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

Leavitt SD, Kraichak E, Nelsen MP, Altermann S, Divakar PK, Alors D, Esslinger TL, Crespo A, Lumbsch HT

Date Published: June 11, 2015

DOI: http://dx.doi.org/10.5061/dryad.5rm6d

 

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Title Supplementary Table S1
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Description Specimens included in the present study.
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Title Supplementary tables S2 - S4_ and figure S1 - S7
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Description 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.
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Title Supplementary text file T1.
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Description Representative sequences from each of the 69 OTUs.
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Title Complete Trebouxia ITS alignment
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Description Complete Trebouxia ITS alignment (n=2356), clades 'A', 'G', 'I', and 'S'.
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Title Trebouxia clade 'A' ITS alignment
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Description Alignment of all Trebouxia ITS sequences belonging to the T. arboricola/gigantea clade
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Title Trebouxia clade 'G' ITS alignment
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Description Alignment of all Trebouxia ITS sequences belonging to the T. galapagensis/usneae clade
Download ITS_clade_G_21May2015_Final.nex (14.34 Kb)
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Title Trebouxia clade 'I' ITS alignment
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Description Alignment of all Trebouxia ITS sequences belonging to the T. impressa/gelatinosa clade
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Title Trebouxia clade 'S' ITS alignment
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Description Alignment of all Trebouxia ITS sequences belonging to the T. simplex/’letharii’/jamesii clade
Download ITS_clade_S_21May2015_Final.nex (363.2 Kb)
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Title Concatenated ITS, COXII, rbcL, and psbJ matrix for representatives of the T. arboricola/gigantea group
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Description Concatenated ITS, COXII, rbcL, and psbJ matrix for representatives of the T. arboricola/gigantea group
Download ITS_COX_rbcL_psbJ_21May2015v1.nex (638.7 Kb)
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When using this data, please cite the original publication:

Leavitt SD, Kraichak E, Nelsen MP, Altermann S, Divakar PK, Alors D, Esslinger TL, Crespo A, Lumbsch HT (2015) Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae. Molecular Ecology 24(14): 3779–3797. http://dx.doi.org/10.1111/mec.13271

Additionally, please cite the Dryad data package:

Leavitt SD, Kraichak E, Nelsen MP, Altermann S, Divakar PK, Alors D, Esslinger TL, Crespo A, Lumbsch HT (2015) 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. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.5rm6d
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