Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla

Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq data sets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the animal tree of life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus infection networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprising Retroviridae, Flaviviridae, and several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.IMPORTANCEThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road toward a deeper understanding of the virome across the animal tree of life.

Functional redundancy of weed seed predation is reduced by intensified agriculture

Intensified agriculture, a driver of biodiversity loss, can diminish ecosystem functions and their stability. Biodiversity can increase functional redundancy and is expected to stabilize ecosystem functions. Few studies, however, have explored how agricultural intensity affects functional redundancy and its link with ecosystem function stability. Here, within a continental-wide study, we assess how functional redundancy of seed predation is affected by agricultural intensity and landscape simplification. By combining carabid abundances with molecular gut content data, functional redundancy of seed predation was quantified for 65 weed genera across 60 fields in four European countries. Across weed genera, functional redundancy was reduced with high field management intensity and simplified crop rotations. Moreover, functional redundancy increased the spatial stability of weed seed predation at the field scale. We found that ecosystem functions are vulnerable to disturbances in intensively managed agroecosystems, providing empirical evidence of the importance of biodiversity for stable ecosystem functions across space.

A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.

Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species

Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype-environment and genotype-phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

Potential implications of shortened rotation length for forest birds, bryophytes, lichens and vascular plants: An example from southern Swedish production forests

The rotation lengths of intensively managed production forests may be altered to achieve a variety of goals, with correspondingly implications for biodiversity. Here we consider the potential implications of shortened rotation times for biodiversity in planted monocultures of the two most common production tree species in Sweden, Scots pine (Pinus sylvestris) and Norway spruce (Picea abies). To do so we surveyed bird, bryophyte, epiphytic lichen and vascular plant diversity in 80 and 55-year-old stands; stand ages which approximate present-day and potential future rotation lengths in this region respectively. We found clear differences in the species communities of the 55 compared to the 80-year-old stands for both understory species and epiphytes, but not for birds. Nevertheless, bird species richness was still highest in the 80-year-old Norway spruce dominated stands. Dead wood amount was also highest the 80-year-old Norway spruce stands. Highest species richness of epiphytic lichens was found in 80-year-old Scots pine stands. However, 55-year-old Scots pine stands had a higher understory species richness and diversity than the older Scots pine stands, including a larger number of open land species. The 80-year-old forest stands examined may be considered old with respect to production forest rotation lengths in Sweden but are relatively young when comparing stand ages of unmanaged natural forest stands. Nevertheless, our results indicate that shortening the rotation time of Scots pine and Norway spruce, in this part of Sweden from 80 to 55 years, could have important consequences for forest biodiversity. These consequences are primarily inferred from the likely implications from shortened rotations for lichens community composition and diversity in both Norway spruce and Scots pine stands, as well as impacts on understory plant species in Norway spruce stands.

Evaluation of domestic animal sperm head morphology via flow cytometric DNA labelling and pulse shape analysis using bull and stallion spermatozoa as model species

The aim of the present study was to test a rapid, robust flow cytometric technique for the detection of sperm head abnormalities of domestic bulls and stallions. The so-called PulSA approach detects the pulse profiles of propidium-iodide labelled spermatozoa. In the first experiment, species-specific threshold values were established on sperm samples that were tested for sperm head abnormalities with a classic visual morphology analysis. In the second experiment, serial mixtures of bull and stallion spermatozoa mimicking different percentages of sperm head abnormalities were analysed. Non-metric multidimensional scaling showed a clear separation between the normal and mixed samples. The PulSA approach may be a useful tool in identifying sub- or infertile breeding males as well as in studying the evolutionary aspects of sperm morphology and morphometry.

