DOI: 10.5061/dryad.hmgqnk9wd
title: Island ontogeny and phylogeography in the Mascarene radiation of <em>Hibiscus</em> sect. <em>Lilibiscus</em>

description: This study tests evolutionary predictions of the General Dynamic Model
 (GDM) of oceanic island biogeography using genomic data from a six-species
 radiation of Hibiscus endemic to the Mascarene Islands (Réunion,
 Mauritius, and Rodrigues). The GDM proposes that as islands age, the
 dominant evolutionary processes shaping biodiversity shift from ecological
 divergence on young islands, to drift on middle-aged islands, and
 ultimately to extinction on older islands. To evaluate these predictions,
 we analyzed phylogenetic and population genetic structure within and among
 Hibiscus species across the three islands. We generated genome-wide SNP
 data for 128 individuals using 2b-RAD sequencing. Raw reads were filtered
 and assembled de novo into uniformly 36 bp loci using ipyrad. Raw sequence
 data are archived in GenBank under BioProject accession PRJNA1271673.
 Phylogenetic relationships were inferred using a maximum-likelihood tree
 in IQ-TREE and a species tree in TETRAD. Patristic distances from the ML
 tree were used to assess interspecific divergence, with differences tested
 using pairwise Wilcoxon rank-sum tests with Bonferroni correction. Genetic
 structure was evaluated using principal component analysis (PCA), uniform
 manifold approximation and projection (UMAP), and model-based clustering
 in STRUCTURE. To test for gene flow versus incomplete lineage sorting, we
 conducted ABBA-BABA (D-statistic) tests using Dsuite. To evaluate
 alternative divergence scenarios and estimate relative divergence times,
 we used Approximate Bayesian Computation with Random Forests in DIYABC-RF.
 Our results support the shifting-process predictions of the GDM:
 ecological differentiation and high intraspecific gene flow were evident
 on the youngest island (Réunion), genetic drift dominated on the
 middle-aged island (Mauritius), and deep divergence patterns consistent
 with extinction were observed on the oldest island (Rodrigues).
 Altogether, our dataset and analytical framework provide a replicable
 approach for testing shifting evolutionary process predictions of the GDM
 using population-level genomic data.
description: # Island ontogeny and phylogeography in the Mascarene radiation of
 *Hibiscus* sect. *Lilibiscus* Dataset DOI:
 [10.5061/dryad.hmgqnk9wd](10.5061/dryad.hmgqnk9wd) ## Description of the
 data and file structure We have included the scripts, data files, and
 parameter files to perform each step of the analysis in our study. The
 data format and scripting language may be unique for each step. The
 analysis steps are as follows: 1\) Sequencing and data processing - files
 for producing the three datasets used in our study. MascPhy08 here is
 referred to as MascPhy_all in the study. Similarly, MascPhy11 =
 MascPhy_sub and MascStr04 = MascStr_in. The files containing
 'KeepList.txt' are lists of samples to include in ipyrad
 assemblies. The 'params' files are necessary to produce
 assemblies in ipyrad. 2\) Phylogenetic reconstruction Maximum likelihood
 phylogenetic reconstruction was performed in iqtree using the
 files run_iqtree.sh and MascPhy08.phy. A species tree was produced in
 Tetrad using MascTetrad.ipynb. Tree figures were produced, and patristic
 distances were calculated in Fig2_MascTrees.Rmd. 3\) Population genetic
 structure Principal component analysis (PCA) and uniform manifold
 approximation and projection (UMAP) were run in HibMasc.ipynb. STRUCTURE
 was run using the bash script run_structure.sh and data
 files MascStr04.str, extraparams, mainparams, and seed.txt. STRUCTURE
 figures were produced in HibMasc.ipynb. 4\) Tests for directional gene
 flow Tests were performed using the program Dsuite. The run_commands.txt
 file runs Dsuite on the following input files: SETS_bypop.txt, SETS.txt,
 simple_tree_bypop.nwk, simple_tree.nwk, and MascPhy08.vcf. Downstream
 analysis dquartets was run with the commands file run_dquartets.txt and
 the input file simple_tree_noout.nwk. 5\) Population genetic diversity
 analyses Basic population genetic measures were calculated in the R script
 Masc_PopGen.R. The input csv file MascStr04_pops.csv provides the
 pertinent population information to run the analysis. 6\) Demographic
