A further new species in the lichen genus Arctomia: A. borbonica from Reunion (Mascarene archipelago)

peer reviewedArctomia borbonica sp. nov. is described as new for science from montane natural and secondary habitats in Reunion in the Mascarene archipelago (Indian Ocean). It has a sterile, foliose, usually wrinkled, thallus whose margins produce goniocysts that disintegrate into a soredioid margin; it looks like a Leptogium species. Its phylogenetic position in the Arctomiaceae (Ostropomycetidae, Ascomycota) has been determined with 3 genes (nuLSU, mtSSU, RPB1) inferences

Do Photobiont Switch and Cephalodia Emancipation Act as Evolutionary Drivers in the Lichen Symbiosis? A Case Study in the Pannariaceae (Peltigerales)

peer reviewedLichen symbioses in the Pannariaceae associate an ascomycete and either cyanobacteria alone (usually Nostoc; bipartite thalli) or green algae and cyanobacteria (cyanobacteria being located in dedicated structures called cephalodia; tripartite thalli) as photosynthetic partners (photobionts). In bipartite thalli, cyanobacteria can either be restricted to a well-delimited layer within the thallus (‘pannarioid’ thalli) or spread over the thallus that becomes gelatinous when wet (‘collematoid’ thalli). We studied the collematoid genera Kroswia and Physma and an undescribed tripartite species along with representatives of the pannarioid genera Fuscopannaria, Pannaria and Parmeliella. Molecular inferences from 4 loci for the fungus and 1 locus for the photobiont and statistical analyses within a phylogenetic framework support the following: (a) several switches from pannarioid to collematoid thalli occured and are correlated with photobiont switches; the collematoid genus Kroswia is nested within the pannarioid genus Fuscopannaria and the collematoid genus Physma is sister to the pannarioid Parmeliella mariana group; (b) Nostoc associated with collematoid thalli in the Pannariaceae are related to that of the Collemataceae (which contains only collematoid thalli), and never associated with pannarioid thalli; Nostoc associated with pannarioid thalli also associate in other families with similar morphology; (c) ancestors of several lineages in the Pannariaceae developed tripartite thalli, bipartite thalli probably resulting from cephalodia emancipation from tripartite thalli which eventually evolved and diverged, as suggested by the same Nostoc present in the collematoid genus Physma and in the cephalodia of a closely related tripartite species; Photobiont switches and cephalodia emancipation followed by divergence are thus suspected to act as evolutionary drivers in the family Pannariaceae

Multilocus-based phylogeny and species recognition within the cosmopolitan Peltigera neopolydactyla-dolichorhiza complex

The Peltigera neopolydactyla/dolichorhiza complex is broadly distributed, growing in boreal and temperate regions from northern Norway to southern Chile, as well as in tropical mountains. Observed morphotype and chemotype variation within this complex suggested the presence of multiple undescribed species. We inferred the phylogeny of Peltigera section Polydactylon with a special focus on the Peltigera neopolydactyla/dolichorhiza complex to determine the full breadth of this species complex, and to assess if taxa from different parts of the worlds but with similar morphological features share a most recent common ancestor. About 525 ITS sequences representing 104 distinct haplotypes were generated for representatives of Peltigera section Polydactylon. We selected a representative of each broadly defined phylotype for which three protein-coding loci: RPB1.1, b-tubulin and EFT2.1 were sequenced. Each of the three protein coding loci provided equivalent or more resolution and support than the ITS locus. The greatest proportion of significantly supported nodes across the tree resulted from β-tubulin alone. Many specimens identified as P. neopolydactyla and P. dolichorhiza are placed outside of this species complex. As currently defined both species represent polyphyletic assemblages of taxa including several potentially undescribed species. Our phylogenies suggest the presence of putatively new species within several complexes across the section.REVSYS: Phylogenetic revision of the lichen-genus Peltigera (Ascomycota): Disentangling cryptic speciation, phenotypic plasticity, and hybridization

