Study species
The pied flycatcher is a small, cavity-nesting, long-distance migratory passerine that breeds in most of Europe and western Siberia, and winters in sub-Saharan Africa. In Finland, pied flycatchers arrive to the breeding grounds in May (Lundberg and Alatalo 1992). At their arrival, the nesting predators have already settled down in the so-called predation risk landscape (Thomson et al. 2006). One of the main predators of small passerine birds in the boreal forests is the pygmy owl (Kellomäki 1977). The pygmy owl poses a risk to pied flycatchers, which is seen for instance in the avoidance of breeding in the vicinity of the owl (Morosinotto et al. 2010). In another passerine, the presence of a pygmy owl also leads to higher antioxidant enzyme activity, which could be reflective of increased oxidative stress (Morosinotto et al. 2018). While the pygmy owl is not the only predator of pied flycatchers, as a diurnal owl and a central place forager it poses a great risk to them (Kellomäki 1977; Morosinotto et al. 2010). Thus, pygmy owl’s presence/absence would most arguably contribute significantly to the overall predation risk perceived by the pied flycatchers.
Field work
Data were collected in 2017 during breeding season in a study area of ca. 500 km2 north of the city of Turku in Southwest Finland. Before the arrival of pied flycatchers, we inspected 195 pygmy owl boxes to locate pygmy owl nests. The owl nest boxes were distributed so that there was approximately one per km2 in the forested parts of the area. At the beginning of the experiment, there were 11 active pygmy owl nests on different sites. Accordingly, we chose 11 control sites, minimum of 1.1 km from the nearest owl site. If possible, we picked control sites where owls had been breeding previously but were not currently breeding, to confirm that the habitat was suitable for pygmy owls (5 out of 11 sites). The other six sites had a pygmy owl box that had never been occupied by an owl, but the forest patches were similar mature forests dominated by spruce and pine to those occupied by the pygmy owls, and they were distributed over the same area as the owl nests. For the experiment, we installed eight nest boxes suitable for pied flycatchers (17 × 17 × 28 cm with entrance hole Ø of 3.2 cm) in the vicinity of each pygmy owl nest box at both owl-inhabited and at control sites. The basic design of spatial configuration of the boxes was always the same: the boxes were 60–90 m away from the pygmy owl nest and ca. 30–40 m from the nearest neighbouring box. The distance to the pygmy owl nest was decided on the basis of previous studies by Morosinotto et al. (2010) and Moks et al. (2016), both of which indicated that flycatchers are aware of the predator presence at this distance from their nest site.
In late May, we checked all the nest boxes to monitor the species inhabiting the boxes. The boxes inhabited by pied flycatchers were thereafter checked every 4 days to monitor the starting date of egg laying and the final clutch size. Once egg laying was completed, we estimated the start of incubation from final clutch size. 10–11 days (average ± SE = 10.7 ± 0.5 days) after the start of incubation, incubating females were caught, weighed and their wing length was measured and a blood sample (50–75 µl) was taken from the wing vein to assess the initial telomere length (from 7 nests in 6 control sites and 11 nests in 8 owl sites). When their nestlings were 10 days old (average ± SE = 13.3 ± 0.5 days after first sampling), the females were caught again, measured, and another blood sample was collected (we were unable to re-catch one female from an owl site). At this time, males were also captured (from 6 nests in 6 control sites and 11 nests in 7 owl sites), measured and sampled. Blood samples were taken with non-heparinized capillary tubes, diluted in 125 µl of PBS and kept chilled while in the field. At the end of the day, the blood samples were stored at − 80 °C.
