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The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics., Trends in Genetics, 39 (7), ISSN:0168-9525

The barn swallow (Hirundo rustica) poses a number of fascinating scientific questions, including the taxonomic status of postulated subspecies. Here, we obtained and assessed the sequence variation of 411 complete mitogenomes, mainly from the European H. r. rustica, but other subspecies as well. In almost every case, we observed subspecies-specific haplogroups, which we employed together with estimated radiation times to postulate a model for the geographical and temporal worldwide spread of the species. The female barn swallow carrying the Hirundo rustica ancestral mitogenome left Africa (or its vicinity) around 280 thousand years ago (kya), and her descendants expanded first into Eurasia and then, at least 51 kya, into the Americas, from where a relatively recent (

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

International audience; In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radio- logical fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem at- tributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This paper is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensi- tive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that ra- diological risk assessments must be designed and informed by rigorous statistical frameworks capable of reveal- ing the causal inference tying radiological exposure to the endpoints selected for measurement.

The objective of this paper is to present the results of discussions at a workshop held as part of the International Congress of Radiation Research (Environmental Health stream) in Manchester UK, 2019. The main objective of the workshop was to provide a platform for radioecologists to engage with radiobiologists to address major questions around developing an Ecosystem approach in radioecology and radiation protection of the environment. The aim was to establish a critical framework to guide research that would permit integration of a pan-ecosystem approach into radiation protection guidelines and regulation for the environment. The conclusions were that the interaction between radioecologists and radiobiologists is useful in particular in addressing field versus laboratory issues where there are issues and challenges in designing good field experiments and a need to cross validate field data against laboratory data and vice versa. Other main conclusions were that there is a need to appreciate wider issues in ecology to design good approaches for an ecosystems approach in radioecology and that with the capture of 'Big Data', novel tools such as machine learning can now be applied to help with the complex issues involved in developing an ecosystem approach.

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.

Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.

Parents are expected to invest more in the sex that benefits most from the local environment. When the quality of breeding sites varies spatially and natal dispersal of males and females differs, parents in high-quality habitats should skew their progeny sex ratio in favor of the less dispersing sex. We tested this prediction in the barn swallow (Hirundo rustica L.), by relating the proportion of male offspring around fledging (secondary sex ratio) of first and second broods to the ecological quality (presence of livestock farming and relative surface of hayfields in the foraging range) and local demographic trends of the farms where the colonies were located. Consistent with our predictions, the proportion of male offspring, which are more philopatric than females, increased with the extent of hayfields, which are high quality, preferred foraging habitats. Moreover, the proportion of male offspring in second broods was smaller in colonies with positive demographic trends, possibly indicating density-dependent effects on sex ratio. Independent of the mechanism generating uneven sex ratio (zygote sex ratio adjustment or sex-related pre-fledging mortality), barn swallows breeding under favorable conditions overproduced the sex that is more likely to benefit from such conditions.

1.Ionizing radiation produces oxidative stress, but organisms can adapt to their exposure with physiological adaptive responses. However, the role of radioadaptive responses in wild populations remains poorly known. 2.At Chernobyl, studies of birds and other taxa including humans show that chronic exposure to radiation depletes antioxidants and increases oxidative damage. Here, we present analyses of levels of the most important intracellular antioxidant (i.e. glutathione, GSH), its redox status, DNA damage and body condition in 16 species of birds exposed to radiation at Chernobyl. We use an approach that allows considering the individual bird as the sampling unit while controlling for phylogenetic effects, thus increasing the statistical power by avoiding the use of species means as done for most previous comparative studies. 3.As a consequence, we found a pattern radically different from previous studies in wild populations, showing that GSH levels and body condition increased, and oxidative stress and DNA damage decreased, with increasing background radiation. Thus, when several species are considered, the overall pattern indicates that birds are not negatively affected by chronic exposure to radiation and may even obtain beneficial hormetic effects following an adaptive response. Analysis of the phylogenetic signal supports the existence of adaptation in the studied traits, particularly in GSH levels and DNA damage. 4.We also show that, under equal levels of radiation, the birds that produce larger amounts of the pigment pheomelanin and lower amounts of eumelanin pay a cost in terms of decreased GSH levels, increased oxidative stress and DNA damage, and poorer body condition. Radiation, however, diminished another potential cost of pheomelanin, namely its tendency to produce free radicals when exposed to radiation, because it induced a change towards the production of less pro-oxidant forms of pheomelanin with higher benzothiazole-to-benzothiazine ratios, which may have facilitated the acclimation of birds to radiation exposure. 5.Our findings represent the first evidence of adaptation to ionizing radiation in wild animals, and confirm that pheomelanin synthesis represents an evolutionary constraint under stressful environmental conditions because it requires GSH consumption

