Phylogenetic relationships and divergent evolution in Pueraria sensu stricto (Fabaceae) based on plastid genomes and...

Despite progress in resolving the polyphyly of Pueraria (Fabaceae) based on multilocus phylogenetic studies, uncertainty remains especially for deep, or backbone relationships among closely related taxa or clades within Pueraria sensu stricto, suggesting a classic case of reticulate evolution.

Comparative chloroplast genomic analysis across 13 Pueraria s.l. species and varieties revealed that simple sequence repeats (SSRs) are abundant and predominantly composed of adenine (A) and thymine (T). Complete comparison and sliding window analysis further demonstrated that non-coding regions exhibited greater sequence divergence than the coding regions. Seventeen highly variable loci such as rpoC2 and ycf1 were detected as potential molecular markers for Pueraria s.l. species identification. Phylogenetic analyses of complete plastomes and nrITS sequences revealed Pueraria s.s. as a monophyletic group, characterized by dorsifixed stipules and the absence of canavanine. These traits show multiple independent transitions across legumes, indicating highly dynamic evolution. Cytonuclear discordance, supported by coalescent simulations, species tree methods and split-network, provides strong evidence of introgression and/or hybridization within Pueraria s.s. Specifically, P. montana var. lobata and P. montana var. thomsonii formed a well-supported clade suggesting that they should be treated as a species or species complex, while P. montana var. culaishanensis nested within P. montana var. montana.

This study offers new insights into the taxonomy and systematic relationships of Pueraria s.s. by integrating comparative chloroplast genomics, phylogenetic inference, and trait evolution. These results enhance our understanding of the lineages within Pueraria s.s. that have undergone reticulate evolution, and inform future studies on legume systematics and adaptive evolution.