DOI: 10.5061/dryad.vhhmgqnzq
title: Data from: Pre‐adaptation and adaptation shape trait‐environment matching in the Neotropics

description: The resources provided here comprise raw and final data sets used in our
 study 'Preadaptation and adaptation shape trait-environment matching
 in the Neotropics' (DOI: 10.1111/geb.13730) comprising curated
 geographic occurrences for 156 Swartzia taxa across its distribution in
 the Neotropics, phylogenetic information for 69 Swartzia taxa, and
 corresponding climatic (i.e. 19 climatic variables taken from WorldClim),
 soil (i.e. sand, nitrogen, and clay content taken from the SoilGrids 2.0
 portal), and trait data for each taxa (i.e. trait measurements
 for lefleats, petals, and fruits). We also provide the script used to
 extract trait information from botanical monographs.
description: The data-sets were collected using various methods. Trait data
 include measurements taken from the literature for leaflets, fruits, and
 petals, mainly from the works of Cowan (1967), and Torke and Mansano
 (2011) (but see detailed references provided in the corresponding
 supplementary files). Additional data for leaflets and fruits were
 obtained from herbarium specimens as described in the paper (see also the
 herbarium references provided in the corresponding supplementary files ).
 Data for nuclear and plastid DNA sequences were obtained from the study of
 Torke and Schall (2008). Phylogenetic trees were generated using BEAST2
 (Bouckaert et al. 2014) , as described in the paper (see Methods). Data on
 occurrences were obtained from herbarium sources and curated posteriorly.
 For the occurrence dataset, we extracted climate data from WorldClim 2
 (Fick & Hijmans 2017) and soil data from SoilGrids 2.0 (Poggio et
 al. 2021). See detailed information for each supplementary file provided
 in the README file.
 <strong>References</strong>
 Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H.,
 Xie, D., Suchard M.A., Rambaut A., Drummond, A. J. (2014). Beast 2: A
 software platform for bayesian evolutionary analysis. PLoS Computational
 Biology, 10(4), e1003537. Cowan, R. S. (1967). Flora
 Neotropica Monograph I. Swartzia (Leguminosae, Caesalpinioideae,
 Swartzieae). Hafner Publishing Company, New York and London.
 Fick, S. E., &
 Hijmans, R. J. (2017). WorldClim 2: New 1‐km spatial resolution climate
 surfaces for global land areas. International Journal of Climatology,
 37(12), 4302–4315. Poggio, L., de Sousa, L. M., Batjes, N. H.,
 Heuvelink, G. B. M., Kempen, B., Ribeiro, E., & Rossiter, D.
 (2021). SoilGrids 2.0: Producing soil information for the globe with
 quantified spatial uncertainty. SOIL, 7(1),
 217–240.  Torke, B. M. & Mansano, V. de F.
 (editors). (2011). The Swartzia Pages The New York Botanical Garden,
 Bronx, NY.
 (https://sweetgum.nybg.org/science/projects/swartzia).<br> Torke, B. M., & Schaal, B. A. (2008). Molecular phylogenetics of the species-rich Neotropical genus Swartzia (Leguminosae, Papilionoideae) and related genera of the swartzioid clade. American Journal of Botany, 95(2), 215–228.
description: The BEAST .xml file can be run using the software BEAST 2
 – 'bayesian
 evolutionary analysis by sampling trees 2'  (Bouckaert et al. 2014).
 All phylogenetic trees can be loaded and visualized in the R
 platform using packages for handling phylogenetic data (i.e.
 'ape'). Alternatively trees can be visualized using  the software
 'Figtree v. 1.4.4.' (Rambaut A. 2010).
 Occurrence, trait and climatic data can be loaded and opened in the R
 platform. The script to extract trait data
 from monographs can be loaded and
 opened in the R platform. Stepwise instructions are provided as commented
 text in the script. Note: NAs in the dataset denote missing data in
 traits or environmental data, which means that the corresponding value was
 not available from the literature or from the environmental
 databases.<br>
 <strong>References</strong>
 Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H.,
 Xie, D., Suchard M.A., Rambaut A., Drummond, A. J. (2014). Beast 2: A
 software platform for bayesian evolutionary analysis. PLoS Computational
 Biology, 10(4), e1003537. Rambaut, A. (2010) FigTree
 v1.3.1. Institute of Evolutionary Biology, University of Edinburgh,
 Edinburgh. https://github.com/rambaut/figtree/releases.