Random and subtle deviations from bilateral symmetry (fluctuating asymmetry) have long been of interest to biologists who wish to study the susceptibility of organisms to changes in environmental quality. However, the reliability of FA as a biomarker has come under question due to inconsistent results in the literature. We conducted a meta-analysis of published literature to test the hypothesis that FA is a reliable biomarker of environmental stress in insects and identify possible sources of variation amongst studies. We expected studies to detect larger, positive magnitudes of effect on FA in lab populations due to the lack of confounding effects from other environmental factors compared to wild populations. Additionally, we predicted that studies that used geometric morphometric approaches to FA in shape and size would be more sensitive to changes in environmental quality compared to linear and meristic measures and thus show larger effects on FA. We also expected anthropogenic stressors to generate significantly larger effects on FA compared to naturally occurring stressors due to the organisms’ inability to buffer developmental pathways against a novel stressor. Finally, we predicted comparatively larger magnitudes of effect in studies that verified the environmental factor acting on the organism was a stressor by detecting negative effects on fitness-related traits. Overall, we found that FA is a sensitive biomarker of environmental stress. Environmental stressors explained 36% of the variation of effect on FA across studies. Studies that demonstrated a negative effect of the stressor on fitness-related traits showed significantly larger, positive magnitudes of effect on FA compared to studies that did not detect an effect from the environmental stressor. Additionally, studies conducted under laboratory conditions detected significantly larger, effects on FA compared to field-based studies. The kind of trait measured and the novelty of the stressor did not significantly account for differences amongst studies. Thus, the use of FA as a biomarker of environmental stress is a legitimate tool particularly when studies verify the biological relevance of stressors for the study organism.

Spermatozoa vary greatly in size and shape among species across the animal kingdom. Postcopulatory sexual selection is thought to be the major evolutionary force driving this diversity. In contrast, less is known about how sperm size varies among populations of the same species. Here, we investigate geographic variation in sperm size in barn swallows Hirundo rustica, a socially monogamous passerine with a wide Holarctic breeding distribution. We included samples from seven populations and three subspecies: five populations of ssp. rustica in Europe (Czech, Italy, Norway, Spain, and Ukraine), one population of ssp. transitiva in Israel, and one population of ssp. erythrogaster in Canada. All sperm traits (head length, midpiece length, tail length, and total length) varied significantly among populations. The variation among the European rustica populations was much lower than the differences among subspecies, indicating that sperm traits reflect phylogenetic distance. We also performed a test of the relationship between the coefficient of between-male variation in total sperm length and extrapair paternity levels across different populations within a species. Recent studies have found a strong negative relationship between sperm size variation and extrapair paternity among species. Here, we show a similar negative relationship among six barn swallow populations, which suggests that the variance in male sperm length in a population is shaped by the strength of stabilizing postcopulatory sexual selection.

Mutagenic and epigenetic effects of environmental stressors and their transgenerational consequences are of interest to evolutionary biologists because they can amplify natural genetic variation. We studied the effect of parental exposure to radioactive contamination on offspring development in lesser marsh grasshopper Chorthippus albomarginatus. We used a geometric morphometric approach to measure fluctuating asymmetry (FA), wing shape and wing size. We measured time to sexual maturity to check whether parental exposure to radiation influenced offspring developmental trajectory and tested effects of radiation on hatching success and parental fecundity. Wings were larger in early maturing individuals born to parents from high radiation sites compared to early maturing individuals from low radiation sites. As time to sexual maturity increased, wing size decreased but more sharply in individuals from high radiation sites. Radiation exposure did not significantly affect FA or shape in wings nor did it significantly affect hatching success and fecundity. Overall, parental radiation exposure can adversely affect offspring development and fitness depending on developmental trajectories although the cause of this effect remains unclear. We suggest more direct measures of fitness and the inclusion of replication in future studies to help further our understanding of the relationship between developmental instability, fitness and environmental stress.

Maternal effects through albumen quality are largely unexplored, despite the fundamental role that albumen exerts as source of proteins and water, as well as for antimicrobial defence of the embryo. We analysed the variation of two major albumen antimicrobials, avidin and lysozyme, by extracting samples from freshly laid eggs of the yellow-legged gull (Larus michahellis) and by correlating their levels to egg features. Lysozyme concentration increased along the laying sequence, while avidin concentration decreased. Both antimicrobials declined during the season. In addition, avidin concentration declined from first- to last-laid male eggs, whereas the opposite was true among the female eggs. We also analysed chick body mass and size and immune response, in relation to albumen antimicrobial levels in their original egg while controlling for potential covariation between egg quality and rearing conditions by cross-fostering eggs between nests. Tarsus length decreased with avidin concentration, particularly early in the season. Avidin concentration negatively predicted tarsus length of chicks and the phytohaemagglutinin response of females, but not males. However, chick phenotype did not covary with lysozyme albumen concentration. This is the first study where maternal effects mediated by albumen antimicrobials are investigated in relation to both sex and egg features in any wild bird species. Whether the observed patterns of variation in antimicrobial concentration are the by-product of maternal physiological constraints, or reflect adaptive allocation strategies, cannot be ascertained. The covariation between chick cell-mediated immunity and albumen avidin concentration might be causal, according to the documented effects of albumen proteins on immunity in other species.

