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1.	Sanli, Kemal, et al. (författare) Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities 2015 Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 6:1192 Tidskriftsartikel (refereegranskat)abstract Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
2.	Radek, Renate, et al. (författare) Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota 2017 Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 25, s. 31-50 Tidskriftsartikel (refereegranskat)abstract Nephridiophagids are poorly known unicellular eukaryotes, previously of uncertain systematic position, that parasitize the Malpighian tubules of insects. Their life cycle includes merogony with multinucleate plasmodia and sporogony leading to small, uninucleate spores. We examined the phylogenetic affiliations of three species of Nephridiophaga, including one new species, Nephridiophaga maderae, from the Madeira cockroach (Leucophaea maderae). In addition to the specific host, the new species differs from those already known by the size of the spores and by the number of spores within the sporogenic plasmodium. The inferred phylogenetic analyses strongly support a placement of the nephridiophagids in the fungal kingdom near its root and with a close, but unresolved, relationship to the chytids (Chytridiomycota). We found evidence for the nephridiophagidean speciation as being strongly coupled to host speciation.
3.	Sigvald, Roland, et al. (författare) Molecular identification of bloodmeals and species composition in Culicoides biting midges 2013 Ingår i: Medical and Veterinary Entomology. - : Wiley. - 0269-283X .- 1365-2915. ; 27, s. 104-112 Tidskriftsartikel (refereegranskat)abstract Investigations of host preferences in haematophagous insects, including Culicoides biting midges (Diptera: Ceratopogonidae), are critical in order to assess transmission routes of vector-borne diseases. In this study, we collected and morphologically identified 164 blood-engorged Culicoides females caught in both light traps and permanent 12-m high suction traps during 20082010 in Sweden. Molecular analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene in the biting midges was performed to verify species classification, discern phylogenetic relationships and uncover possible cryptic species. Bloodmeal analysis using universal vertebrate cytochrome b primers revealed a clear distinction in host selection between mammalophilic and ornithophilic Culicoides species. Host sequences found matches in horse (n = 59), sheep (n = 39), cattle (n = 26), Eurasian elk (n = 1) and 10 different bird species (n = 18). We identified 15 Culicoides species previously recorded in Scandinavia and four additional species haplotypes that were distinctly different from the described species. All ornithophilic individuals (n = 23) were caught exclusively in the suction traps, as were, interestingly, almost all mammalophilic species (n = 41), indicating that many biting midge species may be able to cover long distances after completing a bloodmeal. These results add new information on the composition of Culicoides species and their host preferences and their potential long-distance dispersal while blood-engorged.
4.	Alm Rosenblad, Magnus, 1957, et al. (författare) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota) 2016 Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 13, s. 21-33 Tidskriftsartikel (refereegranskat)abstract During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.
5.	Nilsson, R. Henrik, 1976, et al. (författare) Mycobiome diversity: high-throughput sequencing and identification of fungi. 2019 Ingår i: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109 Forskningsöversikt (refereegranskat)abstract Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
6.	Abarenkov, Kessy, et al. (författare) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden) 2016 Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15 Tidskriftsartikel (refereegranskat)abstract Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
7.	Kõljalg, Urmas, et al. (författare) A price tag on species 2022 Ingår i: Research Ideas and Outcomes_RIO. - : Pensoft Publishers. - 2367-7163. ; 8, s. 1-7 Tidskriftsartikel (refereegranskat)abstract Species have intrinsic value but also partake in a long range of ecosystem services of major economic value to humans. These values have proved hard to quantify precisely, making it all too easy to dismiss them altogether. We outline the concept of the species stock market (SSM), a system to provide a unified basis for valuation of all living species. The SSM amalgamates digitized information from natural history collections, occurrence data, and molecular sequence databases to quantify our knowledge of each species from scientific, societal, and economic points of view. The conceptual trading system will necessarily be very unlike that of the regular stock market, but the looming biodiversity crisis implores us to finally put an open and transparent price tag on symbiosis, deforestation, and pollution
8.	Nilsson, R. Henrik, 1976, et al. (författare) Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms 2022 Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 239-244 Tidskriftsartikel (refereegranskat)abstract DNA sequencing efforts of environmental and other biological samples disclose unprecedented and largely untapped opportunities for advances in the taxonomy, ecology, and geographical distributions of our living world. To realise this potential, DNA-derived occurrence data (notably sequences with dates and coordinates) – much like traditional specimens and observations – need to be discoverable and interpretable through biodiversity data platforms. The Global Biodiversity Information Facility (GBIF) recently headed a community effort to assemble a set of guidelines for publishing DNA-derived data. These guidelines target the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. They cover a choice of terms using a controlled vocabulary, common pitfalls, and good practices, without going into platform-specific details. Our hope is that they will benefit anyone interested in better exposure of DNA-derived occurrence data through general biodiversity data platforms, including national biodiversity portals. This paper provides a brief rationale and an overview of the guidelines, an up-to-date version of which is maintained at https://doi.org/10.35035/doc-vf1a-nr22. User feedback and interaction are encouraged as new techniques and best practices emerge.
9.	Ritter, Camila, et al. (författare) The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia 2019 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1 Tidskriftsartikel (refereegranskat)abstract © 2019, The Author(s). Most knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, litter and insects from four localities on a west-to-east transect across Amazonia. We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three molecular markers. We then compared OTU richness with species richness of two relatively well-studied organism groups in Amazonia: trees and birds. We find that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees. These results suggest that most taxonomic groups respond to the same overall diversity gradients at large spatial scales. However, our results show a different pattern of richness in relation to habitat types, suggesting that the idiosyncrasies of each taxonomic group and peculiarities of the local environment frequently override large-scale diversity gradients. Our findings caution against using the diversity distribution of one taxonomic group as an indication of patterns of richness across all groups.
10.	Unterseher, Martin, et al. (författare) Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition 2018 Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:4, s. 489-500 Tidskriftsartikel (refereegranskat)abstract Multiple biotic and abiotic parameters influence the dynamics of individual fungal species and entire communities. Major drivers for tropical plant endophytes are undoubtedly seasonality, local habitat conditions and biogeography. However, host specialization and tissue preferences also contribute to the structuring of endophytic mycobiomes. To elucidate such specializations and preferences, we sampled two commercially important, unrelated plant species, Amorphophallus albispathus and Camellia sinensis (tea plant) simultaneously at close proximity. The mycobiomes of different tissue types were assessed with high-throughput amplicon sequencing of the internal transcribed spacer DNA region. Both plants hosted different fungal communities and varied in α- and β-diversity, despite their neighboring occurrence. However, the fungal assemblages of Amorphophallus leaflets shared taxa with the mycobiomes of tea leaves, thereby suggesting common driving forces for leaf-inhabiting fungi irrespective of host plant identity. The mycobiome composition and diversity of tea leaves was clearly driven by leaf age. We suggest that the very youngest tea leaves are colonized by stochastic processes, while mycobiomes of old leaves are rather similar as the result of progressive succession. The biodiversity of fungi associated with A. albispathus was characterized by a large number of unclassified OTUs (at genus and species level) and by tissue-specific composition.This study is the first cultivation-independent high-throughput assessment of fungal biodiversity of an Amorphophallus species, and additionally expands the knowledge base on fungi associated with tea plants.
