The Mediterranean region is a center of species and genetic diversity of many plant groups, which served as a source of recolonization of temperate regions of Eurasia in Holocene. We investigate the evolutionary history of species currently classified in
Lotus sect.
Bonjeanea in the context of the evolution of the genus
Lotus as a whole, using phylogenetic, phylogeographic and dating analyses. Of three species of the section,
L. rectus and
L. hirsutus have wide Mediterranean distribution while
L. strictus has a disjunctive range in Bulgaria, Turkey, Armenia, Eastern Kazakhstan, and adjacent parts of Russia and China. We used entire nuclear ribosomal ITS1-5.8S-ITS2 region (nrITS) and a plastid dataset (
rps16 and
trnL-F) to reconstruct phylogenetic relationships within
Lotus with an extended representation of
Bonjeanea group. We analyzed the phylogeographic patterns within each species based on the plastid dataset. For divergence time estimation, the nrITS dataset was analyzed. Our results confirmed the non-monophyletic nature of the section
Bonjeanea. They indicate that
Lotus is likely to have diverged about 15.87 (9.99–19.81) million years ago (Ma), which is much older than an earlier estimate of ca. 5.54 Ma. Estimated divergence ages within
L. strictus,
L. rectus, and
L. hisrutus (6.1, 4.94, and 4.16 Ma, respectively) well predate the onset of the current type of Mediterranean climate. Our data suggest that relatively ancient geological events and/or climatic changes apparently played roles in early diversification of
Lotus and its major clades, as well as in formation of phylogeographic patterns, in at least some species.
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