Mika Bendiksby

• Möller, Erik Johan; Timdal, Einar; Haugan, Reidar & Bendiksby, Mika (2025). Integrative taxonomy and genus delimitation in the Rhizocarpaceae (lichenized Ascomycota). Fungal Systematics and Evolution. 16(1), s. 215–232. doi: 10.3114/fuse.2025.16.12. Fulltekst i vitenarkiv Vis sammendrag

  The Rhizocarpaceae , a family of lichenized fungi within the Ascomycota , comprises approximately 160 species within five genera: Catolechia , Epilichen , Haugania , Poeltinula , and Rhizocarpon . Rhizocarpon is the most species-rich, with about 150 species predominantly inhabiting siliceous rock in boreal and arctic-alpine environments. Molecular phylogenetic studies have revealed that current taxonomy, heavily reliant on morphology, chemistry, and life strategies, renders Rhizocarpon paraphyletic. This study aims to elucidate the phylogenetic relationships and clarify genus delimitation within the Rhizocarpaceae using an integrative taxonomic approach that combines three genetic markers and a diversity of taxa covering the morphological, chemical, and ecological spectrum of the family. Our comprehensive sampling includes 50 species across the Rhizocarpaceae collected from diverse geographical locations and ecological settings. Our phylogenetic hypothesis is based on a concatenated dataset of two nuclear (ITS and MCM7) and one mitochondrial (mtSSU) genetic marker. Ascospore characteristics and thallus pigmentation alongside secondary metabolite profiles were mapped onto this DNA-based evolutionary framework. Our results underscore significant refinements in the classification of the Rhizocarpaceae , highlighting the inadequacy of traditional taxonomic markers alone to infer robust phylogenetic affiliations. We advocate for new circumscriptions of Catolechia , Poeltinula , and Rhizocarpon based on the molecular phylogeny and propose synonymizing Epilichen with Catolechia , the transfer of the species in the R. hochstetteri complex to Poeltinula , and the resurrection of Rehmia . We hence propose 24 new combinations and three typifications. Collectively, this study sets the groundwork for future research and stability in the systematics of the Rhizocarpaceae , augmenting our understanding of their diversity and evolutionary dynamics.

• Ballesteros, Jesus Adrian Chimal; Bendiksby, Mika; Carlsen, Tor & Bjorå, Charlotte Sletten (2025). Shedding light on the Chlorophytum comosum complex through phylogenomics and species distribution modeling. Taxon. ISSN 0040-0262. doi: 10.1002/tax.70072. Fulltekst i vitenarkiv Vis sammendrag

  The taxonomic circumscription of Chlorophytum comosum has been challenged throughout the decades. This name has become an umbrella term for several different genetic lineages. Here we utilize two synergistic approaches to characterize the evolutionary significant units of the C. comosum species complex. These approaches include the first usage in Chlorophytum taxonomy of: (1) target capture and phylogenomics, and (2) species distribution models as a proxy for abiotic niche composition and distribution. Our results identify three genetic lineages within the C. comosum species complex, three distinct environment preferences in three populations, and three semi‐isolated distributions. One lineage distributed in southern Africa displays a clear genetic, niche and distribution independence. As the type specimen was collected by Thunberg on his expedition to South Africa in the 1770s, it is this genetic lineage that should hold the name C. comosum . The other two genetic lineages are found in eastern Africa and are geographically distinct as a Tanzanian lineage and a Ugandan/Ethiopian lineage. As such, we provide evidence that Eastern Africa species previously sunk into C. comosum deserve the rank of species reinstated. The following three other names are suggested reinstated herein: C. miserum (Uganda, Ethiopia), C. rugosum (Tanzanian lineage) and C. kirkii , which represent the East African lineage, a high‐altitude taxon in East Africa, and an East African coastal taxon that does not fit the current description of C. comosum , respectively.

• Kirkhus, Mika Helene; Frisch, Andreas; Evankow, Ann; Blaalid, Rakel; Zane, Rafaelle & Bendiksby, Mika [Vis alle 7 forfattere av denne artikkelen] (2025). Diversity of tremellalean Pertusaria-associated fungi in Norway and the role of secondary metabolites in host specificity. Fungal Biology. ISSN 1878-6146. 129(3), s. 1–12. doi: 10.1016/j.funbio.2025.101563. Fulltekst i vitenarkiv Vis sammendrag

  The diversity and host relationships of lichen-inhabiting tremellalean fungi remain understudied, partly due to their asymptomatic yeast phase. This study employs ITS2 metabarcoding to investigate the diversity and colonization patterns of these fungi within 13 Pertusaria lichen species collected in Norway. We discovered a high prevalence, with tremellalean fungi present in 57% of the examined specimens, representing 12 of the 13 species included, 10 of which were not previously recognized as hosts. Our findings suggest a broad host range for the presumed yeast phase of these fungi, though occurrences of the five most frequent OTUs appeared non-random across different host species. Additionally, negative-binomial general linear models indicated a negative correlation between the presence of tremellalean fungi and the occurrence of specific secondary metabolites, such as thiophaninic acid, fumarprotocetraric acid, and gyrophoric acid, in Pertusaria hosts. These results highlight previously undocumented genetic diversity within tremellalean fungi and suggest that host chemotype significantly influences colonization patterns. Our findings demonstrate a higher frequency of asymptomatic colonization than previously reported, emphasizing the need for further research into their ecological roles and interactions.

• Timdal, Einar; Möller, Erik Johan & Bendiksby, Mika (2024). Rhizocarpon vulgare, a new species in the R. badioatrum species complex. Graphis Scripta. ISSN 0901-7593. 36(4), s. 89–105. Fulltekst i vitenarkiv Vis sammendrag

  Herein, we revise the Rhizocarpon badioatrum species complex in the Nordic countries using molecular phylogenetics combined with morphological/anatomical and chemical data. Bayesian and Maximum Likelihood phylogenetic analyses of the nuclear ribosomal internal transcribed spacer (ITS, the fungal DNA barcode) reveals four strongly supported clades within the R. badioatrum species complex. Based on our assessment of the multiple sources of data included, we recognize R. badioatrum var. badioatrum and var. vulgare at the species level and describe the latter as the new species R. vulgare. Rhizocarpon vulgare receives support also from a phylogeny based on mitochondrial ribosomal small subunit (mtSSU). Rhizocarpon cinereonigrum is the phylogenetic sister species of R. vulgare in both the ITS and mtSSU trees. Rhizocarpon sinense is reported as new to Europe with specimens collected from Iceland and Norway. The secondary chemistry is shown to be largely diagnostic for the species: R. badioatrum is usually acid deficient, R. vulgare contains diffractaic acid, and R. sinense contains gyrophoric acid. However, the concept of R. cinereonigrum, which was previously based on the presence of stictic acid, is shown to be ambiguous because that compound may also occur in R. badioatrum. Lectotypes are designated for Lecidea atrobadia, Rhizocarpon badioatrum, R. rivulare, R. sinense.

• Tomlin, Crystal; Rajaraman, Sitaram; Sebesta, Jeanne Theresa; Scheen, Anne-Cathrine; Bendiksby, Mika & Low, Yee Wen [Vis alle 10 forfattere av denne artikkelen] (2024). Allopolyploid origin and diversification of the Hawaiian endemic mints. Nature Communications. 15(1), s. 1–17. doi: 10.1038/s41467-024-47247-y. Fulltekst i vitenarkiv Vis sammendrag

  Abstract Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides , and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai’i. The three distinct Hawaiian genera, Haplostachys , Phyllostegia , and Stenogyne , are nested inside a fourth genus, Stachys . We uncovered four independent polyploidy events within Stachys , including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin’s thinking about the evolutionary process.

• Nygård, Malene Østreng; Kopatz, Alexander; Speed, James David Mervyn; Martin, Michael David; Prestø, Tommy & Kleven, Oddmund [Vis alle 7 forfattere av denne artikkelen] (2023). SNP genotyping and environmental niche modelling using herbarium specimens of the northern dragonhead, Dracocephalum ruyschiana (Lamiaceae). Bauhinia. ISSN 0067-4605. 29, s. 127–128. doi: 10.12685/bauhinia.1375. Fulltekst i vitenarkiv
• Matten, Damaris Marina; Mienna, Ida Marielle; Bieker, Vanessa Carina; Mishler, Brent D.; Moen, Victoria Stornes & Nygård, Malene Østreng [Vis alle 10 forfattere av denne artikkelen] (2023). Spatial patterns of phylogenetic and species diversity of fennoscandian vascular plants in protected areas. Biodiversity and Conservation. ISSN 0960-3115. 32, s. 4425–4443. doi: 10.1007/s10531-023-02705-9. Fulltekst i vitenarkiv Vis sammendrag

  Protected areas are one of the main strategic means for conserving biodiversity. Yet, the design of protected areas usually neglects phylogenetic diversity, an important diversity measure. In this paper we assess the phylogenetic diversity and species richness of vascular plants in Fennoscandian protected areas. We evaluate how much species richness and phylogenetic diversity is found within and outside protected areas, and the differences in plant diversity between different categories of protected areas. We also assess the differences in the diversity-area relationship of the different protected area categories in terms of both species richness and phylogenetic diversity. We build a multi-locus phylogeny of 1,519 native vascular plants of Norway, Sweden, and Finland. We estimate the phylogenetic diversity and species richness by combining the phylogeny with publicly available occurrence data and the currently protected area system of Fennoscandia. Our results indicate that protected areas in Fennoscandia hold more plant diversity when larger, and that phylogenetic diversity increases faster with area than species richness. We found evidence for more plant diversity outside of protected areas of the different countries of Fennoscandia than inside of protected areas, but no evidence for plant diversity differences between areas with different protection status. Hence, our results indicate that the current protected area system in Fennoscandia is no more effective in conserving phylogenetic diversity and species richness of vascular plants than a random selection of localities. Our results also indicate that planning conservation strategies around phylogenetic diversity, rather than species richness, might be a first step to protect vascular plant diversity more effectively. Biodiversity · Spatial phylogenetics · Conservation · Diversity-area relationship · Flora