11.	Sernland, Emma (författare) Optimal strategies and information in foraging theory 2005 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract In this thesis, I present both theoretical and empirical work where we have studied how humans and animals use information in situations where they need to continually update their information on the density of a resource. We have found that the amount of information, and the way the information is presented, are important factors for how well decisions are adapted to current circumstances. In an empirical study on humans, we found that humans seem to have a default idea of the distribution of a resource. This default idea seems to be plastic, i.e. it is adjusted according to incoming information. The way additional information was presented, as well as the information content, was important for how well the default idea was adjusted to current circumstances.By using mathematical models, we have also studied whether access to information from group members, so called public information, is one of the reasons why some species live in groups. When group members aim to maximize its intake rate of food and share both information and food items found equally, and when each individual has to pay all the cost for travelling between foraging patches, the intake rate of food will decrease with increasing group size. The animals will spend a larger proportion of the time on travelling between patches and less time on foraging the larger the group size. In this case, information sharing on food density in patches is not a reason why animals live in groups.We have also used mathematical models to study the information dynamics in a group of foraging animals that cannot both search for food and information at the same time. The animals aim to maximize their survival, and are given three behavioural choices in each time step: stay and search for food, stay and scan for information, or leave the current patch. The results show that the choice of behaviour depends on the energy reserves of the individual. An animal with low energy reserves searches for food and leaves the patch if its assessment of potential patch quality decreases to a certain level. An animal with high energy reserves chooses to stay in the patch and scan for information. In our model we assume that when one individual leaves the patch, the rest of the group also leaves. This means that it is those individuals that have low energy reserves that will make the leaving decisions for the group.In the end, we use these theories on Bayesian foraging, information updating and decision-making in order to develop a new type of effort-based quota for sustainable fisheries management: an effort-based dynamic quota (EDQ). We show that by using information from ongoing fishing combined with fishing data from earlier years, we can reach a higher maximum sustainable yield compared to using a total allowable catch (TAC).
12.	Nilsson, R. Henrik, 1976, et al. (författare) How, not if, is the question mycologists should be asking about DNA-based typification 2023 Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :96, s. 143-157 Tidskriftsartikel (refereegranskat)abstract Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
13.	Gómez-Martínez, Daniela, et al. (författare) Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican 2023 Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 875 Tidskriftsartikel (refereegranskat)abstract Herbicide pollution poses a worldwide threat to plants and freshwater ecosystems. However, the understanding of how organisms develop tolerance to these chemicals and the associated trade-off expenses are largely unknown. This study aims to investigate the physiological and transcriptional mechanisms underlying the acclimation of the green microalgal model species Raphidocelis subcapitata (Selenastraceae) towards the herbicide diflufenican, and the fitness costs associated with tolerance development. Algae were exposed for 12 weeks (corresponding to 100 generations) to diflufenican at the two environmental concentrations 10 and 310 ng/L. The monitoring of growth, pigment composition, and photosynthetic performance throughout the experiment revealed an initial dose-dependent stress phase (week 1) with an EC50 of 397 ng/L, followed by a time-dependent recovery phase during weeks 2 to 4. After week 4, R. subcapitata was acclimated to diflufenican exposure with a similar growth rate, content of carotenoids, and photosynthetic performance as the unexposed control algae. This acclimation state of the algae was explored in terms of tolerance acquisition, changes in the fatty acids composition, diflufenican removal rate, cell size, and changes in mRNA gene expression profile, revealing potential fitness costs associated with acclimation, such as up-regulation of genes related to cell division, structure, morphology, and reduction of cell size. Overall, this study demonstrates that R. subcapitata can quickly acclimate to environmental but toxic levels of diflufenican; however, the acclimation is associated with trade-off expenses that result in smaller cell size.
14.	Airaud, M, et al. (författare) Biologie - Les manuels visuels pour la Licence 2018 Bok (övrigt vetenskapligt/konstnärligt)abstract En couleurs et très illustré, ce manuel a été conçu pour vous qui débutez un cursus scientifique universitaire. Il vous permettra d’acquérir les connaissances fondamentales en biologie, mais aussi la démarche et la rigueur scientifiques indispensables aux études supérieures. De multiples rubriques vous garantissent un apprentissage progressif et complet : un cours visuel avec de nombreux exemples concrets pour introduire et illustrer les notions et concepts clés ; des encadrés méthodologiques pour vous guider vers les bonnes pratiques et vous faire découvrir les grandes méthodes expérimentales ; des focus sur des applications, sujets de recherche ou thèmes d’actualité ; des repères historiques ; de nombreux QCM et exercices (tous corrigés) pour tester vos acquis et vous entraîner.
15.	Sundblad, Göran (författare) Spatial Modelling of Coastal Fish – Methods and Applications 2010 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Environmental factors influence species and habitats on multiple scales creating a mosaic of distribution patterns. Studying factors shaping these patterns are central to our understanding of population dynamics and ultimately ecosystem functioning. Information on the distribution of resources and conservation values are also highly needed in marine management as coastal areas are increasingly influenced by human activities. In this thesis, large-scale field data is used to explore how strong environmental gradients found on multiple scales in the coastal areas of the Baltic Sea influence fish habitats. The underlying concepts are based in the field of species distribution modelling, whereby habitat maps can be produced using environmental layers in a geographic information system. Distribution modelling is further used to address both ecological and applied questions by examining effects of habitat limitation on fish population sizes and to evaluate management actions aimed at habitat conservation. I show that specific habitat requirements for fish species of both freshwater and marine origin can be described using environmental variables and that species-environment relationships can be used to predict the distribution of early life-stages of fish in the Baltic Sea archipelagos. Further, predicted habitat availability of a specific life-stage was directly related to adult population size of Eurasian perch Perca fluviatilis, signifying that the abundance of large predatory fish can be limited by specific recruitment habitats. Lastly, by predicting the distribution of an assemblage of coastal fish species and their associated habitats, an assessment of a network of marine protected areas was performed. Results revealed large gaps in the current network and identified areas suitable for future protection. By demonstrating how current habitat protection can be improved by including critical habitats for coastal fish population sizes this thesis points to the benefits of integrating nature conservation and fisheries management. Based on these findings I conclude that species distribution modelling provides a suitable analytical framework for assessing the habitat requirements of organisms. An increased understanding of habitat-population relationships and an ability to accurately map ecologically important features will be of great value for an ecosystem-based marine management.
