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1.	Radek, Renate, et al. (author) Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota 2017 In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 25, s. 31-50 Journal article (peer-reviewed)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.
2.	Sigvald, Roland, et al. (author) Molecular identification of bloodmeals and species composition in Culicoides biting midges 2013 In: Medical and Veterinary Entomology. - : Wiley. - 0269-283X .- 1365-2915. ; 27, s. 104-112 Journal article (peer-reviewed)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.
3.	Alm Rosenblad, Magnus, 1957, et al. (author) 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 In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 13, s. 21-33 Journal article (peer-reviewed)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.
4.	Nilsson, R. Henrik, 1976, et al. (author) Mycobiome diversity: high-throughput sequencing and identification of fungi. 2019 In: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109 Research review (peer-reviewed)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.
5.	Forsman, Anders (author) Rethinking the thermal melanism hypothesis: rearing temperature and coloration in pygmy grasshoppers 2011 In: Evolutionary Ecology. - : Springer Science and Business Media LLC. - 0269-7653 .- 1573-8477. ; 25:6, s. 1247-1257 Journal article (peer-reviewed)abstract Selection for efficient conversion of solar radiation to body heat has favored theevolution of dark coloration in many ectotherms. The thermal melanism hypothesis positsthat dark coloration is beneficial under conditions of low ambient temperatures because itresults in faster heating rates and higher body temperatures. Fast heating rates, however,may come at a cost of overheating unless compensated for by thermal physiology orbehaviour. Pygmy grasshopper (Orthoptera, Tetrigidae) populations that inhabit fire-ravagedareas characterized by blackened backgrounds and hot surface temperatures due tohigh absorbance of solar radiation show an increased frequency of black phenotypes. Iraised the progeny of wild-captured Tetrix undulata in cold and hot temperatures and useddata on color patterns and survival in a greenhouse to examine whether a cold thermalenvironment triggered the development of melanic coloration or differently affected survivalof melanic versus non-melanic individuals. My results indicate that melanism was notinfluenced by rearing temperature but by genes or epigenetic maternal effects. Temperaturealso did not affect survival. However, melanic individuals produced by melanic motherssurvived longer than melanic individuals produced by non- melanic mothers, whereas nonmelanicindividuals produced by non-black mothers survived longer than melanic individualsproduced by non-black mothers. This suggests a mismatch between color andphysiology in offspring belonging to a different color morph than their mother. Futureinvestigations into the evolution of melanism should consider conflicting selection pressureson thermal capacity and camouflage as well as the influence of correlated responsesto selection on traits associated with coloration.
6.	Abarenkov, Kessy, et al. (author) 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 In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15 Journal article (peer-reviewed)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. (author) A price tag on species 2022 In: Research Ideas and Outcomes_RIO. - : Pensoft Publishers. - 2367-7163. ; 8, s. 1-7 Journal article (peer-reviewed)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. (author) Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms 2022 In: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 239-244 Journal article (peer-reviewed)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. (author) The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia 2019 In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1 Journal article (peer-reviewed)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. (author) Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition 2018 In: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:4, s. 489-500 Journal article (peer-reviewed)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.	Forsman, Anders, et al. (author) Phenotypic evolution of dispersal-enhancing traits in insular voles 2011 In: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 278:1703, s. 225-232 Journal article (peer-reviewed)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.
12.	Gómez-Martínez, Daniela, et al. (author) Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican 2023 In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 875 Journal article (peer-reviewed)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.
13.	Zhao, M., et al. (author) Phylogenetic position of the Wallcreeper Tichodroma muraria 2016 In: Journal of Ornithology = Journal fur Ornithologie. - : Springer Science and Business Media LLC. - 0021-8375 .- 1439-0361. ; 157:3, s. 913-918 Journal article (peer-reviewed)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.
14.	Alström, Per, et al. (author) A review of the recent advances in the systematics of the avian superfamily Sylvioidea 2013 In: Chinese Birds. - : Chinese Birds (Press). - 1674-7674. ; 4, s. 99-131 Journal article (peer-reviewed)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.
15.	Alström, Per, et al. (author) Dramatic niche shifts and morphological change in two insular bird species 2015 In: Royal Society Open Science. - : The Royal Society. - 2054-5703. ; 2 Journal article (peer-reviewed)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.
16.	Alström, Per, et al. (author) Integrative taxonomy of the Plain-backed Thrush (Zoothera mollissima) complex (Aves, Turdidae) reveals cryptic species, including a new species. 2016 In: Avian research. - : Elsevier BV. - 2053-7166. ; 7:1 Journal article (peer-reviewed)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.
