Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)

Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow

Multiple, distinct intercontinental lineages but isolation of Australian populations in a cosmopolitan lichen-forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota)

Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions. The lichen-forming fungal species Psora decipiens is found on all continents, except Antarctica and occurs in BSCs across diverse habitats, ranging from hot, arid deserts to alpine habitats. In order to better understand factors that shape population structure in cosmopolitan lichen-forming fungal species, we investigated biogeographic patterns in the cosmopolitan taxon P. decipiens, along with the closely related taxa P. crenata and P. saviczii. We generated a multi-locus sequence dataset based on a worldwide sampling of these taxa in order to reconstruct evolutionary relationships and explore phylogeographic patterns. Both P. crenata and P. decipiens were not recovered as monophyletic; and P. saviczii specimens were recovered as a monophyletic clade closely related to a number of lineages comprised of specimens representing P. decipiens. Striking phylogeographic patterns were observed for P. crenata, with populations from distinct geographic regions belonging to well-separated, monophyletic lineages. South African populations of P. crenata were further divided into well-supported sub-clades. While well-supported phylogenetic substructure was also observed for the nominal taxon P. decipiens, nearly all lineages were comprised of specimens collected from intercontinental populations. However, all Australian specimens representing P. decipiens were recovered within a single well-supported monophyletic clade consisting solely of Australian samples. Our study supports up to 10 candidate species-level lineages in P. decipiens, based on genealogical concordance and coalescent-based species delimitation analyses. Our results support the general pattern of the biogeographic isolation of lichen-forming fungal populations in Australia, even in cases where closely related congeners have documented intercontinental distributions. Our study has important implications for understanding factors influencing diversification and distributions of lichens associated with BSC.This research was funded, in part, by a start-up grant from BYU College of Life Sciences to SL; MarW’s and MatW’s work was done within the European Soil Crust Project SCIN (Büdel et al., 2014) funded by the ERA-Net BiodivERsA program, with the national funder The Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS)

Python scripting for network management : PyMIP - TeMIP made simple

Validerat; 20101217 (root

Python scripting for network management : PyMIP - TeMIP made simple

Validerat; 20101217 (root

A monograph of the genus Placomaronea

A monograph of the genus Placomaronea is presented; all species described earlier are revised, a total of six species is recognized, and an identification key is presented. In addition to the three previously known species, P. candelarioides, P. lambii and P. mendozae, three new species are described: Placomaronea kaernefeltii is a large rosette-like species known from one locality in northernmost Chile; Placomaronea fuegiana is a bullate, areolate species described from Tierra del Fuego, Argentina; Placomaronea minima is a small, areolate to minutely lobate species described from Chile and Argentina, and is the first species of Placomaronea to be reported from the African continent. In a phylogenetic analysis of nuclear ITS rDNA, Placomaronea is shown to form a monophyletic group within the Candelariales