The first comprehensive multilocus phylogeny of the lichenized genus Micarea (Ectolechiaceae, Ascomycota)
Data files
Jun 08, 2026 version files 788.28 KB
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combined_data_set_of_232_samples.fas
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README.md
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Abstract
We generated, for the first time, a multilocus phylogeny for Micarea that includes all the main lineages in order to assess phylogenetic relationships in the genus. We specifically examined whether Micarea is monophyletic and whether a broader sampling and the addition of further gene regions can increase the resolution and support in the backbone, and result in a more resolved and better supported phylogeny of Micarea as a whole. The phylogeny of Micarea was reconstructed using five loci (mtSSU rDNA, Mcm7, nuITS rDNA, RPB1 and RPB2) from a worldwide sample of 314 Micarea specimens representing 99 species. 969 new sequences were produced for this study, including molecular data from 18 previously unsequenced species. In the combined analyses, Micarea s. lat. is resolved as a monophyletic group if Fellhaneropsis and Szczawinskia are included, and consists of several strongly supported clades. Furthermore, Micareopsis is included in Micarea based on the separate phylogeny of the Mcm7 data set. We discuss different alternatives to classify the clades and consider the mesogeneric approach as the currently most reasonable taxonomic solution, i.e., to treat Clade M. crassipes, the sister clade to the rest of Micarea, as a separate genus under the name Helocarpon, and to include the remaining clades in the genus Micarea. We reduce Szczawinskia to synonymy with Micarea but conclude that more data are needed to resolve the status of Fellhaneropsis and Micareopsis. Our study shows that the genus contains as yet undescribed diversity. Four lineages are described as new species: Micarea arthonioides van den Boom, Aptroot, Kantelinen & Myllys, Micarea athromelaena Kantvilas, Myllys & Kantelinen, Micarea lignosorediata van den Boom, Aptroot, Kantelinen & Myllys and Micarea regalis Kantvilas & Myllys.
Dataset DOI: 10.5061/dryad.gqnk98t1p
Description of the data and file structure
For the present study, we obtained DNA extractions and sequence data from our previous studies of the genus Micarea (Launis & Myllys, Phytotaxa 409: 179–188 (2019); Launis & al., Lichenologist 51: 7–25. (2019), Mycologia 111: 574–592 (2019); Kantelinen & al., Lichenologist 53: 81–94 (2021), MycoKeys 106: 327–354 (2024)). As many specimens as possible for each species were included in the analyses to examine the infraspecific variation and species delimitation. Furthermore, we tried to cover geographical variation by selecting specimens from different continents. For these purposes, additional samples were collected in areas not included in our recent studies; that is, from Africa, Australia, Japan and East Asia and South America. In addition to our new material, sequences were downloaded from GenBank.
Five markers (two ribosomal RNA-coding and three protein-coding) were selected to infer the Micarea phylogeny: c. 1 kb region of the small subunit of the mitochondrial ribosomal DNA (mtSSU), the complete nuclear ribosomal internal transcribed spacer region (ITS), c. 0.6 kb of the minichromosome maintenance protein 7 gene (Mcm7), c. 0.5 kb (section A–D; see Matheny & al., 2002) of the largest subunit of the RNA polymerase II gene (RPB1), c. 0.5 kb of the second largest subunit of RNA polymerase II gene (RPB2) region 5–7, and c. 0.8 kb of RPB2 region 7–11. PCR products were purified and sequenced by Macrogen Inc., Amsterdam, the Netherlands (www.macrogen.com), or, alternatively, cleaned with ExoSAP (Affymetrix, Santa Clara, California, USA) and sequenced by the Institute for Molecular Medicine Finland FIMM Genomics unit supported by HiLIFE and Biocenter Finland FIMM Genomics. The resulting contig sequences of each specimen were assembled using the program Sequencher (Gene Codes Corp., Ann Arbor, MI, USA).
Files and variables
File: combined_data_set_of_232_samples.fas
Description: This is a five-locus data set to examine phylogenetic relationships in the lichenized fungal genus Micarea. mtSSU = small subunit of the mitochondrial ribosomal DNA (positions 1-740); minichromosome maintenance protein 7 gene (MCM7), partial cds (positions 741-1332); RNA polymerase II largest subunit (RPB1) gene, partial cds (positions 1333-1845); 5.8S ribosomal RNA gene, complete sequence (positions 1846-2015); RNA polymerase II second largest subunit (RPB2) gene, partial cds, region 7-11 (positions 2016-2797); RNA polymerase II second largest subunit (RPB2) gene, partial cds, region 5-7 (positions 2798-3298).
This is a nucelotide sequence alignment (A = adenine, C = cytosine, G = guanine, T = thymine, N = ambiguous, - = deletion).
Code/software
Phylogenetic relationships were inferred using maximum likelihood and Bayesian inference as optimality criteria. Maximum likelihood analysis was performed with RAxML v.8.1.15 (Stamatakis, 2014) located at CSC – IT center for Science (http://www.csc.fi). We divided the data set into 14 partitions: 5.8S, mtSSU and each of the three codon positions of Mcm7, RPB1, RPB2 5–7, and RPB2 7–11. These partitions were analyzed 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 the Akaike information criterion (AIC). The model selected for all loci was SYM+I+G. The Bayesian analyses were performed using MrBayes v. 3.2.6 (Ronquist & al., 2012). Posterior probabilities were approximated by sampling trees using Markov chain Monte Carlo (MCMC). Two simultaneous runs, each with 10 000 000 generations and employing four chains, were executed. Every 1000th tree was saved into a file. The first 25 % of trees were discarded as burn-in. Convergence between chains was assessed using Tracer v. 1.7 (Rambaut & al., 2018), plotting the likelihood versus generation number and the average standard deviation of split frequencies (≤ 0.003).
Access information
Other publicly accessible locations of the data:
- Sequences are deposited in GenBank (https://www.ncbi.nlm.nih.gov/genbank/)
- New taxa (four new species and three new combinations) are deposited in MycoBank (https://www.mycobank.org/)
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 BG, FR, H, HO, LG and UPS (https://sweetgum.nybg.org/science/ih/)