Data from: Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes

Unresolved questions about evolution of the large and diverse legume
family include the timing of polyploidy (whole-genome duplication; WGDs)
relative to the origin of the major lineages within the Fabaceae and to
the origin of symbiotic nitrogen fixation. Previous work has established
that a WGD affects most lineages in the Papilionoideae and occurred some
time after the divergence of the papilionoid and mimosoid clades, but the
exact timing has been unknown. The history of WGD has also not been
established for legume lineages outside the Papilionoideae. We
investigated the presence and timing of WGDs in the legumes by querying
thousands of phylogenetic trees constructed from transcriptome and genome
data from 20 diverse legumes and 17 outgroup species. The timing of
duplications in the gene trees indicates that the papilionoid WGD occurred
in the common ancestor of all papilionoids. The earliest diverging
lineages of the Papilionoideae include both nodulating taxa such as the
genistoids (e.g. lupin), dalbergioids (e.g. peanut), phaseoloids (e.g.
beans), and galegoids (= Hologalegina, e.g. clovers), and clades with
non-nodulating taxa including Xanthocercis and Cladrastis (evaluated in
this study). We also found evidence for several independent WGDs near the
base of other major legume lineages, including the
Mimosoid-Cassiinae-Caesalpinieae (MCC), Detarieae, and Cercideae clades.
Nodulation is found in the MCC and papilionoid clades, both of which
experienced ancestral WGDs. However, there are numerous non-nodulating
lineages in both clades, making it unclear whether the phylogenetic
distribution of nodulation is due to independent gains or a single origin
followed by multiple losses.