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The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors. [ABSTRACT FROM AUTHOR]

Introduction: Atlantic puffin (Fratercula arctica, hereafter "puffin") reproductive success in the Gulf of Maine (GoM) has declined following a recent oceanographic regime shift that has led to rapid warming and increasingly frequent marine heatwaves. Concurrent changes in both the regional forage fish community and puffin chick diets and provisioning rates suggest that inadequate prey resources may be driving this decline. Traditional, noninvasive methods of diet assessment, however, are unable to determine seabird diet at many age classes and breeding stages. Methods: To determine what prey GoM puffins were feeding on during two years of marine heatwave conditions, we assessed puffin diet using two complementary methods: traditional, observational methods that utilize billload photography and emerging methods employing fecal DNA metabarcoding. We then examined the effect of methodology, age, breeding stage, and year on puffin diet composition. Results: We identified a strong correlation between the composition of chick diet as estimated through traditional and emerging methods, supporting the interpretation of DNA relative read abundance as a quantitative metric of diet composition. Both methods identified the same dominant prey groups yet metabarcoding identified a greater number of species and offered higher taxonomic resolution. Additionally, metabarcoding revealed adult puffin diet during the incubation period for the first time. Although puffin adults and chicks fed on many of the same prey types, adults consumed a greater variety of taxa and consumed more low quality prey types than they provisioned chicks. Discussion: For both age classes, diet varied both between and within years, likely reflecting changes in the local forage fish community in response to environmental variability. Puffins exploited unusual abundances of typically-uncommon prey during these two years of marine heatwave conditions, yet low puffin productivity suggests the observed dietary plasticity was not fully able to compensate for apparent prey shortages. Continued refinement of molecular methods and the interpretation of the data they provide will enable better assessments of how seabirds of diverse ages and breeding stages are adapting to changing prey communities. [ABSTRACT FROM AUTHOR]

Aim: Shaped by climate change and sea‐level rise, tidal salt marshes represent ephemeral systems that are home to only a few species. The dynamic ecological histories of these habitats, however, render it challenging to reconstruct the complete biogeographical histories of their endemic taxa. To better understand the evolutionary history of tidal marsh endemic sparrows, we employ genomic data to evaluate the timing and direction of tidal marsh colonization events and leverage these data to test a series of models describing the biogeographical history of our study taxa. Location: North America. Taxon: Ammospiza Sparrows. Methods: We sampled 54 individuals from the Ammospiza clade from freshwater and saltwater habitats. We sequenced whole genomes and generated a dataset containing 21 million SNPs. Detailed phylogenomic analyses were conducted to identify relationships between tidal marsh and freshwater species. These phylogenies were then used to date divergence times and reconstruct the biogeographical history of the clade as well as identify historic signals of introgression. Results: Phylogenies based on several million SNPs supported well‐resolved clades that correspond to all previous species designations. Demographic modelling within A. nelsoni provided further resolution into the subspecies topology. Phylogenetic and biogeographical reconstructions support a series of saltwater to freshwater colonization events, with some endemic taxa exhibiting associations with tidal marsh habitat over longer evolutionary time‐scales and some habitat transitions occurring as recently as 5,000 years ago. Main Conclusions: Biogeographical and phylogenomic reconstructions support an original freshwater origin of the Ammospiza sparrows currently inhabiting tidal marshes in North America. We also found strong evidence for a saltwater to freshwater transition in A. n. subvirgatus as opposed to the long hypothesized freshwater origin of this group. We conclude that the increased resolution from genomic data paired with an integrative framework of phylogenomic, demographic and biogeographical reconstructions is important for resolving evolutionary histories in complex and ephemeral environments. [ABSTRACT FROM AUTHOR]

Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing "green" season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black-throated blue warbler ( Setophaga caerulescens ) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a 2-week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long-legged cobweaver), and Philodromus rufus (white-striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black-throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate-induced changes in insect communities with longer green seasons., Competing Interests: The authors declare we have no competing interests., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)