16.	Zhao, M., et al. (författare) Phylogenetic position of the Wallcreeper Tichodroma muraria 2016 Ingår i: Journal of Ornithology = Journal fur Ornithologie. - : Springer Science and Business Media LLC. - 0021-8375 .- 1439-0361. ; 157:3, s. 913-918 Tidskriftsartikel (refereegranskat)abstract The Wallcreeper Tichodroma muraria is usually placed in a monotypic family or subfamily within the superfamily Certhioidea, with assumed close relationships to Certhia (treecreepers), Sitta (nuthatches) and Salpornis (spotted creepers). Previous studies have suggested that Tichodroma is most closely related to Sitta, alternatively to Salpornis. We analysed the relationships of Tichodroma using two mitochondrial and five nuclear loci. The tree based on concatenated sequences strongly supported a sister relationship between Tichodroma and Sitta, as well as between Salpornis and Certhia. However, species tree analysis (MP-EST) was unable to resolve these relationships, and although the concatenation tree remains the best hypothesis, more data are needed to corroborate this. © 2016, Dt. Ornithologen-Gesellschaft e.V.
17.	Anslan, Sten, et al. (författare) Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding 2018 Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 39, s. 29-40 Tidskriftsartikel (refereegranskat)abstract Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.
18.	Nilsson, R. Henrik, 1976, et al. (författare) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. 2019 Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 47:D1 Tidskriftsartikel (refereegranskat)abstract UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer(ITS) region-and offers all ∼1 000000 public fungal ITS sequences for reference. These are clustered into ∼459000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
19.	Retter, Alice, et al. (författare) Exploring the taxonomic composition of two fungal communities on the Swedish west coast through metabarcoding 2019 Ingår i: Biodiversity Data Journal. - 1314-2828 .- 1314-2836. ; 7 Tidskriftsartikel (refereegranskat)abstract Background Fungi are heterotrophic, unicellular or filamentous organisms that exhibit a wide range of different lifestyles as, e.g., symbionts, parasites, and saprotrophs. Mycologists have traditionally considered fungi to be a nearly exclusively terrestrial group of organisms, but it is now known that fungi have a significant presence in aquatic environments as well. We know little about most fungi in limnic and marine systems, including aspects of their taxonomy, ecology, and geographic distribution. The present study seeks to improve our knowledge of fungi in the marine environment. The fungal communities of two coastal marine environments of the Kattegat sea, Sweden, were explored with metabarcoding techniques using the nuclear ribosomal internal transcribed spacer 2 (ITS2) metabarcode. Our data add new information to the current picture of fungal community composition in benthic and coastal habitats in Northern Europe. New information The dataset describes the number of operational taxonomic units (OTUs) and their taxonomic affiliations in two littoral gradients sampled on the Swedish west coast, Gothenburg municipality. Our data include basic diversity indices as well as chemical and edaphic sediment/soil parameters of the sampling sites. From the sites, 3470 and 4315 fungal OTUs, respectively, were recovered. The number of reads were 673,711 and 779,899, respectively, after quality filtering. Within the benthic sites, more than 80% of the sequences could not be classified taxonomically. The phylum composition of the classifiable sequences was dominated in both localities by Dikarya, which made up around 33% of the OTUs. Within Dikarya, Ascomycota was the dominant phylum. Guild assignment failed for more than half of the classifiable OTUs, with undefined saprotrophs being the most common resolved guild. This guild classification was slightly more common in the ocean sediment samples than in the terrestrial ones. Our metadata indicated that ocean sites contain organisms at a lower trophic level and that there are predominantly endophytic, parasitic, and pathogenic fungi in the marine environments. This hints at the presence of interesting and currently poorly understood fungus-driven ecological processes. It is also clear from our results that a very large number of marine fungi are in urgent need of taxonomic study and formal description.
20.	Boberg, Johanna, et al. (författare) Nitrogen and Carbon Reallocation in Fungal Mycelia during Decomposition of Boreal Forest Litter 2014 Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 9:3, s. e92897- Tidskriftsartikel (refereegranskat)abstract Boreal forests are characterized by spatially heterogeneous soils with low N availability. The decomposition of coniferous litter in these systems is primarily performed by basidiomycete fungi, which often form large mycelia with a well-developed capacity to reallocate resources spatially-an advantageous trait in heterogeneous environments. In axenic microcosm systems we tested whether fungi increase their biomass production by reallocating N between Pinus sylvestris (Scots pine) needles at different stages of decomposition. We estimated fungal biomass production by analysing the accumulation of the fungal cell wall compound chitin. Monospecific systems were compared with systems with interspecific interactions. We found that the fungi reallocated assimilated N and mycelial growth away from well-degraded litter towards fresh litter components. This redistribution was accompanied by reduced decomposition of older litter. Interconnection of substrates increased over-all fungal C use efficiency (i.e. the allocation of assimilated C to biomass rather than respiration), presumably by enabling fungal translocation of growth-limiting N to litter with higher C quality. Fungal connection between different substrates also restricted N-mineralization and production of dissolved organic N, suggesting that litter saprotrophs in boreal forest ecosystems primarily act to redistribute rather than release N. This spatial integration of different resource qualities was hindered by interspecific interactions, in which litters of contrasting quality were colonised by two different basidiomycete species. The experiments provide a detailed picture of how resource reallocation in two decomposer fungi leads to a more efficient utilisation of spatially separated resources under N-limitation. From an ecosystem point of view, such economic fungal behaviour could potentially contribute to organic matter accumulation in the litter layers of boreal forests.
21.	Mikusinska, Anna, et al. (författare) Quantifying landscape change during the last two centuries in Bialowieza Primeval Forest 2013 Ingår i: Applied Vegetation Science. - 1402-2001 .- 1654-109X. ; 16:2, s. 217-226 Tidskriftsartikel (refereegranskat)abstract QuestionWhat changes in character and extent of land use have occurred during the last 200yr in the Biaowiea Primeval Forest (BPF)? Are the landscape transformations described from the multi-temporal analysis of historical maps coherent with vegetation changes expressed by the previous palynological analyses?LocationBiaowiea Primeval Forest, PolishBelarusian border. MethodsWe used five historical maps (from 1793 to 1936) and one digital land-use map (19992000) to quantify the landscape changes. Land-use types according to historical maps were digitized and georeferenced. The maps were then used for both comparing the extent of cover types in each time step and analysing the nature of change through transition matrices. The sequence of changes concerning the proportion of land-use types was then compared with classes of pollen, which were assumed to represent corresponding vegetation types. ResultsMost of the area (>70%) has been continuously covered with forest. In the period between 1793 and 1830, the forest declined, being the main donor to agricultural land and villages. In the 20th century, the trend was reversed. We found a significant correlation between the percentage of the main vegetation types derived from historical maps and the corresponding vegetation types, as indicated by pollen, with a mean time lag of 20yr. ConclusionThe BPF landscape has been quite stable throughout the last 200yr, mainly due to the high continuity of forest cover. The results obtained from landscape analysis based on maps are coherent with pollen data collected in the same area.