 modeling Demographic modeling used the GUI program DIYABC-RF. The
 following files simply summarize the analysis that was performed,
 including scenarios and parameters, for each step of demographic
 modeling: DIYABC_STEP1.txt, DIYABC_STEP2.txt, DIYABC_STEP3.txt ## Files
 and variables ### 1) Sequencing and data processing files #### File:
 MascPhy08_KeepList.txt **Description:** A list of samples to include in
 the assembly to produce MascPhy08 outfiles (=MascPhy_all) #### File:
 MascPhy11_KeepList.txt **Description:** A list of samples to include in
 the assembly to produce MascPhy11 outfiles (=MascPhy_sub) #### File:
 MascStr04_KeepList.txt **Description:** A list of samples to include in
 the assembly to produce MascStr04 outfiles (=MascStr_in) #### File:
 params-MascPhy08.txt **Description:** Params file for running ipyrad to
 produce the MascPhy08 assembly (=MascPhy_all) #### File:
 params-MascPhy11.txt **Description:** Params file for running ipyrad to
 produce the MascPhy11 assembly (=MascPhy_sub) #### File:
 params-MascStr04.txt **Description:** Params file for running ipyrad to
 produce the MascStr04 assembly (=MascStr_in) ### 2) Phylogenetic
 reconstruction files #### File: run_iqtree.sh **Description:** Unix
 commands to run iqtree to produce the maximum likelihood phylogeny. ####
 File: MascPhy08.phy **Description:** Input phylip file for run_iqtree.sh.
 Produced from ipyrad. #### File: Fig2_MascTrees.Rmd **Description:** R
 scripts to produce the tree figures and perform patristic distance test.
 #### File: MascTetrad.ipynb **Description:** Jupyter notebook with python
 commands to produce the Tetrad tree (implemented in ipyrad). ### 3)
 Population genetic structure files #### File: run_structure.sh
 **Description:** Shell script to run STRUCTURE analysis on MascStr04.str
 file. Uses seed.txt, mainparams, and extraparams.  #### File:
 MascStr04.str **Description:** Input structure file for structure
 analysis. Produced from ipyrad. #### File: seed.txt **Description:** Input
 file to repeat structure analysis. #### File: extraparams
 **Description:** Required input params file for structure analysis. ####
 File: mainparams **Description:** Required input params file for structure
 analysis. #### File: HibMasc.ipynb **Description:** Jupyter notebook with
 Python commands for running PCA and UMAP analyses and producing PCA, UMAP,
 and STRUCTURE figures. ### 4) Tests for directional gene flow #### File:
 run_commands.txt **Description:** Unix commands for running ABBA-BABA
 tests in Dsuite. #### File: SETS_bypop.txt **Description:** Pop data text
 file to input into run_commands.txt #### File: SETS.txt
 **Description:** Pop data text file to input into run_commands.txt ####
 File: simple_tree_bypop.nwk **Description:** Tree data newick file to
 input into run_commands.txt #### File: simple_tree.nwk
 **Description:** Tree data newick file to input into run_commands.txt ####
 File: MascPhy08.vcf **Description:** VCF (variant call format) file to
 input into run_commands.txt #### File: run_dquartets.txt
 **Description:** Unix commands for running Dquartets in Dsuite. #### File:
 simple_tree_noout.nwk **Description:** Tree data Newick file to input into
 run_dquartets.txt ### 5) Population genetic diversity analysis files ####
 File: Masc_PopGen.R **Description:** R script for producing population
 genetics statistics. #### File: MascStr04_pops.csv
 **Description:** Population assignments for use in Masc_PopGen.R ### 6)
 Demographic modeling files #### File: DIYABC_STEP1.txt
 **Description:** Summary file of scenarios and parameters for Step1
 demographic modeling in DIYABC-RF. This is a GUI program and must be run
 manually by the user inputting information from this summary file. ####
 File: DIYABC_STEP2.txt **Description:** Summary file of scenarios and
 parameters for Step2 demographic modeling in DIYABC-RF. This is a GUI
 program and must be run manually by the user, inputting information from
 this summary file. #### File: DIYABC_STEP3.txt **Description:** Summary
 file of scenarios and parameters for Step3 demographic modeling in
 DIYABC-RF. This is a GUI program and must be run manually by the user,
 inputting information from this summary file. ## Code/software All
 software versions are detailed in the Methods section of the manuscript.
 ## Access information Raw sequence reads are available on GenBank - SRA
 accession PRJNA1271673.