DOI: 10.5061/dryad.r4xgxd2b1
title: Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees

description: Aim: Miombo woodlands form a characteristic vegetation type covering 2.7
 million km2 in southern and eastern Africa. Despite their wide
 geographical extent, their origin, floristic and spatial evolution through
 time remain understudied. To fill this gap, we studied the evolution of
 Brachystegia trees, one of the most representative genera of these
 woodlands (20 species), also represented in Guineo-Congolian rain forests
 (8 species). Location: Tropical Africa, Guineo-Congolian forests and
 Zambezian savannahs. Methods: We used a genome skimming approach to
 sequence the plastomes of 45 Brachystegia samples, covering 25 of the 29
 existing species, and one outgroup (Julbernardia paniculata). The
 phylogeny of the plastomes was reconstructed and time-calibrated. We
 tested if the genetic divergence between lineages reflected taxonomic
 and/or geographic distances using Mantel tests. Finally, we inferred the
 evolutionary history of Brachystegia based on the age and spatial
 distribution of its lineages. Results: Surprisingly, species represented
 by multiple specimens appear rarely monophyletic while plastid clades
 display strong geographical structuring, independently of the species. Two
 main clades separate woodland and rain forest species, which diverged
 during the late Miocene-Pliocene (95% HPD = 2.78-8.59 Ma). In miombo
 woodlands, three subclades occur in parapatry along an East-West axis,
 ranging from Angola to East Africa. Their divergence started from the
 Plio-Pleistocene (95% HPD = 1.17-3.69 Ma). Divergence dates (TMRCA) within
 miombo subclades decrease from East Africa (1.53 Ma) to Angola (0.76 Ma).
 Main Conclusions: Brachystegia plastomes appear unreliable to identify
 species, probably due to species introgression leading to recurrent
 chloroplast captures. However, they prove very informative for tracking
 the past dynamics of the genus, and suggest a historical westwards
 expansion of miombo Brachystegia, and possibly of miombo vegetation,
 during the Plio-Pleistocene. Further investigations using nuclear DNA are
 needed to assess the species tree as well as speciation and hybridisation
 events between species. 
description: Genome skimming on 45 <em>Brachystegia</em> samples,
 including 25 of the 29 existing species. It allowed us to obtain a
 plastid alignment of 100,400 bp
 (i.e. Plastid_alignment_100400bp.fasta). 
 Additionnal alignment of 45 concatenated plastid genes for 24
 species. 13 <em>Detarioideae</em>, 4
 <em>Dialioideae</em> and 1 <em>Quillajaceae</em>
 sequences came from Koenen et al. (2020). We added data from five
 additional<em> Brachystegia</em> and
 one <em>Julbernardia</em> specimens, sequenced for this study
 using a genome skimming approach
 (i.e. Plastid_45_genes_alignment.fasta).
 Reference: Koenen, Erik JM, et al.
 "Large‐scale genomic sequence data resolve the deepest divergences in
 the legume phylogeny and support a near‐simultaneous evolutionary origin
 of all six subfamilies." New Phytologist 225.3 (2020):
 1355-1369.