• Fjelde, Markus Osaland; Timdal, Einar; Haugan, Reidar & Bendiksby, Mika (2023). Paraphyly and cryptic diversity unveils unexpected challenges in the “naked lichens” (Calvitimela, Lecanoromycetes, Ascomycota). Molecular Phylogenetics and Evolution. ISSN 1055-7903. 190. doi: 10.1016/j.ympev.2023.107944. Fulltekst i vitenarkiv Vis sammendrag

  Molecular phylogenetics has revolutionized the taxonomy of crustose lichens and revealed an extensive amount of cryptic diversity. Resolving the relationships between genera in the crustose lichen family Tephromelataceae has proven difficult and the taxon limits within the genus Calvitimela are only partly understood. In this study, we tested the monophyly of Calvitimela and investigated phylogenetic relationships at different taxonomic levels using an integrative taxonomic approach. We performed a global sampling of all species currently assigned to Calvitimela and conducted additional sampling of C. melaleuca sensu lato across Norway. We included 108 specimens and produced more than 300 sequences from five different loci (ITS, LSU, MCM7, mtSSU, TEF1-α). We inferred phylogenetic relationships and estimated divergence times in Calvitimela. Moreover, we analyzed chemical and morphological characters to test their diagnostic values in the genus. Our molecular phylogenetic results show evolutionarily old and deeply divergent lineages in Calvitimela. The morphological characters are overlapping between divergent subgenera within this genus. Chemical characters, however, are largely informative at the level of subgenera, but are often homoplastic at the species level. The subgenus Calvitimela is found to include four distinct genetic lineages. Detailed morphological examinations of C. melaleuca s. lat. reveal differences between taxa previously assumed to be morphologically cryptic. Furthermore, young evolutionary ages and signs of gene tree discordance indicate a recent divergence and possibly incomplete lineage sorting in the subgenus Calvitimela. Phylogenetic analysis and morphological observations revealed that C. austrochilensis and C. uniseptata are extraneous to Calvitimela (Tephromelataceae). We also found molecular evidence supporting C. septentrionalis being sister to C. cuprea. In the subgenus Severidea, one new grouping is recovered as a highly supported sister to C. aglaea. Lastly, two fertile specimens were found to be phylogenetically nested within the sorediate species C. cuprea. We discuss the need for an updated classification of Calvitimela and the evolution of cryptic species. Through generic circumscription and species delimitation we propose a practical taxonomy of Calvitimela.

• Bendiksby, Mika; Thorbek, Birgitte Lisbeth Graae; Bjorå, Charlotte Sletten & Halvorsen, Rune (2023). Improving procedures for obtaining Sanger sequences from old herbarium specimens. Bauhinia. ISSN 0067-4605. doi: 10.12685/bauhinia.1352. Fulltekst i vitenarkiv Vis sammendrag

  Because DNA degrades over time, extracting DNA of sufficient quality for sequencing is presumed to be more difficult from older than younger herbarium specimens. Although massive parallel sequencing techniques have clear advantages when it comes to sequencing ancient DNA, Sanger sequencing is still in frequent use, prompting us to test and improve its application on herbarium specimens. During molecular phylogenetic investigations of the subfamily Lamioideae (Lamiaceae) and subgroups, we extracted DNA from 651 herbarium specimens collected between 1826 and 2006 using regular mini-prep methods. The aim was to obtain DNA of sufficient quality for Sanger sequencing of various plastid and nuclear genetic markers. Here, we report successful Sanger sequencing of the commonly used plastid marker, rps16, as a conservative measure of DNA quality, and logistic regression to investigate the relationship between age of the material and DNA quality. Our result indicates that the upper age limit for obtaining DNA suitable for Sanger sequencing from herbarium specimens using regular mini-prep DNA extraction methods has not been reached. After simple modifications to the regular DNA mini-prep and PCR procedures, at least one genetic marker was successfully sequenced for about 90 % of the specimens tested, the oldest being 168 years old. Jointly, despite the technique's drawbacks, these results demonstrate a high success rate of Sanger sequencing of herbarium specimens.

• Bjorå, Charlotte Sletten; Bendiksby, Mika; Johannessen, Lars Erik; Løfall, Bjørn Petter & Timdal, Einar (2023). Collections of Arctic Plants, Lichens, and Fungi in the Natural History Museum, University of Oslo, Norway. Collections: A Journal for Museum and Archives Professionals. ISSN 1550-1906. 19(3). doi: 10.1177/15501906231171737. Fulltekst i vitenarkiv Vis sammendrag

  The Arctic has been, and is, an area of focus for the botanical and fungal (lichenized fungi included) collections at the Natural History Museum of Oslo. These collections house more than 233,000 unique Arctic specimens, the oldest dating back more than two centuries. The vascular plants account for 63 percent, lichens 30 percent, and fungi 7 percent. The Arctic collections have a circumpolar representation with emphasis on mainland Norway (48 percent) and Svalbard (13 percent), followed by Arctic America (10 percent), Greenland (9 percent), and Arctic Russia (8 percent). The Oslo herbarium and fungarium house collections from important polar expeditions like Fram-2, Gjøa, and Maud, but also of many expeditions where collecting biological specimens was the main purpose. The number of new collections was highest in the decades 1930 to 1939 and 2000 to 2009 with each around 35,000 new specimens. In the 1990s, a DNA Bank was established for DNA extracts and tissue samples, and it houses today 22,879 Arctic accessions of fungi, lichens, and plants. In times of climatic change and a tense geopolitical situation, the herbarium and fungarium at NHM-Oslo represent an invaluable source for biological information about the Arctic. We welcome the use of our collections for research-, nature management-, and teaching purposes.

• Petersen, Tanja Kofod; Vuorinen, Katariina Elsa M; Bendiksby, Mika & Speed, James David Mervyn (2022). Climate and land-use drive the functional composition of vascular plant assemblages across Norway. Nordic Journal of Botany (NJB). ISSN 0107-055X. 2022(7). doi: 10.1111/njb.03470. Fulltekst i vitenarkiv Vis sammendrag

  Traditionally, biogeography has described the distribution of species. But as plant functional traits and functional diversity underpin ecosystem dynamics, understanding drivers of functional diversity at biogeographical scales is essential to understand spatial variation in ecosystem characteristics, particularly in light of ongoing environmental changes. Here we investigate geographic patterns of functional diversity and -traits of the Norwegian flora. We explore whether climate, land-use or glacial history are important drivers of functional diversity. We combine species occurrence records and assemblage-means of functional traits to assess the spatial distribution of functional traits and -diversity of native vascular plants in Norway in a 20 × 20 km grid. We use multiple-model inference to identify which environmental factors contribute the most in explaining the spatial patterns of trait distributions and functional diversity. Additionally, we use the constructed models to predict potential changes in distributions of traits and functional diversity given different climate change scenarios. Both individual traits and functional diversity display clear geographic patterns, predictable by climate, landscape and glacial history. Traits related to plant size and growth peak in warmer areas and are predicted to increase in the future, as is functional richness and dispersion. In contrast, functional evenness peaks in northern regions and is predicted to decrease in the future. The different environmental drivers vary in degree of importance, effect sizes and -directions on the assemblage-averaged functional traits and -diversity. This underlines the importance of multiple drivers in determining plant assemblage functionality. In the face of climate- and land-use change, Norway is expected to become warmer, wetter and experience a substantial increase in anthropogenic land-uses, such as increased urbanisation. In turn, the functional composition of the Norwegian flora is predicted to shift towards tall, woody, fast-growing species.

• Frisch, Andreas; Ohmura, Yoshihito; Holien, Håkon & Bendiksby, Mika (2022). A phylogenetic survey of the ascomycete genus Arthrorhaphis (Arthrorhaphidaceae, Lecanoromycetes) including new species in Arthrorhaphis citrinella sensu lato. Taxon. ISSN 0040-0262. 71(5), s. 936–962. doi: 10.1002/tax.12718. Fulltekst i vitenarkiv Vis sammendrag

  The genus Arthrorhaphis is a group of ascomycetes comprising lichenised and non-lichenised taxa from temperate to arctic-alpine regions in both hemispheres. Nine species and two infraspecific taxa are currently recognised. Their delimitation, inter-relationships, and phylogenetic placement remain poorly understood. We have used an integrative taxonomic approach to assess taxon limits, phylogenetic placement of the family, and to test the hypothesis that transition to lichenisation has happened only once. We present a first molecular phylogenetic hypothesis of all but one known Arthrorhaphis species based on Bayesian inference and maximum likelihood analyses of multilocus DNA sequence data. Our results support monophyly of Arthrorhaphis, phylogenetic placement in the Ostropomycetidae, and lichenisation having evolved from lichenicolous ancestors only once. The lichenicolous Arthrorhaphis species are well-defined both morphologically and genetically. The lichenised A. alpina s.l. and A. citrinella s.l., however, include multiple genetic clades that are partly supported by phenotypic data. We split A. citrinella s.l. into the following five species: (1) A. bullata sp. nov., (2) A. catolechioides comb. & stat. nov., (3) A. citrinella, (4) A. farinosa sp. nov., and (5) A. vulgaris comb. & stat. nov. A sixth phylogenetic clade from the Neotropics remains undescribed herein due to insufficient data. Five circumarctic accessions of A. alpina s.l. form a genetically distinct but morphologically poorly understood clade sister to the alpina-vacillans clade, which we preliminarily name “A. septentrionalis”. Jointly, our multispecies coalescence analyses, of both single-locus (bGMYC) and multilocus (bPtP, bP&P) datasets, largely support our proposed species hypotheses in Arthrorhaphis.

