Jaelle C. Brealey

Tree bark hosts a unique community of microorganisms, distinct from that of other plant tissues and from the microbial associates of macrophytic epiphytes. These corticolous communities are important components of tree-associated food webs. However, the factors influencing corticolous microbial diversity are understudied. We used amplicon sequencing to characterise and compare the bacterial and aerophytic algal communities colonising the bark of birch trees at three sites in southern Norway with differing histories of nitrogen deposition. Within each site, we investigated associations between the corticolous community and variation in placement on the trunk, including north-facing vs. south-facing aspect, height and trunk diameter. While the most abundant bacterial and algal taxa were similar across the three sites, there were clear differences among sites. Aspect had a strong effect at the most oceanic and open site, with increased abundance of cyanobacteria at northern compared to southern aspects. We observed a higher abundance of nitrogen-fixing cyanobacteria at the site where historical nitrogen deposition had been lowest and correspondingly higher abundance of non-diazotrophic green algae where historical nitrogen deposition had been highest. Generally, the bacterial and algal communities followed similar patterns and co-occurrence network analysis revealed that algal taxa were interspersed among bacterial clusters. Our study provides the first characterisation of both the bacterial and aerophytic algal bark-associated communities of birch, one of the most common and ecologically important trees in Norway. Our results add to the growing body of literature demonstrating that tree bark supports a complex microbial community that varies among sites.

Color polymorphism is an important trait due to its role in defense strategies, feeding habits, environmental responses such as temperature regulation, and overall fitness. While the genetic basis of color polymorphism is well understood in mammals, it remains relatively understudied in non-avian reptiles. Vipera berus, the European adder, is the most widely distributed and northernmost terrestrial snake in the world. Similar to other European vipers, V. berus exhibits a range of dorsal color patterns spanning from zig-zag to complete melanism. However, a unique longitudinal dorsal stripe pattern was recently discovered in the isolated Gossa Island (∼45 km2) population of Norway, where approximately 5% of snakes exhibit this distinct pattern instead of the common dorsal zig-zag pattern. In this study, we investigated the genetic basis of the unique phenotype observed on Gossa by combining low-depth whole-genome shotgun sequencing and pairwise FST genome-scanning. We discovered a moderately sized, significantly differentiated genomic region containing five associated genes, including the premelanosome gene (PMEL) that encodes a well-known transmembrane glycoprotein that is a key component of melanosome organelles. We implicate a functionally relevant variant in the encoded premelanosome protein. Our results provide insight into the evolution and genetic basis of pigmentation of squamate reptiles using the unbiased approach of genome scanning, a method that has rarely been used in this context.

Parasites are ubiquitous in wildlife and can influence health and fitness. Thus, the inclusion of parasites in wildlife monitoring programs could provide important information for understanding declines in population body condition or recruitment rates. However, parasites are often neglected as a factor in wildlife management. We characterised the gastrointestinal parasite community of moose ( Alces alces ) in central Norway over an autumn hunting season and the following winter, using parasitological examination of faecal samples. We identified an age-related effect on parasite communities, including increased prevalence and abundance of Protostrongylidae species and increased community richness in yearlings compared to older moose. We also found that individuals with a lower body mass had higher burdens of Trichostrongylidae and Protostrongylidae species in autumn. There was some evidence for increased parasite burdens in males compared to females, while there was less evidence for seasonal differences between autumn and winter in a subsample of adult females. We found no strong associations between parasite burdens and moose population density. Our results add to the growing body of literature supporting the use of parasite burdens as proxies for an individual’s health status and potentially as predictors for fitness effects. In many Fennoscandian moose populations, the body condition and recruitment rates of individuals are declining, thus further monitoring of parasites may be needed to better understand the mechanisms behind these declines, including the potential role of parasites.

Dental calculus offers an extraordinary window into the past, preserving a rich archive of genetic material that can unlock new insights into ancient ecosystems. By capturing traces of oral microbiomes, dietary components, and even gut microbes regurgitated by ruminants, dental calculus provides an extraordinary window into the past to reconstruct ecological interactions and past environmental conditions. Here, we harness the power of ancient metagenomics to explore the oral microbiome, digestive microbiomes and diet of Pleistocene reindeer ( Rangifer tarandus ) from archaeological sites in France, a region that once served as a glacial refugium before reindeer disappeared from the area. We used shotgun metagenomic sequencing to assemble microbial genomes (MAGs) and classify microbial and dietary reads from dental calculus of 19 ancient reindeer (ca. 12,000 - 23,000 years BP) and 27 modern and historical (1861 - 1958 CE) Scandinavian reindeer. Notably, six bacterial taxa associated with the rumen microbiome were consistently detected across both ancient and modern samples, offering a rare glimpse into the continuity of digestive adaptations over thousands of years. Our recovery of oral microbial and putative dietary plant DNA suggest adaptive capability. Our results suggest a spatio-temporal turnover in oral microbiome and putative dietary plant DNA, which might be explained by ecological differences between Pleistocene France and contemporary Scandinavia. As soft tissue preservation is rare in ancient remains, dental calculus emerges as an exciting and powerful tool for reconstructing the environmental and ecological histories of both past and extinct populations.