17.	Olsson, Urban, 1954, et al. (author) Assessment of species limits in African "brown buntings' (Emberiza, Passeriformes) based on mitochondrial and nuclear sequence data 2013 In: Ibis. - : Wiley. - 0019-1019 .- 1474-919X. ; 155:3, s. 534-543 Journal article (peer-reviewed)abstract We estimated a phylogeny for 10 taxa currently placed in four polytypic species that collectively
18.	Olsson, Urban, 1954, et al. (author) The Lanius excubitor (Aves, Passeriformes) conundrum – Taxonomic dilemma when molecular and non-molecular data tell different stories. 2010 In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 55:2, s. 347-357 Journal article (peer-reviewed)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
19.	Šandová, Markéta, et al. (author) Relationships within Capitotricha bicolor (Lachnaceae, Ascomycota) as inferred from ITS rDNA sequences, including some notes on the Brunnipila and Erioscyphella clades 2018 In: Mycological progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:1-2 / S1, s. 89-101 Journal article (peer-reviewed)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.
20.	Strand, Malin, et al. (author) Size of genera - biology or taxonomy? 2015 In: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 44, s. 106-116 Other publication (peer-reviewed)
21.	Borchert, Erik, et al. (author) Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort 2021 In: mSystems. - 2379-5077 .- 2379-5077. ; 6:1 Journal article (peer-reviewed)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.
22.	Drennan, Regan, et al. (author) Annelid Fauna of the Prince Gustav Channel, a Previously Ice-Covered Seaway on the Northeastern Antarctic Peninsula 2021 In: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 7 Journal article (peer-reviewed)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.
23.	Ritter, Camila, et al. (author) High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia. 2018 In: PeerJ. - : PeerJ. - 2167-8359. ; 6 Journal article (peer-reviewed)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.
24.	Tedersoo, Leho, et al. (author) Novel soil-inhabiting clades fill gaps in the fungal tree of life 2017 In: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5 Journal article (peer-reviewed)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.
25.	Zanne, Amy E, et al. (author) Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. 2020 In: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433 Journal article (peer-reviewed)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.
26.	Abbott, Jessica K., et al. (author) The microevolutionary response to male-limited X-chromosome evolution in Drosophila melanogaster reflects macroevolutionary patterns 2020 In: Journal of Evolutionary Biology. - : Wiley-Blackwell. - 1010-061X .- 1420-9101. ; 33:6, s. 738-750 Journal article (peer-reviewed)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.
27.	Bag, Pushan, 1993- (author) How could Christmas trees remain evergreen? : photosynthetic acclimation of Scots pine and Norway spruce needles during winter 2022 Doctoral thesis (other academic/artistic)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.
28.	Caputo, Andrea, 1988- (author) Genomic and morphological diversity of marine planktonic diatom-diazotroph associations : a continuum of integration and diversification through geological time 2019 Doctoral thesis (other academic/artistic)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.
29.	Jaensson, Thomas, et al. (author) Den fästingöverförda Borreliainfektionen i Sverige 1989 In: Fauna och flora. - 0014-8903. ; 84, s. 124-129 Journal article (pop. science, debate, etc.)
30.	Koch, Kamilla, et al. (author) Morphological differences in the ovary of Libellulidae (Odonata) 2009 In: International Journal of Odonatology. - Oxford : Taylor & Francis. - 1388-7890 .- 2159-6719. ; 12:1, s. 147-156 Journal article (peer-reviewed)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.
31.	Kulma, Katarzyna, et al. (author) Malaria-infected female collared flycatchers (Ficedula albicollis) do not pay the cost of late breeding 2014 In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:1, s. e85822- Journal article (peer-reviewed)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.
32.	Kuparinen, Anna, et al. (author) Developmental threshold model challenged by temperature 2010 In: Evolutionary Ecology Research. - 1522-0613 .- 1937-3791. ; 12:7, s. 821-829 Journal article (peer-reviewed)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.
33.	Quintela, Maria, et al. (author) Detecting hybridization between willow grouse (Lagopus lagopus) and rock ptarmigan (L. muta) in Central Sweden through Bayesian admixture analyses and mtDNA screening 2010 In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11:2, s. 557-569 Journal article (peer-reviewed)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.
