DOI: 10.5061/dryad.s4mw6m996
title: Data for: Brood parasitism of Hooded Warblers by Brown-headed Cowbirds: Severe impact on individual nests but modest consequences for seasonal fecundity and conservation

description: Brood parasitism by Brown-headed Cowbirds (Molothrus ater) often has
 pronounced negative effects on host nests. However, the extent to which
 parasitism reduces annual reproduction and presents conservation
 challenges for host species is unclear. We address this issue with data
 from a color-banded population of Hooded Warblers (Setophaga citrina) in
 Pennsylvania, where Hooded Warblers have increased dramatically despite
 frequent nest parasitism. Our analysis is based on both an extensive
 dataset (8 years, 847 nests) on the per-nest impacts of cowbird
 parasitism, and female-based stochastic simulations that accurately
 reflect the reproductive biology and parasitism rate (30%) of our study
 population. Cowbird parasitism has multiple negative consequences for
 Hooded Warbler nests, including: (1) reduced host clutch size, (2)
 increased nest abandonment, (3) increased risk of complete failure due to
 predation, and (4) in surviving nests increased egg loss, hatching
 failure, and nestling mortality. We estimate that parasitism reduces
 success of Hooded Warbler nests 68%, from 1.29 to 0.41 fledglings per
 nest. For females and populations, however, the consequences of nest
 parasitism are considerably less extreme; female annual fecundity
 decreases 25% for each nesting attempt parasitized, and population-level
 fecundity drops 5.6% for each 10% increase in the frequency of parasitism.
 These more modest impacts are attributable to: (1) steep declines in rates
 of cowbird parasitism as the nesting season progresses, (2) rapid
 re-nesting following abandonment or failure of parasitized nests, and (3)
 regular double brooding, with second broods initiated in late June and
 July when the incidence of cowbird parasitism is low. Our results help
 resolve the paradox of how cowbird parasitism can have both severe
 consequences for individual host nests but more modest and sustainable
 conservation impacts on the seasonal fecundity of females and populations.
 They further underscore the importance of determining population-level
 effects of brood parasites before investing in costly management efforts.
description: <strong>Study site and general
 methods</strong> The study was conducted at
 Hemlock Hill Field Station in Crawford County, Pennsylvania, USA (41.8°N,
 79.9°W). The study site comprises 125 ha of primarily beech-maple-hemlock
 forest located within a complex rural matrix of agricultural land,
 abandoned fields, and forest fragments. Data for the present study come
 from the 8 years 2013–2020, when intensive efforts were made to capture
 and color-band all breeding adult Hooded Warblers and find and monitor all
 nests during the May–August nesting season. Nests were checked every 3–5
 days, and more frequently around expected dates of hatching and fledging.
 About half (48%) of all nests were found before the onset of incubation,
 but when a nest with a complete clutch of eggs or nestlings was found, the
 date of nest initiation (date the first egg was laid) was estimated based
 on either the date of hatching, assuming eggs were laid on consecutive
 days and a 12-day incubation period (Mumme et al. 2023), or the date a
 previous nesting attempt by the same female had failed. These estimated
 dates of nest initiation were likely accurate to within 1–2 days. In
 total, 847 nests were included in the complete dataset.
 <strong>Statistical analysis</strong>
 The date of nest initiation, which we defined as the day the
 first egg is laid (FEDay) and recorded as the number of days elapsed since
 30 April, is an important determinant of several Hooded Warbler
 reproductive variables, including probability of nest parasitism, clutch
 size, and probability of nest predation (Harrod 2021, Lignac 2022). We
 therefore examined the effects of cowbird parasitism on Hooded Warbler
 nesting success with generalized linear mixed models (GLMM) or generalized
 linear models (GLM) that included FEDay as a fixed factor. Year was
 included in these models as either a random effect in a GLMM or a fixed
 factor in a GLM; the latter approach was used when we encountered model
 convergence or singularity issues with GLMM. All statistical analyses were
 conducted using JMP Pro 15.2 (SAS Institute, Cary, North Carolina, USA)
 and R version 4.2.1 (R Core Team 2022) with package lme4 version 1.1-30
 (Bates et al. 2015). Timing of parasitism, clutch size,
 and nest abandonment. We analyzed the relationship between the date of
 nest initiation (FEDay) and probability of parasitism using a logistic
 GLMM with year included as a random effect. We used a Poisson GLM to
 examine the effects of cowbird parasitism on the number of Hooded Warbler
 eggs in the complete clutch. The number of cowbird eggs in the nest,
 FEDay, and year were included as fixed factors. A logistic GLM was used to
 examine the probability of nest abandonment, with cowbird parasitism,
 FEDay, and year entered as fixed factors. Nest survival
 to hatching and hatching failure. The effect of cowbird parasitism on the
 probability of nests surviving to hatching was examined using a logistic
