Phylogenomics of Brachystegia (Fabaceae, Detarioideae): Insights into the origin of African miombo woodlands

Premise of study: Phylogenetic approaches can provide valuable insights on
how and when a biome emerged and developed using its structuring species.
In this context, Brachystegia Benth, a dominant genus of trees in miombo
woodlands, appears as a key witness of the history of the largest woodland
and savanna biome of Africa. Methods: We reconstructed the evolutionary
history of the genus using targeted-enrichment sequencing on
60 Brachystegia specimens for a near complete species sampling.
Phylogenomic inferences used supermatrix (RAxML-NG) and summary-method
(ASTRAL-III) approaches. Conflicts between species and gene trees were
assessed and the phylogeny was time-calibrated in BEAST. Introgression
between species was explored using Phylonet. Key results: Phylogenies are
globally congruent regardless of the method used. Most of the species were
recovered as monophyletic, unlike previous plastid phylogenetic
reconstructions where lineages were shared among geographically close
individuals independently of species identity. Still, most of the
individual gene trees have low levels of phylogenetic information and are
mostly in conflict with the reconstructed species trees, when informative.
It suggests incomplete lineage sorting and/or reticulate evolution, the
latter being supported by network analyses. BEAST analysis supports a
Pliocene origin for the genus, with most of the diversification events
dated to the Pliocene-Pleistocene. Conclusions: These results suggest a
recent origin of species of the miombo, congruently with their spatial
expansion documented from plastid data. Brachystegia species appear to
behave potentially as a syngameon, a group of interfertile but still
relatively well-delineated species, an aspect that deserves further
investigations.