Common ash (Fraxinus excelsior) is under intensive attack from the invasive alien pathogenic fungus Hymenoscyphus fraxineus, causing ash dieback at epidemic levels throughout Europe. Previous studies have found significant genetic variation among genotypes in ash dieback susceptibility and that host phenology, such as autumn yellowing, is correlated with susceptibility of ash trees to H. fraxineus; however, the genomic basis of ash dieback tolerance in F. excelsior requires further investigation. Here, we integrate quantitative genetics based on multiple replicates and genome‐wide association analyses with machine learning to reveal the genetic architecture of ash dieback tolerance and of phenological traits in F. excelsior populations in six European countries (Austria, Denmark, Germany, Ireland, Lithuania, Sweden). Based on phenotypic data of 486 F. excelsior replicated genotypes we observed negative genotypic correlations between crown damage caused by ash dieback and intensity of autumn leaf yellowing within multiple sampling sites. Our results suggest that the examined traits are polygenic and using genomic prediction models, with ranked single nucleotide polymorphisms (SNPs) based on GWAS associations as input, a large proportion of the variation was predicted by unlinked SNPs. Based on 100 unlinked SNPs, we can predict 55% of the variation in disease tolerance among genotypes (as phenotyped in genetic trials), increasing to a maximum of 63% when predicted from 9155 SNPs. In autumn leaf yellowing, 52% of variation is predicted by 100 unlinked SNPs, reaching a peak of 72% using 3740 SNPs. Based on feature permutations within genomic prediction models, a total of eight nonsynonymous SNPs linked to ash dieback crown damage and autumn leaf yellowing (three and five SNPs, respectively) were identified, these were located within genes related to plant defence (pattern triggered immunity, pathogen detection) and phenology (regulation of flowering and seed maturation, auxin transport). We did not find an overlap between genes associated with crown damage level and autumn leaf yellowing. Hence, our results shed light on the difference in the genomic basis of ADB tolerance and autumn leaf yellowing despite these two traits being correlated in quantitative genetic analysis. Overall, our methods show the applicability of genomic prediction models when combined with GWAS to reveal the genomic architecture of polygenic disease tolerance enabling the identification of ash dieback tolerant trees for breeding or conservation purposes.

Studying host–microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.

Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high‐arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest‐induced demographic bottleneck that occurred during the 17–20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene‐specific differentiation during and after this overharvesting event. Using whole‐genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near‐extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre‐harvest diversity and a complex post‐harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high‐arctic case study therefore emphasize the need to understand the long‐term interplay of past, current, and future stressors in wildlife conservation.

Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus) , endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20 ^th century. Here we investigate changes in genetic diversity, population structure and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient nuclear ( n = 11) and mitochondrial ( n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences ( n = 90), to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation and 400 years of genetic drift have altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 23%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long- term interplay of past, current, and future stressors in wildlife conservation.

Animals and their associated microbiota share long evolutionary histories. Both host genotype and associated microbiota influence phenotypes such as growth and disease resilience. We applied a hologenomic approach to explore the relationship between host and microbiota in shaping lifetime growth and parasitic cestode infection in farmed Atlantic salmon. Genomes, transcriptomes, metabolomes and metagenomes were generated from the guts of 460 harvest-aged salmon, 82% of which were naturally infected with an intestinal cestode. One salmonid-specific Mycoplasma dominated the gut microbiota of uninfected salmon. However, the microbiota was perturbed in smaller, parasitised fish, with increased abundance of Vibrionaceae and other Mycoplasma species previously linked to the cestode microbiota. The cestode-associated Mycoplasma carry more virulence-associated genes than the salmonid Mycoplasma . Colonisation by one cestode-associated Mycoplasma was associated with a region of the salmon genome encoding several long noncoding RNA genes previously associated with host control of intestinal microbiota. Integrating the multiple omic datasets revealed coordinated changes in the salmon gut transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitised fish. Our results suggest that cestode infections introduce new microbes and trigger host responses, altering the gut microbiota with increases in potentially pathogenic microbes. Establishment of these microbes is partially shaped by the genetic background of the host. Our study highlights the value of a hologenomic approach for gaining an in-depth understanding of trilateral interactions among host, microbiota and parasite.

Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant’s remarkable success as an invasive species.