The gut microbiota of three avian species living in sympatry.

Background: Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation.

Genomic and fitness consequences of a near-extinction event in the northern elephant seal.

Understanding the genetic and fitness consequences of anthropogenic bottlenecks is crucial for biodiversity conservation. However, studies of bottlenecked populations combining genomic approaches with fitness data are rare. Theory predicts that severe bottlenecks deplete genetic diversity, exacerbate inbreeding depression and decrease population viability.

The gut microbiota-immune-brain axis in a wild vertebrate: dynamic interactions and health impacts.

The gut microbiota-immune-brain axis is a feedback network which influences diverse physiological processes and plays a pivotal role in overall health and wellbeing. Although research in humans and laboratory mice has shed light into the associations and mechanisms governing this communication network, evidence of such interactions in wild, especially in young animals, is lacking. We therefore investigated these interactions during early development in a population of common buzzards () and their effects on individual condition.

Characterizing offshore polar ocean soundscapes using ecoacoustic intensity and diversity metrics.

Polar offshore environments are considered the last pristine soundscapes, but accelerating climate change and increasing human activity threaten their integrity. In order to assess the acoustic state of polar oceans, there is the need to investigate their soundscape characteristics more holistically. We apply a set of 14 ecoacoustic metrics (EAMs) to identify which metrics are best suited to reflect the characteristics of disturbed and naturally intact polar offshore soundscapes.

Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness.

The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability.

Runs of homozygosity reveal contrasting histories of inbreeding across global lineages of the edible porcini mushroom, Boletus edulis.

Inbreeding, the mating of individuals that are related through common ancestry, is of central importance in evolutionary and conservation biology due to its impacts on individual fitness and population dynamics. However, while advanced genomic approaches have revolutionised the study of inbreeding in animals, genomic studies of inbreeding are rare in plants and lacking in fungi. We investigated global patterns of inbreeding in the prized edible porcini mushroom Boletus edulis using 225 whole genomes from seven lineages distributed across the northern hemisphere.

Life-history stage influences immune investment and oxidative stress in response to environmental heterogeneity in Antarctic fur seals.

Immune defenses are crucial for survival but costly to develop and maintain. Increased immune investment is therefore hypothesized to trade-off with other life-history traits. Here, we examined innate and adaptive immune responses to environmental heterogeneity in wild Antarctic fur seals.

Early-life factors shaping the gut microbiota of Common buzzard nestlings.

Background: Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited.

No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals.

Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background.

Ninety years of change, from commercial extinction to recovery, range expansion and decline for Antarctic fur seals at South Georgia.

With environmental change, understanding how species recover from overharvesting and maintain viable populations is central to ecosystem restoration. Here, we reconstruct 90 years of recovery trajectory of the Antarctic fur seal at South Georgia (S.W.

Genetic diversity and demographic history of the leopard seal: A Southern Ocean top predator.

Leopard seals (Hydrurga leptonyx) are top predators that can exert substantial top-down control of their Antarctic prey species. However, population trends and genetic diversity of leopard seals remain understudied, limiting our understanding of their ecological role. We investigated the genetic diversity, effective population size and demographic history of leopard seals to provide fundamental data that contextualizes their predatory influence on Antarctic ecosystems.

Editorial: Polar Genomics in a Changing World.

Polar regions play critical roles in the function of the Earth's climate system, many of which are underpinned by their endemic biota [...

Heavy metal contamination in pristine environments: lessons from the Juan Fernandez fur seal ().

Heavy metals, including mercury (Hg) and cadmium (Cd), occur naturally or anthropogenically and are considered toxic to the environment and human health. However, studies on heavy metal contamination focus on locations close to industrialized settlements, while isolated environments with little human activity are often ignored due to perceived low risk. This study reports heavy metal exposure in Juan Fernandez fur seals (JFFS), a marine mammal endemic to an isolated and relatively pristine archipelago off the coast of Chile.

Effects of hunting on genetic diversity, inbreeding and dispersal in Finnish black grouse ().

Intensive hunting activities such as commercial fishing and trophy hunting can have profound influences on natural populations. However, less intensive recreational hunting can also have subtle effects on animal behaviour, habitat use and movement, with implications for population persistence. Lekking species such as the black grouse () may be especially prone to hunting as leks are temporally and spatially predictable, making them easy targets.

Evolution of the germline mutation rate across vertebrates.

The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles.

Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species.

Two commercially important scallop species of the genus are found in Europe: the north Atlantic and the Mediterranean whose distributions abut at the Almeria-Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the genome is unknown. Here, we mapped RADseq data from 235 and 27 to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation.

Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals.

The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species.

Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals.

Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose.

The genetic consequences of captive breeding, environmental change and human exploitation in the endangered peninsular pronghorn.

Endangered species with small population sizes are susceptible to genetic erosion, which can be detrimental to long-term persistence. Consequently, monitoring and mitigating the loss of genetic diversity are essential for conservation. The Peninsular pronghorn (Antilocapra americana peninsularis) is an endangered pronghorn subspecies that is almost entirely held in captivity.

Low heritability and high phenotypic plasticity of salivary cortisol in response to environmental heterogeneity in a wild pinniped.

Individuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or environmental stressors often produce an individualized response of the hypothalamic-pituitary-adrenal (HPA) axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the factors shaping individual variation in baseline cortisol in Antarctic fur seal pups and their mothers.

Demographic Reconstruction of Antarctic Fur Seals Supports the Krill Surplus Hypothesis.

Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the 'krill surplus hypothesis'. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling.

A stable foraging polymorphism buffers Galápagos sea lions against environmental change.

Understanding the ability of animals to cope with a changing environment is critical in a world affected by anthropogenic disturbance. Individual foraging strategies may influence the coping ability of entire populations, as these strategies can be adapted to contrasting conditions, allowing populations with foraging polymorphisms to be more resilient toward environmental change. However, environmentally dependent fitness consequences of individual foraging strategies and their effects on population dynamics have not been conclusively documented.

Origin and expansion of the world's most widespread pinniped: Range-wide population genomics of the harbour seal (Phoca vitulina).

The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonized its current range. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic single nucleotide polymorphisms from 286 individuals sampled from 22 localities across the species' range.

50,000 years of ice and seals: Impacts of the Last Glacial Maximum on Antarctic fur seals.

Ice is one of the most important drivers of population dynamics in polar organisms, influencing the locations, sizes, and connectivity of populations. Antarctic fur seals, , are particularly interesting in this regard, as they are concomitantly reliant on both ice-associated prey and ice-free coastal breeding areas. We reconstructed the history of this species through the Last Glacial Maximum (LGM) using genomic sequence data from seals across their range.

Sweepstake reproductive success and collective dispersal produce chaotic genetic patchiness in a broadcast spawner.

A long-standing paradox of marine populations is chaotic genetic patchiness (CGP), temporally unstable patterns of genetic differentiation that occur below the geographic scale of effective dispersal. Several mechanisms are hypothesized to explain CGP including natural selection, spatiotemporal fluctuations in larval source populations, self-recruitment, and sweepstake reproduction. Discriminating among them is extremely difficult but is fundamental to understanding how marine organisms reproduce and disperse.