• Frisch, Andreas; Holien, Håkon; Klepsland, Jon T.; Suija, Ave & Bendiksby, Mika (2022). New data on lichenicolous fungi in Norway. Graphis Scripta. ISSN 0901-7593. 34(7), s. 59–133. Fulltekst i vitenarkiv
• Nygaard, Malene; Kopatz, Alexander; Speed, James David Mervyn; Martin, Michael David; Prestø, Tommy & Kleven, Oddmund [Vis alle 7 forfattere av denne artikkelen] (2022). Spatiotemporal monitoring of the rare northern dragonhead (Dracocephalum ruyschiana, Lamiaceae) — SNP genotyping and environmental niche modeling herbarium specimens. Ecology and Evolution. 12(8). doi: 10.1002/ece3.9187. Fulltekst i vitenarkiv Vis sammendrag

  The species we have studied the spatiotemporal genetic change in the northern dragonhead, a plant species that has experienced a drastic population decline and habitat loss in Europe. We have added a temporal perspective to the monitoring of northern dragonhead in Norway by genotyping herbarium specimens up to 200 years old. We have also assessed whether northern dragonhead has achieved its potential distribution in Norway. To obtain the genotype data from 130 herbarium specimens collected from 1820 to 2008, mainly from Norway (83) but also beyond (47), we applied a microfluidic array consisting of 96 SNP markers. To assess temporal genetic change, we compared our new genotype data with existing data from modern samples. We used sample metadata and observational records to model the species' environmental niche and potential distribution in Norway. Our results show that the SNP array successfully genotyped all included herbarium specimens. Hence, with the appropriate design procedures, the SNP array technology appears highly promising for genotyping old herbarium specimens. The captured genetic diversity correlates negatively with distance from Norway. The historical-modern comparisons reveal similar genetic structure and diversity across space and limited genetic change through time in Norway, providing no signs of any regional bottleneck (i.e., spatiotemporal stasis). The regional areas in Norway have remained genetically divergent, however, both from each other and more so from populations outside of Norway, rendering continued protection of the species in Norway relevant. The ENM results suggest that northern dragonhead has not fully achieved its potential distribution in Norway and corroborate that the species is anchored in warmer and drier habitats.

• Zhao, Fei; Chen, Ya-Ping; Salmaki, Yasaman; Drew, Bryan T.; Wilson, Trevor C. & Scheen, Anne-Cathrine [Vis alle 15 forfattere av denne artikkelen] (2021). An updated tribal classification of Lamiaceae based on plastome phylogenomics. BMC Biology. 19(2). doi: 10.1186/s12915-020-00931-z. Fulltekst i vitenarkiv Vis sammendrag

  Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification.

• Nygård, Malene Østreng; Kemppainen, Petri; Speed, James D. M.; Elven, Reidar; Flatberg, Kjell Ivar & Galten, Leif Persen [Vis alle 9 forfattere av denne artikkelen] (2021). Combining population genomics and ecological niche modeling to assess taxon limits between Carex jemtlandica and C. lepidocarpa. Journal of Systematics and Evolution. ISSN 1674-4918. 59(4), s. 627–641. doi: 10.1111/jse.12743. Fulltekst i vitenarkiv Vis sammendrag

  Carex section Ceratocystis (Cyperaceae) is a group of recently evolved plant species, in which hybridization is frequent, introgression is documented, taxonomy is complex, and morphological boundaries are vague. Within this section, a unified taxonomic treatment of the Carex jemtlandica–Carex lepidocarpa species complex does not exist, and Norway may currently be the sole country accepting species rank for both. Carex jemtlandica is mainly confined to Fennoscandia and is thus a Fennoscandian conservation responsibility. This motivated us to test the principal hypothesis that both C. jemtlandica and C. lepidocarpa represent evolutionary significant units, and that both deserve their current recognition at species level. We investigated their evolutionary distinctiveness in Norway, using restriction site-associated DNA sequencing and ecological niche modeling. Our genomic results reveal two genetic clusters, largely corresponding to C. jemtlandica and C. lepidocarpa that also remain distinct in sympatry, despite clear indications of ongoing hybridization and introgression. The ecological niche modeling suggests that they occupy different environmental niches. Jointly, our results clearly show that C. jemtlandica and C. lepidocarpa represent separately evolving entities that should qualify recognition as evolutionary significant units. Given the high level of introgression compared to other hybridizing species pairs in Carex we recommend treating C. jemtlandica as a subspecies of C. lepidocarpa.

• Grant, Danielle; Brodnicke, Ole Bjørn; Evankow, Ann; Ferreira, André O.; Fontes, João T. & Hansen, Aslak Kappel [Vis alle 21 forfattere av denne artikkelen] (2021). The Future of DNA Barcoding: Reflections from Early Career Researchers. Diversity. 13(7). doi: 10.3390/d13070313. Fulltekst i vitenarkiv Vis sammendrag

  Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions

• Crous, Pedro W.; Lombard, L.; Sandoval-Denis, M; Seifert, K.A; Schroers, H.-J & Chavern, P [Vis alle 50 forfattere av denne artikkelen] (2021). Fusarium: more than a node or a foot-shaped basal cell. Studies in Mycology. ISSN 0166-0616. 98(4). doi: 10.1016/j.simyco.2021.100116. Fulltekst i vitenarkiv Vis sammendrag

  Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).

• Speed, James David Mervyn; Austrheim, Gunnar; Bendiksby, Mika; Kolstad, Anders Lorentzen & Vuorinen, Katariina (2020). Increasing Cervidae populations have variable impacts on habitat suitability for threatened forest plant and lichen species. Forest Ecology and Management. ISSN 0378-1127. 473. doi: 10.1016/j.foreco.2020.118286. Fulltekst i vitenarkiv Vis sammendrag

  Large herbivores play a key role in temperate and boreal forest ecosystems. Cervidae (deer) population densities and community structure have undergone drastic changes in many parts of the world over the past decades, often with deer populations increasing. Many studies show impacts of Cervidae on multiple ecosystem properties, including vegetation and biodiversity, at local spatial scales. At larger spatial scales, however, impacts of changing Cervidae populations on forest ecosystems are less known. Although both abiotic and biotic dimensions contribute to shaping species’ niches, abiotic variables are generally given prominence when modelling species habitats and ranges. This is despite biotic changes, including changes in trophic structure, being an important component of global environmental change. In this study, we examined the potential contribution of Cervidae densities to the habitat suitability for rare plant and lichen species across the temperate and boreal forests of Norway, where cervid densities have increased over the past 60 years. We also examined how these changes in herbivore communities may have shaped habitat suitability for rare lichens and plants and discuss the results in light of continuing shifts in herbivore assemblages. We ran habitat suitability models for 47 species of rare plants and lichens, which were selected based on herbivory reported as a criterion for placement on the national red list for species. Climate (temperature and precipitation), forest (forest type and productivity), soil pH and Cervidae densities (moose Alces alces, red deer Cervus elaphus and roe deer Capreolus capreolus) were used as independent variables. Densities of one or more of the three Cervidae species were inferred to be associated with the distribution of 14 (ten lichen, one bryophyte and three vascular plant species) of these 47 species. We found a range of habitat suitability associations with Cervidae densities, including positive, negative and hump-backed responses. Increases in Cervidae densities over the past 60 years may have led to different spatial trends in habitat suitability across the 14 species. Our results suggest that Cervidae densities are associated with the distribution of rare forest plant and lichen species differently at large spatial scales; experimental studies should test the causality of these associations. If causal, this implies that Cervidae management should find a balance between high and low densities to conserve several plant and lichen species. The preponderance of epiphytic lichens species, for which habitat suitability was associated with Cervidae densities, calls for field studies to focus on Cervidae impacts on forest lichens.

• Timdal, Einar; Westberg, Martin; Haugan, Reidar; Hofton, Tom Hellik; Holien, Håkon & Speed, James David Mervyn [Vis alle 8 forfattere av denne artikkelen] (2020). Integrative taxonomy reveals a new species, Nephroma orvoi, in the N. parile species complex (lichenized Ascomycota). Graphis Scripta. ISSN 0901-7593. 32(4), s. 70–85. Fulltekst i vitenarkiv Vis sammendrag

  Our knowledge of the diversity and distribution of many groups of lichens remains poor due to unclear species boundaries and challenging species identification. We have studied the medium sized to large foliose lichen Nephroma parile, which is known to be heterogeneous in chemistry and genetics. Our aim has been to assess the potential presence of evolutionary significant units within the Nephroma parile species complex that may be worthy of recognition at species level. Using phylogenetic analysis of the fungal DNA-barcode marker (ITS) in combination with studies of morphology and chemistry, we discover two distinct lineages in the N. parile species complex. For the strongly supported clade that corresponds to chemotype II, we describe the new species Nephroma orvoi. The new species is known from Norway, Sweden, Finland, Switzerland, Canada (Alberta and British Columbia), USA (Washington), and Greenland.