22.	Witzgall, Peter, et al. (författare) "This is not an Apple"-Yeast Mutualism in Codling Moth 2012 Ingår i: Journal of Chemical Ecology. - : Springer Science and Business Media LLC. - 1573-1561 .- 0098-0331. ; 38:8, s. 949-957 Tidskriftsartikel (refereegranskat)abstract The larva of codling moth Cydia pomonella (Tortricidae, Lepidoptera) is known as the worm in the apple, mining the fruit for food. We here show that codling moth larvae are closely associated with yeasts of the genus Metschnikowia. Yeast is an essential part of the larval diet and further promotes larval survival by reducing the incidence of fungal infestations in the apple. Larval feeding, on the other hand, enables yeast proliferation on unripe fruit. Chemical, physiological and behavioral analyses demonstrate that codling moth senses and responds to yeast aroma. Female moths are attracted to fermenting yeast and lay more eggs on yeast-inoculated than on yeast-free apples. An olfactory response to yeast volatiles strongly suggests a contributing role of yeast in host finding, in addition to plant volatiles. Codling moth is a widely studied insect of worldwide economic importance, and it is noteworthy that its association with yeasts has gone unnoticed. Tripartite relationships between moths, plants, and microorganisms may, accordingly, be more widespread than previously thought. It, therefore, is important to study the impact of microorganisms on host plant ecology and their contribution to the signals that mediate host plant finding and recognition. A better comprehension of host volatile signatures also will facilitate further development of semiochemicals for sustainable insect control.
23.	Zhao, Tao, 1969-, et al. (författare) Fungal associates of the tree-killing bark beetle, Ips typographus, vary in virulence, ability to degrade conifer phenolics and influence bark beetle tunning behavior 2019 Ingår i: Fungal ecology. - Amsteradam : Elsevier. - 1754-5048 .- 1878-0083. ; 38, s. 71-79 Tidskriftsartikel (refereegranskat)abstract The bark beetle Ips typographus carries numerous fungi that could be assisting the beetle in colonizing live Norway spruce (Picea abies) trees. Phenolic defenses in spruce phloem are degraded by the beetle's major tree-killing fungus Endoconidiophora polonica, but it is unknown if other beetle associates can also catabolize these compounds. We compared the ability of five fungi commonly associated with I. typographus to degrade phenolic compounds in Norway spruce phloem. Grosmannia penicillata and Grosmannia europhioides were able to degrade stilbenes and flavonoids faster than E. polonica and grow on minimal growth medium with spruce bark constituents as the only nutrients. Furthermore, beetles avoided medium amended with phenolics but marginally preferred medium colonized by fungi. Taken together our results show that different bark beetle-associated fungi have complementary roles in degrading host metabolites and thus might improve this insect's persistence in well defended host tissues.
24.	Alström, Per, et al. (författare) A review of the recent advances in the systematics of the avian superfamily Sylvioidea 2013 Ingår i: Chinese Birds. - : Chinese Birds (Press). - 1674-7674. ; 4, s. 99-131 Tidskriftsartikel (refereegranskat)abstract The systematics of the avian superfamily Sylvioidea are reviewed, focusing on studies of relationships among families and within genera, more superficially on taxonomic studies at the species level. For the families Bernieridae and Phylloscopidae, new analyses based on already published sequence data are presented. Our understanding of relationships has been vastly improved in recent years due to a large number of molecular studies. However, the relationships among the different families remain largely obscured, probably mainly as a result of rapid divergence of the different primary lineages (families). Also, species level taxonomy has been much improved in recent years due to a large number of studies applying molecular markers and/or vocalizations and other life-history data. It seems likely that the number of species will continue to increase, as new groups are being studied with modern integrative methods.
25.	Alström, Per, et al. (författare) Dramatic niche shifts and morphological change in two insular bird species 2015 Ingår i: Royal Society Open Science. - : The Royal Society. - 2054-5703. ; 2 Tidskriftsartikel (refereegranskat)abstract Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.
26.	Alström, Per, et al. (författare) Integrative taxonomy of the Plain-backed Thrush (Zoothera mollissima) complex (Aves, Turdidae) reveals cryptic species, including a new species. 2016 Ingår i: Avian research. - : Elsevier BV. - 2053-7166. ; 7:1 Tidskriftsartikel (refereegranskat)abstract Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly sympatric. Methods: We revise the Z. mollissima–Z. dixoni complex by integrating morphological, acoustic, genetic (two mito- chondrial and two nuclear markers), ecological and distributional datasets. Results: In earlier field observations, we noted two very different song types of“Plain-backed”Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and Sichuan, China (“Alpine Thrush”); a forest breeder in the eastern Himalayas and northwest Yunnan (at least), China (“Himalayan Forest Thrush”); and a forest breeder in central Sichuan (“Sichuan Forest Thrush”). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is prob- ably true also for Alpine and Sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists (“Yunnan Thrush”). However, we find no consistent morphological differences from Alpine Thrush, and its breed- ing range is unknown. Molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative “Yunnan Thrush” as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato (s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocin- cla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto (s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest Thrush. Conclusions: The Plain-backed Thrush Z. mollissima s.l. comprises at least three species: Alpine Thrush Z. mollissima s.s., with a widespread alpine breeding distribution; Sichuan Forest Thrush Z. griseiceps, breeding in central Sichuan forests; and Himalayan Forest Thrush, breeding in the eastern Himalayas and northwest Yunnan (at least), which is described herein as a new species. “Yunnan Thrush” requires further study.
27.	Halwachs, Bettina, et al. (författare) Critical Issues in mycobiota analysis 2017 Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8 Tidskriftsartikel (refereegranskat)abstract Fungi constitute an important part of the human microbiota and they play a significant role for health and disease development. Advancements made in the culture-independent analysis of microbial communities have broadened our understanding of the mycobiota, however, microbiota analysis tools have been mainly developed for bacteria (e.g., targeting the 16S rRNA gene) and they often fall short if applied to fungal marker-gene based investigations (i.e., internal transcribed spacers, ITS). In the current paper we discuss all major steps of a fungal amplicon analysis starting with DNA extraction from specimens up to bioinformatics analyses of next-generation sequencing data. Specific points are discussed at each step and special emphasis is placed on the bioinformatics challenges emerging during operational taxonomic unit (OTU) picking, a critical step in mycobiota analysis. By using an in silico ITS1 mock community we demonstrate that standard analysis pipelines fall short if used with default settings showing erroneous fungal community representations. We highlight that switching OTU picking to a closed reference approach greatly enhances performance. Finally, recommendations are given on how to perform ITS based mycobiota analysis with the currently available measures.
