Mid-Pleistocene origin and phylogeographical signatures of recurrent expansion-fragmentation of a highly inbred and endangered African timber legume

Abstract Past climatic oscillations have influenced the genetic diversity and distribution patterns of tropical African tree species, and possibly their mating system. To explore these effects, we investigated the phylogeography of Pericopsis elata (Fabaceae), an endangered timber species with a high selfing rate and a fragmented Guineo-Congolian distribution with three gene pools: Upper Guinea (UG, west Africa), the Sangha River Interval (SRI, western Central Africa), and Congolia (C, Congo Basin). Our dated phylogeny of 51 plastomes indicates that P. elata diverged from P. angolensis, a dry woodland species, during the Mid-Pleistocene and had spread to UG by 210 000 years ago. Central African plastomes diverged 99 000 years ago but those from the SRI show more recent divergence. Nuclear microsatellites confirm the strong differentiation between the C and SRI clusters, and reveal contrasting evolutionary histories. While the C cluster exhibited moderate inbreeding and secondary selfing rate, the SRI cluster displayed a westward decay of diversity with high secondary selfing rate and strong fine-scale spatial genetic structure. Our findings suggest recurrent range expansion–fragmentation of P. elata since the Mid-Pleistocene, with a probable refugium in northern Republic of Congo, followed by a recent westward expansion into Cameroon facilitated by selfing, providing clues about the vegetation history of the SRI. The genetic peculiarities of the different gene pools must be considered in efforts to conserve and exploit this species sustainably.