• Kistenich, Sonja Daniela; Bendiksby, Mika; Weerakoon, Gothamie & Timdal, Einar (2020). A revision of the genus Aciculopsora (Ramalinaceae) with the description of one new species and one new combination. Plant and Fungal Systematics. ISSN 2544-7459. 65(1), s. 200–209. doi: 10.35535/pfsyst-2020-0015. Fulltekst i vitenarkiv Vis sammendrag

  The tropical lichen genus Aciculopsora is still very poorly collected. Only eleven collections are known worldwide. We present a molecular phylogenetic tree based on mtSSU and nrITS sequence data from six Aciculopsora specimens. Our results corroborate the monophyly of the genus. We conclude that Aciculopsora consists of three species: A. cinerea, A. longispora comb. nov. (≡ Phyllopsora longispora, = A. salmonea syn. nov.) and A. srilankensis sp. nov. Aciculopsora cinerea occurs in Brazil, A. longispora in Argentina, Costa Rica, Ecuador, and Kenya, and A. srilankensis in Sri Lanka. As such, the genus is new for the Paleotropics, Argentina and Ecuador.

• Frisch, Andreas; Moen, Victoria Stornes; Grube, Martin & Bendiksby, Mika (2020). Integrative taxonomy confirms three species of Coniocarpon (Arthoniaceae) in Norway. MycoKeys. ISSN 1314-4057. 62, s. 27–51. doi: 10.3897/mycokeys.62.48480. Fulltekst i vitenarkiv
• Frisch, Andreas; Klepsland, Jon T; Palice, Zdenek; Bendiksby, Mika; Tønsberg, Tor & Holien, Håkon (2020). New and noteworthy lichens and lichenicolous fungi from Norway. Graphis Scripta. ISSN 0901-7593. 32(1), s. 1–47. Fulltekst i vitenarkiv Vis sammendrag

  Twelve species of lichens and lichenicolous fungi are reported as new to Fennoscandia. Additionally, we report 19 species as new to Norway. New localites are given for 47 rare or seldom collected species. The new combination Reichlingia anombrophila (Coppins & P. James) Frisch is proposed. Most collections were made in the boreo-nemoral and boreal rainforests during the NBIC funded project Three storied diversity – mapping and barcoding crustose lichens and lichenicolous fungi in the Norwegian rainforests and associated fieldwork in recent years. With the present contribution, we hope to raise awareness on previously neglected groups of lichenised and lichenicolous fungi and encourage further fieldwork in understudied habitats in Norway.

• Kistenich, Sonja Daniela; Bendiksby, Mika; Ekman, Stefan; Caceres, MES; Hernández, Jesus E. & Timdal, Einar (2019). Towards an integrative taxonomy of Phyllopsora (Ramalinaceae). The Lichenologist. ISSN 0024-2829. 51(4), s. 323–392. doi: 10.1017/S0024282919000252. Fulltekst i vitenarkiv
• Kistenich, Sonja; Halvorsen, Rune; Schrøder-Nielsen, Audun; Thorbek, Birgitte Lisbeth Graae; Timdal, Einar & Bendiksby, Mika (2019). DNA Sequencing Historical Lichen Specimens. Frontiers in Ecology and Evolution. 7. doi: 10.3389/fevo.2019.00005. Fulltekst i vitenarkiv Vis sammendrag

  Biological specimens in natural history collections worldwide are increasingly being used in biogeographical, environmental, and taxonomic studies. For their meaningful use, correct species identification is crucial. For example, clarifying if a species is new to science requires an overview of what has already been described. This includes comparisons with existing authoritative specimens (types). Most type specimens are rather old and their DNA expected to be degraded to various extents. Comparative DNA sequence analysis is in regular use in taxonomic research of today and is essential for identifying and delimiting species. In this study, we focus on lichenized fungi (lichens), in which many species groups are highly inconspicuous and impossible to identify to species based on morphology alone. Our aim was to test the non-mutually exclusive hypotheses that DNA quality of lichens depends on (1) time since collection, (2) taxonomic affinity, and/or (3) habitat/ecology. We included two species from each of four different lichen genera (i.e., Cladonia, Nephroma, Peltigera, and Ramalina), each species pair with a different autecology. For each species, we included samples from approximately every 25 years from present to about 150 years back in time. We used a two-step PCR-based approach followed by sequencing on an Ion Torrent PGM to produce target sequences (mtSSU) of degraded DNA. We received satisfactory DNA sequence information for 54 of 56 specimens. We recovered full-length sequences for several more than 100-years-old specimens, including a 127-years-old specimen, and retrieved enough sequence information for species identification of a 150-years-old specimen. As expected, sequencing success was negatively correlated with age of the specimens. It also varied with taxonomic affinity. We found no significant correlation between sequencing success and habitat ecology of the investigated specimens. The herein tested Ion Torrent sequencing approach outperformed Sanger sequencing with regard to sequencing success and efficiency. We find the protocol used herein highly suitable for obtaining sequences from both young and old lichen specimens and discuss potential improvements to it.

• Kistenich, Sonja Daniela; Ekman, Stefan; Bendiksby, Mika & Timdal, Einar (2019). (2687) Proposal to conserve the name Phyllopsora against Triclinum and Crocynia (Ramalinaceae, lichenized Ascomycota). Taxon. ISSN 0040-0262. 68(3), s. 590–592. doi: 10.1002/tax.12075. Fulltekst i vitenarkiv
• Kistenich, Sonja Daniela; Bendiksby, Mika; Vairappan, Charles S.; Weerakoon, Gothamie; Wijesundara, Siril & Wolseley, Patricia [Vis alle 7 forfattere av denne artikkelen] (2019). A regional study of the genus Phyllopsora (Ramalinaceae) in Asia and Melanesia. MycoKeys. ISSN 1314-4057. 53, s. 23–72. doi: 10.3897/mycokeys.53.33425. Fulltekst i vitenarkiv Vis sammendrag

  Phyllopsora is a crustose to squamulose lichen genus inhabiting the bark of trees in moist tropical forests and rainforests. Species identification is generally challenging and is mainly based on ascospore morphology, thallus morphology and anatomy, vegetative dispersal units, and on secondary chemistry. While regional treatments of the genus have been conducted for Africa, South America and Australia, there exists no study focusing on the Asian and Melanesian species. Previously, 24 species of Phyllopsora s. str. have been reported from major national studies and checklists representing 13 countries. We have studied herbarium material of 625 Phyllopsora specimens from 18 countries using morphology, anatomy, secondary chemistry, and molecular data to investigate the diversity of Phyllopsora species in Asia and Melanesia. We report the occurrence of 28 species of Phyllopsora including the following three species described as new to science: P. sabahana from Malaysia, P. siamensis from Thailand and P. pseudocorallina from Asia and Africa. Eight species are reported as new to Asia. A key to the Asian and Melanesian species of Phyllopsora is provided.

• Mienna, Ida Marielle; Speed, James David Mervyn; Bendiksby, Mika; Thornhill, Andrew H.; Mishler, Brent D. & Martin, Michael David (2019). Differential patterns of floristic phylogenetic diversity across a post-glacial landscape. Journal of Biogeography. ISSN 0305-0270. 47, s. 915–926. doi: 10.1111/jbi.13789. Fulltekst i vitenarkiv Vis sammendrag

  Aim: In this study, we explored spatial patterns of phylogenetic diversity (PD) and end-emism in the flora of Norway and tested hypothesized post-glacial environmental drivers of PD, including temperature, precipitation, edaphic factors and time since glacial retreat.Location: Norway.Taxon: Vascular plants (Trachaeophyta).Methods: We produced a multi-locus maximum-likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and se-quences available from public repositories. We combined the phylogeny with species occurrence data to estimate PD and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model infer-ence to identify environmental variables that contributed the most to the patterns of PD. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history.Results: Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and charac-terized by neo-endemism, while the mild and wet regions were characterized by both paleo- and neo-endemism. PD was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway.Main conclusions: Both contemporary ecological factors (climate and habitat het-erogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper line-ages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.

• Zamora, Juan Carlos; Svensson, Måns; Kirschner, Roland; Olariaga, Ibai; Ryman, Svengunnar & Parra, Luis Alberto [Vis alle 50 forfattere av denne artikkelen] (2018). Considerations and consequences of allowing DNA sequence data as types of fungal taxa. IMA Fungus. ISSN 2210-6340. 9(1), s. 167–175. doi: 10.5598/imafungus.2018.09.01.10. Fulltekst i vitenarkiv Vis sammendrag

  Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

• Bendiksby, Mika; Næsborg, Rikke Reese & Timdal, Einar (2018). Xylopsora canopeorum (Umbilicariaceae), a new lichen species from the canopy of Sequoia sempervirens. MycoKeys. ISSN 1314-4057. 30, s. 1–15. doi: 10.3897/mycokeys.30.22271. Fulltekst i vitenarkiv Vis sammendrag

  Xylopsora canopeorum Timdal, Reese Næsborg & Bendiksby is described as a new species occupying the crowns of large Sequoia sempervirens trees in California, USA. The new species is supported by morphology, anatomy, secondary chemistry and DNA sequence data. While similar in external appearance to X. friesii, it is distinguished by forming smaller, partly coralloid squamules, by the occurrence of soralia and, in some specimens, by the presence of thamnolic acid in addition to friesiic acid in the thallus. Molecular phylogenetic results are based on nuclear (ITS and LSU) as well as mitochondrial (SSU) ribosomal DNA sequence alignments. Phylogenetic hypotheses obtained using Bayesian Inference, Maximum Likelihood and Maximum Parsimony all support X. canopeorum as a distinct evolutionary lineage belonging to the X. caradocensis–X. friesii clade.

