DOI: 10.5061/dryad.ksn02v72w
title: Data from: Evolution and biogeography of Memecylon

description: Premise The woody plant
 group Memecylon (Melastomataceae) is a large clade
 occupying diverse forest habitats in the Old World tropics and exhibiting
 high regional endemism. Its phylogenetic relationships have been
 previously studied using ribosomal DNA with extensive sampling from Africa
 and Madagascar. However, divergence times, biogeography, and character
 evolution of Memecylon remain uninvestigated. We present
 a phylogenomic analysis of Memecylon to provide a broad
 evolutionary perspective of this clade. Methods One hundred supercontigs
 of 67 Memecylon taxa were harvested from target
 enrichment. The data were subjected to coalescent and concatenated
 phylogenetic analyses. A timeline was provided
 for Memecylon evolution using fossils and secondary
 calibration. The calibrated Memecylon phylogeny was used
 to elucidate its biogeography and ancestral character states. Results
 Relationships recovered by the phylogenomic analyses are strongly
 supported in both maximum likelihood and coalescent-based species
 trees. Memecylon is inferred to have originated in
 Africa in the Eocene and subsequently dispersed predominantly eastward via
 long-distance dispersal (LDD), although a reverse dispersal from South
 Asia westward to the Seychelles was postulated. Morphological data
 exhibited high levels of homoplasy, but also showed that several
 vegetative and reproductive characters were phylogenetically informative.
 Conclusions The current distribution
 of Memecylon appears to be the result of multiple
 ancestral LDD events. Our results demonstrate the importance of the
 combined effect of geographic and paleoclimatic factors in shaping the
 distribution of this group in the Old World
 tropics. Memecylon includes a number of evolutionarily
 derived morphological features that contribute to diversity within the
 clade.
description: Silica-dried tissue samples of
 <i>Memecylon</i> leaves were collected in the field, mainly
 from Sri Lanka, India, Singapore, Thailand, Philippines, Indonesia,
 Seychelles, Madagascar, and South Africa. Additional samples of
 <i>Memecylon</i> and an outgroup, <i>Mouriri,
 </i>were taken from herbarium specimens. Total genomic DNA was
 extracted following a modified CTAB extraction protocol (Jantzen et al.,
 2020). Target-capture was employed to enrich genomic regions of interest
 for the rest of the samples. All accessions were processed according to a
 workflow described in detail in Jantzen et al. (2020). Cleaned
 target-capture reads were assembled with the Burrows-Wheeler alignment
 version of HybPiper v.1.3.1 using the template sequences used for probe
 design as references (Johnson et al., 2016). Genome-skims were assembled
 using a modified HybPiper script. The postprocessing scripts in the
 HybPiper were used to retrieve intron regions flanking targeted exons and
 the supercontigs (Johnson et al., 2016). The supercontigs were
 individually aligned using MAFFT v7.215 (Katoh and Standley, 2013). The
 alignments were trimmed using trimAl v1.2 (Capella-Gutiérrez et al.,
 2009). Gene trees were generated for each of the individual gene
 alignments using maximum-likelihood (ML) analysis performed with RAxML
 v8.2.12 (Stamatakis, 2014), assuming a GTRGAMMA model. Genes (i.e. 100
 supercontigs) were concatenated, and a partition scheme was provided using
 Phyx v8.2.0 (Brown et al., 2017). ML analysis was performed following the
 above RAxML parameters for the concatenated dataset. To infer a coalescent
 species tree, the 100 optimal gene trees generated from RAxML were input
 to ASTRAL-III v5.0.3 (Zhang et al., 2018). As informative branch lengths are
 required for downstream analyses, the resulting ASTRAL-III
 topology was constrained on the ML analysis. A time-calibrated phylogeny was
 produced using two fossils and two secondary calibrations
 from Berger et al. (2016). The calibrated
 <i>Memecylon</i> phylogeny was used to elucidate its
 biogeography and ancestral character-states.
description: In the alignment of low copy nuclear loci, the sequences of
 <em>M. fruticosum</em> <em>M. elaeagni</em>,
 <em>M. lateriflorum</em><em>, M.
 lanceolatum</em><em>, M. magnifoliatum</em><em>,
 </em>and <em>M. symplociforme</em> contained a
 significant amount of missing data due to low success in target capture
 for these samples. However, these samples were retained in the analysis,
 because some of them showed important relationships in the resulting
 phylogeny. In the morphological data matrix, some data are missing because
 these specimens were sterile.