10.5061/DRYAD.5RM6D
Leavitt, Steven D.
Field Museum of Natural History
University of Chicago
Kraichak, Ekaphan
Field Museum of Natural History
Kasetsart University
Nelsen, Matthew P.
Stanford University
Altermann, Susanne
Complutense University of Madrid
Divakar, Pradeep K.
Complutense University of Madrid
Alors, David
Complutense University of Madrid
Esslinger, Theodore L.
North Dakota State University
Crespo, Ana
Complutense University of Madrid
Lumbsch, H. Thorsten
Field Museum of Natural History
Lumbsch, Thorsten
Field Museum of Natural History
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
dataset
2015
Trebouxia
specificity
photobiont
Coevolution
mycobiont
2015-06-11T16:52:22Z
2015-06-11T16:52:22Z
en
https://doi.org/10.1111/mec.13271
6325517 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 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