• Kistenich, Sonja; Timdal, Einar; Bendiksby, Mika & Ekman, Stefan (2018). Molecular systematics and character evolution in the lichen family Ramalinaceae (Ascomycota: Lecanorales). Taxon. ISSN 0040-0262. 67(5), s. 871–904. doi: 10.12705/675.1. Fulltekst i vitenarkiv Vis sammendrag

  The Ramalinaceae is the fourth‐largest family of lichenized ascomycetes with 42 genera and 913 species exhibiting considerable morphological variation. Historically, generic boundaries in the Ramalinaceae were primarily based on morphological characters. However, molecular systematic investigations of subgroups revealed that current taxonomy is at odds with evolutionary relationships. Tropical members of the family remain particularly understudied, including the large genus Phyllopsora. We have generated and collected multilocus sequence data (mtSSU, nrITS, nrLSU, RPB1, RPB2) for 149 species associated with the Ramalinaceae and present the first comprehensive molecular phylogeny of the family. We used ancestral state reconstructions on our molecular family phylogeny to trace the evolution of character states. Our results indicate that the Ramalinaceae have arisen from an ancestor with long, multiseptate ascospores living in humid temperate forests, and that the phyllopsoroid growth form has evolved multiple times within the family. Based on our results using integrative taxonomy, we discuss sister‐relations and taxon‐delimitation within five well‐supported clades: The Bacidia, Biatora‐, Ramalina‐, Rolfidium‐, and Toninia‐groups. We reduce six genera into synonymy and make 49 new nomenclatural combinations. The genera Bacidia, Phyllopsora, Physcidia and Toninia are polyphyletic and herein split into segregates. We describe the two genera Bellicidia and Parallopsora and resurrect the genera Bibbya, Kiliassia, Sporacestra, and Thalloidima. According to our new circumscription, which also includes some additional changes, the family Ramalinaceae now comprises 39 genera.

• Speed, James David Mervyn; Bendiksby, Mika; Finstad, Anders Gravbrøt; Hassel, Kristian; Kolstad, Anders Lorentzen & Prestø, Tommy (2018). Contrasting spatial, temporal and environmental patterns in observation and specimen based species occurrence data. PLOS ONE. 13(4). doi: 10.1371/journal.pone.0196417. Fulltekst i vitenarkiv Vis sammendrag

  Species occurrence data records the location and time of an encounter with a species, and is valuable for many aspects of ecological and evolutionary analyses. A key distinction within species occurrence data is between (1) collected and preserved specimens that can be taxonomically validated (i.e., natural history collections), and (2) observations, which are more error prone but richer in terms of number and spread of observations. In this study we analyse the distribution in temporal, spatial, taxonomic and environmental coverage of specimen- and observation based species occurrence data for land plants in Norway, a region with strong climatic and human population density gradients. Of 4.8 million species occurrence records, the majority (78%) were observations. However, there was a greater species richness in the specimen record (N = 4691) than in the observation record (N = 3193) and most species were recorded more as specimens than observations. Specimen data was on average older, and collected later during the year. Both record types were highly influenced by a small number of prolific contributors. The species most highly represented in the observation data set were widespread or invasive, while in the specimen records, taxonomically challenging species were overrepresented. Species occurrence records were unevenly spatially distributed. Both specimen and observation records were concentrated in regions of Norway with high human population density and with high temperatures and precipitation, but in different regions within Norway. Observation and specimen records thus differ in taxonomic, temporal, spatial and environmental coverage for a well-sampled group and study region, potentially influencing the ecological inferences made from studies utilizing species occurrence data. The distribution of observation data dominates the dataset, so inferences of species diversity and distributions do not correspond to the evolutionary or physiological knowledge of species, which is based on specimen data. We make recommendations for users of biodiversity data, and collectors to better exploit the complementary strengths of these distinct biodiversity data types.

• Armstrong, Ellie E.; Prost, Stefan; Ertz, Damien; Westberg, Martin; Frisch, Andreas & Bendiksby, Mika (2018). Draft genome sequence and annotation of the lichen-forming fungus Arthonia radiata. Microbiology Resource Announcements (MRA). 6(14), s. e00281–18. doi: 10.1128/genomeA.00281-18. Fulltekst i vitenarkiv Vis sammendrag

  We report here the draft de novo genome assembly, transcriptome assembly, and annotation of the lichen-forming fungus Arthonia radiata (Pers.) Ach., the type species for Arthoniomycetes, a class of lichen-forming, lichenicolous, and saprobic Ascomycota. The genome was assembled using overlapping paired-end and mate pair libraries and sequenced on an Illumina HiSeq 2500 instrument.

• Bjelland, Torbjørg; Bendiksby, Mika & Frisch, Andreas (2017). Geographically disjunct phylogenetic lineages in Leptogium hibernicum reveal Leptogium krogiae sp. nov. from East Africa. The Lichenologist. ISSN 0024-2829. 49(3), s. 239–251. doi: 10.1017/S0024282916000645. Fulltekst i vitenarkiv Vis sammendrag

  Phylogenetic analyses of nuclear (Mcm7, nrITS, nrLSU) and mitochondrial (mrSSU) DNA sequences revealed geographically disjunct lineages in Leptogium hibernicum. One of these lineages is here described as Leptogium krogiae, which differs from L. hibernicum in the thinner thallus (190–210 µm vs. 390–480 µm), shallowly striate lobes instead of deeply furrowed lobes, isidia that are seldom distinctly flattened , and apothecia with a subhymenial euparaplectenchymatous layer. Leptogium krogiae is a widespread epiphyte in mist-affected woodlands and montane forests in East Africa and appears to be a rather common species.

• Struck, Torsten H; Feder, Jeffrey L.; Bendiksby, Mika; Birkeland, Siri; Oliveira, Josè Cerca De & Gusarov, Vladimir [Vis alle 13 forfattere av denne artikkelen] (2017). Finding Evolutionary Processes Hidden in Cryptic Species. Trends in Ecology & Evolution. ISSN 0169-5347. 33(3), s. 153–163. doi: 10.1016/j.tree.2017.11.007. Fulltekst i vitenarkiv Vis sammendrag

  Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes cryptic species based on their low levels of phenotypic (morphological) disparity relative to their degree of genetic differentiation and divergence times as compared to non-cryptic species. We discuss how application of a more rigorous definition of cryptic species in taxonomic practice will lead to more accurate estimates of their prevalence in nature, better understanding of their distribution patterns on the tree of life, and increased abilities to resolve the processes underlying their evolution.

• Timdal, Einar; Bendiksby, Mika; Kahraman, Arife Merve & Halici, Mehmet Gökhan (2017). Psora taurensis (Psoraceae, Lecanorales), a new lichen species from Turkey. MycoKeys. ISSN 1314-4057. 21, s. 1–12. doi: 10.3897/mycokeys.21.11726. Fulltekst i vitenarkiv Vis sammendrag

  Herein we describe the new species, Psora taurensis, from two localities in the Taurus Mountains in Turkey at ca. 1000 m altitude. Investigations of anatomy, secondary chemistry and DNA sequences (ITS and mtSSU) of P. taurensis and presumed close relatives suggest that P. taurensis is a distinct evolutionary lineage with P. tenuifolia as its sister, although it is morphologically more similar to P. russellii and P. vallesiaca.

• Grube, Martin; Gaya, Ester; Kauserud, Håvard; Smith, Adrian M.; Avery, Simon V. & Fernstad, Sara F. [Vis alle 11 forfattere av denne artikkelen] (2017). The next generation fungal diversity researcher. Fungal Biology Reviews. ISSN 1749-4613. 31(3), s. 124–130. doi: 10.1016/j.fbr.2017.02.001. Fulltekst i vitenarkiv Vis sammendrag

  Fungi are more important to our lives than is assumed by the general public. They can comprise both devastating pathogens and plant-associated mutualists in nature, and several species have also become important workhorses of biotechnology. Fungal diversity research has in a short time transcended from a low-tech research area to a methodintensive high-tech discipline. With the advent of the new genomic and post-genomic methodologies, large quantities of new fungal data are currently becoming available each year. Whilst these new data and methodologies may help modern fungal diversity researchers to explore and discover the yet hidden diversity within a context of biological processes and organismal diversity, they need to be reconciled with the traditional approaches. Such a synthesis is actually difficult to accomplish given the current discouraging situation of fungal biology education, especially in the areas of biodiversity and taxonomic research. The number of fungal diversity researchers and taxonomists in academic institutions is decreasing, as are opportunities for mycological education in international curricula. How can we educate and stimulate students to pursue a career in fungal diversity research and taxonomy and avoid the situation whereby only those few institutions with strong financial support are able to conduct excellent research? Our short answer is that we need a combination of increased specialization and increased collaboration, i.e. that scientists with specialized expertise (e.g., in data generation, compilation, interpretation, and communication) consistently work together to generate and delivernew fungal knowledge in a more integrative manner e closing the gap between both traditional and modern approaches and academic and non-academic environments. Here we discuss how this perspective could be implemented in the training of the ‘next generation fungal diversity researcher’.

• Bjorå, Charlotte Sletten; Elden, Marte; Nordal, Inger; Brysting, Anne Krag; Awas, Tesfaye & Sebsebe, Demissew [Vis alle 7 forfattere av denne artikkelen] (2017). Speciation in the genera Anthericum and Chlorophytum (Asparagaceae) in Ethiopia — a molecular phylogenetic approach. Phytotaxa. ISSN 1179-3155. 297(2), s. 139–156. doi: 10.11646/phytotaxa.297.2.2. Fulltekst i vitenarkiv Vis sammendrag

  Sister group relations of Ethiopian species of Anthericum and Chlorophytum and variation patterns in the C. gallabatense and C. comosum complexes are studied using molecular phylogenetic analyses, morphometrics, and scanning electron microscopy of seed surfaces. Our results indicate that molecular data largely support previous morphological conclusions, and that speciation has occurred in Ethiopia at least three times in Anthericum and repeatedly within different subclades of Chlorophytum. Areas particularly rich in endemic species are the lowland area around Bale Mountains in SE Ethiopia and in the Beninshangul Gumuz regional state in W Ethiopia near the border to Sudan. A new species, Chlorophytum mamillatum sp. nov., is described, and the names Chlorophytum tordense Chiov. and Chlorophytum tetraphyllum f. are re-erected.