28.	Olsson, Urban, 1954, et al. (författare) Assessment of species limits in African "brown buntings' (Emberiza, Passeriformes) based on mitochondrial and nuclear sequence data 2013 Ingår i: Ibis. - : Wiley. - 0019-1019 .- 1474-919X. ; 155:3, s. 534-543 Tidskriftsartikel (refereegranskat)abstract We estimated a phylogeny for 10 taxa currently placed in four polytypic species that collectively
29.	Olsson, Urban, 1954, et al. (författare) The Lanius excubitor (Aves, Passeriformes) conundrum – Taxonomic dilemma when molecular and non-molecular data tell different stories. 2010 Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 55:2, s. 347-357 Tidskriftsartikel (refereegranskat)abstract The phylogeny of 18 taxa in the Lanius excubitor complex, and the related species L. sphenocercus, L. ludovicianus and L. somalicus, was estimated based on the mitochondrial cytochrome b gene and the non-coding D-loop (in total ∼1.3 kb). According to the mitochondrial gene tree, Lanius excubitor s.l. is non-monophyletic, with some of its subspecies being more closely related to L. sphenocercus, L. ludovicianus, and L. somalicus. Also the division of the L. excubitor complex into a northern (L. excubitor) and a southern (L. meridionalis) species, as has been proposed based on morphological and ecological similarity and geographical distributions, is not compatible with the mitochondrial tree. Overall, genetic divergences among the ingroup taxa are small, indicating a recent radiation. A tree based on the nuclear ornithine decarboxylase (ODC) introns 6–7 is unresolved with respect to the ingroup, but provides strong support for a clade containing the Lanius excubitor complex, L. sphenocercus, L. ludovicianus and L. somalicus. We discuss the incongruence between the current taxonomy and the mitochondrial gene tree, and conclude that based on the latter the Lanius excubitor complex may be treated as at least six species, L. borealis, L. elegans, L. excubitor, L. lahtora, L. meridionalis, and L. uncinatus, but that other taxonomic treatments are also possible. However, uncertainty regarding to which extent the mitochondrial gene tree reflects the species phylogeny prevents us from recommending taxonomic change without further investigation. This study highlights the possible danger of relying on a single molecular marker, such as mitochondrial DNA, in taxonomic revisions and phylogenetic inference
30.	Šandová, Markéta, et al. (författare) Relationships within Capitotricha bicolor (Lachnaceae, Ascomycota) as inferred from ITS rDNA sequences, including some notes on the Brunnipila and Erioscyphella clades 2018 Ingår i: Mycological progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:1-2 / S1, s. 89-101 Tidskriftsartikel (refereegranskat)abstract DNA sequences of Capitotricha bicolor from Quercus, Fagus sylvatica, Alnus alnobetula, and Nothofagus, and C. rubi from Rubus idaeus were obtained from apothecia to establish whether specimens from different hosts belong to separate species. The obtained ITS1–5.8S–ITS2 rDNA sequences were examined with Bayesian and parsimony phylogenetic analyses. Intra- and interspecific variation was also investigated based on molecular distances in the ITS region. The phylogenetic analyses supported the specific distinctness of Capitotricha rubi and the Capitotricha from Nothofagus, but also suggest specific distinctness between samples from Quercus, Fagus, and Alnus. The interspecific distances were larger than intraspecific distances for all examined units. The smallest distance was found between the “Alnus alnobetula” and “Fagus sylvatica” units. Two new sequences of Brunnipila are published. Capitotricha, Lachnum, and Erioscyphella are compared to each other based on hair and excipulum characteristics.
31.	Strand, Malin, et al. (författare) Size of genera - biology or taxonomy? 2015 Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 44, s. 106-116 Annan publikation (refereegranskat)
32.	Subhash, Santhilal, 1987, et al. (författare) Sperm Originated Chromatin Imprints and LincRNAs in Organismal Development and Cancer 2020 Ingår i: iScience. - : Elsevier BV. - 2589-0042. ; 23:6 Tidskriftsartikel (refereegranskat)abstract Importance of sperm-derived transcripts and chromatin imprints in organismal development is poorly investigated. Here using an integrative approach, we show that human sperm transcripts are equally important as oocyte. Sperm-specific and sperm-oocyte common transcripts carry distinct chromatin structures at their promoters correlating with corresponding transcript levels in sperm. Interestingly, sperm-specific H3K4me3 patterns at the lincRNA promoters are not maintained in the germ layers and somatic tissues. However, bivalent chromatin at the sperm-specific protein-coding gene promoters is maintained throughout the development. Sperm-specific transcripts reach their peak expression during zygotic genome activation, whereas sperm-oocyte common transcripts are present during early preimplantation development but decline at the onset of zygotic genome activation. Additionally, there is an inverse correlation between sperm-specific and sperm-oocyte lincRNAs throughout the development. Sperm-lincRNAs also show aberrant activation in tumors. Overall, our observations indicate that sperm transcripts carrying chromatin imprints may play an important role in human development and cancer.
33.	Bengtsson-Palme, Johan, 1985, et al. (författare) Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker 2018 Ingår i: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 34:23, s. 4027-4033 Tidskriftsartikel (refereegranskat)abstract Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.We evaluated the Metaxa2 Database Builder on eleven commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.Supplementary data are available at Bioinformatics online.
34.	Borchert, Erik, et al. (författare) Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort 2021 Ingår i: mSystems. - 2379-5077 .- 2379-5077. ; 6:1 Tidskriftsartikel (refereegranskat)abstract The marine bone biome is a complex assemblage of macro- and microor- ganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic colla- gen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of micro- bial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia con- tained the most diverse gene repertoires. We postulate that demineralization of inor- ganic bone components is achieved by a timely succession of a closed sulfur biogeo- chemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone sur- face communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia. IMPORTANCE Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment. We here demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.
35.	Drennan, Regan, et al. (författare) Annelid Fauna of the Prince Gustav Channel, a Previously Ice-Covered Seaway on the Northeastern Antarctic Peninsula 2021 Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 7 Tidskriftsartikel (refereegranskat)abstract The Prince Gustav Channel is a narrow seaway located in the western Weddell Sea on the northeastern-most tip of the Antarctic Peninsula. The channel is notable for both its deep (>1200 m) basins, and a dynamic glacial history that most recently includes the break-up of the Prince Gustav Ice Shelf, which covered the southern portion of the channel until its collapse in 1995. However, the channel remains mostly unsampled, with very little known about its benthic biology. We present a preliminary account of the benthic annelid fauna of the Prince Gustav Channel in addition to samples from Duse Bay, a sheltered, glacier-influenced embayment in the northwestern portion of the channel. Samples were collected using an Agassiz Trawl, targeting megafaunal and large macrofaunal sized animals at depths ranging between 200–1200 m; the seafloor and associated fauna were also documented in situ using a Shallow Underwater Camera System (SUCS). Sample sites varied in terms of depth, substrate type, and current regime, and communities were locally variable across sites in terms of richness, abundance, and both taxonomic and functional composition. The most diverse family included the motile predator/scavenger Polynoidae, with 105 individuals in at least 12 morphospecies, primarily from a single site. This study provides first insights into diverse and spatially heterogeneous benthic communities in a dynamic habitat with continuing glacial influence, filling sampling gaps in a poorly studied region of the Southern Ocean at direct risk from climate change. These specimens will also be utilized in future molecular investigations, both in terms of describing the genetic biodiversity of this site and as part of wider phylogeographic and population genetic analyses assessing the connectivity, evolutionary origins, and demographic history of annelid fauna in the region.
36.	Ritter, Camila, et al. (författare) High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia. 2018 Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 6 Tidskriftsartikel (refereegranskat)abstract Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.We used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.Soil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, várzea, igapó and campina) than between substrates (soil and litter).In spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world's largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity.
