Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies

Abstract

Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event

“…We used sets of homolog clusters generated prior to extracting orthologs for species tree inference using the Yang and Smith (2014) pipeline, derived from genomes and transcriptomes of representatives of five of the six legume subfamilies and an extensive eudicot outgroup (Table S1) assembled by Koenen et al (2020). We do not http://mc.manuscriptcentral.com/systbiol PHYLOGENOMIC COMPLEXITY AND POLYPLOIDY IN LEGUMES 11 include the monospecific subfamily Duparquetioideae for which large-scale nuclear genomic data are presently unavailable.…”

“…Additionally, an analysis was run with two additional polytomies within the legume backbone, since ILS likely occurred among the first divergences in the family (Koenen et al, 2020). All other internodes within the legume family are considered to be wellsupported (Koenen et al, 2020), suggesting that ILS will have less impact on these.…”

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

“…With the development of next-generation sequencing (NGS), complete plastome sequencing has increased dramatically. In recent years, phylogenomic studies of cp genomes have provided new insights into subfamilial relationships and species diversification within Fabaceae [ 18 , 19 , 20 ]. In Desmodieae, cp genomes of 10 species representing seven genera have been published [ 20 , 21 ], but the cp genomes of Christia and Urariopsis species are still unknown.…”

The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes

“…With the increased application of high-throughput sequencing technology, the number of characterized chloroplast genomes of angiosperms is increasing rapidly 55 . In this study, we found that the two newly sequenced Gleditsia species have similar quadripartite structure and gene contents to the published chloroplast genomes of other members of the Caesalpinioideae sub-family 15,[56][57][58] . According to phylogenetic analysis results, the genus Gleditsia forms a monophyletic clade with strong bootstrap values, which is consistent with the results of previous studies 22,[48][49][50] .…”