• Timdal, Einar; Obermayer, Walter & Bendiksby, Mika (2016). Psora altotibetica (Psoraceae, Lecanorales), a new lichen species from the Tibetan part of the Himalayas. MycoKeys. ISSN 1314-4057. 13, s. 35–48. doi: 10.3897/mycokeys.13.8824. Fulltekst i vitenarkiv Vis sammendrag

  In the present study, we describe the new species, Psora altotibetica, from nine localities in China (Tibetan area) and Nepal. The study includes analyses of anatomy, secondary chemistry, and DNA sequence data of P. altotibetica and presumed close relatives. Psora altotibetica resembles P. indigirkae morphologically, but is phylogenetically closer to P. tenuifolia and P. vallesiaca. It differs from P. indigirkae in the colour of the apothecia, the size of the ascospores, and in the secondary chemistry. The species is terricolous and was collected in the alpine zone of the Great Himalayas between 4230 and 5000 m altitude. Psora tenuifolia and P. vallesiaca are here reported as new to China and the Himalayas.

• Holien, Håkon; Frisch, Andreas; Jonsson, Fredrik; Klepsland, Jon T.; Millanes, Ana M. & Motiejunaite, Jurga [Vis alle 12 forfattere av denne artikkelen] (2016). Interesting lichenized and lichenicolous fungi found during the Nordic Lichen Society excursion in Nord-Trøndelag, Norway 2015. Graphis Scripta. ISSN 0901-7593. 28(1-2), s. 55–64. Fulltekst i vitenarkiv Vis sammendrag

  In August 2015, the Nordic Lichen Society held its 21st bi-annual meeting and excursion in Steinkjer, Nord- Trøndelag, Norway. During the excursion various habitats, including boreal rainforest, calcareous rocks with pine forest, coastal heath, heavy metal containing rock and montane spruce forest, were investigated. The most interesting findings are recorded herewith. Didymocyrtis pseudeverniae and Unguiculariopsis manriquei are new to Scandinavia, and six species are new to Norway: Absconditella celata, Catillaria aphana, Micarea contexta, Scytinium aquale, Tremella wirthii and Verrucaria sparsiuscula. Notes on a number of red-listed and/or rarely collected species in Norway are also provided.

• McCune, Bruce; Timdal, Einar & Bendiksby, Mika (2016). Rhizocarpon quinonum, a new anthraquinone-containing species from the Alaska Peninsula. The Lichenologist. ISSN 0024-2829. 48(5), s. 367–375. doi: 10.1017/S0024282916000347. Fulltekst i vitenarkiv
• Salmaki, Yasaman; Bendiksby, Mika & Heubl, GÜNTHER (2015). Molecular phylogeny confirms the placement of enigmatic Stachys persepolitana in Lamium (Lamiaceae; subfam. Lamioideae). Phytotaxa. ISSN 1179-3155. 192(4), s. 254–266. doi: 10.11646/phytotaxa.192.4.3. Fulltekst i vitenarkiv

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• Naranjo-Ortiz, Miguel Angel; Skrede, Inger; Peris, David; Krabberød, Anders Kristian; Lü, Dabao Sun & Bendiksby, Mika (2025). Expansive pangenome sin the Agaricomycetes. Fulltekst i vitenarkiv Vis sammendrag

  Trichaptum abietinum (Dicks.) Ryvarden (Hymenochaetales) is a pioneer wood rot mushroom common across the Northern Hemisphere, usually growing on conifer wood. The species has emerged in recent years as a model for mushroom genomics, and extensive genomic resources are available. Here, we have analyzed patterns of gene presence-absence variation across a dataset covering T. abietinum known intraspecific geographical and genetic diversity. Our results suggest that Trichaptum abietinum has a large proportion of its genome under Presence-Absence variation, over 40% of all genes for any particular strain. This pattern seem to be common across Agaricomycetes, but not across other groups of Fungi. Core and accessory genes have distinct properties. Core genes also tend to cluster towards chromosome centers, while accessory genes are more abundant at the extremes. Core genes tend to be longer, have more introns and appear closer to other genes. Distribution of Accessory genes across the species depends on genetic distance, but this variable alone can only explain a fraction of the observed pattern. Unlike most other groups of fungi that tend to be haploid, Agaricomycetes spend most of their life cycle as a dikaryotic mycelium. Cell division in this mycelium is typically tightly regulated, which would be unnecessary were this a simple diploid. We hypothesize that extensive PAV has the potential of causing interference during mitotic recombination events, thus promoting genomic unstability. This is then prevented by keeping the two nuclei separated until meiosis. This life cycle would allow these fungi to access a much larger gene pool than it would be possible for any single haploid genet.

• Bjorå, Charlotte Sletten; Ballesteros, Jesus Adrian Chimal; Bendiksby, Mika; Carlsen, Tor & Nordal, Inger (2025). Genus and species delimitation in Chlorophytum (Asparagaceae) over again, what is improved by high throughput sequencing? Fulltekst i vitenarkiv
• Winden, Veerle Van; Bendiksby, Mika; Naranjo-Ortiz, Miguel Angel & Bjorå, Charlotte Sletten (2025). PhyloFun - Spatial Phylogenetics of Fungi in Norway for Biodiversity Management. Fulltekst i vitenarkiv Vis sammendrag

  Fungi are among the most understudied branches of life, despite their great diversity and crucial ecological roles. The PhyloFun project explores patterns of fungal diversity from an evolutionary perspective using Norway as a model. PhyloFun integrates occurrence records with phylogenetic information to carry out a spatial phylogenetic assessment. Occurrence data are harvested from various online data repositories, including both observational as well as specimens-based records. In addition, PhyloFun uses DNA sequence data systematically produced within the NorBol barcoding project combined with sequences harvested from GenBank. To reduce imbalance in taxon and marker sampling, PhyloFun also produces new DNA sequence data from both fungarium specimens and freshly collected materials. An existing, systematically organised framework, Nature in Norway (NiN), provides an important and innovative data source, with which to compare the distribution patterns of clades at all levels. With its extensive fungal occurrence data, its diverse habitat, and the NiN system Norway represents an ideal location to undertake this research. Focusing on Norway as a model system, the PhyloFun project hopes to assess how evolutionary relationships shape fungal community composition across spatial scales.

• Winden, Veerle Van; Bendiksby, Mika; Naranjo-Ortiz, Miguel Angel & Bjorå, Charlotte Sletten (2024). PhyloFun: spatial phylogenetics of fungi in Norway. doi: https:/www.forbio.uio.no/events/meeting/2024/biosystematikk_program.pdf. Fulltekst i vitenarkiv Vis sammendrag

  The PhyloFun project aims to map the spatial distribution of fungal phylogenetic diversity and endemism across various Norwegian ecosystems by integrating molecular phylogenetic data with species occurrence records. The project pioneers the first spatial phylogenetic study of fungi, using Norway as a model system to explore the evolutionary and ecological diversity of these crucial organisms. Occurrence data will be combined with phylogenetic techniques to uncover patterns of phylogenetic diversity, identify environmental variables influencing these patterns, and assess spatial phylogenetic diversity across Norway's ecosystems. For this, we will supplement existing barcode data with newly generated sequences derived from Norway’s natural history collections. Besides the aim to fill a critical knowledge gap in fungal biodiversity, we also aim to enhance biodiversity management practices through phylogenetically informed conservation strategies. By integrating the Nature in Norway (NiN) framework with spatial phylogenetic methods, PhyloFun will provide novel insights into the distribution and ecological significance of fungi in Norway. The outcomes will set the stage for future parallel studies in other regions, such as California, and contribute to a broader understanding of global fungal diversity. PhyloFun will advance the field of biodiversity research, promoting a deeper understanding of the intrinsic and extrinsic factors which determine the diversity of fungi, as well as their evolutionary and ecological roles in maintaining healthy ecosystems.

• Frisch, Andreas; Bendiksby, Mika; Kantelinen, Annina & Thor, Göran (2024). Epiphytic forest lichens and lichen-associated fungi in Saxnäs, Sweden. Funga. Fulltekst i vitenarkiv
• Ortiz, Miguel Angel Naranjo; Skrede, Inger; Bendiksby, Mika; Lü, Dabao Sun; Navarro, David Peris & Krabberød, Anders Kristian (2024). Pangenome analyses of the mushroom Trichaptum abietinum (Hymenochaetales) reveals extensive presence-absence variation. Fulltekst i vitenarkiv
• Bendiksby, Mika (2023). The potential of fungarium specimens and DNA barcodes in fungal research. Fulltekst i vitenarkiv
• Nygaard, Malene; Kopatz, Alexander; Speed, James David Mervyn; Martin, Michael David; Prestø, Tommy & Kleven, Oddmund [Vis alle 7 forfattere av denne artikkelen] (2023). SNP genotyping and environmental niche modelling using herbarium specimens of the northern dragonhead, Dracocephalum ruyschiana (Lamiaceae). Bauhinia. ISSN 0067-4605. 29, s. 127–128. Fulltekst i vitenarkiv
• Matten, Damaris Marina; Bendiksby, Mika; Martin, Michael David & Speed, James David Mervyn (2023). Spatial patterns of species and phylogenetic diversity of vascular plants in Norway and Fennoscandia. Fulltekst i vitenarkiv
• Bendiksby, Mika (2023). Nytt fra fungariet. Funga. 1(1), s. 6–7. Fulltekst i vitenarkiv
• Bendiksby, Mika (2023). Hva er et fungarium og hva er poenget? Funga. 1(1), s. 4–5. Fulltekst i vitenarkiv Vis sammendrag

  Fungariene huser referansemateriale for arter, populasjoner og genetiske ressurser i tid og rom og representerer sånn sett en viktig infrastruktur for biomangfoldsforskning

• Bendiksby, Mika & Wollan, Anders K. (2023). Slørsoppmiddagen (https://radio.nrk.no/podkast/abels_taarn). [Radio]. NRK P2: Abels tårn. Fulltekst i vitenarkiv Vis sammendrag

  Hanne Aass drar på en middag der soppeksperter serverer slørsopp, en slekt som sopplukkere har blitt bedt om å styre langt unna. Noen av slørsoppene er nemlig blant våre dødeligste giftsopper.