 GLMM, with cowbird parasitism and FEDay as fixed factors and year as a
 random effect. This analysis was limited to 356 nests found before the
 onset of incubation that were not abandoned. To examine the effects of
 cowbird parasitism on Hooded Warbler hatching failure and egg loss during
 incubation, we used Poisson GLMs to analyze the effect of cowbird
 parasitism on both the number of eggs that failed to hatch and the number
 of warbler eggs that disappeared during incubation. In these analyses, the
 number of cowbird eggs, FEDay, and year were entered as fixed factors,
 with the total number of Hooded Warbler eggs in the clutch serving as the
 offset variable. These analyses were limited to a sample of 373 nests that
 were found no later than the fourth day of the 12-day incubation period
 and did not experience abandonment or complete nest failure before
 hatching. Nest and nestling survival from hatching to
 fledging. We used a logistic GLM to examine the probability of nests with
 and without a cowbird nestling surviving to fledging. This analysis was
 limited to 492 nests found before hatching that were not abandoned and
 included FEDay, year, and the presence/absence of a cowbird chick as fixed
 factors. We also created Kaplan-Meier survival curves to examine the
 pattern of nest survival during the nestling period. For 359 nests that
 survived from hatching to fledging, a Poisson GLM was used to determine if
 the presence of a cowbird chick increased the number of Hooded Warbler
 hatchlings that disappeared and presumably died before fledging; the
 number of warbler nestlings that hatched was used as the offset variable
 in this analysis, and FEDay and year were included as fixed
 factors. <strong>Cumulative effects of cowbird
 parasitism on success per nest</strong> We
 estimated the cumulative effects of cowbird parasitism on mean success per
 nest at Hemlock Hill by calculating its separate impacts on five
 components of per-nest success: (1) the number of Hooded Warbler eggs in
 the final clutch, (2) the probability that the nest is not depredated,
 abandoned, or a victim of complete nest failure prior to hatching, (3) the
 proportion of Hooded Warbler eggs in surviving nests that hatch
 successfully, (4) the probability that the nest is not depredated,
 abandoned, or a victim of complete nest failure between hatching and
 fledging, and (5) the proportion of Hooded Warbler nestlings in surviving
 nests that fledge successfully. We used GLMs to estimate the effect of
 cowbird parasitism on the five components of nest success listed above
 while simultaneously controlling for the potentially confounding effects
 of FEDay. An additional complication of calculating the
 cumulative effect of nest parasitism is including the probability that the
 cowbird egg (or eggs) in a parasitized nest will fail to hatch,
 effectively turning a parasitized nest into a non-parasitized nest during
 the nestling stage. We incorporated this probability into our
 calculations, using a 0.75 probability that each cowbird egg would hatch
 (McMaster and Sealy 1997) and our finding that 15.6% of parasitized nests
 contain more than one cowbird egg.
 <strong>Effects of cowbird parasitism on seasonal
 fecundity</strong> Because we removed cowbird
 eggs from some Hooded Warbler nests late in incubation as part of other
 experimental studies, and because some females move onto or off of the
 study between nesting attempts, we do not have unbiased data that allow a
 direct assessment of the impact of cowbird parasitism on female
 reproductive histories and population productivity. Instead, we generated
 a realistic female-based stochastic simulation of Hooded Warbler
 reproduction to extend our estimates of the per-nest impacts of cowbird
 parasitism to both per-season effects on individual females, and
 population-level effects on the reproductive performance of entire
 populations. We used data from the Hemlock Hill study population to
 parameterize the simulation with realistic variation in the timing of
 first reproduction, the probability of nest parasitism, clutch size,
 hatching success, the probability of complete nest failure, nestling
 survival, the timing and probability of renesting after nest failure, and
 the timing and probability of attempting a second brood following a
 successful nest. One baseline simulation was created to mimic the
 parasitism and reproductive characteristics of the Hemlock Hill study
 population, and this simulation was used to estimate the effect of cowbird
 parasitism on per-season success of individual females. However, we also
 created 7 additional simulations that altered the overall nest parasitism
 rate by realistically modifying the logistic regression equation relating
 the probability of nest parasitism to the date of nest initiation (see
 Results). Collectively, the 8 simulations allowed us to explore the
 population-level reproductive consequences of simulated variation in the
 overall rate of nest parasitism. For each of the 8
 simulations, we ran 25 replicates of 400 females; we chose 400 females for
 these replicates because 400 approximates the number of females whose
 reproductive histories we followed each year (~50) multiplied by the
 number of complete breeding seasons (8, 2013–2020) used in our analyses.
