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Summary: Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.

The 2010 Deepwater Horizon (DWH) disaster led to extensive oil deposition in Louisiana’s coastal wetlands, followed two years later by Hurricane Isaac. These disturbances led to changes in saltmarsh invertebrate communities, potentially affecting higher-level predators and the saltmarsh food web. Seaside Sparrows (Ammospiza maritima) are ubiquitous, year-round residents of the coastal saltmarsh affected by the DWH spill, where they consume diverse invertebrates and may be considered an indicator species for the ecosystem’s integrity. We used DNA metabarcoding to evaluate prey consumed by Seaside Sparrows to understand how sparrows responded to residual contamination from the DWH oil spill and ecosystem disturbance caused by Hurricane Isaac. To do so, we evaluated metrics of diet (prey richness, diversity, overall diet composition) and resource use (total niche width, individual specialization) from 2011 to 2017 on oiled, unoiled, and reference sites. We found that while diet composition varied across years and site type, Hurricane Isaac had an even greater effect on the richness and diversity of prey consumed. Resource use—as measured by the total niche width of the populations and degree of individual specialization—was most stable on unoiled sites compared to unoiled and reference sites. Finally, we analyzed resource use for each combination of site type and year (i.e.: “2014 oiled sites”), which indicated a strong correlation between individual specialization and total niche width: as total niche width increased, individuals became more specialized, following the predictions of the Niche Variation Hypothesis.

Abstract Bayou orthohantavirus (BAYV) is one of several hantaviruses in the United States that cause hantavirus pulmonary syndrome in humans. Its host reservoir, the marsh rice rat (Oryzomys palustris), inhabits coastal saltmarshes of Louisiana, a region extensively impacted by anthropogenic disturbances, such as the 2010 Deepwater Horizon (DWH) oil spill. The oil spill presents an opportunity to investigate how a large‐scale ecological disturbance can influence the hantavirus host–pathogen dynamic by examining BAYV presence in its reservoir host species in areas with different oiling histories. Here, we: (1) quantify BAYV prevalence in the rice rat in coastal saltmarshes of Louisiana; (2) assess whether prevalence is driven by rice rat demographics, seasonality, or association with habitat characteristics; and (3) determine whether these factors differ by marsh oiling history. We collected mark–recapture data and blood and tissue samples over 5 years (2013–2017) at oiled, unoiled, and reference sites. Testing of the samples for BAYV revealed an antibody and RNA prevalence of 13.7%. Logistic regression analysis found that prevalence varied seasonally and inter‐annually, and in July of 2016 reached 30.8%. Sex (male) and increasing cover of Sporobolus alterniflorus and open water compared to Juncus roemerianus and bare ground were the strongest predictors of hantavirus prevalence. Abundance estimates derived from Huggins closed‐capture models were greatest at oiled sites, but oiling treatment had no residual influence on BAYV prevalence, and abundance and prevalence were not correlated. This study supports the hypothesis that habitat is a main driver of hantavirus prevalence in the host and implies that continued and future disturbances in the region will likely impact the rice rat–BAYV dynamic by altering plant communities and landscape structure.

Bioindicator species are commonly used as proxies to help identify the ecological effects of oil spills and other stressors. However, the utility of taxa as bioindicators is dependent on understanding their trophic niche and life history characteristics, as these factors mediate their ecological responses. Seaside sparrows (Ammospiza maritima) and marsh rice rats (Oryzomys palustris) are two ubiquitous terrestrial vertebrates that are thought to be bioindicators of oil spills in saltmarsh ecosystems. To improve the utility of these omnivorous taxa as bioindicators, we used carbon and nitrogen stable isotope analysis to quantify their trophic niches at saltmarshes in coastal Louisiana with differing oiling histories. We found that rats generally had lower trophic positions and incorporated more aquatic prey relative to seaside sparrows. The range of resources used (i.e.,trophic niche width) varied based on oiling history. Seaside sparrows had wider trophic niches than marsh rice rats at unoiled sites, but not at oiled sites. Trophic niche widths of conspecifics were less consistent at oiled sites, although marsh rice rats at oiled sites had wider trophic niches than rats at unoiled sites. These results suggest that past oiling histories may have imparted subtle, yet differing effects on the foraging ecology of these two co-occurring species. However, the temporal lag between initial oiling and our study makes identifying the ultimate drivers of differences between oiled and unoiled sites challenging. Even so, our findings provide a baseline quantification of the trophic niches of sympatric seaside sparrows and marsh rice rats that will aid in the use of these species as indicators of oiling and other environmental stressors in saltmarsh ecosystems.