Recolonization following past persecution questions the importance of persistent snow cover as a range limiting factor for wolverines

Globally, climate is changing rapidly, which causes shifts in many species' distributions, stressing the need to understand their response to changing environmental conditions to inform conservation and management. Northern latitudes are expected to experience strongest changes in climate, with milder winters and decreasing snow cover. The wolverine (Gulo gulo) is a circumpolar, threatened carnivore distributed in northern tundra, boreal, and subboreal habitats. Previous studies have suggested that wolverine distribution and reproduction are constrained by a strong association with persistent spring snow cover. We assess this hypothesis by relating spatial distribution of 1589 reproductive events, a fitness-related proxy for female reproduction and survival, to snow cover over two decades. Wolverine distribution has increased and number of reproductive events increased 20 times in areas lacking spring snow cover during our study period, despite low monitoring effort where snow is sparse. Thus, the relationship between reproductive events and persistent spring snow cover weakened during this period. These findings show that wolverine reproductive success and hence distribution are less dependent on spring snow cover than expected. This has important implications for projections of future habitat availability, and thus distribution, of this threatened species. Our study also illustrates how past persecution, or other factors, that have restricted species distribution to remote areas can mask actual effects of environmental parameters, whose importance reveals when populations expand beyond previously restricted ranges. Overwhelming evidence shows that climate change is affecting many species and ecological processes, but forecasting potential consequences on a given species requires longitudinal data to revisit hypotheses and reassess the direction and magnitude of climate effects with new data. This is especially important for conservation-oriented management of species inhabiting dynamic systems where environmental factors and human activities interact, a common scenario for many species in different ecosystems around the globe.

Reduced brain connectivity along the autism spectrum controlled for familial confounding by co-twin design

Previous studies on brain connectivity correlates of autism have often focused on selective connections and yielded inconsistent results. By applying global fiber tracking and utilizing a within-twin pair design, we aimed to contribute to a more unbiased picture of white matter connectivity in association with clinical autism and autistic traits. Eighty-seven twin pairs (n = 174; 55% monozygotic; 24 with clinical autism) underwent diffusion tensor imaging. Linear regressions assessed within-twin pair associations between structural brain connectivity of anatomically defined brain regions and both clinical autism and autistic traits. These were explicitly adjusted for IQ, other neurodevelopmental/psychiatric conditions and multiple testing, and implicitly for biological sex, age, and all genetic and environmental factors shared by twins. Both clinical autism and autistic traits were associated with reductions in structural connectivity. Twins fulfilling diagnostic criteria for clinical autism had decreased brainstem-cuneus connectivity compared to their co-twins without clinical autism. Further, twins with higher autistic traits had decreased connectivity of the left hippocampus with the left fusiform and parahippocampal areas. These associations were also significant in dizygotic twins alone. Reduced brainstem-cuneus connectivity might point towards alterations in low-level visual processing in clinical autism while higher autistic traits seemed to be more associated with reduced connectivity in networks involving the hippocampus and the fusiform gyrus, crucial especially for processing of faces and other (higher order) visual processing. The observed associations were likely influenced by both genes and environment.

Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data

The applicability domain of machine learning models trained on structural fingerprints for the prediction of biological endpoints is often limited by the lack of diversity of chemical space of the training data. In this work, we developed similarity-based merger models which combined the outputs of individual models trained on cell morphology (based on Cell Painting) and chemical structure (based on chemical fingerprints) and the structural and morphological similarities of the compounds in the test dataset to compounds in the training dataset. We applied these similarity-based merger models using logistic regression models on the predictions and similarities as features and predicted assay hit calls of 177 assays from ChEMBL, PubChem and the Broad Institute (where the required Cell Painting annotations were available). We found that the similarity-based merger models outperformed other models with an additional 20% assays (79 out of 177 assays) with an AUC > 0.70 compared with 65 out of 177 assays using structural models and 50 out of 177 assays using Cell Painting models. Our results demonstrated that similarity-based merger models combining structure and cell morphology models can more accurately predict a wide range of biological assay outcomes and further expanded the applicability domain by better extrapolating to new structural and morphology spaces.

