Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost?

The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW; Protonotaria citrea) that were either parasitized or non-parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter-specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness.

Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host-Symbiont Coevolution.

Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host-symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: Amerodectes protonotaria) from four individual Prothonotary Warblers (Parulidae: Protonotaria citrea). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host-symbiont coevolution at multiple evolutionary scales.

Novel insights into symbiont population structure: Globe-trotting avian feather mites contradict the specialist-generalist variation hypothesis.

Researchers often examine symbiont host specificity as a species-level pattern, but it can also be key to understanding processes occurring at the population level, which are not as well understood. The specialist-generalist variation hypothesis (SGVH) attempts to explain how host specificity influences population-level processes, stating that single-host symbionts (specialists) exhibit stronger population genetic structure than multi-host symbionts (generalists) because of fewer opportunities for dispersal and more restricted gene flow between populations. However, this hypothesis has not been tested in systems with highly mobile hosts, in which population connectivity may vary temporally and spatially. To address this gap, we tested the SGVH on proctophyllodid feather mites found on migratory warblers (family Parulidae) with contrasting host specificities, Amerodectes protonotaria (a host specialist of Protonotaria citrea) and A. ischyros (a host generalist of 17 parulid species). We used a pooled-sequencing approach and a novel workflow to analyse genetic variants obtained from whole genome data. Both mite species exhibited fairly weak population structure overall, and contrary to predictions of the SGVH, the generalist was more strongly structured than the specialist. These results may suggest that specialists disperse more freely among conspecifics, whereas generalists sort according to geography. Furthermore, our results may reflect an unexpected period for mite transmission - during the nonbreeding season of migratory hosts - as mite population structure more closely reflects the distributions of hosts during the nonbreeding season. Our findings alter our current understanding of feather mite biology and highlight the potential for studies to explore factors driving symbiont diversification at multiple evolutionary scales.

The Complete Genome Sequence of Protonotaria citrea, the Prothonotary Warbler.

The Prothonotary Warbler (Protonotaria citrea) is a nearctic-neotropical migratory songbird that breeds in forested swamps and riparian areas in the eastern-central United States and southern Ontario. It is the sole eastern North American wood-warbler that nests in cavities, the only species in the genus Protonotaria, and is one of the few hole-nesting hosts of the Brown-headed Cowbird (Molothrus ater), an obligate brood parasite. We present the whole genome sequence of this wood-warbler species. Illumina sequencing was performed on a genetic sample from a single female individual. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR19579445) and Assembly (JAOYNP000000000).

Niche construction through a Goldilocks principle maximizes fitness for a nest-sharing brood parasite.

Generalist brood parasites that share nests with host nestlings can optimize resource acquisition from host parents by balancing the benefits that host nest-mates provide, including attracting increased provisions to the nest, against the costs of competing with the same host young over foster parental resources. However, it is unclear how parasitic chicks cope when faced with more nest-mates than are optimal for their survival upon hatching. We suggest that, in the obligate brood parasitic brown-headed cowbird (Molothrus ater), chicks use a niche construction strategy and reduce larger, more competitive host broods to maximize the parasites' survival to fledging. We experimentally altered brood sizes to test for Goldilocks principle patterns (i.e. a 'just right' intermediate brood size) of cowbird survival in nests of prothonotary warbler (Protonotaria citrea) hosts. We found that intermediate brood sizes of two host nestlings maximized cowbird fledging success relative to 0 or 4 host nest-mates at hatching. Specifically, cowbird nestlings lowered host brood sizes towards this optimum when placed in broods with more host nestlings. The results suggest that cowbirds reduce, but do not eliminate, host broods as a niche construction mechanism to improve their own probability of survival.

The effect of avian brood parasitism on physiological responses of host nestlings.

Avian obligate brood parasites lay their eggs in the nests of other species that may provide care for the foreign offspring. Brood parasitism often imparts substantial fitness losses upon host nestlings when they are raised alongside the typically more competitive, larger, and older parasitic chick(s). Whereas fitness costs due to reduced host offspring survival in parasitized broods have been studied in detail, the physiological changes in host nestlings caused by parasitic nestmate(s) are less well known. We compared prothonotary warbler (Protonotaria citrea) nestlings, a host of the nest-sharing brown-headed cowbird (Molothrus ater), in experimentally parasitized vs. non-parasitized broods. Our aim was to determine whether cohabitation with brood parasitic young impacted host nestling baseline corticosterone plasma concentrations, immune responses, body condition, and mortality. Corticosterone levels and body condition of host nestlings were similar between nests with or without a cowbird nestmate, whereas host immune responses were lower and nestling mortality was greater in parasitized broods, irrespective of variation in brood size or total brood mass. We detected no trade-offs of baseline corticosterone levels with either immune responses or with body condition. These results suggest that this host species' nestlings experience some adverse fitness-relevant physiological effects in parasitized broods, but are also resilient in other aspects when coping with brood parasitism.

Physiological responses of host parents to rearing an avian brood parasite: An experimental study.