 In addition, for each of the 8 simulations we also ran one replicate based
 on a much larger simulated population of 40,000 females. All simulations
 were created with JMP Pro 15.2 (SAS Institute, Cary, North Carolina,
 USA). Complete details on the simulation models and
 their validation are provided in Supplementary Materials 1. However, we
 note here that the baseline simulation consistently replicated important
 reproductive characteristics of the Hemlock Hill study population that
 were not explicitly built into the simulation, including overall mean ± SD
 of nest initiation dates (13 June ± 18 days simulated vs. 14 June ± 18
 days observed), overall mean ± SD of Hooded Warbler clutch size (3.00 ±
 0.97 simulated vs. 3.02 ± 0.93 observed), overall rate of cowbird
 parasitism (29.7% simulated vs. 30.3% observed), and overall mean ± SD
 number of young fledged from successful non-parasitized nests (2.78 ± 0.88
 simulated vs. 2.83 ± 0.88 observed). <strong>The baseline
 simulation</strong> To explore the effects of
 Brown-headed Cowbird nest parasitism on the annual reproductive output of
 Hooded Warbler females and populations subjected to varying levels of
 parasitism, we created a realistic female-based stochastic simulation of
 Hooded Warbler reproduction. We used data from our Hemlock Hill study
 population to parameterize the simulation with realistic variation in the
 timing of the initial nesting, the probability of nest parasitism, clutch
 size, hatching success, the probability of complete nest failure, nestling
 survival, the timing and probability of renesting after nest failure, and
 the timing and probability of attempting a second brood following a
 successful nest.  <strong>Initial
 nest</strong> We simulated the date of nest
 initiation (laying of the first egg, FEDay) for the first nest with a
 four-parameter sinh-arcsinh (SHASH) distribution that closely fit our
 observed data: 23.24 + 8.30(SinH((ArcSinH(RandomNormal)
 + 0.70)/1.61)) In our baseline simulation of 40,000
 females, the simulated first egg date for the initial nesting attempt was
 27 May ± 5 days (mean ± SD), range 15 May–15 June.  For
 each of the 40,000 simulated initial nests, we then simulated whether it
 was parasitized based on the logistic regression equation relating the
 probability of cowbird nest parasitism to the date of nest initiation
 (FEDay; Figure 2A); 45.1% of the 40,000 initial nests in our baseline
 simulation were parasitized. Host clutch size was then simulated based on
 both the date of nest initiation (FEDay) and whether the nest was
 parasitized (Figure 2B); this approach therefore accounted for both the
 seasonal decline in clutch size and the reduction in host clutch size
 associated with nest parasitism (Figure 2B). The
 probability of the nest surviving to hatching was simulated based on our
 observed logistic regression equation relating nest survival to both FEDay
 and whether the nest was parasitized; all causes of complete nest failure
 prior to hatching (e.g., abandonment, clutch predation, nest destruction)
 were included in the logistic regression analysis. If a simulated nest did
 not survive to hatching, a simulated failure date was assigned, based on a
 uniform random distribution over the time period between laying of the
 first egg and expected hatching date (12 days after clutch completion). If
 the nest did survive to hatching and was not parasitized, the number of
 Hooded Warbler eggs hatching was simulated based on the observed hatching
 probability of eggs in surviving non-parasitized nests, 0.89 (Figure 3C).