Limited effects of macro-nutrient ratios on thiamin content and transfer in phytoplankton and copepods

Vitamin B₁ (thiamin) is primarily produced by bacteria, phytoplankton and fungi in aquatic food webs and transferred to higher trophic levels by ingestion. However, much remains unknown regarding the dynamics this water-soluble, essential micronutrient; e.g. how it relates to macronutrients (carbon, nitrogen and phosphorous). Nutrient limitation has been found to be related to periods of thiamin deficiency as well as in models. Hence, thiamin transfer to copepods from three phytoplankton species from different taxa was investigated, along with the effect of various nutrient regimes on thiamin content. Nutrient levels did not affect thiamin content of phytoplankton nor the transfer to copepods. Instead, phytoplankton displayed species-specific thiamin and macronutrient contents and whilst a higher thiamin content in the prey lead to higher levels in copepods, the transfer was lower for Skeletonema compared to Dunaliella and Rhodomonas. In all, thiamin transfer to copepods is not only dependent on thiamin content of the prey, but also the edibility and/or digestibility is of importance. Thiamin is essential for all organisms, and this study offers insights into the limited effect of macronutrients on the dynamics and transfer of thiamin in the aquatic food webs.

Addressing indirect sourcing in zero deforestation commodity supply chains

The trade in agricultural commodities is a backbone of the global economy but is a major cause of negative social and environmental impacts, not least deforestation. Commodity traders are key actors in efforts to eliminate deforestation-they are active in the regions where commodities are produced and represent a "pinch point" in global trade that provides a powerful lever for change. However, the procurement strategies of traders remain opaque. Here, we catalog traders' sourcing across four sectors with high rates of commodity-driven deforestation: South American soy, cocoa from Côte d'Ivoire, Indonesian palm oil, and Brazilian live cattle exports. We show that traders often source more than 40% of commodities "indirectly" via local intermediaries and that indirect sourcing is a major blind spot for sustainable sourcing initiatives. To eliminate deforestation, indirect sourcing must be included in sectoral initiatives, and landscape or jurisdictional approaches, which internalize indirect sourcing, must be scaled up.

Organic nitrogen enhances nitrogen nutrition and early growth of Pinus sylvestris seedlings

Boreal trees are capable of taking up organic nitrogen (N) as effectively as inorganic N. Depending on the abundance of soil N forms, plants may adjust physiological and morphological traits to optimize N uptake. However, the link between these traits and N uptake in response to soil N sources is poorly understood. We examined Pinus sylvestris L. seedlings' biomass growth and allocation, transpiration and N uptake in response to additions of organic N (the amino acid arginine) or inorganic N (ammonium nitrate). We also monitored in situ soil N fluxes in the pots following an addition of N, using a microdialysis system. Supplying organic N resulted in a stable soil N flux, whereas the inorganic N resulted in a sharp increase of nitrate flux followed by a rapid decline, demonstrating a fluctuating N supply and a risk for loss of nitrate from the growth medium. Seedlings supplied with organic N achieved a greater biomass with a higher N content, thus reaching a higher N recovery compared with those supplied inorganic N. In spite of a higher N concentration in organic N seedlings, root-to-shoot ratio and transpiration per unit leaf area were similar to those of inorganic N seedlings. We conclude that enhanced seedlings' nutrition and growth under the organic N source may be attributed to a stable supply of N, owing to a strong retention rate in the soil medium.

Wheat Stem Rust Back in Europe: Diversity, Prevalence and Impact on Host Resistance

