DOI: 10.5061/dryad.9zw3r22ks
title: Data from: A phylogenetic analysis of Marcetia (Melastomataceae, Marcetieae) and three new sprawling species from Bahia, Brazil

description: This dataset contains: -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. -Binary
 images of leaves and anther connectives of Marcetia alba, M.
 barbadensis, M. minima, and M. serratifolia. These
 images were used to generate outlines for the shape analyses in Momocs.
description: 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
 <em>Marcetia</em> (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. Binary images
 -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 an 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.
description: # Data from: A phylogenetic analysis of Marcetia (Melastomataceae,
 Marcetieae) and three new sprawling species from Bahia, Brazil. ## 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.