In avian species, maternal provisioning to the eggs is predicted to be more valuable for the offspring under adverse environmental conditions and intense sibling competition. However, studies manipulating both the amount of maternal pre-hatching resources and the harshness of post-hatching environment have seldom been performed to date. In this experimental study of Barn Swallow (Hirundo rustica) nestlings, we tested the consequences of a reduction in the albumen content of the eggs for fitness-related offspring traits, while performing an unbalanced partial cross-fostering soon after hatching, either increasing or decreasing brood size by one nestling. By molecular sexing of the chicks, we additionally tested for sex-specific sensitivity of individual nestlings to experimental treatments and to sex ratio variation in nestmates. We predicted that chicks hatching from albumen-deprived eggs should suffer more than control chicks from the harsher rearing conditions of enlarged broods. However, although albumen removal depressed chick body mass, chicks hatching from control eggs did not fare better than those hatching from eggs with reduced albumen content in enlarged vs. reduced broods. Albumen removal had sex-specific effects on immunity, with males, but not females, hatching from eggs with reduced albumen content showing a lower T-cell-mediated immune response than controls, suggesting that the two sexes were differentially susceptible to resource deprivation during early ontogeny. In addition, both immune response and chick body mass at age 7 days, when maximum growth rate is attained, declined with an increasing proportion of male nestmates. The effect of brood size manipulation on chick body mass at age 12 days, when peak body mass is attained, was also found to depend on brood sex composition, in that an increase in the proportion of male nestmates depressed offspring body mass in reduced broods, while the reverse was true in enlarged broods. On the whole, these findings suggest that sex differences may exist in environmental sensitivity and patterns of resource allocation among different body functions, and that brood size variation and sex composition may affect offspring fitness-related traits.

Summary 1Egg size is an important maternal trait that can have major consequences on offspring phenotype. However, the effects of the variation of different components of cleidoic eggs have been little investigated. 2Here, we addressed whether a reduction of the relative egg albumen content within the natural range of variation affects viability, time to hatching, early post-natal begging displays, morphology and immune response of yellow-legged gull Larus michahellis chicks. 3Egg mass strongly positively predicted chick size and mass at all ages, while time to hatching positively predicted tarsus length and immune response, irrespective of albumen removal. Variation in time to hatching may thus affect immune system maturation. 4Albumen removal resulted in a lower embryonic viability and increased time to hatching of individual eggs. The probability that an egg originated a chick surviving until 8 days of age increased with original egg mass among controls, but not among chicks hatching from eggs with reduced albumen content (‘albumen chicks’). 5Begging rate increased with laying order among albumen chicks while it decreased among controls. Concomitantly, begging rate decreased with egg mass among controls while it did not vary among albumen chicks. Surprisingly, albumen removal did not affect body mass or tarsus length except at 8 days of age, when control chicks were lighter than albumen chicks. 6In conclusion, our study indicates that a reduction of the relative egg albumen content can have complex effects on offspring development, behaviour and viability of a semiprecocial bird, suggesting that the relative albumen content of the eggs represents an important mechanism of maternal effects.

A number of studies have assessed or modeled the distribution of the radionuclides released by the accident at the Fukushima-Daiichi Nuclear Power Plant (FDNPP). Few studies however have investigated its consequences for the local biota. We tested whether exposure of barn swallow (Hirundo rustica) nestlings to low dose ionizing radiation increased genetic damage to their peripheral erythrocytes. We estimated external radiation exposure by using thermoluminescent dosimeters and by measuring radioactivity of the nest material. We then assessed DNA damage by means of the neutral comet assay. In addition, we conducted standard point-count censuses of barn swallows across environmental radiation levels and estimated their abundance and local age ratio. Radioactivity of nest samples was in the range 479–143,349 Bq kg−1, while external exposure varied between 0.15 and 4.9 mGy. Exposure to radioactive contamination did not correlate with higher genetic damage in nestlings. However, at higher levels of radioactive contamination the number of barn swallows declined and the fraction of juveniles decreased, indicating lower survival and lower reproduction and/or fledging rate. Thus, genetic damage to nestlings does not explain the decline of barn swallows in contaminated areas and a proximate mechanism for the demographic effects documented here remains to be clarified.