Discordance in a South African Memecylon clade (Melastomataceae): Evidence for reticulate evolution

Premise of research. Evergreen forests in eastern South Africa have high
biodiversity but are limited in extent and have a highly fragmented
distribution. Populations of forest plants are thus geographically
isolated, and fine-scale evolutionary studies of these lineages might
yield important insights into the history and assembly of the forests
themselves. Despite their morphological diversity, a prior study showed
that three South African Memecylon taxa in Melastomataceae (M.
natalense, M. bachmannii, and M. australissimum) had
almost identical nuclear ribosomal spacer sequences. Our study
investigates phylogenetic relationships within this clade using multiple
samples collected across populations and a next-generation phylogenomic
approach. Methodology. We used 87 low-copy nuclear (LCN) loci to examine
relationships among these taxa using both concatenated and coalescent
methods. We further used LCN loci to estimate phylogenetic networks and
SNPs derived from LCN genes for STRUCTURE analysis of South African
Memecylon populations. Finally, we employed two approaches (flow cytometry
and SNPs) to infer the ploidy levels of these three taxa. Pivotal results.
Our investigations showed discordance among gene trees and the species
tree, and low statistical support for relationships indicating that
species monophyly cannot be recovered from this phylogenomic analysis.
Phylogenetic networks and population structures showed that the South
African Memecylon clade may be affected by gene flow and reticulate
evolution. Flow cytometry and SNP-based estimations provided evidence for
polyploidy within this group. Conclusions. We found no evidence of
monophyly for species within the South African Memecylon clade, which we
infer to be the consequence of reticulation and recent and rapid
evolution. More cytological studies and genomic data are needed to
elucidate the evolutionary history of this group. Additionally, our study
identifies priority populations within the South African Memecylon clade
for conservation.