34.	Schneider, Nicole, et al. (author) Influence and value of different water regimes on avian species richness in arid inland Australia 2009 In: Biodiversity and Conservation. - : Springer Science and Business Media LLC. - 0960-3115 .- 1572-9710. ; 18:2, s. 457-471 Journal article (peer-reviewed)abstract Riparian habitats in arid landscapes are recognised for their structurally diverse vegetation and diverse bird species assemblages. In the extensive semi-arid and arid centre of Australia, riparian woodland habitats are impacted by pastoral land-use which may negatively influence vegetation structure and avian species composition. However, pastoralism has promoted the establishment of artificial water bodies, so that additional riparian vegetation may occur in the landscape. In this study, we surveyed the importance of different water regimes (i.e. artificial lakes, natural waterholes, desert sites) together with their associated vegetation on avian species richness in north-western New South Wales, Australia. Our results show that bird species richness was highest at water locations, in particular at artificial lakes. Avian species richness was negatively associated with distance to water bodies, both in desert vegetation types and in the riparian vegetation type along dry creeks. Moreover, riparian habitats supported larger avian assemblages and especially those of sedentary bird species compared to the surrounding shrub-steppe landscape. This indicates that artificial water bodies may be of significance for arid zone bird species and might gain in importance with changing water availabilities due to climatic changes.
35.	Alström, Per, et al. (author) The Arctic Warbler Phylloscopus borealis - three anciently separated cryptic species revealed 2011 In: Ibis. - 0019-1019 .- 1474-919X. ; 153:2, s. 395-410 Journal article (peer-reviewed)abstract The Arctic Warbler Phylloscopus borealis breeds across the northern Palaearctic and northwestern-most Nearctic, from northern Scandinavia to Alaska, extending south to southern Japan, and winters in Southeast Asia, the Philippines and Indonesia. Several subspecies have been described based on subtle morphological characteristics, although the taxonomy varies considerably among different authors. A recent study (T. Saitoh et al. (2010) BMC Evol. Biol. 10: 35) identified three main mitochondrial DNA clades, corresponding to: (1) continental Eurasia and Alaska, (2) south Kamchatka, Sakhalin and northeast Hokkaido, and (3) most of Japan (Honshu, Shikoku, Kyushu). These three clades were estimated to have diverged during the late Pliocene to early Pleistocene (border at c. 2.6 million years ago). Differences in morphometrics have also been reported among members of the three clades (T. Saitoh et al. (2008) Ornithol. Sci. 7: 135-142). Here we analyse songs and calls from throughout the range of the Arctic Warbler, and conclude that these differ markedly and consistently among the populations representing the three mitochondrial clades. Kurile populations, for which no sequence data are available, are shown to belong to the second clade. To determine the correct application of available scientific names, mitochondrial DNA was sequenced from three name-bearing type specimens collected on migration or in the winter quarters. Based on the congruent variation in mitochondrial DNA, morphology and vocalizations, we propose that three species be recognized: Arctic Warbler Phylloscopus borealis (sensu stricto) (continental Eurasia and Alaska), Kamchatka Leaf Warbler Phylloscopus examinandus (Kamchatka (at least the southern part), Sakhalin, Hokkaido and Kurile Islands), and Japanese Leaf Warbler Phylloscopus xanthodryas (Japan except Hokkaido).
36.	Hooper, D. M., et al. (author) The Rusty-tailed Flycatcher (Muscicapa ruficauda; Ayes: Muscicapidae) is a member of the genus Ficedula 2016 In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 102, s. 56-61 Journal article (peer-reviewed)abstract The phylogenetic relationships of the avian family Muscicapidae (Old World chats and flycatchers) have historically been enigmatic and remain an active area of study. Widespread instances of non-monophyly resulting from misleading morphological and behavioral similarities have merited numerous taxonomic revisions to the group. Here we report one such instance with regard to the Rusty-tailed Flycatcher Muscicapa ruficauda, which has recently been placed in the newly proposed monotypic genus Ripleyia, due to inferred sister relationship to the genus Muscicapa and related genera (Voelker et al., 2016a). This name was later replaced by Ripleyornis, as it was realized that Ripleyia is a junior homonym of a genus of Mollusca (Voelker et al., 2016b). Using a Bayesian phylogenetic assessment of the Muscicapidae with near-complete taxon sampling of the genus Ficedula for five loci, along with an acoustic comparison of M. ruficauda to a subset of other flycatcher species, we show that this species should be reassigned to the genus Ficedula and accordingly that the names Ripleyia and Ripleyornis are both junior synonyms of Ficedula. (C) 2016 Elsevier Inc. All rights reserved.