Raising an obligate avian brood parasite is costly for host parents because it redirects valuable parental resources from one's own offspring to genetically unrelated young. The costs of raising a brood parasite may be mediated by physiological stressors for foster parents if it requires greater or biased parental effort compared to raising non-parasitized broods. For example, upregulating glucocorticoid hormones or reducing immune responses may mediate a trade-off between resource allocation to a current brood versus future reproductive opportunities, but published data on parasitized hosts' physiology are scarce. Here we used an experimental approach to test if host parents respond to the presence of brood parasitic young through dynamic changes in their own physiology. We conducted our experiments with parasitic brown-headed cowbirds (Molothrus ater) fostered into nests of host prothonotary warblers (Protonotaria citrea). Relative to parents caring for non-parasitized control broods, parasitism increased baseline corticosterone levels and reduced body mass in adult male, but not in female, hosts. Immune responses to a novel antigen were depressed in both parents of parasitized broods compared to parents of non-parasitized broods. Additionally, we found that immune function increased along the breeding season regardless of treatment. These experiments also confirmed prior observational data that parasitized adult males have reduced return rates to breeding sites in years subsequent to raising cowbirds. The findings demonstrate diverse physiological effects of parasitism on the foster parents in our particular host-brood parasite system, yet we found no evidence of individual trade-offs between endocrine and immune responses of adult hosts.

Greater opportunities for sexual selection in male than in female obligate brood parasitic birds.

Females are expected to have evolved to be more discriminatory in mate choice than males as a result of greater reproductive investment into larger gametes (eggs vs. sperm). In turn, males are predicted to be more promiscuous than females, showing both a larger variance in the number of mates and a greater increase in reproductive success with more mates, yielding more intense sexual selection on males vs. females (Bateman's Paradigm). However, sex differences in costly parental care strategies can either reinforce or counteract the initial asymmetry in reproductive investment, which may be one cause for some studies failing to conform with predictions of Bateman's Paradigm. For example, in many bird species with small female-biased initial investment but extensive biparental care, both sexes should be subject to similar strengths of sexual selection because males and females are similarly restricted in their ability to pursue additional mates. Unlike 99% of avian species, however, obligate brood parasitic birds lack any parental care in either sex, predicting a conformation to Bateman's Paradigm. Here we use microsatellite genotyping to demonstrate that in brood parasitic brown-headed cowbirds (Molothrus ater), per capita annual reproductive success increases with the number of mates in males, but not in females. Furthermore, also as predicted, the variance of the number of mates and offspring is greater in males than in females. Thus, contrary to previous findings in this species, our results conform to predictions of the Bateman's Paradigm for taxa without parental care.

A generalist brood parasite modifies use of a host in response to reproductive success.

Avian obligate brood parasites, which rely solely on hosts to raise their young, should choose the highest quality hosts to maximize reproductive output. Brown-headed cowbirds (Molothrus ater) are extreme host generalists, yet female cowbirds could use information based on past reproductive outcomes to make egg-laying decisions thus minimizing fitness costs associated with parasitizing low-quality hosts. We use a long-term (21 years) nest-box study of a single host, the prothonotary warbler (Protonotaria citrea), to show that local cowbird reproductive success, but not host reproductive success, was positively correlated with the probability of parasitism the following year. Experimental manipulations of cowbird success corroborated that female cowbirds make future decisions about which hosts to use based on information pertaining to past cowbird success, both within and between years. The within-year pattern, in particular, points to local cowbird females selecting hosts based on past reproductive outcomes. This, coupled with high site fidelity of female cowbirds between years, points to information use, rather than cowbird natal returns alone, increasing parasitism rates on highly productive sites between years.

Juvenile survival in a neotropical migratory songbird is lower than expected.

Attempts to estimate and identify factors influencing first-year survival in passerines, survival between fledging and the first reproductive attempt (i.e. juvenile survival), have largely been confounded by natal dispersal, particularly in long-distance migratory passerines. We studied Prothonotary Warblers (Protonotaria citrea) breeding in nest boxes to estimate first-year survival while accounting for biases related to dispersal that are common in mark-recapture studies. The natal dispersal distribution (median = 1420 m; n = 429) and a distance-dependent recruitment rate, which controls for effects of study site configuration, both indicated a pattern of short-distance natal dispersal. This pattern was consistent with results of a systematic survey for birds returning outside the nest box study sites (up to 30 km in all directions) within a majority (81%) of total available bottomland forest habitat, further suggesting that permanent emigration outside of the study system was rare. We used multistate mark-recapture modeling to estimate first-year survival and incorporated factors thought to influence survival while accounting for the potential confounding effects of dispersal on recapture probabilities for warblers that fledged during 2004-2009 (n = 6093). Overall, the average first-year survival for warblers reared without cowbird nestmates was 0.11 (95% CI = 0.09-0.13), decreased with fledging date (0.22 early to 0.03 late) and averaged 40% lower for warblers reared with a brood parasite nestmate. First-year survival was less than half of the rate thought to represent population replacement in migratory passerines (∼0.30). This very low rate suggests that surviving the first year of life for many Neotropical migratory species is even more difficult than previously thought, forcing us to rethink estimates used in population models.