In 2010, the Deepwater Horizon oil spill released an estimated 4.9 million barrels of oil into the Gulf of Mexico, damaging coastal ecosystems. Seaside Sparrows (Ammospiza maritima)—a year-round resident of Gulf Coast salt marshes—were exposed to oil, as shown by published isotopic and molecular analyses, but fitness consequences have not been clarified. We monitored nests around two bays in Plaquemines Parish, Louisiana, USA from 2012–2017 to assess possible impacts on the nesting biology of Seaside Sparrows. A majority of nests failed (76% of known-fate nests, N = 252 nests, 3521 exposure-days) during our study, and predation was the main cause of nest failure (~91% of failed nests). Logistic exposure analysis revealed that daily nest survival rate: (1) was greater at nests with denser vegetation at nest height, (2) was higher in the more sheltered bay we studied, (3) decreased over the course of the breeding season in each year, and (4) was not correlated with either sediment polycyclic aromatic hydrocarbon concentrations or estimated predator abundance during the years for which we had those data. Although the Deepwater Horizon spill impacted other aspects of Seaside Sparrow ecology, we found no definitive effect of initial oiling or oiled sediment on nest survival during 2012–2017. Because predation was the overwhelming cause of nest failure in our study, additional work on these communities is needed to fully understand demographic and ecological impacts of storms, oil spills, other pollutants, and sea-level rise on Seaside Sparrows and their predators.

In 2010, the Deepwater Horizon oil spill released an estimated 4.9 million barrels of oil into the Gulf of Mexico, damaging coastal ecosystems. Seaside Sparrows (Ammospiza maritima)-a year-round resident of Gulf Coast salt marshes-were exposed to oil, as shown by published isotopic and molecular analyses, but fitness consequences have not been clarified. We monitored nests around two bays in Plaquemines Parish, Louisiana, USA from 2012-2017 to assess possible impacts on the nesting biology of Seaside Sparrows. A majority of nests failed (76% of known-fate nests, N = 252 nests, 3521 exposure-days) during our study, and predation was the main cause of nest failure (~91% of failed nests). Logistic exposure analysis revealed that daily nest survival rate: (1) was greater at nests with denser vegetation at nest height, (2) was higher in the more sheltered bay we studied, (3) decreased over the course of the breeding season in each year, and (4) was not correlated with either sediment polycyclic aromatic hydrocarbon concentrations or estimated predator abundance during the years for which we had those data. Although the Deepwater Horizon spill impacted other aspects of Seaside Sparrow ecology, we found no definitive effect of initial oiling or oiled sediment on nest survival during 2012-2017. Because predation was the overwhelming cause of nest failure in our study, additional work on these communities is needed to fully understand demographic and ecological impacts of storms, oil spills, other pollutants, and sea-level rise on Seaside Sparrows and their predators.

BackgroundFollowing the Chernobyl nuclear power plant accident, large amounts of radionuclides were emitted and spread in the environment. Animals living in such contaminated areas are predicted to suffer fitness costs including reductions in the quality and quantity of gametes.Methodology/principal findingsWe studied whether aspermy and sperm quality were affected by radioactive contamination by examining ejaculates from wild caught birds breeding in areas varying in background radiation level by more than three orders of magnitude around Chernobyl, Ukraine. The frequency of males with aspermy increased logarithmically with radiation level. While 18.4% of males from contaminated areas had no sperm that was only the case for 3.0% of males from uncontaminated control areas. Furthermore, there were negative relationships between sperm quality as reflected by reduced sperm velocity and motility, respectively, and radiation.Conclusions/significanceOur results suggest that radioactive contamination around Chernobyl affects sperm production and quality. We are the first to report an interspecific difference in sperm quality in relation to radioactive contamination.

Carbon isotopic evidence revealed Deepwater Horizon (DWH) oil entering coastal planktonic and lower terrestrial food webs. The integration of spilled oil into higher terrestrial trophic levels, however, remains uncertain. We measured radiocarbon ( ^14 C) and stable carbon ( ^13 C) in seaside sparrow ( Ammodramus maritimus ) feathers and crop contents. Lower ^14 C and ^13 C values in feathers and crop contents of birds from contaminated areas indicated incorporation of carbon from oil. Our results, although based on a small sample of birds, thus reveal a food-web link between oil exposure and a terrestrial ecosystem. They also suggest that the reduction in reproductive success previously documented in the same population might be due to the (direct) toxic effect of oil exposure, rather than to (indirect) ecological effects. We recommend future studies test our results by using larger samples of birds from a wider area in order to assess the extent and implications of DWH oil incorporation into the terrestrial food web.

