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DNA metabarcoding is a popular tool for animal diet studies to address a variety of research topics across disciplines and taxa. Despite its widespread use, there has been relatively little focus on how digestion influences prey DNA detection and the description of a predator's diet. Fecal samples are a compelling source of dietary DNA because they are collected non-invasively. However, these samples may provide incomplete or inaccurate descriptions of diet because of differential digestion and DNA degradation across prey taxa during gut passage. This is especially pertinent for avian diet studies, which have widely adopted the use of fecal samples as a proxy for overall diet. To explore how digestion affects the recovery and detection of prey DNA in passerines, we used DNA metabarcoding to compare the recovery of prey DNA from paired stomach contents and fecal samples in Seaside Sparrows (Ammospiza maritima). Stomach contents produced ~2.5 times greater DNA concentrations than fecal samples and--while this difference in DNA concentration was not statistically significant--stomach contents produced significantly more read identifications than fecal samples. However, these differences did not influence the description of diet, as similar measures of richness and diversity were found in both sample types. The relative read abundance of common prey families remained consistent between sample types, suggesting that while less DNA may survive digestion, the proportions of prey remain largely unaffected. We found no difference in the description of diet based on sample type at the population level, but our results show that comparing stomach and fecal samples from the same individual can reveal distinct foraging bouts. With no clear benefit to using stomach contents, we conclude that fecal samples are the preferred sample type for avian metabarcoding diet studies, unless research goals necessitate otherwise. [ABSTRACT FROM AUTHOR]

Genotoxic chemicals, through damage and alteration of the genetic material of wild organisms, pose significant threats to the persistence of wild animal populations. Their damaging effects can ultimately impair the health of the ecosystem and its provision of services to human society. Bird species are good candidates for the role of sentinels of the effects of genotoxins, thanks to (i) the diversity of their ecological niches, (ii) their ubiquity across environments, (iii) their conspicuousness, abundance and approachability, together with (iv) their well-known life histories and the availability of historical data series. Avian diversity increases the likelihood that adequate model species be available for monitoring genotoxicants and assessing their impact. This paper reviews the methods utilized by genetic ecotoxicological studies of wild birds, highlighting their benefits and shortcomings. It also summarizes the genetic ecotoxicological studies so far conducted. In spite of a paucity of studies, several classes of genotoxicants have already been investigated across a variety of species and environments, thus supporting the versatility of birds as monitors of genotoxic contamination. Future technical advancements and applications are suggested, with particular reference to the analysis of mutational events, gene expression and methylation patterns. Finally, I argue that the development of avian genetic ecotoxicology will contribute to the understanding of natural variation in the underlying machinery for coping with DNA damage and oxidative stress, both of which are increasingly recognized as proximate factors in the evolution of life history adaptations. [ABSTRACT FROM AUTHOR]

Females of several vertebrate species selectively mate with males on the basis of the major histocompatibility complex (MHC) genes. As androgen-mediated maternal effects have long-lasting consequences for the adult phenotype, both mating and reproductive success may depend on the combined effect of MHC genotype and exposure to androgens during early ontogeny. We studied how MHC-based mate choice in ring-necked pheasants ( Phasianus colchicus) was influenced by an experimental in ovo testosterone (T) increase. There was no conclusive evidence of in ovo T treatment differentially affecting mate choice in relation to MHC genotype. However, females avoided mating with males with a wholly different MHC genotype compared with males sharing at least one MHC allele. Females also tended to avoid mating with MHC-identical males, though not significantly so. These findings suggest that female pheasants preferred males with intermediate MHC dissimilarity. Male MHC heterozygosity or diversity did not predict the expression of ornaments or male dominance rank. Thus, MHC-based mating preferences in the ring-necked pheasant do not seem to be mediated by ornaments' expression and may have evolved mainly to reduce the costs of high heterozygosity at MHC loci for the progeny, such as increased risk of autoimmune diseases or disruption of coadapted gene pools. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Maternal effects mediated by egg quality are important sources of offspring phenotypic variation and can influence the course of evolutionary processes. Mothers allocate to the eggs diverse antioxidants that protect the embryo from oxidative stress. In the yellow-legged gull ( Larus michahellis), yolk antioxidant capacity varied markedly among clutches and declined considerably with egg laying date. Analysis of bioptic yolk samples from clutches that were subsequently partially cross-fostered revealed a positive effect of yolk antioxidant capacity on embryonic development and chick growth, but not on immunity and begging behaviour, while controlling for parentage and common environment effects. Chick plasma antioxidant capacity varied according to rearing environment, after statistically partitioning out maternal influences mediated by egg quality. Thus, the results of this study indicate that egg antioxidants are important mediators of maternal effects also in wild bird populations, especially during the critical early post-hatching phase. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]