37.	Tedersoo, Leho, et al. (författare) Novel soil-inhabiting clades fill gaps in the fungal tree of life 2017 Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5 Tidskriftsartikel (refereegranskat)abstract Background - Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results - We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions - This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
38.	Zanne, Amy E, et al. (författare) Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. 2020 Ingår i: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433 Tidskriftsartikel (refereegranskat)abstract Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
39.	Lanzén, Anders, et al. (författare) Benthic eDNA metabarcoding provides accurate assessments of impact from oil extraction, and ecological insights 2021 Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X. ; 130 Tidskriftsartikel (refereegranskat)abstract Apart from its contribution to climate change, offshore oil and gas extraction is also a potential threat to the diversity and function of marine ecosystems. Routine monitoring of the environmental status of affected areas is therefore critical for effective management. While current morphology-based monitoring is relatively time consuming, costly and prone to identification bias, environmental DNA metabarcoding offers an attractive alternative for assessing the impacts of oil drilling, extraction or spills. However, to be ready for routine monitoring, its performance needs to be demonstrated through agreement with assessments based on physicochemical measurements and current bioindicators. To this end, we applied metabarcoding to sequence the metazoan (COI) and total eukaryotic (18S) benthic components. We targeted a range of sites, with a gradient of low to high level of impact, located near active production installations and reference sites, in the North and Barents Seas. Alpha diversity and community structure of both datasets correlated strongly with a physicochemical pressure index (PI) based on total hydrocarbons (THC), PAH16, Ba and Cu. Calculations of the macroinvertebrate-based Norwegian Sensitivity Index (NSI) based on COI metabarcoding data agreed well with corresponding morpho-taxonomy values and with the PI. Further, we identified a set of bioindicator taxa from both metabarcoding datasets, to develop novel biotic indices and demonstrate their predictive performance using cross-validation. Finally, we compared co-occurrence networks from impacted vs. non-impacted sites, to improve the understanding of the ecological consequences of impacts. Our study demonstrates that metabarcoding can act as a meaningful and relatively accurate complement to the current morpho-taxonomic approach.
40.	Abbott, Jessica K., et al. (författare) The microevolutionary response to male-limited X-chromosome evolution in Drosophila melanogaster reflects macroevolutionary patterns 2020 Ingår i: Journal of Evolutionary Biology. - : Wiley-Blackwell. - 1010-061X .- 1420-9101. ; 33:6, s. 738-750 Tidskriftsartikel (refereegranskat)abstract Due to its hemizygous inheritance and role in sex determination, the X-chromosome is expected to play an important role in the evolution of sexual dimorphism and to be enriched for sexually antagonistic genetic variation. By forcing the X-chromosome to only be expressed in males over >40 generations, we changed the selection pressures on the X to become similar to those experienced by the Y. This releases the X from any constraints arising from selection in females and should lead to specialization for male fitness, which could occur either via direct effects of X-linked loci or trans-regulation of autosomal loci by the X. We found evidence of masculinization via up-regulation of male-benefit sexually antagonistic genes and down-regulation of X-linked female-benefit genes. Potential artefacts of the experimental evolution protocol are discussed and cannot be wholly discounted, leading to several caveats. Interestingly, we could detect evidence of microevolutionary changes consistent with previously documented macroevolutionary patterns, such as changes in expression consistent with previously established patterns of sexual dimorphism, an increase in the expression of metabolic genes related to mito-nuclear conflict and evidence that dosage compensation effects can be rapidly altered. These results confirm the importance of the X in the evolution of sexual dimorphism and as a source for sexually antagonistic genetic variation and demonstrate that experimental evolution can be a fruitful method for testing theories of sex chromosome evolution.
41.	Bag, Pushan, 1993- (författare) How could Christmas trees remain evergreen? : photosynthetic acclimation of Scots pine and Norway spruce needles during winter 2022 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Plants and other green organisms harvest sunlight by green chlorophyll pigments and covertit to chemical energy (sugars) and oxygen in a process called photosynthesis providing the foundation for life on Earth. Although it is unanimously believed that oceanic phytoplanktons are the main contributors to the global photosynthesis, the contribution of coniferous boreal forests distributed across vast regions of the northern hemisphere cannot be undermined. Hence boreal forests account signifificantly for social, economical and environmental sustainability. Not only do conifers thrive in the tundra regions with extreme climate, but they also maintain their needles green over the boreal winter. A question remains; what makes them so resilient? In this respect, we aimed to understand the remarkable winter adaptation strategies in two dominant boreal coniferous species,i.e., Pinus sylvestris and Picea abies. First, we mapped the transcriptional landscape in Norway spruce (Picea abies) needles over the annual cycle. Transcriptional changes in the nascent needles reflflected a sequence of developmental processes and active vegetative growth during early summer and summer. Later after maturation, transcriptome reflflected activated defense against biotic factors and acclimationin response to abiotic environmental cues such as freezing temperatures during winter. Secondly, by monitoring the photosynthetic performance of Scot pine needles, we found that the trees face extreme stress during the early spring (Feb-Mar) when sub-zero temperatures are accompanied by high solar radiation. At this time, drastic changes occur in the thylakoid membranes of the chloroplast that allows the mixing of photosystem I and photosystem II that typically remain laterally segregated. This triggers direct energy transfer from PSII to PSI and thus protects PSII from damage. Furthermore, we found that this loss of lateral segregation may be a consequence of triple phosphorylationof Lhcb1 (Light harvesting complex1 of photosystem II). The structural changes in thylakoid membranes also lead to changes inthe thylakoid macro domain organisationand pigment protein composition. Furthermore, we discovered that while PSII is protected by direct energy transfer, the protection of PSI is provided through photoreduction of oxygen by flavodiiron proteins, which in turn allows P700 to stay in an oxidised state necessary for direct energy transfer. These coordinated cascades of changes concomitantly protect both PSI and PSII to maintain the needles green over the winter.
42.	Blake, Chelsea A., et al. (författare) Conspecific boldness and predator species determine predation-risk consequences of prey personality 2018 Ingår i: Behavioral Ecology and Sociobiology. - : Springer-Verlag New York. - 0340-5443 .- 1432-0762. ; 72:8, s. 1-7 Tidskriftsartikel (refereegranskat)abstract Abstract: Individual variation in the behavior of prey can influence predation risk in complex ways. We ran individual roach (Rutilus rutilus), a common freshwater fish, through a standard refuge emergence protocol to characterize their boldness, a key animal personality trait. We then paired a bold and a shy roach and exposed the pair to one of two predator species that have contrasting hunting modes to ascertain how personality traits shaped their survival during predator encounters. When a paired bold and shy prey fish interacted with a perch predator (active foraging mode), bold and shy prey were consumed in almost equal numbers. However, pike predators (ambush foraging mode) selectively consumed more shy prey, and prey body size and boldness score both contributed significantly to which prey fish was eaten. Our findings support the idea that multiple predators with different foraging modes, and hence differential selection on prey personality, could contribute to maintaining variation in personality in prey populations. Furthermore, for social species, including shoaling fish, the ultimate consequences of an individual’s personality may depend upon the personality of its nearby conspecifics. Significance statement: Animals of the same species often look similar, but individuals show differences in their behavior that can have important consequences, for instance when these individuals interact with predators. The common roach is a freshwater fish that shows inter-individual variation in its propensity to take risks, a key personality trait often termed boldness. Variation in boldness may affect the outcome when roach interact with predators, i.e., if they get eaten or survive. However, we found the impact of roachs’ personality type depends on what species of predatory fish they face. When we put a shy and a bold roach together with predatory perch, the roachs’ personality did not significantly affect which individual was eaten. But when the predator was a pike, the predators selectively ate more shy roach, and the likelihood an individual would be eaten depended on their body size.
