Dataset DOI: 10.5061/dryad.0vt4b8hcq

Description of the data and file structure

dryad_submission.tar.gz

Here you can find the analyzes divided in:

- Biogeography

- Dating

- Diversification

- Niche

- Phylonet

Each directory contains a RMarkdown notebook, depicting how that particular set of analysis was conducted. The Phylonet dir contains only the files, since all the commands necessary for PhyloNet are included in the input nexus file

Some files are freely available in their original repository:

Bioclimatic variables are freely available in their original repository: CHELSA. https://www.chelsa-climate.org/datasets/chelsa_bioclim

If something it's not clear here, please contact me via email (marvin.danque@gmail.com)

M. V. Dantas-Queiroz

Files and variables

Directory: biogeography

Description:  Files and Scripts used for the biogeographic analyzes, in BiogeoBEARS, including the tree figure and the coded areas depicted in the original manuscript,

Required inputs:

• tree file in Newick format (e.g., ./biogeography/parental_v_r_h_ML_calibrated_2024_wo_outgroup.nwk)
• geography file, with the categorization of your areas of interest (e.g., ./biogeography/geo_without_v_2024.txt)

Refer to BioGeoBEARS website for more info about the inputs and how to run the script.

Directory: dating_trees

Description:  Files and Scripts used for dating the Zingiberales and Curcuma trees.

Required inputs:

• tree files in Newick format (e.g., ./dating_trees/0_trees/all_contrees/gene*.contree)
• aligned sequence files in fasta format (e.g., ./dating_trees/1_alignments/parental_alignments/parental_v_r_h/*.fas

Directory: diversification

Description: Files and Scripts used to test the diversification of Curcuma. It includes BAMM, BiSSE, GeoHiSSE and RPANDA.

Required inputs:

• a tree file in Newick format (e.g., ./biogeography/parental_v_r_h_ML_calibrated_2024_wo_outgroup.nwk)
• a distribution file, with the categorization of your areas of interest (e.g., ./diversification/test_geohisse/curcuma_areas_high_vs_low_seasonality.txt)
• the environmental datasets to be tested. Here, monsoon intensity (AsianMonsoonsfrom_15_Ma.txt) and global temperature variability over the last 15 Mya (sd_means_asia.csv) are being tested.

Directory: niche

Description: Files and Scripts used to reconstruct the niche of sublineages of Curcuma, as well as test their overlap and similarity using ecospat.

Required inputs:

• raster files of your area of interest. For this I downloaded 19 climatic variables of CHELSA (30 seconds), cropping their extension to Asia (62.86653, 113.9249, 1.566527, 37.66653) (xmin, xmax, ymin, ymax).
• a file with the lat long info for your samples of interest: (./niche/from_bijay_to_extract_niche_overlapping_cleanned.csv)

Directory: phylonet

Description: Files used in our reticulation analyzes in Phylonet.

Required inputs:

• tree files in nexus format (e.g., ./phylonet/trees_good_treeshrink_red_phylonet0.nex)

Code/software

Most of the code used here was implemented in R and bash, as depicted in the RMarkdown notebooks. The dating was conducted in the MEGA software v. 11.