The objective of this study was to investigate the re-emergence of a previously important crop pathogen in Europe, Puccinia graminis f.sp. tritici, causing wheat stem rust. The pathogen has been insignificant in Europe for more than 60 years, but since 2016 it has caused epidemics on both durum wheat and bread wheat in local areas in southern Europe, and additional outbreaks in Central- and West Europe. The prevalence of three distinct genotypes/races in many areas, Clade III-B (TTRTF), Clade IV-B (TKTTF) and Clade IV-F (TKKTF), suggested clonal reproduction and evolution by mutation within these. None of these genetic groups and races, which likely originated from exotic incursions, were detected in Europe prior to 2016. A fourth genetic group, Clade VIII, detected in Germany (2013), was observed in several years in Central- and East Europe. Tests of representative European wheat varieties with prevalent races revealed high level of susceptibility. In contrast, high diversity with respect to virulence and Simple Sequence Repeat (SSR) markers were detected in local populations on cereals and grasses in proximity to Berberis species in Spain and Sweden, indicating that the alternate host may return as functional component of the epidemiology of wheat stem rust in Europe. A geographically distant population from Omsk and Novosibirsk in western Siberia (Russia) also revealed high genetic diversity, but clearly different from current European populations. The presence of Sr31-virulence in multiple and highly diverse races in local populations in Spain and Siberia stress that virulence may emerge independently when large geographical areas and time spans are considered and that Sr31-virulence is not unique to Ug99. All isolates of the Spanish populations, collected from wheat, rye and grass species, were succesfully recovered on wheat, which underline the plasticity of host barriers within P. graminis. The study demonstrated successful alignment of two genotyping approaches and race phenotyping methodologies employed by different laboratories, which also allowed us to line up with previous European and international studies of wheat stem rust. Our results suggest new initiatives within disease surveillance, epidemiological research and resistance breeding to meet current and future challenges by wheat stem rust in Europe and beyond.

GIGANTEA influences leaf senescence in trees in two different ways

GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to "autumn environmental cues" inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally-the phenotype followed the genotype of the branch, independent of its position on the tree-and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.

The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels

Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs–the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.

As a consequence of selective breeding, specific disease-causing mutations have become more frequent in certain dog breeds. Whether the breeding practice also resulted in a general increase in the overall number of disease-causing mutations per dog genome is however not clear. To address this question, we compare the amount of harmful, potentially disease-causing, mutations in dogs from eight common breeds that have experienced varying degrees of intense selective breeding. We find that individuals belonging to the breed affected by the most intense breeding—cavalier King Charles spaniel (cKCs)—carry more harmful variants than other breeds, indicating that past breeding practices may have increased the overall levels of harmful genetic variation in dogs. The most common disease in cKCs is myxomatous mitral valve disease (MMVD). To identify variants linked to this disease we next characterize mutations that are common in cKCs, but rare in other breeds, and then investigate if these mutations can predict MMVD in dachshunds. We find that variants that regulate the expression of the gene NEBL in papillary muscles may increase the risk of the disease, indicating that loss of papillary muscle integrity could contribute to the development of MMVD.

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

Modelling past and future peatland carbon dynamics across the pan-Arctic

The majority of northern peatlands were initiated during the Holocene. Owing to their mass imbalance, they have sequestered huge amounts of carbon in terrestrial ecosystems. Although recent syntheses have filled some knowledge gaps, the extent and remoteness of many peatlands pose challenges to developing reliable regional carbon accumulation estimates from observations. In this work, we employed an individual- and patch-based dynamic global vegetation model (LPJ-GUESS) with peatland and permafrost functionality to quantify long-term carbon accumulation rates in northern peatlands and to assess the effects of historical and projected future climate change on peatland carbon balance. We combined published datasets of peat basal age to form an up-to-date peat inception surface for the pan-Arctic region which we then used to constrain the model. We divided our analysis into two parts, with a focus both on the carbon accumulation changes detected within the observed peatland boundary and at pan-Arctic scale under two contrasting warming scenarios (representative concentration pathway-RCP8.5 and RCP2.6). We found that peatlands continue to act as carbon sinks under both warming scenarios, but their sink capacity will be substantially reduced under the high-warming (RCP8.5) scenario after 2050. Areas where peat production was initially hampered by permafrost and low productivity were found to accumulate more carbon because of the initial warming and moisture-rich environment due to permafrost thaw, higher precipitation and elevated CO₂ levels. On the other hand, we project that areas which will experience reduced precipitation rates and those without permafrost will lose more carbon in the near future, particularly peatlands located in the European region and between 45 and 55°N latitude. Overall, we found that rapid global warming could reduce the carbon sink capacity of the northern peatlands in the coming decades.