43.	Caputo, Andrea, 1988- (författare) Genomic and morphological diversity of marine planktonic diatom-diazotroph associations : a continuum of integration and diversification through geological time 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Symbioses between eukaryotes and nitrogen (N2)-fixing cyanobacteria (or diazotrophs) are quite common in the plankton community. A few genera of diatoms (Bacillariophyceae) such as Rhizosolenia, Hemiaulus and Chaetoceros are well known to form symbioses with the heterocystous diazotrophic cyanobacteria Richelia intracellularis and Calothrix rhizosoleniae. The latter are also called diatom-diazotroph associations, or DDAs. Up to now, the prokaryotic partners have been morphologically and genetically characterized, and the phylogenetic reconstruction of the well conserved nifH gene (encodes for the nitrogenase enzyme) placed the symbionts in 3 clusters based on their host-specificity, i.e. het-1 (Rhizosolenia-R. intracellularis), het-2 (Hemiaulus-R. intracellularis), and het-3 (Chaetoceros-C- rhizosoleniae). Conversely, the diatom-hosts, major representative of the phytoplankton community and crucial contributors to the carbon (C) biogeochemical cycle, have been understudied.The first aim of this thesis was to genetically and morphologically characterize the diatom-hosts, and to reconstruct the evolutionary background of the partnerships and the symbiont integration in the host. The molecular-clock analysis reconstruction showed the ancient appearance of the DDAs, and the traits characterizing the ancestors. In addition, diatom-hosts bearing internal symbionts (with more eroded draft genomes) appeared earlier than diatom-hosts with external symbionts. Finally a blast survey highlighted a broader distribution of the DDAs than expected.The second aim of this thesis was to compare genetic and physiological characteristics of the DDAs symbionts with the other eukaryote-diazotroph symbiosis, i.e. prymnesiophyte-UCYN-A (or Candidatus Atelocyanobacterium thalassa). The genome comparison highlighted more genes for transporters in het-3 (external symbiont) and in the UCYN-A based symbiosis, suggesting that symbiont location might be relevant also for metabolic exchanges and interactions with the host and/or environment. Moreover, a summary of methodological biases that brought to an underestimation of the DDAs is reported.The third aim of this thesis was to determine the distribution of the DDAs in the South Pacific Ocean using a quantitative polymerase chain reaction (qPCR) approach and to outline the environmental drivers of such distribution. Among the het-groups, het-1 was the most abundant/detected and co-occurred with the other 2 symbiotic strains, all responding similarly to the influence of abiotic factors, such as temperature and salinity (positive and negative correlation, respectively). Globally, Trichodesmium dominated the qPCR detections, followed by UCYN-B. UCYN-A phylotypes (A-1, A-2) were detected without their proposed hosts, for which new oligonucleotides were designed. The latter suggested a facultative symbiosis. Finally, microscopy observations of the het-groups highlighted a discrepancy with the qPCR counts (i.e. the former were several order of magnitudes lower), leading to the idea of developing a new approach to quantify the DDAs. The fourth aim of this thesis was to develop highly specific in situ hybridization assays (CARD-FISH) to determine the presence of alternative life-stages and/or free-living partners. The new assays were applied to samples collected in the South China Sea and compared with abundance estimates from qPCR assays for the 3 symbiotic strains. Free-living cells were indeed detected along the transect, mainly at deeper depths. Free-living symbionts had two morphotypes: trichomes and single-cells. The latter were interpreted as temporary life-stages. Consistent co-occurrence of the 3 het-groups was also found in the SCS and application of a SEM model predicted positive interactions between the het groups. We interpreted the positive interaction as absence of intra-specific competition, and consistent with the previous study, temperature and salinity were predicted as major drivers of the DDAs distribution.
44.	Comstedt, Daniel, et al. (författare) Autotrophic and heterotrophic soil respiration in a Norway spruce forest : estimating the root decomposition and soil moisture effects in a trenching experiment 2011 Ingår i: Biogeochemistry. - : Springer. - 0168-2563 .- 1573-515X. ; 104:1-3, s. 121-132 Tidskriftsartikel (refereegranskat)abstract The two components of soil respiration, autotrophic respiration (from roots, mycorrhizal hyphae and associated microbes) and heterotrophic respiration (from decomposers), was separated in a root trenching experiment in a Norway spruce forest. In June 2003, cylinders (29.7 cm diameter) were inserted to 50 cm soil depth and respiration was measured both outside (control) and inside the trenched areas. The potential problems associated with the trenching treatment, increased decomposition of roots and ectomycorrhizal mycelia and changed soil moisture conditions, were handled by empirical modelling. The model was calibrated with respiration, moisture and temperature data of 2004 from the trenched plots as a training set. We estimate that over the first 5 months after the trenching, 45% of respiration from the trenched plots was an artefact of the treatment. Of this, 29% was a water difference effect and 16% resulted from root and mycelia decomposition. Autotrophic and heterotrophic respiration contributed to about 50% each of total soil respiration in the control plots averaged over the two growing seasons. We show that the potential problems with the trenching, decomposing roots and mycelia and soil moisture effects, can be handled by a modelling approach, which is an alternative to the sequential root harvesting technique.
45.	Forsman, Anders, et al. (författare) Phenotypic evolution of dispersal-enhancing traits in insular voles 2011 Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 278:1703, s. 225-232 Tidskriftsartikel (refereegranskat)abstract Evolutionary theory predicts that in metapopulations subject to rapid extinction-recolonization dynamics, natural selection should favour evolution of traits that enhance dispersal and recolonization ability. Metapopulations of field voles (Microtus agrestis) on islands in the Stockholm archipelago, Sweden, are characterized by frequent local extinction and recolonization of subpopulations. Here, we show that voles on the islands were larger and had longer feet than expected for their body size, compared with voles from the mainland; that body size and size-specific foot length increased with increasing geographical isolation and distance from mainland; and that the differences in body size and size-specific foot length were genetically based. These findings provide rare evidence for relatively recent (less than 1000 years) and rapid (corresponding to 100-250 darwins) evolution of traits facilitating dispersal and recolonization in island metapopulations.