description: ### Title of Dataset Preadaptation and adaptation shape trait
 environment-matching in the Neotropics ### Abstract The resources provided
 here comprise raw and final data sets used in our study
 'Preadaptation and adaptation shape trait-environment matching in the
 Neotropics' (DOI: 10.1111/geb.13730) comprising curated geographic
 occurrences for 156 *Swartzia* taxa across its distribution in the
 Neotropics, phylogenetic information for 69 *Swartzia* taxa, and
 corresponding climatic (i.e. 19 climatic variables taken from WorldClim),
 soil (i.e. sand, nitrogen, and clay content taken from the SoilGrids 2.0
 portal), and trait data for each taxa (i.e. trait measurements for
 lefleats, petals, and fruits). We also provide the script used to extract
 trait information from botanical monographs. ### Description of the data
 **Supplementary file 1**: BEAST setup used to date and obtain a series of
 posterior trees in extensible markup language (xml) file format. The file
 also includes the DNA partitions and sequences that were used. The
 *Swartzia* DNA sequences were taken from Torke and Schaal (2008) and are
 available under the study ID S2154 in www.treebase.org. **Supplementary
 file 2**: Contains a data set of posterior trees generated by BEAST 2. The
 file contains the raw set of 30000 trees that were obtained after running
 BEAST 2 for 300 million iterations and sampling every 10000. The trees
 contain all taxa as in Torke and Schaal (2008). **Supplementary file 3**:
 Maximum clade credibility tree including the same taxa as in the study of
 Torke & Schaal (2008). **Supplementary file 4**: Cropped version
 of the maximum clade credibility tree containing only *Swartzia* taxa and
 a single taxa per species or subspecies / variety. **Supplementary file
 5**: 1000 posterior trees evenly sampled from the set of posterior trees
 in Supplementary file 2. Trees are cropped to contain a single *Swartzia*
 taxa per species or subspecies / variety. **Supplementary file 6**:
 Curated *Swartzia* occurrences from herbaria with at least 5 records per
 taxa (i.e. 3688 occurrences for 156 taxa of *Swartzia* including
 subspecies and varieties). Details on the corresponding hebaria and
 collectors are also provided. **Supplementary file 7**: Leaflet trait
 measurements (raw dataset collected from the literature). The file
 includes references to the original sources from which the data was
 derived, the species name as described in the original reference, the
 accepted species name for each taxon, the final species name after
 correcting for synonyms according to Torke & Manasano (2011), and
 corresponding measurements. **Supplementary file 8**: Fruit trait
 measurements (raw dataset extracted from the literature). The file
 includes references to the original sources from which the data was
 derived, the species name as described in the original reference, the
 accepted species name for each taxon, the final species name after
 correcting for synonyms according to Torke & Manasano (2011), and
 corresponding measurements. **Supplementary file 9**: Petal trait
 measurements (raw dataset collected from the literature). The file
 includes references to the original sources from which the data was
 derived, the species name as described in the original reference, the
 accepted species name for each taxon, the final species name after
 correcting for synonyms according to Torke & Manasano (2011), and
 corresponding measurements. **Supplementary file 10**: Script for
 extracting trait information from the monograph of Cowan R.S. (1967). The
 instructions for running the script are contained in the script as
 commented text. **Supplementary file 11**: Leaflet measurements from
 herbarium specimens with associated references. **Supplementary file 12**:
 Fruit measurements from herbarium specimens with associated references.
 **Supplementary file 13**: Data set of leaflet measurements with
 corresponding climate and soil variables averaged per taxa.
 **Supplementary file 14**: Data set of fruit measurements with
 corresponding climate and soil variables averaged per taxa.
 **Supplementary file 15**: Data set of petal measurements with
 corresponding climate and soil variables averaged per taxa.
 **Supplementary file 16**: Credits and licensing for photographs used in
 Figure 3. ### Sharing/Access information DNA data was derived from the
 following sources: Torke & Schaal (2008) available in
 www.treebase.org, study ID S2154. Trait data was derived from the
 following sources: References provided in the data references and in the
 excel files from Supp. files 7, 8, 9, 10 and 12 for each taxa. ###
 Code/Software Supplementary file 10 contains the R Script to extract trait
 information from the monograph of Cowan R.S. (1967). The instructions on
 how to run the script are included as commented text in the script. ###
 References Torke, B. M., & Schaal, B. A. (2008). Molecular
 phylogenetics of the species-rich Neotropical genus Swartzia (Leguminosae,
 Papilionoideae) and related genera of the swartzioid clade. American
 Journal of Botany, 95(2), 215–228. Torke, B. M. and Mansano, V. de F.
 (editors). (2011). The Swartzia Pages The New York Botanical Garden,
 Bronx, NY. (https://sweetgum.nybg.org/science/projects/swartzia). Cowan,
 R. S. (1967). Flora Neotropica Monograph I. Swartzia (Leguminosae,
 Caesalpinioideae, Swartzieae). Hafner Publishing Company, New York and
 London.