Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.
Supplementary Table S1
Specimens included in the present study.
Supp_Table_S1.xlsx
Supplementary tables S2 - S4_ and figure S1 - S7
Supplementary Table S2. Summary of the taxonomic and geographic sampling of fungal genera for this study.
Supplementary Table S3. Specificity indices for Trebouxia OTUs represented by ≥ 10 sequences per OTU, based on fungal genera included in this study.
Supplementary Table S4. Summary of OTUs inferred using the ABGD detection program (Puillandre et al. 2012) represented by at least ten sequences and/or including sequences generated from UTEX and SAG cultures (UTEX and SAG cultures are shown in bold). Cultures and/or provisional names from previous studies, geographic distributions, and associated mycobiont hosts are reported. Other lichen mycobiont genera associated with Trebouxia OTUs were inferred using a BLAST search against the GenBank Nucleotide sequence database (searched 15 Nov 2014), where sequences with ≥ 98% similarity to a representative sequence from each OTU were assumed to belong to the OTU. The majority of OTUs were largely consistent with 97.5% sequence similarity clusters, with the exception of OTU ‘I01’, which was split into ten OTUs at 97.5%. The 97.5% sequence similarity clusters for OTUs ‘I01’ are shown parenthetically for each mycobiont host.
Supplementary Figure S1. Relative proportion of Trebouxia OTUs associated with sampled fungal genera
Supplementary Figure S2. ITS gene tree for a subset of specimens in the T. arboricola/gigantea group inferred using the program RAxML.
Supplementary Figure S3. Mitochondrial COXII gene tree for a subset of specimens in the T. arboricola/gigantea group inferred using the program RAxML.
Supplementary Figure S4. Chloroplast rbcL gene tree for a subset of specimens in the T. arboricola/gigantea group inferred using the program RAxML.
Supplementary Figure S5. Chloroplast psbJ-L gene tree for a subset of specimens in the T. arboricola/gigantea group inferred using the program RAxML. Ambiguous regions of the alignment were removed using the program Gblocks.
Supplementary Figure S6. Chloroplast topology for a subset of specimens in the T. arboricola/gigantea group inferred from concatenated rbcL and psJ-L alignments using the program RAxML.
Supplementary Figure S7. A “total evidence” phylogeny for the T. arboricola/gigantea, inferred from concatenated nuclear ITS, mitochondrial COXII, and the chloroplast markers rbcL and psbJ-L using the program RAxML.
tables2_4_figsS1_S7.pdf
Supplementary text file T1.
Representative sequences from each of the 69 OTUs.
Supp_Text_T1_v1.fasta
Complete Trebouxia ITS alignment
Complete Trebouxia ITS alignment (n=2356), clades 'A', 'G', 'I', and 'S'.
ITS_alignment_21May2015_Final.nex
Trebouxia clade 'A' ITS alignment
Alignment of all Trebouxia ITS sequences belonging to the T. arboricola/gigantea clade
ITS_clade_A_21May2015_Final.nex
Trebouxia clade 'G' ITS alignment
Alignment of all Trebouxia ITS sequences belonging to the T. galapagensis/usneae clade
ITS_clade_G_21May2015_Final.nex
Trebouxia clade 'I' ITS alignment
Alignment of all Trebouxia ITS sequences belonging to the T. impressa/gelatinosa clade
ITS_clade_I_21May2015_Final.nex
Trebouxia clade 'S' ITS alignment
Alignment of all Trebouxia ITS sequences belonging to the T. simplex/’letharii’/jamesii clade
ITS_clade_S_21May2015_Final.nex
Concatenated ITS, COXII, rbcL, and psbJ matrix for representatives of the T. arboricola/gigantea group
Concatenated ITS, COXII, rbcL, and psbJ matrix for representatives of the T. arboricola/gigantea group
ITS_COX_rbcL_psbJ_21May2015v1.nex