Tropical crustose lichens account for a substantial portion of the biodiversity of lichenized fungi, but we know comparatively little about their species identity, evolutionary history and photobiont interactions. We used a collection of lecanoroid lichens from Bolivia to fill gaps in our understanding of tropical Lecanoraceae phylogeny and investigate patterns in the mycobiont–Trebouxia interaction. Out of a total sampling of over 550 specimens, we selected approximately 100 specimens with diverse morphologies and ecologies for molecular investigation. Mycobiont nrITS and nrLSU sequence data show that most specimens fall into three genus-level clades: Lecanora s.str., Myriolecis, and the Lecanora polytropa group. Within Lecanora s.str., relatively few sequences correspond to previously sequenced species, and morphological study is required to determine whether the many unique sequences represent new species or previously described species for which molecular data were lacking. We also obtained photobiont nrITS sequences from the same specimens and inferred their phylogenetic relationships within the genus Trebouxia. Some of the photobionts represent previously described Trebouxia species, including T. corticola, T. gelatinosa, T. incrustata s.lat., T. jamesii, T. simplex, and T. usneae s.lat. However, most of the photobionts belong to well-supported groups that have been detected as clades or OTUs in previous studies but have not been formally described as species, and one small clade comprised only of sequences generated in this study that represent a previously unknown species. In general, saxicolous species of Lecanora s.str. associate with different Trebouxia species than their corticolous counterparts. This research has received funding from the National Science Centre, Poland (project no. 2016/21/B/NZ8/02463).
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