We estimated the hatching date from the date of the last laid egg. Nest boxes were checked a day before the estimated hatching day and every day after that until the hatching. Chicks were partially cross-fostered between owl and control sites when they were 3 days old (hatching day = day 0). The cross-fostering study design enables distinguishing genetic/prenatal and environmental effects on a trait by placing full siblings in different rearing environments (Merilä 1996). Cross-fostering nest pairs were matched according to hatching date and original clutch size. On average, pied flycatcher chicks at owl sites hatched later than control chicks due to delayed nest construction and later egg laying, and for this reason five of the owl site nests could not be matched with a control nest on the original sites. We thus had to resort to five additional control site boxes that were out of our study area, to complete the cross-fostering. Only chicks (not adults) from those sites were used in the analyses. Matching the cross-fostering pairs according to the hatching day diminishes the differences in environmental conditions experienced by the chicks and ensures that the chick-rearing period is the same for adults from both control and owl sites despite the general later hatching of the owl site chicks. If there were eggs in the nest that had not hatched by day 3, extra chicks were brought to the nest from extra nests hatched on the same day, to match the original clutch size. If a suitable extra chick was not found, no chicks were added (in four out of ten cases). Extra chicks were not sampled. Two to three chicks (depending on the brood size) were picked randomly and exchanged between the nest pairs, while the rest of the chicks remained in their original nest throughout the study (sample size for chicks per treatment C–C = 33, C–O = 36, O–O = 31, O–C = 36; treatment = original site-rearing site, c = control, o = owl site; cross-fostered chicks are in groups C–O and O–C and those remaining in their own nests in groups C–C and O–O). All exchanges happened within 5 days. During the cross-fostering the chicks were made identifiable by removing gently the feather tufts either from the head or the back. When chicks were 5 days old, they were ringed, weighed and a first blood sample (about 35 µl) was taken. Blood samples were diluted in 65 µl of PBS and kept chilled until stored at − 80 °C at the end of the day. Because less blood was taken from chicks than from adults, PBS volume for chick samples was lower to standardize the dilution factor. When the chicks were 12 days old (2–3 days before fledging), they were weighed and sampled for the second time.
We determined box occupancy, average date of first egg laid, average clutch size, average number of nestlings and fledglings and mean parental body mass between control and owl sites (Table 1). As suggested by Morosinotto et al. (2010), pied flycatchers may have actively avoided breeding near pygmy owls, as box occupancy at owl site was little more than 30% compared to almost 80% at control sites. On average, females at owl sites started egg laying 1 day later than control-site females, but despite of that we observed no significant differences in average clutch size and number of nestlings or fledglings between control and owl sites (Table 1). Adults at control sites were a little heavier than owl site adults, although the differences were not statistically significant.
Table 1 General breeding characteristics between control and owl sites Telomere length assessment
Two months after data collection, the DNA was extracted from whole blood samples using salt extraction alcohol precipitation method (Aljanabi and Martinez 1997). Extracted DNA was diluted in elution buffer BE for DNA preservation and aliquoted. DNA concentration and quality were quantified with Spectrophotometer NanoDrop 2000. Samples were then diluted to concentration of 2.5 ng/µl for subsequent qPCR analysis.
We used quantitative PCR method to measure relative telomere length: the amount of telomeric sequence relative to the amount of a control gene (i.e. non-variable copy number gene) sequence, as previously described in birds (Criscuolo et al. 2009). qPCR analysis was performed on a QuantStudio™ 12 K Flex Real-Time PCR System (Thermo Fisher) using 384-well qPCR plates. We used a final reaction volume of 10µL, 5 ng of genomic DNA, 200 nM of forward and reverse primers and SensiFAST SYBR Lo-ROX mix as MasterMix. qPCR conditions were: an initial denaturation (1 cycle of 3 min at 95 °C), 40 cycles with first step of 10 s at 95 °C, second step of 15 s at 58 °C and third step of 10 s at 72 °C, and finally a melting curve analysis. We used Tel 1b as a forward telomere primer (5′-CGGTTTGTTTGGGTTTGGGTTTGGGTTTGGGTTTGGGTT-3′) and Tel 2b as a reverse telomere primer (5′-GGCTTGCCTTACCCTTACCCTTACCCTTACCCTTACCCT-3′). We used GAPDH as a control gene and designed primers based on collared flycatcher (Ficedula albicollis, a close relative of the pied flycatcher) genome, as pied flycatcher genome assembly was not available (forward primer 5′-AACCAGCCAAGTACGATGACAT-3′ and reverse primer 5′-CCATCAGCA GCAGCCTTCA-3′). Before qPCR we performed normal PCR with our GAPDH primers and used gel electrophoresis to confirm the amplification of the pied flycatcher gene. In addition, we checked the specificity of our primers by analysing qPCR melting curves and confirming the presence of a single narrow peak.
