DOI: 10.6078/d1wx3s
title: Data from: The rapid radiation of <em>Bomarea</em> (Alstroemeriaceae: Liliales), driven by the rise of the Andes

description: Geological events such as mountain uplift affect how, when, and where
 species diversify, but measuring those effects is a longstanding
 challenge. Andean orogeny impacted the evolution of regional biota by
 creating barriers to gene flow, opening new habitats, and changing local
 climate. Bomarea (Alstroemeriaceae) are tropical plants with (often)
 small, isolated ranges; in total, Bomarea species occur from central
 Mexico to central Chile. This genus appears to have evolved rapidly and
 quite recently, and rapid radiations are often challenging to resolve with
 traditional phylogenetic inference. In this study, we apply
 phylogenomics—with hundreds of loci, gene-tree-based data curation, and a
 multispecies-coalescent approach—to infer the phylogeny of Bomarea. We
 used this phylogeny to untangle the potential drivers of diversification
 and biogeographic history. In particular, we test if Andean orogeny
 contributed to the diversification of Bomarea. We find that Bomarea
 originated in the central Andes during the mid-Miocene, then spread north,
 following the trajectory of mountain uplift. Furthermore, Andean lineages
 diversified faster than non-Andean relatives. Bomarea thus demonstrates
 that—at least in some cases—geological change rather than environmental
 stability has driven high species diversity in a tropical biodiversity
 hotspot. These results also demonstrate the utility (and danger) of
 genome-scale data for making macroevolutionary inferences.
description: # The rapid radiation of *Bomarea* (Alstroemeriaceae: Liliales), driven by
 the rise of the Andes [Access this dataset on
 Dryad](https://doi.org/10.6078/D1WX3S) This dataset contains the data to
 fully reproduce analyses on the evolutionary history, diversification, and
 biogeography of *Bomarea* and outgroups in Alstroemeriaceae. These data
 include intermediate and processed molecular data (raw molecular data is
 on NCBI SRA, link below), the results of phylogenetic analyses,
 biogeographic data on species' ranges, and the results of
 diversification and biogeographic analyses. ## Description of the data and
 file structure ### This repository contains a series of analysis-specific
 folders and relevant files compressed in a single zipped directory. ###
 bom_phy_data.zip Zipped directory containing the subdirectories listed
 below.  #### [Dir] aln_editing Alignments and scripts for editing and
 curating alignments. All code is in R, which is available from
 [CRAN](https://cran.r-project.org/). * \[Dir] original_alns # alignments
 produced by the assembly pipeline described in Endara & Burleigh
 (2023, in prep) * \[Dir] final_alns # alignments used in the analyses
 after curating with the code files listed below *
 1_get_loci_for_genetrees.R * 2_sort_loci_highcoverage_good_gt.R *
 3_revise_alns.R * 4_split_loci.R * 5_trim_alns.R * 6_concatenate_loci.R *
 7_make_bom_edu_subset.R * 8_make_bpp_input_aln.R #### [Dir] astral Scripts
 and data to make gene trees and run astral from alignments. Code is in
 bash and calls [IQ-TREE](http://www.iqtree.org/), a maximum likelihood
 phylogenetic reconstruction method, and
 [ASTRAL](https://github.com/smirarab/ASTRAL), an approximate coalescent
 phylogenetic reconstruction method. * \[Dir] alignments # input data for
 building gene trees with iqtree * \[Dir] gene_trees # output from iqtree *
 astral.tre # output of astral * gene_trees.sh # build gene trees *
 in_BS10.trees # input of astral * run_astral.sh # code for running astral
 #### [Dir] contaiminant_ID Script and files for IDing contaminant
 sequences in alignments in [R](https://cran.r-project.org/). *
 blast_bad_seqs.R * contamination_blast.csv * seqs_to_remove.txt #### [Dir]
 dec_alstr Scripts and data/ output for Alstroemeriaceae-wide DEC analysis.
 Code is in Rev, implemented in [RevBayes](https://revbayes.github.io/),
 for specifying phylogenetic probabilistic graphical models. * \[Dir] data
 # input data for RevBayes analysis * \[Dir] data_prep # prepping input
 data for RevBayes analysis, code is in [R](https://cran.r-project.org/) *
 \[Dir] output # RevBayes output files * \[Dir]] scripts # RevBayes code
 #### [Dir] dec_bom_only Scripts and data/ output for Bomarea only DEC
 analysis. Code is in Rev, implemented in
 [RevBayes](https://revbayes.github.io/), for specifying phylogenetic
 probabilistic graphical models. * \[Dir] data # input data for RevBayes
 analysis and plotting. tierney2020_temp.csv provides global average
 temperature in degrees celsius from DOI:
 [10.1038/s41586-020-2617-x](https://doi.org/10.1038/s41586-020-2617-x) *
 \[Dir] data_prep # prepping input data for RevBayes analysis, code is in
 [R](https://cran.r-project.org/) * \[Dir] output # RevBayes output files *
 \[Dir] scripts # RevBayes code #### [Dir] genesortR_bom Files for running
 [genesortR](https://github.com/mongiardino/genesortR) script to choose
 loci for dating, including the following directories. * \[Dir] alns_all #
 alignment input files * \[Dir] genes_selected_15 # output of selected 15
 gene regions * \[Dir] rooted_gt # all rooted gene trees * \[Dir] scripts #
 scripts for prepping the data #### [Dir] iqtree_part Files for estimating
 a maximum likelihood tree using [IQ-TREE](http://www.iqtree.org/), and the
 output of the analysis. #### [Dir] lsbdp Lineage-specific birth-death
 process analysis on Bomarea tree. Code is in Rev, implemented in
 [RevBayes]{[https://revbayes.github.io/}](https://revbayes.github.io/}),
 for specifying phylogenetic probabilistic graphical models. * \[Dir] data
 # input data for RevBayes analysis * \[Dir] output # RevBayes output files
 * \[Dir] scripts # RevBayes code ### [Dir] **metadata** A few files for
 making figures and tables: * LociPerSample.txt * sample_info.csv ###
 [Dir] **misc_plotting_scripts** A few scripts for figure plotting:  \-
 make_tip_labels.R \- makeSpecimenTable.R \- matchNodeLabels.R \-
 plotMyTrees.R #### [Dir] partitionfinder Files to identify partitions for
 ML analysis using
 [PartitionFinder](https://www.robertlanfear.com/partitionfinder/) and the
 output of the analysis #### [Dir] relaxed_dating Relaxed-clock data of
 astral topology. Code is in Rev, implemented in
 [RevBayes]{[https://revbayes.github.io/}](https://revbayes.github.io/}),
 for specifying phylogenetic probabilistic graphical models. * \[Dir] data
 # input data for RevBayes analysis * \[Dir] data_prep # prepping input
 data for RevBayes analysis, code is in [R](https://cran.r-project.org/) *
 \[Dir] output # RevBayes output files * \[Dir] scripts # RevBayes code ##
 Sharing/Access information Links to other publicly accessible locations of
 data: * Raw molecular data is available on on NCBI SRA BioProject ID
 PRJNA881339 Biogeographic data was derived from the following source: *
 [Kew's Plants of the World Online](https://powo.science.kew.org/) ##
 Code/Software Additional code is available on GitHub at
 [https://github.com/cmt2/bom_phy_analysis](https://github.com/cmt2/bom_phy_analysis)