DOI: 10.5061/dryad.fj6q5746j
title: Data from: Spatial phylogenetics of the native Colombian flora

description: This dataset underpins the first nationwide analysis of spatial
 phylogenetic diversity and endemism in Colombia’s native vascular flora.
 Using 278,551 georeferenced records and DNA-based phylogenies comprising
 8,337 species, 1,839 genera, and 266 families, we identified 17 centers of
 phylogenetic diversity. Randomization tests revealed pronounced
 clustering, with the Andes harboring the highest evolutionary diversity
 and endemism. Our phylogentic results show that high elevation
 areas tend to have more short-range restricted lineages or neoendemism
 centres (cradles); mid-to high elevations areas act as a mix of both
 biodiversity cradles and museums; while lowlands more often preserve
 ancient lineages with long branches or paleoendemism centres
 (museums). Three major phylogenetically distinct biogeographic
 regions emerged: Andean region with 2 clusters, and lowlands 
 with cluster 1.
description: # Data from: Spatial phylogenetics of the native Colombian flora ## File
 1: Species Occurrences Native Flora of Colombia File 1 is not available in
 Dryad. Instead, it can be accessed on Zenodo at the following DOI:
 10.5281/zenodo.17513490. As part of the spatial data, a species occurrence
 dataset was downloaded from BIEN 4.2.8 (Maitner et al. 2018;
 [http://bien.nceas.ucsb.edu/bien/](http://bien.nceas.ucsb.edu/bien/);
 downloaded March 14, 2024\) containing 268,159 records corresponding to
 8,583 species. The script and parameters to download the data are provided
 Description of the data and file structure. Species occurrences of
 Colombia´s native flora. name: Sp_ocurr_Col_native_Flora.csv
 Sp_ocurr_Col_native_Flora.csv: Contains multiple information of all taxa
 used in the study. ID: Unique ID going from 1 to 278552 for each species
 occurrences. X: Unique datasource number scrubbed_species_binomial:
 Scientific name for each taxon used in the study. Columns with other
 fields contained in the .csv are: TAXONOMIC: verbatim_family
 verbatim_scientific_name family_matched name_matched name_matched_author
 higher_plant_group scrubbed_taxonomic_status scrubbed_family ORIGIN:
 scrubbed_author native_status native_status_reason native_status_sources
 is_introduced native_status_country native_status_state_province
 native_status_county_parish GEOGRAPHIC: country state_province county
 locality elevation_m latitude longitude is_new_world CUSTODIANS:
 date_collected datasource dataset data owner custodial_institution_codes
 collection_code datasource_id `Script_download_BIENoccurrence.R` Summary
 script for downloading BIEN occurrence data for PARAMETERS: occ &lt;-
 BIEN_occurrence_species(species = species_in_phylogeny, new.world = T,
 all.taxonomy = T, native.status = T, natives.only = F,
 political.boundaries = T, only.geovalid = T) Next, the occurrences were
 merged to one table, subset with country==”Colombia” ORCHIDS DATA: This
 dataset included information comprising 10,392 records of Colombian
 orchids, representing 730 species, extracted from GBIF (access to data at:
 DOI: 10.15468/dl.v2gwxv). These data are freely available as part of the
 supplementary material of the following paper: Pérez-Escobar, O. A. et al.
 (2024). The origin and speciation of orchids. New Phytologist, 242,
 700–716. --- ## File 2: Species Phylogeny of Native Colombian Flora
 Dataset DOI:
 [https://doi.org/10.5061/dryad.fj6q5746j](https://doi.org/10.5061/dryad.fj6q5746j) Description of the data and file structure. NEXUS file containing 10,853 terminals of native plant species for Colombia. File name: Colombia_native_plants_orderedt.tre content genes: eight loci (ITS, rbcL, atpB, matK, matR, trnF, ndhF, and trnK) Sequences source: GeneBank (Table with all details of the sequences in File 4). --- ## File 3: Family Phylogeny of Native Colombian Flora Dataset DOI: [https://doi.org/10.5061/dryad.fj6q5746j](https://doi.org/10.5061/dryad.fj6q5746j) Description of the data and file structure. Newick format as a .TRE file containing 266 terminals of native plant families for Colombian flora. name: S03_R20160415_euphyllophyte.new.ed.210829.tre repared originally by: Gastauer and Meira (2017) Source: Angiosperm Phylogeny Group IV classification (APG IV 2016), Version used here adapted by: Diazgranados (2022) by reconciling the nomenclature with the taxonomic backbone of World Flora Online (WFO 2023) and pruning the tree to include as terminals only the families represented in our dataset (266 families). --- ## File 4: Loci per species and GenBank IDs of Colombian native flora Dataset DOI: [https://doi.org/10.5061/dryad.fj6q5746j](https://doi.org/10.5061/dryad.fj6q5746j) Description of the data and file structure. name: Loci_per_species_and_Genbank_IDs.xlsx Loci per species and GenBank IDs.excel: Table that contains names of all taxa used in the study, with Loci type and GenBank IDs. Taxon: 10,855 rows with species names of Colombian native flora. No of charsets: number of locis identified in GenBank. 8 columns with loci names and Genbank IDs: ndhf ITS_binomials atpB_binomials matK_binomials matR_binomials rbcL_binomials trnF_binomials trnL_binomials --- ## File 5: Alignment Colombian native Flora Dataset DOI: [https://doi.org/10.5061/dryad.fj6q5746j](https://doi.org/10.5061/dryad.fj6q5746j) Dataset Description: A concatenated alignment in Phylip format containing ndhf, ITS, atpB, matK, matR, rbcL, trnF, and trnL. This dataset contains the concatenated DNA sequence alignment used for the phylogenetic and spatial analyses of Colombia’s native flora. The dataset was compiled as part of a study assessing patterns of phylogenetic diversity and endemism across Colombian plant lineages. Data Content The dataset includes aligned DNA sequences from eight loci commonly used in plant phylogenetics: ITS (Internal Transcribed Spacer) rbcL (ribulose-bisphosphate carboxylase large chain) atpB (ATP synthase beta subunit) matK (maturase K) matR (maturase R) trnF (transfer RNA phenylalanine) ndhF (NADH dehydrogenase subunit F) trnK (transfer RNA lysine) These loci were concatenated into a single alignment using SequenceMatrix version 1.9, resulting in 10,853 terminals (species-level entries) representing the native flora of Colombia. File Information File name: Colombia.phy Format: .phy Software used: SequenceMatrix v1.9 Number of loci: 8 Intended Use The data are provided for phylogenetic, macroevolutionary, and biodiversity analyses. Users may employ these sequences to replicate the phylogenetic tree reconstruction or to conduct independent analyses of evolutionary relationships among Colombian plant taxa.