IMA Fungus 11(1): e33872, doi: 10.1186/s43008-020-00051-x

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

Felix Grewe^‡, Claudio Ametrano^§, Todd J. Widhelm^§, Steven Leavitt^|, Isabel Distefano^¶, Wetchasart Polyiam^#, David Pizarro^¤, Mats Wedin^«, Ana Crespo^¤, Pradeep K. Divakar^¤, H. Thorsten Lumbsch^¶

‡ The Field Museum, Chicago, United States of America§ Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, Chicago| Brigham Young University, Department of Biology and M. L. Bean Life Science Museum, Provo¶ Grainger Bioinformatics Center, Field Museum, Department of Science and Education, Chicago# Ramkhamhaeng University, Lichen Research Unit, Biology Department, Faculty of Science, Bangkok, Thailand¤ Universidad Complutense de Madrid, Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Madrid, Spain« Swedish Museum of Natural History, Department of Botany, Stockholm, Sweden

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Citation: Grewe F, Ametrano C, Widhelm TJ, Leavitt S, Distefano I, Polyiam W, Pizarro D, Wedin M, Crespo A, Divakar PK, Lumbsch HT (2020) Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota). IMA Fungus 11(1): e33872. https://doi.org/10.1186/s43008-020-00051-x

Abstract

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.

Keywords

Next-generation sequencing, Target capture, HybPiper, Phylogenomics, Maximum likelihood, Bayesian interference, ASTRAL, Parmotrema, Parmelioideae, Protoparmelioideae