37.	Li, Xinlei, et al. (author) Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of White Wagtail Motacilla alba (Aves: Passeriformes). 2016 In: Journal of Avian Biology. - : Wiley. - 0908-8857 .- 1600-048X. ; 47, s. 263-274 Journal article (peer-reviewed)abstract We studied the phylogeography and population history of the white wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of white wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in central and south Europe; and clade SE was distributed in central and east Asia. e deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of east Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. e recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.
38.	Olsson, Urban, 1954, et al. (author) Mitochondrial phylogeny of the Eurasian/African reed warbler complex (Acrocephalus, Aves). Disagreement between morphological and molecular evidence and cryptic divergence: A case for resurrecting Calamoherpe ambigua Brehm 1857 2016 In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 102, s. 30-44 Journal article (peer-reviewed)abstract A tree based on the mitochondrial cyt b gene for 278 samples from throughout the range of the Eurasian Reed Warbler Acrocephalus scirpaceus - African Reed Warbler A. baeticatus complex shows well supported geographically structured divergence for eight distinct lineages. The phylogenetic structuring together with the clarification of priority, provided by sequence data from seven type specimens, suggests that both taxonomy and distribution boundaries are in need of revision. The Iberian and Moroccan populations form a well-supported Glade, and we propose that these are treated as taxonomically distinct, under the name ambiguus (Brehm, 1857). We propose that the names scirpaceus, fuscus, avicenniae, ambiguus, minor, cinnamomeus, hallae and baeticatus are used for the well supported clades in the complex, which we recommend to treat as one polytypic species, A. scirpaceus, pending studies of gene flow and assortative mating in the contact zones. (C) 2016 Elsevier Inc. All rights reserved.
39.	Wintersparv Stervander, Martin, et al. (author) Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae) 2016 In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 102, s. 233-245 Journal article (peer-reviewed)abstract The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision. (C) 2016 Elsevier Inc. All rights reserved.
40.	Affonso, Igor de Paiva, et al. (author) Light-induced eye-fluke behavior enhances parasite life cycle 2017 In: Frontiers in Ecology and the Environment. - : John Wiley & Sons. - 1540-9295 .- 1540-9309. ; 15:6, s. 340-341 Journal article (peer-reviewed)
41.	An, Junghwa, et al. (author) Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009 2010 In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408 Journal article (peer-reviewed)abstract This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
42.	Barber, I., et al. (author) Behavioural responses to simulated avian predation in female three spined sticklebacks the effect of experimental Schistocephalus solidus infections 2004 In: Behaviour. - 0005-7959 .- 1568-539X. ; 141, s. 1425-1440 Journal article (peer-reviewed)abstract Plerocercoid larvae of Schistocephalus solidus are common parasites of three-spined sticklebacks that require the ingestion of stickleback hosts by birds to complete their life cycle. Amongst wild-caught sticklebacks, infection is associated with a reduction in antipredator behaviour; however, to date no study has examined the escape responses of experimentally infected sticklebacks, and thus assigning causality remains difficult. Here, we compare aspects of the antipredator behaviour of five experimentally infected female sticklebacks with shamexposed controls over a 16 post-exposure week period. During weeks 1-7 post-exposure, the escape responses of infected fish did not differ significantly from those of sham-exposed fish. However, over weeks 9-15, when infected fish had developed plerocercoids of >50 mg—the size at which they become infective to birds —a lower proportion of infected fish performed directional responses and reached cover within 2 s of the strike. Infected fish also performed a lower frequency of ‘staggered dashes’, and a higher frequency of ‘slow swims’, than shamexposed fish over weeks 9-15. Amongst sham-exposed fish, re-emergence from cover was uncommon throughout the study, but infected fish regularly left cover during weeks 9-15. Our results support those of previous studies examining behavioural change in naturally infected fish and, although other explanations remain possible, our finding that behaviour change in experimentally-infected fish is limited to hosts harbouring single infective parasites provides further evidence that the behaviour changes may be parasite adaptations.
43.	Barber, I., et al. (author) Effects of experimental Schistocephalus solidus infections on growth, morphology and sexual development of female three-spined sticklebacks, Gasterosteus aculeatus 2003 In: Parasitology. - 0031-1820 .- 1469-8161. ; 126, s. 359-367 Journal article (peer-reviewed)abstract The use of naturally infected hosts in studies attempting to identify parasite-induced changes in host biology is problematical because it does not eliminate the possibility that infection may be a consequence, rather than a cause, of host trait variation. In addition, uncontrolled concomitant infections may confound results. In this study we experimentally infected individual laboratory-bred female three-spined sticklebacks Gasterosteus aculeatus L. with the pseudophyllidean cestode Schistocephalus solidus [Muller], and compared the morphology and growth patterns of infected females with sham-exposed controls over a 16-week period. Fish were fed a ration of 8% body weight per day. Non-invasive image analysis techniques allowed the growth of individual plerocercoids to be tracked in vivo throughout the course of infection, and patterns of host and parasite growth were determined. Females that developed infections diverged morphometrically from unexposed control females and exposed-uninfected females at 6 weeks post-infection, with the width of the body at the pectoral fins giving the earliest indication of infection success. When including the plerocercoid, infected females gained weight more quickly than controls, but when plerocercoid weight was removed this trend was reversed. There was no effect of infection on the increase in fish length. Plerocercoids grew at different rates in individual hosts, and exhibited measurable sustained weight increases of up to 10% per day. Final estimates of plerocercoid weight from morphometric analysis prior to autopsy were accurate to within +/-17% of actual plerocercoid weight. At autopsy, infected female sticklebacks had significantly lower perivisceral fat reserves but had developed significantly larger ovaries than controls. The results are discussed in relation to previous studies examining natural infections, and the value of utilizing experimental infections to examine ecological aspects of host-parasite interactions is discussed.
44.	Betzholtz, Per-Eric, et al. (author) Mobility is related to species traits in noctuid moths 2011 In: Ecological Entomology. - : Wiley. - 0307-6946 .- 1365-2311. ; 36, s. 369-376 Journal article (peer-reviewed)abstract Abstract. 1. Mobility is important for the understanding of how species survive infragmented landscapes and cope with increasing rates of habitat and climate change.However, mobility is a difficult trait to explore and is poorly known in most taxa.Species traits have been studied in relation to range shifts, extinction risks, andresponses to habitat area and isolation, and have also been suggested as good estimatorsof mobility. Here we explore the relation between mobility and species traits in noctuidmoths.2. We sampled noctuid moths by an automatic light-trap on an island far out in theBaltic Sea. We compared traits of the non-resident species on the island with traits ofa species pool of assumed potential migrants from the Swedish mainland.3. Mobility was significantly related to adult activity period, length of flightperiod, and the interaction between host-plant specificity and distribution area. Widelydistributed host-plant generalists were more mobile than host-plant specialists withmore restricted distribution, and species with an adult activity period in August toSeptember moved to the island to a higher extent than species with an adult activityperiod in May to July. Our results remained qualitatively robust in additional analyses,after controlling for phylogeny and including all species recorded on the island, exceptfor the trait ‘length of flight period’.4. Our results highlight the importance of the relation between mobility and speciestraits. Noctuid moths with certain traits move over longer distances than earlier known.This finding is important to include when predicting range dynamics in fragmentedand changing landscapes, and when conservation measures of species are devised.
45.	De Chiara, Matteo, et al. (author) Domestication reprogrammed the budding yeast life cycle 2022 In: Nature Ecology & Evolution. - : Springer Science and Business Media LLC. - 2397-334X .- 2397-334X. ; 6 Journal article (peer-reviewed)abstract Domestication of plants and animals is the foundation for feeding the world human population but can profoundly alter the biology of the domesticated species. Here we investigated the effect of domestication on one of our prime model organisms, the yeast Saccharomyces cerevisiae, at a species-wide level. We tracked the capacity for sexual and asexual reproduction and the chronological life span across a global collection of 1,011 genome-sequenced yeast isolates and found a remarkable dichotomy between domesticated and wild strains. Domestication had systematically enhanced fermentative and reduced respiratory asexual growth, altered the tolerance to many stresses and abolished or impaired the sexual life cycle. The chronological life span remained largely unaffected by domestication and was instead dictated by clade-specific evolution. We traced the genetic origins of the yeast domestication syndrome using genome-wide association analysis and genetic engineering and disclosed causative effects of aneuploidy, gene presence/absence variations, copy number variations and single-nucleotide polymorphisms. Overall, we propose domestication to be the most dramatic event in budding yeast evolution, raising questions about how much domestication has distorted our understanding of the natural biology of this key model species.