Keeping pace with forestry: Multi-scale conservation in a changing production forest matrix

The multi-scale approach to conserving forest biodiversity has been used in Sweden since the 1980s, a period defined by increased reserve area and conservation actions within production forests. However, two thousand forest-associated species remain on Sweden's red-list, and Sweden's 2020 goals for sustainable forests are not being met. We argue that ongoing changes in the production forest matrix require more consideration, and that multi-scale conservation must be adapted to, and integrated with, production forest development. To make this case, we summarize trends in habitat provision by Sweden's protected and production forests, and the variety of ways silviculture can affect biodiversity. We discuss how different forestry trajectories affect the type and extent of conservation approaches needed to secure biodiversity, and suggest leverage points for aiding the adoption of diversified silviculture. Sweden's long-term experience with multi-scale conservation and intensive forestry provides insights for other countries trying to conserve species within production landscapes.

Browning of freshwaters: Consequences to ecosystem services, underlying drivers, and potential mitigation measures

Browning of surface waters, as a result of increasing dissolved organic carbon and iron concentrations, is a widespread phenomenon with implications to the structure and function of aquatic ecosystems. In this article, we provide an overview of the consequences of browning in relation to ecosystem services, outline what the underlying drivers and mechanisms of browning are, and specifically focus on exploring potential mitigation measures to locally counteract browning. These topical concepts are discussed with a focus on Scandinavia, but are of relevance also to other regions. Browning is of environmental concern as it leads to, e.g., increasing costs and risks for drinking water production, and reduced fish production in lakes by limiting light penetration. While climate change, recovery from acidification, and land-use change are all likely factors contributing to the observed browning, managing the land use in the hydrologically connected parts of the landscape may be the most feasible way to counteract browning of natural waters.

Hiding from the climate: Characterizing microrefugia for boreal forest understory species

Climate warming is likely to shift the range margins of species poleward, but fine-scale temperature differences near the ground (microclimates) may modify these range shifts. For example, cold-adapted species may survive in microrefugia when the climate gets warmer. However, it is still largely unknown to what extent cold microclimates govern the local persistence of populations at their warm range margin. We located 99 microrefugia, defined as sites with edge populations of 12 widespread boreal forest understory species (vascular plants, mosses, liverworts and lichens) in an area of ca. 24,000 km² along the species' southern range margin in central Sweden. Within each population, a logger measured temperature eight times per day during one full year. Using univariate and multivariate analyses, we examined the differences of the populations' microclimates with the mean and range of microclimates in the landscape, and identified the typical climate, vegetation and topographic features of these habitats. Comparison sites were drawn from another logger data set (n = 110), and from high-resolution microclimate maps. The microrefugia were mainly places characterized by lower summer and autumn maximum temperatures, late snow melt dates and high climate stability. Microrefugia also had higher forest basal area and lower solar radiation in spring and autumn than the landscape average. Although there were common trends across northern species in how microrefugia differed from the landscape average, there were also interspecific differences and some species contributed more than others to the overall results. Our findings provide biologically meaningful criteria to locate and spatially predict potential climate microrefugia in the boreal forest. This opens up the opportunity to protect valuable sites, and adapt forest management, for example, by keeping old-growth forests at topographically shaded sites. These measures may help to mitigate the loss of genetic and species diversity caused by rear-edge contractions in a warmer climate.

