DOI: 10.5061/dryad.625tn
title: Data from: Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera

description: How species interactions shape global biodiversity and influence
 diversification is a central – but also data-hungry – question in
 evolutionary ecology. Microbially-based mutualisms are widespread and
 could cause diversification by ameliorating stress and thus allowing
 organisms to colonize and adapt to otherwise unsuitable habitats. Yet the
 role of these interactions in generating species diversity has received
 limited attention, especially across large taxonomic groups. In the
 massive angiosperm family Leguminosae, plants often associate with
 root-nodulating bacteria that ameliorate nutrient stress by fixing
 atmospheric nitrogen. These symbioses are ecologically-important
 interactions, influencing community assembly, diversity, and succession,
 contributing ~100-290 million tons of N annually to natural ecosystems,
 and enhancing growth of agronomically-important forage and crop plants
 worldwide. In recent work attempting to determine whether mutualism with
 N-fixing bacteria led to increased diversification across legumes, we were
 unable to definitively resolve the relationship between diversification
 and nodulation. We did, however, succeed in compiling a very large
 searchable, analysis-ready database of nodulation data for 749 legume
 genera (98% of Leguminosae genera; LPWG 2017), which, along with
 associated phylogenetic information, will provide a valuable resource for
 future work addressing this question and others. For each legume genus, we
 provide information about the species richness, frequency of nodulation,
 subfamily association, and topological correspondence with an additional
 data set of 100 phylogenetic trees curated for database compatibility. We
 found 386 legume genera were confirmed nodulators (i.e., all species
 examined for nodulation nodulated), 116 were non-nodulating, 4 were
 variable (i.e., containing both confirmed nodulators and confirmed
 non-nodulators), and 243 had not been examined for nodulation in published
 studies. Interestingly, data exploration revealed that nodulating legume
 genera are ~3× more species-rich than non-nodulating genera, but we did
 not find evidence that this difference in diversity was due to differences
 in net diversification rate. Our metadata file describes in more detail
 the structure of these data that provide a foundational resource for
 future work as more nodulation data become available, and as greater
 phylogenetic resolution of this ca. 19,500-species family comes into
 focus.
description: DataS1 - Nodulation and
 phylogenetic data for legume genera.DataS1.zip includes the
 following files: [1] File name: Nodulation_clade.csv; Size: 749 rows
 excluding header; Format and storage mode: comma-separated values format,
 no compression; Header Information: See Header_explanation.csv;
 Description: Analysis-ready, searchable database of nodulation data for
 749 legume genera with species diversity, subfamily associations, and
 phylogenetic information corresponding to family-wide trees (curated and
 pruned from LPWG 2013; available in pruned_tree.zip). [2] File name:
 Header_explanation.csv; Size: 6 rows excluding header; Format and storage
 mode: comma-separated values format, no compression; Header Information:
 NA; Description: Table providing description of each column contents of
 Nodulation_clade.csv. [3] File name: pruned_tree.zip
 (pruned.legume.1.date.tre - pruned.legume.100.date.tre); Size: 100
 phylogenetic trees; Format and storage mode: zip (.tre format within zip
 folder); Header Information: NA; Description: The set of 100 sampled trees
 from the LPWG (2013) pruned down to 157 shared or “consensus” clades to
 achieve a distribution of backbone phylogenies representing the deep
 phylogenetic structure of the legumes. Our curation and pruning allows for
 compatibility of phylogenetic information with available nodulation data
 (available in Nodulation_clade.csv database). [4] Table S1.pdf; Size: 1
 pg; Format and storage mode: pdf, no compression; Header Information:
 Provided in file; Description: Phylogenetic ANOVA result – difference in
 net diversification rates between nodulating and non-nodulating legume
 clades with ‘unknown’ data included as either all “nodulating’ or all
 ‘non-nodulating’.DataS1.zip