Samples were analysed in triplicate and distributed on 384-well plates accordingly: (1) samples from cross-fostering pairs on a same plate; (2) both samples from one individual on the same plate; and (3) if possible, samples from individuals from the same site on the same plate. In the end, the samples were distributed on six different plates. All plates included three internal standards (= same sample on every plate) and one negative control. We used a LinRegPCR version 2017.1 (Ruijter et al. 2009) to determine the baseline fluorescence, the qPCR efficiencies of each reaction (average ± SE efficiencies for telomere and GAPDH reactions were 1.922 ± 0.008 and 1.904 ± 0.003, respectively) and the quantification cycle (Cq) values. Relative telomere length (T/S ratio, hereafter telomere length) was calculated based on plate-specific efficiencies using the mathematical model presented in Pfaffl (2001). The average intra-plate coefficient of variation (CV ± SE) for T/S ratio was 11.5 ± 0.56%. The average inter-plate CV based on the three internal standards was 6.9 ± 2.9%. The technical repeatability of triplicate telomere lengths was 0.865 (95% Cl: 0.837–0.886, p < 0.001). Chromosomes contain terminal and interstitial telomeric sequences (ITS), but only terminal sequences shorten with age. The qPCR measures both sequences, which can decrease considerably statistical power when studying terminal telomeres due to between-individual differences in ITS amount (Foote et al. 2013). To ensure the validity of our qPCR protocol, we therefore analysed 13 individuals (10 chicks and 3 adults) with both in-gel TRF (i.e. measuring only terminal telomeres) and qPCR. We found a strong correlation between methods (r = 0.74, p = 0.004, see Online Resource 1), thereby validating the use of qPCR in the pied flycatcher.
Statistical analyses
We used general linear models and general linear mixed models to examine the effect of predation threat on telomere dynamics in adults and their chicks. As we only had one telomere measurement for parent males at chick rearing, we started by fitting a model including all the adults sampled at chick-rearing stage (males and females with final measurement, n = 35), with telomere length as the dependent variable and predator presence (owl or control), sex and their interaction as fixed effects. Because this dataset contained breeding pairs, nest identity was included as a random effect to control for possible similarities in telomere length caused by sharing the same nest. To investigate the rate of telomere change (i.e. telomere length at chick rearing minus telomere length at incubation) in females (n = 18), we fitted a model with predator presence (control or owl) and initial telomere length as fixed effects. To avoid statistical artefacts due to regression to the mean phenomenon, the ‘telomere change’ values were corrected using the equation by Verhulst et al. (2013). As control-site females seemed to be consistently a little heavier than owl-site females, we assessed this further by running a repeated-measures model with female body mass as dependent variable and breeding stage, predator presence and their interaction as independent variables.
To test the effects of prenatal and/or early, as well as later parental and environmental components on nestling telomere length (244 measurements from 136 chicks from 24 nests, 12 from control and 12 from owl sites), we fitted a repeated-measures model with, as fixed factors, nestling age (5 or 12 days), predator presence at original nest (control or owl), predator presence at rearing nest (control or owl), their interaction (to address origin-specific responses to the cross-fostering treatment), and the interactions between nestling age and predator presence at original nest as well as nestling age and predator presence at rearing nest. We also used cross-fostering pair (duplicate), and both original and rearing nest box nested within duplicate as random effects. The original nest includes all genetic and prenatal effects as well as early parental effects, while rearing nest includes post-swapping parental effects. The term duplicate reflects variation of nestling traits related to differences between nest pairs such as time of season (Norte et al. 2009). Compound symmetry was used as a covariance structure to model the repeated measures within chicks. We used a similar approach for testing the effect of predation risk on nestling growth rate (i.e. body mass measured at 5 and 12 days). As telomere measurements may vary slightly between different qPCR plates, we tested this ‘plate effect’ by adding plate ID as a random effect to all the telomere models. Ultimately, plate ID was removed from the models as it did not have any obvious effect on the results.
The models were estimated using restricted maximum-likelihood (REML) and Kenward–Roger method was used to calculate degrees of freedom of fixed factors and assess parameter estimates and their standard errors. Normality and heteroscedasticity assumptions were checked visually from the model residuals and deemed satisfactory. Statistical analyses were conducted with SAS statistical software version 9.4 (SAS Institute, Cary, NC, USA).