Skip to main content
Dryad

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

Cite this dataset

Boom, Arthur et al. (2024). Phylogenomics of Brachystegia (Fabaceae, Detarioideae): Insights into the origin of African miombo woodlands [Dataset]. Dryad. https://doi.org/10.5061/dryad.ngf1vhj28

Abstract

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.

README: Phylogenomics of Brachystegia (Fabaceae, Detarioideae): Insights into the Origin of African Miombo Woodlands

Targeted enrichment sequencing of 61 samples of Brachystegia and outgroup, using the Detarioideae baits set designed by Ojeda et al. (2019) [link to the study -> https://doi.org/10.1016/j.ympev.2019.05.002].

Data and File Structure

**global_DNA_alignment.fasta: Final alignment of 214,545 bp used for the RAxML-NG.

**BEAST-DNA_alignment-21-orthologs.fasta: Alignment of the 21 orthologs used for the BEAST analysis.

**BEAST-DNA_alignment-21-orthologs_additionnal_outgroups.fasta: Alignment of the 21 orthologs used for the BEAST analysis, with two additional outgroups.

**Individual-alignment: Folder containing 226 different text files (fasta). Each file corresponds to one of the DNA alignments used for gene tree inferences. The names of the different files correspond to the loci used as reference (for more detail, see dataset S2 file in Ojeda et al. (2019).

** Two outgroups (Aphanocalyx microphyllus and Tetraberlinia korupensis) were provided by the authors of [https://doi.org/10.1111/jbi.13971].

Funding

Fund for Scientific Research, Award: 5208718F

Fund for Scientific Research, Award: 5129216F

Fund for Scientific Research, Award: J.0292.17F

Fund for Scientific Research, Award: T.0075.23F

Belgian Federal Science Policy Office, Award: BR/132/A1/AFRIFORD