Eco-phylogenetic study of Trebouxia in southern Africa reveals interbiome connectivity and potential endemism in a green algal lichen photobiont.

Premise: Southern Africa is a biodiversity hotspot rich in endemic plants and lichen-forming fungi. However, species-level data about lichen photobionts in this region are minimal. We focused on Trebouxia (Chlorophyta), the most common lichen photobiont, to understand how southern African species fit into the global biodiversity of this genus and are distributed across biomes and mycobiont partners.

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria.

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification.

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

Biotic 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.

The taxonomy of the complex: a phylogenomic approach.

The medically relevant 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. , and are currently accepted as separate species.

Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism.

Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe.

Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens.

Understanding the evolutionary history of symbiotic Cyanobacteria at a fine scale is essential to unveil patterns of associations with their hosts and factors driving their spatiotemporal interactions. As for bacteria in general, Horizontal Gene Transfers (HGT) are expected to be rampant throughout their evolution, which justified the use of single-locus phylogenies in macroevolutionary studies of these photoautotrophic bacteria. Genomic approaches have greatly increased the amount of molecular data available, but the selection of orthologous, congruent genes that are more likely to reflect bacterial macroevolutionary histories remains problematic.

Corrigendum: Spjut R, Simon A, Guissard M, Magain N, Sérusiaux E (2020) The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history. MycoKeys 73: 1-68. https://doi.org/10.3897/mycokeys.73.47287.

[This corrects the article DOI: 10.3897/mycokeys.73.

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

We 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 north-western Mexico and the coastal desert in Namibia. We generate a four-locus DNA sequence dataset for accessions of and two additional loci for and . Four genera are strongly supported: the subcosmopolitan , the new genus endemic to SW Africa, and a duo formed by and , endemic to the New World except the sorediate that disjunctly occurs in Namibia.

T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees.

The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.

Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus .

Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus , section . We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries.

Bioclimatic factors at an intrabiome scale are more limiting than cyanobiont availability for the lichen-forming genus Peltigera.

Premise Of The Study: Factors shaping spatiotemporal patterns of associations in mutualistic systems are poorly understood. We used the lichen-forming fungi Peltigera and their cyanobacterial partners Nostoc to investigate the spatial structure of this symbiosis at an intrabiome scale and to identify potential factors shaping these associations.

Methods: Ninety-three thalli were sampled in Québec, Canada, along a south-north and an east-west transect of ~1300 km each.

High diversity, high insular endemism and recent origin in the lichen genus Sticta (lichenized Ascomycota, Peltigerales) in Madagascar and the Mascarenes.

Lichen biodiversity and its generative evolutionary processes are practically unknown in the MIOI (Madagascar and Indian Ocean Islands) biodiversity hotspot. We sought to test the hypothesis that lichenized fungi in this region have undergone a rapid radiation, following a single colonization event, giving rise to narrow endemics, as is characteristic of other lineages of plants. We extensively sampled specimens of the lichen genus Sticta in the Mascarene archipelago (mainly Réunion) and in Madagascar, mainly in the northern range (Amber Mt and Marojejy Mt) and produced the fungal ITS barcode sequence for 148 thalli.

Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon.

Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore the potential of this approach, we found 125 Collinear Orthologous Regions (COR) ranging from 1 to >10kb across nine genomes representing the Lecanoromycetes and Eurotiomycetes (Pezizomycotina, Ascomycota).

Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).

• Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the phylogenetic placement of section Hydrothyriae within Peltigera. We delimited species within the section and identified their symbiotic cyanobacteria.

Do photobiont switch and cephalodia emancipation act as evolutionary drivers in the lichen symbiosis? A case study in the Pannariaceae (Peltigerales).

Lichen 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.

Microsatellite primers in the Peltigera dolichorhiza complex (lichenized ascomycete, Peltigerales).

Premise Of The Study: Microsatellite primers were developed for the lichen-forming fungus Peltigera dolichorhiza to investigate partitioning of genetic variation in a widespread, morphologically and chemically variable taxon likely to represent a complex of cryptic lineages, including P. neopolydactyla. •

Methods And Results: Using next generation shotgun sequence reads, 331 primer pairs were designed to amplify microsatellite sequences from an African accession of P.