46.	Gross, Elisabeth, et al. (author) Allelochemical interactions among aquatic primary producers 2012. - 1 In: Chemical Ecology in Aquatic Systems. - Oxford : Oxford University Press. - 9780199583102 ; , s. 196-209 Book chapter (peer-reviewed)abstract Allelopathy is the study of biochemically-driven organismic interactions among primary producers. One organism affects others by the release of allelochemicals that are transported to the target cells, and cause a negative (or positive) response. Most aquatic allelochemicals are amphiphilic, thus have a sufficient solubility in the water, and at the same time can bind to and penetrate lipophilic cell membranes. Allelopathic interactions are not static but are influenced by variable environmental stressors. Resource availability can both affect the production and release of allelochemicals by the producing organism, but also influence the susceptibility of the target cells. The biosynthesis and excretion of allelochemicals might involve costs for the producing organism, and these costs will only be balanced if a net gain, i.e. better resource availability such as space or nutrients or secondary benefits, e.g. predator deterrence, are achieved. Allelopathic effects against cooccurring organisms might lead to coevolutionary responses, i.e. a lower susceptibility of target cells or to more advanced allelochemicals. Target organisms from different habitats might be more susceptible, especially if they are not acquainted with the allelochemicals. The transfer of laboratory results on allelopathy to realistic field conditions is complex, and might in the long run benefit from advanced analytical and molecular methods identifying specific target cell responses in situ.
47.	Karpestam, Einat, et al. (author) Matching habitat choice by experimentally mismatched phenotypes 2012 In: Evolutionary Ecology. - : Springer Science and Business Media LLC. - 0269-7653 .- 1573-8477. ; 26:4, s. 893-907 Journal article (peer-reviewed)abstract Gene flow is often regarded a random process that homogenizes differencesbetween populations and constrains local adaptation. However, the matching habitat choicehypothesis posits that individuals actively choose those microhabitats that best match theirspecific phenotype to maximize fitness. Dispersal (and possibly gene flow) may thus bedirected. Many studies report associations between habitats and phenotypes, but they mayreflect selection, plasticity or adaptation rather than matching choice. Here, we test twopredictions from the matching habitat choice hypothesis by manipulating the dorsal colourof Tetrix subulata, a pygmy grasshopper. (1) Is microhabitat choice flexible such thatdifferently manipulated phenotypes distribute themselves differently in a microclimaticand solar radiation mosaic? (2) If they do, are their fitness prospects higher in the morepreferred microhabitat? We find that individuals painted white or black do distributethemselves differently, with black individuals residing in habitats with less radiation, onaverage, than white individuals, demonstrating that microhabitat choices are plastic. Furthermore,white females had more hatchlings than black ones in the increased radiationtreatment, and this was mainly due to increased mortality of black females under increasedradiation. These findings provide rare experimental evidence in line with predictions fromthe matching habitat choice hypothesis.
48.	Lehtonen, Topi K., et al. (author) Adjustment of brood care behaviour in the absence of a mate in two species of Nicaraguan crater lake cichlids 2011 In: Behavioral Ecology and Sociobiology. - : Springer Science and Business Media LLC. - 0340-5443 .- 1432-0762. ; 65:4, s. 613-619 Journal article (peer-reviewed)abstract In many taxa, parental strategies can vary among individuals. This is especially true in species with biparental care, with males, more often than females, deserting their mates. While there is an abundance of theoretical predictions and empirical data on factors inducing mate abandonment by males, much less is known about what consequences this may have on female behaviour, particularly in the field and in non-avian systems. Here, we compared brood defence rate, behavioural defence types, and brood success of solitary and paired females in two species of Neotropical cichlid fish in their natural habitat. In terms of the rate of territorial aggression towards potential brood predators, solitary females were able to fully compensate in the absence of a male but, in so doing, ended up maintaining smaller territories, which appeared to compromise offspring fitness in at least one of the two species. Hence, our results suggest that even extensive quantitative compensation in parental effort by solitary females may not be enough to ensure adequate qualitative compensation for the lack of male participation, highlighting the importance of distinguishing between these two aspects of compensatory parental care.
49.	Liu, B. Y., et al. (author) Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family 2017 In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 7:16, s. 6346-6357 Journal article (peer-reviewed)abstract Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino-Himalayan Mountains or these mountains and Central Asia-Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid-Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo-/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacialperiods, followed by fragmentation during interglacials-contrary to the usual view that glacial periods resulted mainly in fragmentations.
50.	Watz, Johan, 1977-, et al. (author) Egg production in Arion vulgaris: density dependence in A. vulgaris and interspecific effects of Limax maximus 2022 In: Journal of molluscan studies. - Oxford : Oxford University Press. - 0260-1230 .- 1464-3766. ; 88:3, s. 1-3 Journal article (peer-reviewed)

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