Plastome sequences shed light on phylogenetic relationships, divergence time, and biogeography of the enigmatic endemism Eokochia saxicola (Amaranthaceae)

Abstract Eokochia saxicola is one of the rarest plants in Europe and together with Spirobassia hirsuta they are the only Eurasian members of the Chenolea clade (Camphorosmeae, Amaranthaceae). This is a relict clade represented by only six species with a highly disjoint distribution in four continents. To investigate the phylogenetic origin and biogeographical history of E. saxicola we performed a plastome sequence analysis of E. saxicola and its related S. hirsuta and compared their plastomes with related Amaranthaceae plastomes. The investigation revealed a progressive plastid genome size reduction, from E. saxicola to S. hirsuta, ruling out a progenitor-derivative origin of the rare endemism from the widespread S. hirsuta. Plastome phylogenetic analysis also offered insights into the branching lineages of the Chenolea clade, revealing E. saxicola and S. hirsuta as sister taxa to Bassia. Camphorosmeae originated towards the end of the Oligocene, and Bassia emerged as a vicariant sister taxon to E. saxicola and S. hirsuta, with an estimated divergence time of 9.7 Mya. Ancestral area reconstruction and divergence time estimation suggest a vicariant origin for the endemic perennial E. saxicola and for the widespread annual S. hirsuta ~4 Mya in the European continent, a much more recent time than previously estimated.