DOI: 10.5061/dryad.8cz8w9gqw
title: Discordance in a South African Memecylon clade (Melastomataceae): Evidence for reticulate evolution

description: 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.
description: The DNA sequences were obtained from silica-dried tissue samples
 of <i>Memecylon</i> that were collected from South Africa
 (KwaZulu-Natal, Eastern Cape, and Mpumalanga provinces). These samples
 include <i>Memecylon natalense</i>, <i>M.
 bachmannii,</i> and <i>M. australissimum. </i>Additional
 samples of outgroups, <i>M. soutpansbergense </i>and<i>
 M. kosiense, </i>were collected from Limpopo and KwaZulu-Natal
 provinces. Target capture was employed to enrich genomic regions of
 interest for the samples. The probe set from Jantzen et al.(2020) was used
 to capture low-copy nuclear (LCN) genes. Total genomic DNAs were extracted
 following a modified CTAB extraction protocol for Melastomataceae (Jantzen
 et al. 2020). Preparation and quantification of double-barcoded genomic
 libraries and target enrichment were performed by RAPiD Genomics,
 Gainesville, Florida, USA. All accessions were processed as described in
 Jantzen et al. (2020). Cleaned reads were assembled with HybPiper v.1.3.1
 using the template sequences used for probe design as references (Johnson
 et al. 2016). Potential paralogs identified by HybPiper scripts were
 removed (Jantzen et al. 2020). The LCN sequences were individually aligned
 using MAFFT v7.215 (Katoh and Standley 2013), with the default gap opening
 penalty. The alignment was then trimmed using trimAl v1.2
 (Capella-Gutierrez et al. 2009) with a gap threshold of 0.9. Gene trees
 were generated for each of the individual gene alignments using Maximum
 Likelihood (ML) in RAxML v8 (Stamatakis 2014), with 500 rapid bootstrap
 pseudoreplicates combined with a ML tree search using the GTRGAMMA
 model. The remaining genes were concatenated, and a partition scheme was
 generated using Phyx v8.2.0 (Brown et al. 2017). Although maximum
 Likelihood analyses of the concatenated dataset were repeated for
 supercontigs, exons, and introns using the RAxML parameters as described
 above, we archived phylogenies only from introns here because 87
 individual introns were
 informative at the population level and resulted in phylogenies with
 higher bootstrap support (BS) compared to the individual
 supercontig and exon datasets. To infer a coalescent species
 tree, 87 ML gene trees (derived from introns) generated from RAxML were
 input to ASTRAL-III v5.0.3 (Zhang et al. 2018).
description: The alignments and phylogenies included in this dataset are
 generated only from 87 introns because they were informative at the
 population level of this South African <em>Memecylon</em>.
 Cleaned sequence reads used to generate this data have been deposited on
 the NCBI Sequence Read Archive (PRJNA576018).