Transcriptome analysis reveals that fertilization with cryopreserved sperm downregulates genes relevant for early embryo development in the horse

Artificial insemination with cryopreserved spermatozoa is a major assisted reproductive technology in many species. In horses, as in humans, insemination with cryopreserved sperm is associated with lower pregnancy rates than those for fresh sperm, however, direct effects of sperm cryopreservation on the development of resulting embryos are largely unexplored. The aim of this study was to investigate differences in gene expression between embryos resulting from fertilization with fresh or cryopreserved sperm. Embryos were obtained at 8, 10 or 12 days after ovulation from mares inseminated post-ovulation on successive cycles with either fresh sperm or frozen-thawed sperm from the same stallion, providing matched embryo pairs at each day. RNA was isolated from two matched pairs (4 embryos) for each day, and cDNA libraries were built and sequenced. Significant differences in transcripts per kilobase million (TPM) were determined using (i) genes for which the expression difference between treatments was higher than 99% of that in the random case (P < 0.01), and (ii) genes for which the fold change was ≥ 2, to avoid expression bias in selection of the candidate genes. Molecular pathways were explored using the DAVID webserver, followed by network analyses using STRING, with a threshold of 0.700 for positive interactions. The transcriptional profile of embryos obtained with frozen-thawed sperm differed significantly from that for embryos derived from fresh sperm on all days, showing significant down-regulation of genes involved in biological pathways related to oxidative phosphorylation, DNA binding, DNA replication, and immune response. Many genes with reduced expression were orthologs of genes known to be embryonic lethal in mice. This study, for the first time, provides evidence of altered transcription in embryos resulting from fertilization with cryopreserved spermatozoa in any species. As sperm cryopreservation is commonly used in many species, including human, the effect of this intervention on expression of developmentally important genes in resulting embryos warrants attention.

Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.

Earlier occurrence and increased explanatory power of climate for the first incidence of potato late blight caused by Phytophthora infestans in Fennoscandia

BACKGROUND

Late blight (caused by Phytophthora infestans) is a devastating potato disease that has been found to occur earlier in the season over the last decades in Fennoscandia. Up until now the reasons for this change have not been investigated. Possible explanations for this change are climate alterations, changes in potato production or changes in pathogen biology, such as increased fitness or changes in gene flow within P. infestans populations. The first incidence of late blight is of high economic importance since fungicidal applications should be typically applied two weeks before the first signs of late blight and are repeated on average once a week.

METHODS

We use field observations of first incidence of late blight in experimental potato fields from five sites in Sweden and Finland covering a total of 30 years and investigate whether the earlier incidence of late blight can be related to the climate.

RESULTS

We linked the field data to meteorological data and found that the previous assumption, used in common late blight models, that the disease only develops at relative humidity levels above 90% had to be rejected. Rather than the typically assumed threshold relationship between late blight disease development and relative humidity we found a linear relationship. Our model furthermore showed two distinct responses of late blight to climate. At the beginning of the observation time (in Sweden until the early 90s and in Finland until the 2000s) the link between climate and first incidence was very weak. However, for the remainder of the time period the link was highly significant, indicating a change in the biological properties of the pathogen which could for example be a change in the dominating reproduction mode or a physiological change in the response of the pathogen to climate.

CONCLUSIONS

The study shows that models used in decision support systems need to be checked and re-parametrized regularly to be able to capture changes in pathogen biology. While this study was performed with data from Fennoscandia this new pathogen biology and late blight might spread to (or already be present at) other parts of the world as well. The strong link between climate and first incidence together with the presented model offers a tool to assess late blight incidence in future climates.

"Generality of mis-fit"? The real-life difficulty of matching scales in an interconnected world

A clear understanding of processes at multiple scales and levels is of special significance when conceiving strategies for human-environment interactions. However, understanding and application of the scale concept often differ between administrative-political and ecological disciplines. These mirror major differences in potential solutions whether and how scales can, at all, be made congruent. As a result, opportunities of seeking "goodness-of-fit" between different concepts of governance should perhaps be reconsidered in the light of a potential "generality of mis-fit." This article reviews the interdisciplinary considerations inherent in the concept of scale in its ecological, as well as administrative-political, significance and argues that issues of how to manage "mis-fit" should be awarded more emphasis in social-ecological research and management practices. These considerations are exemplified by the case of reindeer husbandry in Fennoscandia. Whilst an indigenous small-scale practice, reindeer husbandry involves multi-level ecological and administrative-political complexities-complexities that we argue may arise in any multi-level system.