 If the nest was parasitized, hatching probability for each Hooded Warbler
 egg was set at the observed value of 0.72 (Figure 3C). For parasitized
 nests, the probability of a cowbird nestling hatching in a surviving nest
 was set at 0.784, based on a 0.75 probability that each cowbird egg would
 hatch (McMaster and Sealy 1997) and our finding that 15.6% of parasitized
 nests contain more than one cowbird egg.  For nests
 that survived to hatching, we then simulated whether the nest would
 survive to fledging, based on the logistic regression relating the
 probability of post-hatching nest survival to both FEDay and whether a
 cowbird nestling was present in the nest (see Figure 4); all causes of
 complete post-hatching nest failure were included in the logistic
 regression analysis. In our baseline simulation, the probability of
 survival from hatching to fledging was 0.733 for 13,621 simulated
 non-parasitized nests and 0.524 for 5616 simulated nests where a cowbird
 nestling was present. For surviving nests, we also simulated the
 probability that each Hooded Warbler nestling fledged successfully, using
 the observed probability of 0.96 for nestlings from successful nests
 without a cowbird chick, and 0.85 for those from successful nests with a
 cowbird chick. For nests that did not survive from hatching to fledging,
 we simulated a failure date based on a uniform random distribution over
 the time period between hatching and the expected date of fledging, 9 days
 after hatching. <strong>Subsequent
 nests</strong> If the initial nesting attempt
 failed before fledging, we simulated renesting as follows. First, because
 data from Hemlock Hill indicate that renesting females require 6 days from
 failure of the previous attempt to laying of the first egg for the
 subsequent nest, we added 6 days to the simulated failure date described
 above for the female’s new estimated date of nest initiation (FEDay). If
 this new date was before June 30, we considered the probability that the
 female would renest to be 100%. However, if the new date was July 1 or
 later, the probability of renesting was set to (number of days remaining
 in July/31); July 31 is the latest nest initiation date ever recorded for
 a nest at Hemlock Hill, so this linear decrease in the probability of
 renesting through the month of July is realistic and closely matches the
 observed breeding biology of Hooded Warblers at Hemlock Hill. 
 If the initial nesting was successful, we simulated the laying of
 a second brood as follows. Because females who attempt a second brood at
 Hemlock Hill average 12 days between fledging and the first egg of the
 subsequent nest, we added 12 days to the date of fledging of the prior
 attempt to estimate the first egg date for the second brood. If this new
 date was before June 30, we considered the probability that the female
 would attempt to nest again to be 100%. However, if the new date was July
 1 or later, the probability of renesting was set to (number of days
 remaining in July/31), as described above. For each
 subsequent attempt we modeled the probability of cowbird parasitism,
 clutch size, nest survival to hatching, hatching success, nest survival to
 fledging, and nestling survival to fledging using the same approaches as
 described above for the initial nest, adjusting for the date of nest
 initiation (FEDay) to account for the seasonal changes in nest parasitism
 (Figure 2A), clutch size (Figure 2B), and nest predation. Because 5
 nesting attempts in a single season is the most we have ever observed by
 an individual female at Hemlock Hill, we set 5 as the maximum number of
 nesting attempts that a female might make. However, in our baseline
 simulation, &lt;1% (308 of 40,000 simulated females) made 5 nesting
 attempts, and the mean ± SD was 2.6 ± 0.7 attempts per season. 
 <strong>Simulation validation</strong>
 The simulation realistically models Hooded Warbler reproduction
 and accurately reflects the breeding biology of our Hemlock Hill study
 population. This conclusion is best illustrated by Figure S1, which shows
 the observed and simulated distribution of nest initiation dates. The two
 distributions are remarkably similar; overall mean ± SD nest initiation
 date was 14 June ± 18 days (range 17 May–31 July) for 847 observed nests,
 vs. 13 June ± 18 days (range 15 May–30 July) for 103,258 simulated nests.
 Most impressively, our simulation also produced the bimodal distribution
 observed in our study population, with a smaller second peak of nesting
 occurring in late June and early July (Figure S1). This second peak of
 nesting was not explicitly built into the simulation, but emerged from the
 realistic parameterization of the simulation with data on the timing and
 probability of renesting following failure, and the timing and probability
 of attempting a second brood following a successful nesting
 attempt. Our baseline simulation also replicated other
 important reproductive characteristics of the Hemlock Hill study
 population that were not explicitly built into the simulation, included
 overall Hooded Warbler clutch size (Figure S2), overall rate of cowbird
 parasitism (30.3% observed vs. 29.7% simulated), and overall mean ± SD
 number of young fledged from successful non-parasitized nests (2.83 ± 0.88
 observed vs. 2.78 ± 0.88 simulated).
 <strong>Simulating variation in rates of nest
 parasitism</strong> After creating the baseline
 simulation to mimic the parasitism and reproductive characteristics of the
 Hemlock Hill study population, we then created 7 additional simulations
 that altered the overall nest parasitism rate by realistically modifying
 the intercept and slope of the logistic regression equation relating the
 probability of nest parasitism to the date of nest initiation (Table S1,
 Figure 2A). All 7 of the modified logistic regression equations retained
 the essential feature that the probability of cowbird nest parasitism was
 highest early in the nesting season and declined to low levels in July
 (Figure 2A). Collectively, the 8 simulations allowed us to explore the
 population-level reproductive consequences of simulated variation in the
 overall rate of nest parasitism. 
description: JMP Pro 15.2 (SAS Institute, Cary, North Carolina, USA) and R
 version 4.2.1 (R Core Team 2022) with package lme4 version 1.1-30 (Bates
 et al. 2015).