Species delimitation at a global scale reveals high species richness with complex biogeography and patterns of symbiont association in Peltigera section Peltigera (lichenized Ascomycota: Lecanoromycetes)

Abstract

This comprehensive phylogenetic revision of sections Peltigera and Retifoveatae of the cyanolichen genus Peltigera is based on DNA sequences from more than 500 specimens from five continents. We amplified five loci (nrITS, β-tubulin and three intergenic spacers part of colinear orthologous regions [COR]) for the mycobiont, and the rbcLX locus for the cyanobacterial partner Nostoc. Phylogenetic inferences (RAxML, BEAST) and species delimitation methods (bGMYC, bPTP, bPP) suggest the presence of 88 species in section Peltigera, including 50 species new to science, hence uncovering a surprisingly high proportion of previously unnoticed biodiversity. The hypervariable region in ITS1 (ITS1-HR) is a powerful marker to identify species within sections Peltigera and Retifoveatae. Most newly delimited species are restricted to a single biogeographic region, however, up to ten species have a nearly cosmopolitan distribution. The specificity of mycobionts in their association with Nostoc cyanobionts ranges from strict specialists (associate with only one Nostoc phylogroup) to broad generalists (up to eight Nostoc phylogroups uncovered), with widespread species recruiting a broader selection of Nostoc phylogroups than species with limited distributions. In contrast, species from the P. didactyla clade characterized by small thalli and asexual vegetative propagules (soredia) associate with fewer Nostoc phylogroups (i.e., are more specialized) despite their broad distributions, and show significantly higher rates of nucleotide substitutions.

Species diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera

“…We assembled a dataset of Peltigera-Nostoc interaction pairs summing up all information from the literature for which we could confidently assess the identity of the Peltigera species and Nostoc phylogroups or haplotypes (Chagnon et al, 2018;Lu et al, 2018;Magain, Miadlikowska, Goffinet, et al, 2017a;Magain, Miadlikowska, Mueller, et al, 2017b;Magain et al, 2018;Miadlikowska et al, 2014Miadlikowska et al, , 2018O'Brien, Miadlikowska, & Lutzoni, 2005;O'Brien, Miadlikowska, & Lutzoni, 2013;Pardo De la Hoz et al, 2018). The total dataset consisted of 1,026 thalli, or interaction pairs, representing 155 Peltigera species and 95 Nostoc phylogroups or haplotypes (Tables S1 and S2).…”

“…To infer a phylogeny for the entire genus Peltigera, we gathered published data from all currently validated species (Chagnon et al, 2018;Magain, Miadlikowska, Goffinet, et al, 2017a;Magain, Miadlikowska, Mueller, et al, 2017b;Magain et al, 2018;Miadlikowska et al, 2014Miadlikowska et al, , 2018Pardo De la Hoz et al, 2018) for seven loci (ITS, nrLSU, β-tubulin, RPB1, COR1b, COR3, COR16). We selected one representative per species with the highest number of sequenced loci, or two representatives per species when sets of available loci were mostly non-overlapping between two specimens of a species.…”

“…Because each locus was analysed separately in previous studies to detect potential topological conflicts, with appropriate corrections made when needed (Chagnon et al, 2018;Magain, Miadlikowska, Goffinet, et al, 2017a;Magain, Miadlikowska, Mueller, et al, 2017b;Magain et al, 2018;Miadlikowska et al, 2014Miadlikowska et al, , 2018Pardo De la Hoz et al, 2018), we concatenated these seven loci using in-house PERL scripts (Magain, 2018). Our concatenated dataset consisted of 205 specimens and 10,064 characters.…”

“…These modules include 1-to-1 strict F I G U R E 2 Close-ups of the seven-locus chronogram of the genus Peltigera: (a) POLY clade, that is, sections Chloropeltigera, Peltidea, Phlebia and Polydactylon, and (b) PELT clade, that is, sections Horizontales, Peltigera and Retifoveatae. Branch lengths are proportional to relative time, and each terminal tip represents a species indicated on the far right, or putative species resulting from recent studies (Magain, Miadlikowska, Goffinet, et al, 2017a;Magain et al, 2018;Pardo De La Hoz et al, 2018;Miadlikowska et al, 2018). The coloured capital letters immediately to the right of the terminal branch tips represent the network modules of each species, based on results of the modularity analyses (Figure 1).…”

New Estonian records: Lichenized fungi

“…-Peltigera castanea was described quite recently from North America (Canada) and belongs to Peltigera didactyla complex (Goffinet et al, 2003). This taxon is confirmed to be a well-delimited species occurring also in Eurasia (Russia, Krasnoyarsk Territory) (Magain et al, 2018). Peltigera cas tanea thallus is foliose, small, to 6-8 cm across; lobes to 1.0-1.5 cm wide, with a smooth, shiny, chestnut brown, mostly non-tomentose upper cortex.…”