• Evankow, Ann; Bendiksby, Mika & Timdal, Einar (2023). Cryptic diversity of the lichen genus Psora in cryptogam collections. Fulltekst i vitenarkiv
• Bendiksby, Mika (2022). Stort ukjent soppmangfold. Fulltekst i vitenarkiv
• Bendiksby, Mika; Thorbek, Birgitte Lisbeth Graae; Bjorå, Charlotte Sletten & Halvorsen, Rune (2022). Simple procedures for obtaining DNA sequences from old herbarium specimens. Fulltekst i vitenarkiv
• Bjorå, Charlotte Sletten; Bendiksby, Mika; Løfall, Bjørn Petter & Timdal, Einar (2022). Collections from the cold solving hot questions. Fulltekst i vitenarkiv
• Ballesteros, Jesus Adrian Chimal; Bjorå, Charlotte Sletten; Bendiksby, Mika & Carlsen, Tor (2022). Target-capture and angiosperm-353 probe-set on Chlorophytum: a viable way to determine species complexes? Fulltekst i vitenarkiv
• Løken, Solveig Bua; Bendiksby, Mika & Stedje, Brita (2022). A HTS approach for delimiting taxa of Drimiopsis, Ledebouria and Resnova (Asparagaceae, subfamily Scilloidea). Fulltekst i vitenarkiv
• Evankow, Ann; Bendiksby, Mika; Speed, James David Mervyn & Timdal, Einar (2021). INTEGRATIVE TAXONOMY OF THE Psoraceae. Fulltekst i vitenarkiv
• Moen, Victoria Stornes & Bendiksby, Mika (2020). Kjære leser – du er omgitt av sopp. Harvest Magazine. Fulltekst i vitenarkiv
• Bendiksby, Mika (2020). The future of collections-based research in Systematic Mycology. Fulltekst i vitenarkiv
• Bendiksby, Mika (2020). DNA-navigering i lav: strekkoding, kryptisk artsmangfold og andre overraskelser. Fulltekst i vitenarkiv
• Moen, Victoria Stornes & Bendiksby, Mika (2020). Soppevangeliet. Gemini. ISSN 0802-085X. Fulltekst i vitenarkiv
• Nygård, Malene Østreng & Bendiksby, Mika (2020). Vi måler tempen på forskningsfeltet biosystematikk. Biolog. ISSN 0801-0722. 2, s. 14–21. Fulltekst i vitenarkiv
• Bendiksby, Mika (2020). Progress and activities in the researcher group «Integrative Taxonomy and DNA barcoding» (TAXA). Fulltekst i vitenarkiv
• Løken, Solveig Bua; Bendiksby, Mika & Stedje, Brita (2020). Phylogeny, character state evolution and species delimitation in Drimiopsis, Ledebouria and Resnova (Asparagaceae, subfamily Scilloidea). Fulltekst i vitenarkiv
• Matten, Damaris Marina; Bendiksby, Mika; Martin, Michael David & Speed, James David Mervyn (2020). Phylogenetic diversity of Fennoscandian vascular plants: Do we protect the relevant areas? Fulltekst i vitenarkiv
• Matten, Damaris Marina; Bendiksby, Mika; Martin, Michael David & Speed, James David Mervyn (2020). Phylogenetic diversity of Fennoscandian vascular plants: Do we protect the relevant areas? Fulltekst i vitenarkiv
• Evankow, Ann; Bendiksby, Mika & Timdal, Einar (2020). Integrative taxonomy of the Psoraceae (Lichenized Ascomycota). Fulltekst i vitenarkiv
• Moen, Victoria Stornes & Bendiksby, Mika (2019). Naturhistoriske samlinger som ressurs for samfunnet. Orebladet. ISSN 1501-4924. 1, s. 25–30. Fulltekst i vitenarkiv
• Moen, Victoria Stornes; Bendiksby, Mika; Frisch, Andreas & Grube, Martin (2019). Molecular systematics and species delimitation in Coniocarpon and Arthonia punctiformis sensu lato (Arthoniaceae) in Norway. Fulltekst i vitenarkiv
• Bendiksby, Mika (2019). “Lav og lavboende sopper i norske regnskoger”. Fulltekst i vitenarkiv
• Bendiksby, Mika; Frisch, Andreas & Holien, Håkon (2019). A phylogenetic survey of Arthrorhaphis (Arthrorhaphidaceae) including new taxa in the A. citrinella species complex. Fulltekst i vitenarkiv
• Moen, Victoria Stornes; Bendiksby, Mika & Frisch, Andreas (2019). Molecular systematics and species delimitation in Coniocarpon and Arthonia punctiformis s.lat. in Norway. Fulltekst i vitenarkiv
• Bendiksby, Mika (2019). Multifaceted diversity in a fascinating branch of ascomycete associations. Fulltekst i vitenarkiv
• Løken, Solveig Bua; Bendiksby, Mika & Stedje, Brita (2019). LEDEBOURIA & FRIENDS - Phylogeny, character state evolution and species delimitation in three African monocot genera: Drimiopsis, Ledebouria and Resnova (Asparagaceae, subfamily Scilloidea). Fulltekst i vitenarkiv
• Frisch, Andreas & Bendiksby, Mika (2019). Hidden treasures in your front yard: Crustose lichens and lichenicolous fungi in the Norwegian boreo-nemoral and boreal rain forests. Fulltekst i vitenarkiv
• Bendiksby, Mika (2019). DEN NORSKE JUNGELEN. Boreal regnskog ̶ Hva er det? Hvor finnes den? Hva skal vi med den? Fulltekst i vitenarkiv
• Mienna, Ida Marielle; Speed, James David Mervyn; Martin, Michael David; Bendiksby, Mika; Thornhill, Andrew H & Mishler, Brent D (2018). Patterns and drivers of vascular plant phylogenetic diversity and endemism across Norway. Fulltekst i vitenarkiv
• Mienna, Ida Marielle; Speed, James David Mervyn; Martin, Michael David; Bendiksby, Mika; Thornhill, Andrew H & Mishler, Brent D (2018). The Spatial Distribution Of Phylogenetic Diversity And Endemism In The Norwegian Vascular Flora. Fulltekst i vitenarkiv
• Struck, Torsten H; Feder, Jeffrey L.; Bendiksby, Mika; Birkeland, Siri; Oliveira, Josè Cerca De & Gusarov, Vladimir [Vis alle 13 forfattere av denne artikkelen] (2018). Cryptic Species – More Than Terminological Chaos: A Reply to Heethoff. Trends in Ecology & Evolution. ISSN 0169-5347. 33(5), s. 310–312. doi: 10.1016/j.tree.2018.02.008. Fulltekst i vitenarkiv
• Bjorå, Charlotte Sletten; Stedje, Brita; Bendiksby, Mika; Kativu, Shakkie & Nordal, Inger (2017). A phylogenetic analysis of Anthericum and Chlorophytum. Fulltekst i vitenarkiv
• Bjorå, Charlotte Sletten; Stedje, Brita & Bendiksby, Mika (2017). A phylogenetic analysis of Anthericum L. and Chlorophytum Ker Gawl. (Asparagaceae). Fulltekst i vitenarkiv
• Marthinsen, Gunnhild; Bendiksby, Mika; Brandrud, Tor Erik; Dima, Bálint; Hansen, Lars Ove & Johnsen, Arild [Vis alle 8 forfattere av denne artikkelen] (2017). Discordance between morphology and DNA barcodes in lichens, fungi and insects. Fulltekst i vitenarkiv
• Mienna, Ida M; Thornhill, Andrew H; Mishler, Brent D; Bendiksby, Mika; Speed, James David Mervyn & Martin, Michael David (2017). Spatial phylogenetics of the Norwegian vascular plant flora. Fulltekst i vitenarkiv
• Košuthová, Alica; Fačkovcová, Zuzana; Guttová, Anna; Holien, Håkon; Timdal, Einar & Wedin, Mats [Vis alle 8 forfattere av denne artikkelen] (2016). DNA barcoding of lichens and biosystematics; the case studies of genera: Cladonia, Placynthium and Solenopsora. Fulltekst i vitenarkiv Vis sammendrag

  The main motivation for this project is a situation of shared research questions, complementary competences, and a desire for knowledge and data sharing, both taxonomically and methodologically, between Masaryk University and NTNU. On the lichenology side, there was a motivation for nourishing and fomalizing a dawning network of european lichen systematists. All involved, both the core participants (Bendiksby, Holien and Košuthová) and the accompanyiong scientists (Guttová, Steinová, Timdal, Wedin and Westberg), have some form of ongoing work with at least one participant of this project. However, their respective networks and competences are not the same, and new connections within the group has been made in the present project.