46.	Koch, Kamilla, et al. (författare) Morphological differences in the ovary of Libellulidae (Odonata) 2009 Ingår i: International Journal of Odonatology. - Oxford : Taylor & Francis. - 1388-7890 .- 2159-6719. ; 12:1, s. 147-156 Tidskriftsartikel (refereegranskat)abstract All female Odonata have been assumed to produce oocytes continuously during their mature life span. However, a recent study of ovariole orientation and development led to the suggestion that Libellulidae are divided into two groups of species, one with continuous, the other with stepwise oocyte production. To find more evidence of this division, we compared the size variation and growth within the vitellarium of the ovary, studying oocytes, and follicle cells. We found that morphological characters discriminate between the two ovary types in eight of the 10 investigated species. In both types we found an increase in all measurements from the anterior to the posterior end of the vitellarium. The increase in oocyte width and follicle cell length was significantly higher in species with a continuous oocyte production. We also noted that follicle cells may have more than one nucleus and that their number can vary during vitellogenesis. Our study confirmed the hypotheses that two different ovary types exist in Libellulidae. The two species not fitting into this grouping could be an artefact of small samp le size due to intraspecific phenotypic plasticity, or else there might be more than two ovary groups, or even a continuum. We could not offer an explanation as to how the process of stepwise oocyte production differs from continuous based production on morphological characters.
47.	Kulma, Katarzyna, et al. (författare) Malaria-infected female collared flycatchers (Ficedula albicollis) do not pay the cost of late breeding 2014 Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:1, s. e85822- Tidskriftsartikel (refereegranskat)abstract Life-history theory predicts that the trade-off between parasite defense and other costly traits such as reproduction may be most evident when resources are scarce. The strength of selection that parasites inflict on their host may therefore vary across environmental conditions. Collared flycatchers (Ficedula albicollis) breeding on the Swedish island Oland experience a seasonal decline in their preferred food resource, which opens the possibility to test the strength of life-history trade-offs across environmental conditions. We used nested-PCR and quantitative-PCR protocols to investigate the association of Haemosporidia infection with reproductive performance of collared flycatcher females in relation to a seasonal change in the external environment. We show that despite no difference in mean onset of breeding, infected females produced relatively more of their fledglings late in the season. This pattern was also upheld when considering only the most common malaria lineage (hPHSIB1), however there was no apparent link between the reproductive output and the intensity of infection. Infected females produced heavier-than-average fledglings with higher-than-expected recruitment success late in the season. This reversal of the typical seasonal trend in reproductive output compensated them for lower fledging and recruitment rates compared to uninfected birds earlier in the season. Thus, despite different seasonal patterns of reproductive performance the overall number of recruits was the same for infected versus uninfected birds. A possible explanation for our results is that infected females breed in a different microhabitat where food availability is higher late in the season but also is the risk of infection. Thus, our results suggest that another trade-off than the one we aimed to test is more important for explaining variation in reproductive performance in this natural population: female flycatchers appear to face a trade-off between the risk of infection and reproductive success late in the season.
48.	Kuparinen, Anna, et al. (författare) Developmental threshold model challenged by temperature 2010 Ingår i: Evolutionary Ecology Research. - 1522-0613 .- 1937-3791. ; 12:7, s. 821-829 Tidskriftsartikel (refereegranskat)abstract Question: Does the L-shape of the reaction norm for age and size at ontogenetic transitions arise irrespective of temperature? The developmental threshold model suggests that this shape arises due to a threshold in body size to undertake the transition. Data studied: Ages and sizes at metamorphosis measured in a common garden experiment in Rana temporaria originating from six populations along a latitudinal gradient. Individuals were exposed to three temperature treatments and two levels of food. Search method: Population-specific age and size at metamorphosis were plotted against each other, and the shape of the reaction norm across populations was further illustrated by an exponential decay function. The observed patterns were further explored via linear mixed-effect models. Conclusion: The L-shape of the reaction norm depends on temperature, suggesting that at low temperature a developmental threshold in age rather than in size regulates the process of metamorphosis.
49.	Norrström, Niclas (författare) Artificial neural networks in models of specialization and sympatric speciation 2009 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract This thesis deals with specialization and how it is linked to sympatric speciation. The trait driving specialization is a cue recognition trait modelled with artificial neural networks that exploiters use to discriminate beneficial resources from detrimental resources based on the signals of the resources. Paper I investigates how haploid exploiters and the resources coevolve when the signals of the resources can evolve through mutations. We find that this coevolution can be a cyclic process with saltational changes between different stages and that evolution is only directional and the exploiters are only specialists in parts of this cycle. In simulations underlying Paper II the signals of the resources can not mutate but the exploiters have a diploid genome and the organisms reproduce sexually. We show that the disruptive selection stemming from exploiters specializing on different resources can overcome the homogenizing effect of sexual recombination when exploiters mate randomly and produce a functional genetic polymorphism with specialized exploiters. A functional genetic polymorphism removes the force of reinforcement but we run simulations where the exploiters have a mating gene determining if mating is random or if exploiters should mate assortatively in Paper III. We find that assortative invades the exploiter population and homozygote specialists evolve because the genetic polymorphism pays a cost by having some alleles being silenced (that is they do not contribute to the complete phenotype) in certain genotypes so a mutation in these silenced alleles is not selected against, which cause these alleles to accumulate deleterious mutations. The homozygote specialists, mating assortatively, are much more efficiently removing deleterious mutations from the population and hence can invade the population. Finally, in Paper IV we investigate the effects of resource and resource signal arrangements in the environment. We show that the environment can influence the evolution of specialization and sympatric speciation. By modelling a resource discrimination trait based on the interaction of epistatic genes we find a novel force promoting sympatric speciation over genetic polymorphisms.
50.	Quintela, Maria, et al. (författare) Detecting hybridization between willow grouse (Lagopus lagopus) and rock ptarmigan (L. muta) in Central Sweden through Bayesian admixture analyses and mtDNA screening 2010 Ingår i: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11:2, s. 557-569 Tidskriftsartikel (refereegranskat)abstract Willow grouse (L. lagopus) and rock ptarmigan (L. muta) are sibling species with similar phenotypic and life histories that coexist sympatrically in wide areas of their distribution range. These grouse are amongst the most popular game birds in Scandinavia but contrary to other quarry species, no restocking with captive-bred animals has ever been performed. The discovery of two individuals with intermediate plumage features evoked the question of possible hybridization events between both species, an idea that did not seem too unlikely on the basis of habitat overlap. Thus, to assess whether any genetic exchange is occurring, we used different Bayesian-based admixture analyses of multilocus genotypes determined at twelve microsatellite loci. We also obtained mitochondrial COI-sequences from a selected number of individuals to infer the maternal geneflow and potential introgression. The capacity of our panel of microsatellite markers to detect hybridization was verified using assignments of simulated genotypes. We then evaluated the extent of hybridization in an actual sample of 111 individuals collected in a 100-km(2) area in the Scandinavian mountain range. An admixed condition was verified in one of the suspected hybrids, that seemed to carry a L. muta genotype with partial L. lagopus introgression. In addition, more than 4% of L. lagopus showed signs of hybridization under the most conservative scenario with respect to discrepancies between population assignment methods. This was unexpected, given that no L. lagopus displayed any apparent intermediate plumage features. Furthermore, interspecific geneflow of mtDNA haplotypes was lower than expected; which suggests that Haldane's rule might apply for these two grouse species. Hence, plumage identification of hybrid ancestry is not always reliable and might lead to biases in the estimation of hybridization rates. Hybridisation may be expected to increase if the climate gets warmer as the habitat overlap between the species will become more extensive. We discuss whether hybridisation is a threat to the long-term survival of any of the two species.

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