DOI: 10.5061/dryad.5rm6d
title: Data from: Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae

description: 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.
description: Supplementary Table
 S1Specimens included in
 the present study.Supp_Table_S1.xlsxSupplementary tables S2 - S4_ and figure S1 - S7Supplementary 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.pdfSupplementary text file T1.Representative sequences from each of the 69 OTUs.Supp_Text_T1_v1.fastaComplete Trebouxia ITS alignmentComplete Trebouxia ITS alignment (n=2356), clades 'A', 'G', 'I', and 'S'.ITS_alignment_21May2015_Final.nexTrebouxia clade 'A' ITS alignmentAlignment of all Trebouxia ITS sequences belonging to the T. arboricola/gigantea cladeITS_clade_A_21May2015_Final.nexTrebouxia clade 'G' ITS alignmentAlignment of all Trebouxia ITS sequences belonging to the T. galapagensis/usneae cladeITS_clade_G_21May2015_Final.nexTrebouxia clade 'I' ITS alignmentAlignment of all Trebouxia ITS sequences belonging to the T. impressa/gelatinosa cladeITS_clade_I_21May2015_Final.nexTrebouxia clade 'S' ITS alignmentAlignment of all Trebouxia ITS sequences belonging to the T. simplex/’letharii’/jamesii cladeITS_clade_S_21May2015_Final.nexConcatenated ITS, COXII, rbcL, and psbJ matrix for representatives of the T. arboricola/gigantea groupConcatenated ITS, COXII, rbcL, and psbJ matrix for representatives of the T. arboricola/gigantea groupITS_COX_rbcL_psbJ_21May2015v1.nex