Description of the data and file structure

This submission includes seven datasets:

Bryoria_its_mcm7_igs_gapdh_mtssu_tsr1_align.fas. This is a six-locus data set to examine infrageneric classification of the lichen-forming fungal genus Bryoria. GAPDH = glyceraldehyde 3-phosphate dehydrogenase gene, IGS = intergenic spacer of the nuclear rDNA, its = nuclear ribosomal internal transcribed spacer region, mcm7 = minichromosome maintenance protein 7 gene, mtSSU = small subunit of the mitochondrial ribosomal DNA, Tsr1 = ribosome biogenesis protein

The following six data sets were used to examine phylogenetic relationships and species delimitation in section Divaricatae.
GAPDH_Divaricatae.fas.
igs_Divaricatae.fas
its_Divaricatae.fas
mcm7_Divaricatae.fas
mtssu_Divaricatae.fas
Tsr1_Divaricatae.fas

These are nucelotide sequences alignments (A=adenine, C=cytosine, G=guanine, T=thymine, N=ambiguous, -=deletion).

Sharing/Access information

Links to other publicly accessible locations of the data:

• Sequences are deposited in GenBank (https://www.ncbi.nlm.nih.gov/genbank/)

Data was derived from the following sources:

• Already published sequences were obtained from GenBank (https://www.ncbi.nlm.nih.gov/genbank/). New sequences were obtained from own material and herbarium specimens deposited in H, UPS, UBC, KPABG, OULU and KUN (https://sweetgum.nybg.org/science/ih/)

Code/Software

For all seven data sets, we performed maximum parsimony, maximum likelihood, and, Bayesian analyses. Parsimony analyses were performed in TNT version 1.1 for Windows (Goloboff et al. 2008) using the option Traditional Search with the following settings: random addition of sequences with 100 replicates and TBR branch swapping algorithm. Ten trees were saved for each replicate. The bootstrapping method as implemented in TNT was used with 1000 replicates to estimate node support. Maximum likelihood analyses were performed with RAxML v.8.1.15 (Stamatakis 2014) located at CSC IT center for Science (https://www.csc.fi/). We divided the data set into 23 partitions: ITS1, 5.8S, ITS2, IGS, mtSSU, each three codon positions of Mcm7, GAPDH and Tsr1, and introns of GAPDH. These partitions were analysed under the universal GTR-GAMMA model. Node support was estimated with 1000 bootstrap replicates using the rapid bootstrap algorithm.
For the Bayesian analyses, the optimal substitution model for each locus was calculated in jmodeltest (Posada 2008), using Akaike information criterion (AIC). The models selected were: TrNef+G for ITS1, IGS rDNA, GAPDH; JC for 5.8S; K80+G for ITS2; TrNef+I+G for Mcm7; SYM+I+G for mtSSU; SYM+G for Tsr1.
The Bayesian analyses were run in MrBayes 3.2.6 (Ronquist et al. 2012) in CIPRES Science Gateway v. 3.1 (Miller et al. 2010). For the concatenated analysis 23 partitions were considered and the models selected by jmodeltest were used. The posterior probabilities were approximated by sampling trees using Markov Chain Monte Carlo (MCMC). Two simultaneous runs with 20 000 000 generations each, starting with a random tree and employing 4 simultaneous chains, were executed. Every 1 000th tree was saved into a file. The first 25% trees were deleted as burn-in. The convergence between chains was assessed in Tracer v. 1.7 (Rambaut et al. 2018), plotting the likelihood versus generation number and the average standard deviation of split frequencies ( 0.01).