「上海遊記」の「徐家匯」 : 基督教受容史に芥川の見出した「近代」

千葉大学社会文化科学研究科研究プロジェクト報告書第120集『日本近代文学と宗教』所

The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history

peer reviewedWe present phylogenetic analyses of the fruticose Ramalinaceae based on extensive collections from many parts of the world, with a special focus on the Vizcaíno deserts in northwestern Mexico and the coastal desert in Namibia. We generate a four-locus DNA sequence dataset for accessions of Ramalina and two additional loci for Niebla and Vermilacinia. Four genera are strongly supported: the subcosmopolitan Ramalina, the new genus Namibialina endemic to SW Africa, and a duo formed by Niebla and Vermilacinia, endemic to the New World except the sorediate V. zebrina that disjunctly occurs in Namibia. The latter three genera are restricted to coastal desert and chaparral where vegetation depends on moisture from ocean fog. Ramalina is subcosmopolitan and much more diverse in its ecology. We show that Ramalina and its sister genus Namibialina diverged from each other at c. 48 Myrs, whereas Vermilacinia and Niebla split at c. 30 Myrs. The phylogeny of the fruticose genera remains unresolved to their ancestral crustose genera. Species delimitation within Namibialina and Ramalina is rather straightforward. The phylogeny and taxonomy of Vermilacinia are fully resolved, except for the two youngest clades of corticolous taxa, and support current taxonomy, including four new taxa described here. Secondary metabolite variation in Niebla generally coincides with major clades which are comprised of species complexes with still unresolved phylogenetic relationships. A micro-endemism pattern of allopatric species is strongly suspected for both genera, except for the corticolous taxa within Vermilacinia. Both Niebla and saxicolous Vermilacinia have chemotypes unique to species clades that are largely endemic to the Vizcaíno deserts. The following new taxa are described: Namibialina gen. nov. with N. melanothrix (comb. nov.) as type species, a single new species of Ramalina (R. krogiae) and four new species of Vermilacinia (V. breviloba, V. lacunosa, V. pustulata and V. reticulata). The new combination V. granulans is introduced. Two epithets are reintroduced for European Ramalina species: R. crispans (= R. peruviana auct. eur.) and R. rosacea (= R. bourgeana auct. p.p). A lectotype is designated for Vermilacinia procera. A key to saxicolous species of Vermilacinia is presented

Molybdenum threshold for ecosystem scale alternative vanadium nitrogenase activity in boreal forests

Biological nitrogen fixation (BNF) by microorganisms associated with cryptogamic covers, such as cyanolichens and bryophytes, is a primary source of fixed nitrogen in pristine, high-latitude ecosystems. On land, low molybdenum (Mo) availability has been shown to limit BNF by the most common form of nitrogenase (Nase), which requires Mo in its active site. Vanadium (V) and iron-only Nases have been suggested as viable alternatives to countering Mo limitation of BNF; however, field data supporting this long-standing hypothesis have been lacking. Here, we elucidate the contribution of vanadium nitrogenase (V-Nase) to BNF by cyanolichens across a 600-km latitudinal transect in eastern boreal forests of North America. Widespread V-Nase activity was detected (∼15–50% of total BNF rates), with most of the activity found in the northern part of the transect. We observed a 3-fold increase of V-Nase contribution during the 20-wk growing season. By including the contribution of V-Nase to BNF, estimates of new N input by cyanolichens increase by up to 30%. We find that variability in V-based BNF is strongly related to Mo availability, and we identify a Mo threshold of ∼250 ng·glichen−1 for the onset of V-based BNF. Our results provide compelling ecosystem-scale evidence for the use of the V-Nase as a surrogate enzyme that contributes to BNF when Mo is limiting. Given widespread findings of terrestrial Mo limitation, including the carbon-rich circumboreal belt where global change is most rapid, additional consideration of V-based BNF is required in experimental and modeling studies of terrestrial biogeochemistry

The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach

The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex

Macroclimatic structuring of spatial phylogenetic turnover in liverworts

Phylogenetic turnover has emerged as a powerful tool to identify the mechanisms by which biological communities assemble. When significantly structured along environmental gradients, phylogenetic turnover evidences phylogenetic niche conservatism, a critical principle explaining patterns of species distributions at different spatio-temporal scales. Here, we quantify the contribution of geographic or macroclimatic drivers to explain patterns of phylogenetic turnover in an entire phylum of land plants, namely liverworts. We further determine whether climatic niche conservatism has constrained the distribution of liverworts in the course of their evolutionary history. Two datasets, one insular, focused on 60 archipelagos and including 2346 species, and the second global, including 6334 species in 451 oceanic and continental Operational Geographic Units (OGUs) worldwide, were assembled. Phylogenetic turnover among OGUs was quantified through πst statistics. πst-throughtime profiles were generated at 1 myr intervals along the phylogenetic time-scale and used to compute the correlation between πst, current geographic distance and macroclimatic variation with Mantel tests based on Moran spectral randomization to control for spatial autocorrelation. The contribution of macroclimatic variation to phylogenetic turnover was about four-times higher than that of geographic distance, a pattern that was consistently observed in island and global geographic settings, and with datasets including or excluding species-poor OGUs. The correlation between phylogenetic turnover and geographic distance rapidly decayed at increasing phylogenetic depth, whereas the relationship with macroclimatic variation remained constant until 100 mya. Our analyses reveal that changes in the phylogenetic composition among liverwort floras across the globe are primarily shaped by macroclimatic variation. They demonstrate the relevance of macroclimatic niche conservatism for the assembly of liverwort floras over very large spatial and evolutionary time scales, which may explain why such a pervasive biodiversity pattern as the increase of species richness towards the tropics also applies to organisms with high dispersal capacities

Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks

peer reviewedBiotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α-diversity. To calculate the PSS index, we then compare observed partner phylogenetic α-diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed-dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much-needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss