DNA alignment

A fasta file containing DNA sequences for 107 species of Marcetieae (Melastomataceae). This alignment was imported into RAxML 8.2.12 (Stamatakis 2014) and used in phylogenetic analyses.

Description of the data and file structure - DNA alignment

Total genomic DNA was extracted from silica-dried leaves or herbarium specimens. We amplified and sequenced the ribosomal markers ETS and ITS and the chloroplast markers accD-psaI, atpF-atpH, trnS-trnG, psbK-psbL, ndhF and rbcL. We sampled a total of 107 terminals comprising 107 species. The sampling included 35 species of Marcetia (ingroup), plus 72 species from the other 18 genera of Marcetieae (outgroups).
The ends of all matrices were trimmed in Mega X (Kumar et al. 2018). Each marker was aligned separately using the package DECIPHER (Wright 2016) implemented in the R
The concatenated sequences were analyzed using Maximum likelihood (ML) in RAxML 8.2.12 (Stamatakis 2014) with the GTR+Γ model, partitioned by region, and employing the ‘-f a’ setting in the configuration file.
The partition code used in RAxmL is:

DNA, ACCD=1-685
DNA, ATPH=686-1377
DNA, ETS=1378-2085
DNA, ITS=2086-3103
DNA, NDHF=3104-3731
DNA, PSBK=3732-3918
DNA, RBCL=3919-5192
DNA, TRNS=5193-6035

Outlines

Binary images of leaves and anther connectives of Marcetia alba, M. barbadensis, M. minima, M. serratifolia.The binary images were imported into R and converted to lists of coordinates using the Momocs library (Bonhomme et al. 2014), are were used in morphometric analyses.

Description of the data and file structure - outlines

For obtaining outlines, high-resolution photographs of mature leaves (n=10 for each species) and anther connectives in lateral view (n=5) were taken using a stereoscope with attached camera.
Based on these photographs, we used GIMP 2.10.32 (http://www.gimp.org) to generate binary images with the leaves and connectives as black shapes on a white background, and export them as jpg files

Sharing/Access information

Bonhomme, V., S. Picq, C. Gaucherel, and J. Claude. 2014. Momocs: Outline analysis using R. Journal of Statistical Software 56:124.
GIMP 2.10.32 (http://www.gimp.org)
Kumar, S., G. Stecher, M. Li, C. Knyaz, and K. Tamura. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35:15–47.
Stamatakis, A. 2014. Raxml Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313.
Wright, E. S. 2016. Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R. The R Journal 8:352–359.