Discordance in a South African Memecylon Clade (Melastomataceae): Evidence for Reticulate Evolution

Abstract

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. A prior study showed that, despite their morphological diversity, three South African Memecylon taxa in Melastomataceae (Memecylon 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 single-nucleotide polymorphisms (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 for conservation within the South African Memecylon clade.