BackgroundRadiation has negative effects on survival of animals including humans, although the generality of this claim is poorly documented under low-dose field conditions. Because females may suffer disproportionately from the effects of radiation on survival due to differences in sex roles during reproduction, radiation-induced mortality may result in male-skewed adult sex ratios.Methodology/principal findingWe estimated the effects of low-dose radiation on adult survival rates in birds by determining age ratios of adults captured in mist nets during the breeding season in relation to background radiation levels around Chernobyl and in nearby uncontaminated control areas. Age ratios were skewed towards yearlings, especially in the most contaminated areas, implying that adult survival rates were reduced in contaminated areas, and that populations in such areas could only be maintained through immigration from nearby uncontaminated areas. Differential mortality in females resulted in a strongly male-skewed sex ratio in the most contaminated areas. In addition, males sang disproportionately commonly in the most contaminated areas where the sex ratio was male skewed presumably because males had difficulty finding and acquiring mates when females were rare. The results were not caused by permanent emigration by females from the most contaminated areas because none of the recaptured birds had changed breeding site, and the proportion of individuals with morphological abnormalities did not differ significantly between the sexes for areas with normal and higher levels of contamination.Conclusions/significanceThese findings are consistent with the hypothesis that the adult survival rate of female birds is particularly susceptible to the effects of low-dose radiation, resulting in male skewed sex ratios at high levels of radiation. Such skewed age ratios towards yearlings in contaminated areas are consistent with the hypothesis that an area exceeding 30,000 km(2) in Chernobyl's surroundings constitutes an ecological trap that causes dramatic excess mortality.

Normal and pathological processes entail the production of oxidative substances that can damage biological molecules and harm physiological functions. Organisms have evolved complex mechanisms of antioxidant defense, and any imbalance between oxidative challenge and antioxidant protection can depress fitness components and accelerate senescence. While the role of oxidative stress in pathogenesis and aging has been studied intensively in humans and model animal species under laboratory conditions, there is a dearth of knowledge on its role in shaping life-histories of animals under natural selection regimes. Yet, given the pervasive nature and likely fitness consequences of oxidative damage, it can be expected that the need to secure efficient antioxidant protection is powerful in molding the evolutionary ecology of animals. Here, we test whether overall antioxidant defense varies with age and predicts long-term survival, using a wild population of a migratory passerine bird, the barn swallow (Hirundo rustica), as a model.Plasma antioxidant capacity (AOC) of breeding individuals was measured using standard protocols and annual survival was monitored over five years (2006-2010) on a large sample of selection episodes. AOC did not covary with age in longitudinal analyses after discounting the effect of selection. AOC positively predicted annual survival independently of sex. Individuals were highly consistent in their relative levels of AOC, implying the existence of additive genetic variance and/or environmental (including early maternal) components consistently acting through their lives.Using longitudinal data we showed that high levels of antioxidant protection positively predict long-term survival in a wild animal population. Present results are therefore novel in disclosing a role for antioxidant protection in determining survival under natural conditions, strongly demanding for more longitudinal eco-physiological studies of life-histories in relation to oxidative stress in wild populations.

Animals living in areas contaminated by radioactive material from Chernobyl suffer from increased oxidative stress and low levels of antioxidants. Therefore, normal development of the nervous system is jeopardized as reflected by high frequencies of developmental errors, reduced brain size and impaired cognitive abilities in humans. Alternatively, associations between psychological effects and radiation have been attributed to post-traumatic stress in humans.Here we used an extensive sample of 550 birds belonging to 48 species to test the prediction that even in the absence of post-traumatic stress, there is a negative association between relative brain size and level of background radiation. We found a negative association between brain size as reflected by external head volume and level of background radiation, independent of structural body size and body mass. The observed reduction in brain size in relation to background radiation amounted to 5% across the range of almost a factor 5,000 in radiation level. Species differed significantly in reduction in brain size with increasing background radiation, and brain size was the only morphological character that showed a negative relationship with radiation. Brain size was significantly smaller in yearlings than in older individuals.Low dose radiation can have significant effects on normal brain development as reflected by brain size and therefore potentially cognitive ability. The fact that brain size was smaller in yearlings than in older individuals implies that there was significant directional selection on brain size with individuals with larger brains experiencing a viability advantage.