Data from: Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera

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.

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