegging. Laying date was also correlated with yolk testosteronelevel; however, when we controlled for it, male age still remaineda strong determinant of testosterone allocation.     

MATERNAL EFFECTS AND THE PERVASIVE IMPACT OF NESTLING HISTORY ON EGG SIZE IN A PASSERINE BIRD

Environmental conditions experienced during ontogeny may have important and permanent consequences for life-history traits of individuals. The aim of this work was to determine whether conditions experienced during early life, as expressed by prefledgling condition, have any bearing on the volume of eggs subsequently laid by females in a small passerine bird species, the pied flycatcher (Ficedula hypoleuca). I first show a genetic influence on egg volume by dam-offspring regression. The existence of maternal effects is shown by comparing resemblances between average egg volumes of offspring to those of their paternal and maternal grandmothers. Path analysis shows that when controlling for the influence of maternal egg volume, the average volume of eggs produced in a lifetime is positively related to the body condition of a female measured while she is still at the nest. Thus, body condition at fledgling affects egg volume beyond the ability of maternal egg volume to predict offspring egg volume. Although there may be a persistent maternal effect of egg volume on itself or linked to a property correlated with egg volume, the maternal performance trait involved remains unknown, except for maternal egg volume itself. Given the effects that egg volume may have on reproductive success, which are partly determined prior to leaving the nest, maternal effects may have important consequences for lifetime fitness of offspring.     

Fear factor: prey habitat selection and its consequences in a predation risk landscape

Predation risk influences prey use of space. However, little is known about how predation risk influences breeding habitat selection and the fitness consequences of these decisions. The nest sites of central-place foraging predators may spatially anchor predation risk in the landscape. We explored how the spatial dispersion of avian predator nests influenced prey territory location and fitness related measures. We placed 249 nest boxes for migrant pied flycatchers Ficedula hypoleuca , at distances between 10 and 630 m, around seven different sparrowhawk nests Accipiter nisus . After closely monitoring flycatcher nests we found that flycatcher arrival dates, nest box occupation rates and clutch size showed a unimodal relationship with distance from sparrowhawk nests. This relationship suggested an optimal territory location at intermediate distances between 330 and 430 m from sparrowhawk nests. Furthermore, pied flycatcher nestling quantity and quality increased linearly with distance from sparrowhawk nests. These fitness related measures were between 4 and 26% larger in flycatcher nestlings raised far from, relative to those raised nearby, sparrowhawk nests. Our results suggest that breeding sparrowhawk affected both flycatcher habitat selection and reproductive success. We propose that nesting predators create predictable spatial variation in predation risk for both adult prey and possibly their nests, to which prey individuals are able to adaptively respond. Recognising predictable spatial variation in perceived predation risk may be fundamental for a proper understanding of predator-prey interactions and indeed prey species interactions.     

Discrepancies in population differentiation at microsatellites, mitochondrial DNA and plumage colour in the pied flycatcher--inferring evolutionary processes

Genetic differentiation between three populations of the pied flycatcher Ficedula hypoleuca (Norway, Czech Republic and Spain, respectively) was investigated at microsatellite loci and mitochondrial DNA (mtDNA) sequences and compared with the pattern of differentiation of male plumage colour. The Czech population lives sympatrically with the closely related collared flycatcher (F. albicollis) whereas the other two are allopatric. Allopatric populations are on average more conspicuously coloured than sympatric ones, a pattern that has been explained by sexual selection for conspicuous colour in allopatry and a character displacement on breeding plumage colour in sympatry that reduces the rate of hybridization with the collared flycatcher. The Czech population was genetically indistinguishable from the Norwegian population at microsatellite loci and mtDNA sequences. Recent isolation and/or gene flow may explain the lack of genetic differentiation. Accordingly, different selection on plumage colour in the two populations is either sufficiently strong so that gene flow has little impact on the pattern of colour variation, or differentiation of plumage colour occurred so recently that the (presumably) neutral, fast evolving markers employed here are unable to reflect the differentiation. Genetically, the Spanish population was significantly differentiated from the other populations, but the divergence was much more pronounced at mtDNA compared to microsatellites. This may reflect increased rate of differentiation by genetic drift at the mitochondrial, compared with the nuclear genome, caused by the smaller effective population size of the former genome. In accordance with this interpretation, a genetic pattern consistent with effects of small population size in the Spanish population (genetic drift and inbreeding) were also apparent at the microsatellites, namely reduced allelic diversity and heterozygous deficiency.     

No evidence for pre-copulatory sexual selection on sperm length in a passerine bird

There is growing evidence that post-copulatory sexual selection, mediated by sperm competition, influences the evolution of sperm phenotypes. Evidence for pre-copulatory sexual selection effects on sperm traits, on the other hand, is rather scarce. A recent paper on the pied flycatcher, Ficedula hypoleuca, reported phenotypic associations between sperm length and two sexually selected male traits, i.e. plumage colour and arrival date, thus invoking pre-copulatory sexual selection for longer sperm. We were unable to replicate these associations with a larger data set from the same and two additional study populations; sperm length was not significantly related to either male plumage colour or arrival date. Furthermore, there was no significant difference in sperm length between populations despite marked differences in male plumage colour. We also found some evidence against the previously held assumption of longer sperm being qualitatively superior; longer sperm swam at the same speed as shorter sperm, but were less able to maintain speed over time. We argue that both empirical evidence and theoretical considerations suggest that the evolution of sperm morphology is not primarily associated with pre-copulatory sexual selection on male secondary sexual traits in this or other passerine bird species. The relatively large between-male variation in sperm length in this species is probably due to relaxed post-copulatory sexual selection.     

Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post-zygotic barriers to gene exchange

Introgression is the incorporation of alleles from one species or semispecies into the gene pool of another through hybridization and backcrossing. The rate at which this occurs depends on the frequency of hybridization and the fitness of hybrids and backcrosses compared to 'pure' individuals. The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) co-exist and hybridize at low to moderate frequencies in a clinal hybrid zone in Central Europe and on the islands of Gotland and Oland off the Swedish east coast. Data on hatching success suggest that hybrids are less fertile in Central Europe compared to on the islands. Direct fitness estimates using molecular markers to infer paternity are consistent with the demographic data. Applying a tag-array-based minisequencing assay to genotype interspecific substitutions and single nucleotide polymorphisms we demonstrate that the amount of introgression from the pied to the collared flycatcher is higher in the two island populations (Gotland and Oland) than in two geographically distinct areas from the Central European hybrid zone (Czech Republic and Hungary). In all areas the amount of introgression from collared to pied flycatchers is very low or seemingly absent. The different patterns of introgression are consistent with regional differences in rates of hybridization and fitness of hybrids. We suggest that barriers to gene exchange may have been partly broken down on the islands due to asymmetric gene flow from allopatry. Alternatively, or in addition, more pronounced reinforcement of prezygotic isolation in Central Europe might have increased post-zygotic isolation through hitchhiking, since genes affecting pre and post-zygotic isolation are both sex-linked in these birds. One of our genetic markers appears to introgress from pied to collared flycatchers at a much higher rate than the other markers. We discuss the possibility that the introgressed marker may be linked to a gene which is under positive selection in the novel genetic background.     

Density dependence of avian clutch size in resident and migrant species: is there a constraint on the predictability of competitor density?

The presence of density dependence of clutch size is tested in 57 long-term population studies of 10 passerine bird species. In about half of the studies of tit species Parus spp. density dependence of clutch size was found, while none was found in studies of two flycatcher species Ficedula spp. One hypothesis explaining this difference is that migrants are less able to predict the final competitor density, because new pairs are still settling when the first females start laying eggs. Such unpredictability is only a problem for early laying females. If this explanation is true, the commonly observed negative correlation between clutch size and laying date should be stronger in high-density years. I tested this prediction in three populations of Pied Flycatcher Ficedula hypoleuca , and compared the results with three populations of Great Tit Parus major . In none of the six populations was there a significant correlation between the strength of the seasonal decline in clutch size and population density. Thus the lack of density dependence of clutch size in Pied Flycatchers was not consistent with the idea that this is caused by the unpredictability of final density at the time of egg-laying of the earliest females in the population. Furthermore, density does not have any adverse effect on reproductive output of Pied Flycatchers, and therefore they do not adjust clutch size to density.     

Pollution related effects on immune function and stress in a free-living population of pied flycatcher Ficedula hypoleuca

We investigated whether exposure to heavy metal pollution affected the immune function of individuals in a free living population of a small insectivorous passerine bird, the pied flycatcher Ficedula hypoleuca . We measured humoral immune responses in two study areas: a polluted area in the vicinity of a copper smelter and a control area far from the smelter. Plasma corticosterone level and blood heterophil/lymphocyte ratio (H/L) were used as more general physiological measures of stress. The immune response of F. hypoleuca was not suppressed by pollution stress. In contrast, we found that F. hypoleuca males showed stronger humoral immune responses to a novel antigen (tetanus toxoid) in the polluted environment than in the unpolluted one. After the immunization of males, numbers of lymphocytes rose significantly more in the polluted area, leading to a smaller H/L ratio than in males from the control area. Females showed no pollution related effects on their immune responses. Corticosterone levels of males and nestlings were not related to pollution levels. Nestlings showed somewhat higher H/L ratios and lower fledging success in the polluted area, both factors indicating increased stress levels in a polluted area. Our results suggest that humoral immune response of male F. hypoleuca may be enhanced under moderate levels of heavy metal pollution. Enhanced immune function may, however, also be costly for birds and the higher humoral immune responses in polluted areas may thus have negative effects on the birds' breeding performance and survival.     

Determinants of the Mating Success of Polyterritorial Pied Flycatcher Males

Much attention has been paid to the polyterritorial mating system of some passerine birds. Here we report how a male's mating success is related to the behavioral traits of polyterritorial pied flycatcher (Ficedula hypoleuca) males. We found no evidence that the timing of polyterritoriality in relation to egg laying in the primary nest or the singing behavior of males have any influence on mating success. However, results show clearly that male mating success was improved with an increase in the distance between territories up to a distance of about 200–300 m whereupon there was no further enhancement of mating success. This finding is crucial for both the deception hypothesis and female-female aggression hypothesis which have been put forward to explain polyterritorial polygyny. Males who establish a distant second territory seemed to allocate more time to singing there. The association, although weak, between singing activity and distance between territories makes it more difficult for females to use song rate as a cue to discriminate males with a secondary territory far from the primary territory, and these are the males that are least likely to feed the young of a second female. Males who established a second territory late in relation to egg laying in the primary nest did not take over a close second territory as might be predicted from female-female aggression hypothesis.