• Frisch, Andreas; Holien, Håkon; Ohmura, Yoshihito & Bendiksby, Mika (2016). Molecular systematics of Arthrorhaphis with special consideration of the A. alpina ― A. citrinella species complex. Fulltekst i vitenarkiv Vis sammendrag

  Background: Arthrorhaphis Th. Fr. includes c. 11 species and varieties of lichenised and lichenicolous fungi. The genus thrives in temperate to arctic-alpine regions of the Northern Hemisphere. Arthrorhaphis alpina, A. citrinella and A. grisea extend their distributions into the Southern Hemisphere [1], and A. citrinella var. catolechioides is restricted to Australasia [1]. Arthrorhaphis is well-studied in Europe and Central Asia [2,3,4], but species delimitation of taxa containing pulvinic acid derivates remains problematic. Arthrorhaphis alpina and A. citrinella in particular show considerable morphological variation at the world level that is presently not well understood. Material and Methods: New mitochondrial (mtSSU) and nuclear (nLSU, RPB1 and ITS 2) DNA sequences were generated for 142 specimens representing all currently described Arthrorhaphis species except A. aeruginosa*. We sequenced specimens from all continents. Due to the availability of collections, our sampling is biased towards northern and central Europe and parts of central and eastern Asia. All specimens were identified following current species concepts and the key morphological characters were noted. We applied Bayesian methods of phylogenetic tree reconstruction to the concatenated alignment of all four gene loci. Principal results: All lichenised species of Arthrorhaphis containing pulvinic acid derivates are monophyletic and apparently closely related Except for A. jungens, all species are recovered in our phylogeny according to the current morphology based concepts Ascospore type and presence / absence of Ca-oxalate crystals are confirmed as good characters for separating A. alpina s.l. (incl. A. vacillans and A. jungens) and A. citrinella s.l. A. alpina s.l. and A. citrinella s.l. comprise several genetically distinct lineages being correlated with morphology and / or geographical distribution The obligate parasitic taxa are separated by long branches and placed together in a basal position on the phylogenetic tree

• Haugan, Reidar; Timdal, Einar; Frisch, Andreas; Rui, Siri & Bendiksby, Mika (2016). Miriquidica – yet another non-monophyletic lichen genus rich in cryptic species. Fulltekst i vitenarkiv Vis sammendrag

  Background: Miriquidica Hertel & Rambold comprises about 30 saxicolous, mainly alpine species worldwide. The genus was originally delimited by the presence of miriquidic acid in most of the species and by asci of the “Lecanora-type”. The species are often difficult to identify without chemical and microscopical investigations. Although they are common rock lichens in some regions in the Northern Hemisphere, many Miriquidica species remain poorly understood. Material and Methods: We have collected Miriquidica extensively throughout Fennoscandia, over wide climatic, geographical and ecological gradients. We studied this, and additional material of available Miriquidica species and presumed close relatives, using TLC, microscopy, and multi-locus DNA-sequencing. We have compiled a dataset with 187 accessions representing specimens collected as Miriquidica, their presumed close relatives, and appropriate outgroups. Some sequences were downloaded from genbank (mainly from Singh et al. 2013). The molecular work was undertaken as described in Bendiksby et al. (2013). A partitioned concatenated dataset of one mitochondrial (mtSSU) and two nuclear genetic regions (ITS and MCM7) was analysed phylogenetically using Maximum likelihood (ML) on the CIPRES Science Gateway (Miller et al. 2010). For the ML analysis, we used the RAxML-HPC black box with rapid bootstrapping and full ML analysis under the GTR+GAMMA approximation. Results: We have discovered several new species, many of them so-called cryptic and Miriquidica hence falls into the line of crustose genera showing a high degree of cryptic speciation (Fig. 1). Our results also show that Miriquidica, as currently circumscribed, is polyphyletic, i.e. one species (M. pycnocarpa) is extraneous in the genus. After its removal from Miriquidica, the genus remains paraphyletic, with species of Protoparmelia (cfr. Singh et al. 2013), Lecanora, Lecidea s.lat., and Myochroidea nested. We recognize several new species, of which we include two in Fig. 1 (M. scoriae and M. ymei), and recombine 11 others.

• Toreskaas, Anne Karin; Bendiksby, Mika & Timdal, Einar (2016). Molecular systematics of the lichen genus Eschatogonia. Fulltekst i vitenarkiv
• Dahl, Malin Stapnes; Bendiksby, Mika & Timdal, Einar (2016). Molecular systematics of the lichen genus Sporacestra and relatives (Ramalinaceae, Ascomycota). Fulltekst i vitenarkiv
• Toreskaas, Anne Karin; Bendiksby, Mika & Timdal, Einar (2016). Molecular systematics of the lichen genus Eschatogonia. Fulltekst i vitenarkiv
• Kistenich, Sonja Daniela; Timdal, Einar; Bendiksby, Mika & Ekman, Stefan (2016). Molecular phylogenetics and taxonomy of the lichen family Ramalinaceae. Fulltekst i vitenarkiv
• Bendiksby, Mika (2016). Pizzakrydder: mat, botanikk og genetikk. Fulltekst i vitenarkiv
• Dahl, Malin Stapnes; Bendiksby, Mika & Timdal, Einar (2016). Molecular systematics of the lichen genus Sporacestra and relatives (Ramalinaceae, Ascomycota). Fulltekst i vitenarkiv
• Kistenich, Sonja Daniela; Timdal, Einar; Bendiksby, Mika & Ekman, Stefan (2016). Molecular phylogenetics and taxonomy of the lichen family Ramalinaceae. Fulltekst i vitenarkiv
• Nygaard, Malene; Bendiksby, Mika; Speed, James David Mervyn & Martin, Mike (2022). Integrative biosystematics and conservation genomics – holistic studies of two red-listed plants in Norway. Norges teknisk-naturvitenskapelige universitet. ISSN 9788232663392. Fulltekst i vitenarkiv Vis sammendrag

  We are currently facing a rapid decline in biodiversity. More than 20% of all plants are threatened by extinction. Loss of plants may have drastic effects on our lives as they represent a fundamental part of the biodiversity providing food, timber, medicine, and other ecosystem services. To conserve biodiversity, we must first understand what it consists of as well as the processes shaping it. The purpose of this study was to contribute toward a greater understanding of plant diversity and distribution in Norway in order to guide conservation of threatened plants. We combined different types of data (morphological, genetic, geographical) and methods (population genetics, phylogenetics, ecological niche modeling) to study taxonomic, ecological, evolutionary and conservation aspects of two red-listed plants. The value of natural history collection in biodiversity studies was evaluated through the use of herbarium material within two of the included articles. A kinship hypothesis, also called a phylogenetic tree, can be used for a variety of downstream analyses. Integrated, these analyses may contribute towards holistic biodiversity knowledge. In this study we developed and tested a set of Hyb-Seq probes for the Carex genus (Cyperaceae), with the ultimate goal of unraveling its internal relationships. We further performed a literature search to study the use of phylogenies within different biological disciplines during the last 50 years, and the relevance of resolved phylogenies for biodiversity conservation practices.

• Niroula, Dhirendra; Bendiksby, Mika & Martin, Michael David (2018). Global functional genomics of the Irish potato famine pathogen Phytophthora infestans. NTNU Vitenskapsmuseet. Fulltekst i vitenarkiv
• Mienna, Ida Marielle; Martin, Michael David; Speed, James David Mervyn & Bendiksby, Mika (2018). Patterns and Drivers of Phylogenetic Diversity and Endemism in the Norwegian Vascular Flora. Norges teknisk-naturvitenskapelige universitet. Fulltekst i vitenarkiv Vis sammendrag

  Biodiversity is commonly measured as the local abundance of discrete species. This approach fails to incorporate evolutionary relationships among species and gives an incomplete picture of the diversity in a given region. Recently developed methods for spatial phylogenetics combine species occurrence datasets with molecular phylogenetic data to recover information about the spatial distribution of phylogenetic diversity and endemism across a geographic region. In this study, we applied these methods on vascular plants across Norway, a region that was covered by the Fennoscandian ice sheet until about 10 kyr BP. Our primary aim was to test whether patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) for 1238 native vascular plant species are non-randomly distributed across Norway and to seek causal mechanisms for the revealed patterns. A multi-locus concatenated alignment was produced using a combination of GenBank data and newly produced sequence data from herbarium specimens, and a corresponding phylogenetic hypothesis was inferred. We combined this data with occurrence data from GBIF, and then calculated PD, PE, relative phylogenetic diversity (RPD), and relative phylogenetic endemism (RPE). To assess areas of statistical significance we performed a spatial randomisation of these indices. To determine if PD outlier regions are associated with various environmental explanatory variables, we performed pairwise linear correlation analyses. We also performed range-weighted turnover analyses and compared these maps with previous studies on vegetation zones in Norway. Our results revealed significantly high PD and RPD (phylogenetic overdispersion) along the coast of southern Norway and significantly low PD and RPD (phylogenetic clustering) in the mountainous areas. The best fitted statistical models showed that the PD pattern could best be explained by temperature, time since last glaciation cover, and topographic heterogeneity. For PE and RPE, we found a concentration of short restricted branches (neo-endemics) in northern Norway, and a mix of short and long restricted branches (both neo-endemics and paleo-endemics) on the coast of southern Norway, with temperature inferred as a likely driver for the revealed patterns. The range-weighted turnover analyses showed an evolutionary signal in the way the flora is distributed. This study emphasizes the importance of incorporating evolutionary relationships between species to see patterns of diversity and endemism that would normally not be seen by examining species diversity alone. Moreover, it shows that spatial phylogenetics can be meaningfully applied to a region of short evolutionary history as opposed to previous studies restricted to regions with long evolutionary history (e.g. Australia and California).

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