DOI: 10.5061/dryad.pk0p2ngtf
title: Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography

description: The general dynamic model (GDM) of oceanic island biogeography views
 oceanic islands predominantly as sinks rather than sources of dispersing
 lineages. To test this, we conducted a biogeographic analysis of a highly
 successful insular plant taxon, Cyrtandra and inferred
 directionality of dispersal and founder events throughout the four
 biogeographical units of the Indo-Australian Archipelago (IAA), namely
 Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major
 source area, followed by Wallacea, a system of oceanic islands. The
 relatively high number of events originating from Wallacea is attributed
 to its central location in the IAA and its complex geological history
 selecting for increased dispersibility. We also tested if diversification
 dynamics in Cyrtandra follow predictions of adaptive radiation, which is
 the dominant process as per the GDM. Diversification dynamics of
 dispersing lineages of Cyrtandra in the Southeast Asian grade showed early
 bursts followed by a plateau, which is consistent with adaptive radiation.
 We did not detect signals of diversity-dependent diversification, and this
 is attributed to Southeast Asian cyrtandras occupying various niche
 spaces, evident by their wide morphological range in habit and floral
 characters. The Pacific clade, which arrived at the immaturity phase of
 the Pacific Islands, showed diversification dynamics predicted by the
 Island Immaturity Speciation Pulse (IISP) model, wherein rates increase
 exponentially, and their morphological range is controlled by the least
 action effect favoring woodiness and fleshy fruits. Our study provides a
 first step toward a framework for investigating diversification dynamics
 as predicted by the GDM in highly successful insular taxa.
description: Software requirements: R, MrBayes and BEAST.
description: # Data from: **Early diversification dynamics in a highly successful
 insular plant taxon are consistent with the general dynamic model of
 oceanic island biogeography** Persistent Identifier: doi:
 (10.5061/dryad.pk0p2ngtf) Dataset Contributors: Jay Edneil C. Olivar,
 Frank Hauenschild, Hannah J. Atkins, Gemma L.C. Bramley & Alexandra N.
 Muellner-Riehl ## Contact Information Jay Edneil C. Olivar Department of
 Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute
 of Biology, Leipzig University, D-04103 Leipzig, Germany
 Alexandra N. Muellner-Riehl
 Department of Molecular Evolution and Plant Systematics & Herbarium
 (LZ), Institute of Biology, Leipzig University, D-04103 Leipzig, Germany
 German Centre for Integrative Biodiversity Research (iDiv)
 Halle-Jena-Leipzig, D-04103 Leipzig, Germany
 --- ## Methodological Information *
 Methods of data collection/generation: see manuscript for details --- ##
 Description of the data and file structure ## Data and File Overview ##
 Summary Metrics * File count: 20 * Total file size: 6.8 MB * Range of
 individual file sizes: 59 bytes - 4 MB * File formats: .cut1000, .nex,
 .newick, .pdf, .R, .tre, .txt, .xml ## Naming Conventions * File naming
 scheme: Files are named after an analysis where they were used and/or
 produced. ## Table of Contents * BAMM_control_diversification.txt *
 BAMM_myPriors.txt * BAYES_tree.tre * BEAST_bdi_input.xml * BEAST_tree.tre
 * BEAST_yule_input.xml * complete_BioGeoBeaRs_script.R *
 continental_source_manual_dispersal_multipliers.txt * cyr_alignment.nex *
 DEC + J_100BSMs_v1.pdf * DEC + J_single_stochastic_map_n1.pdf *
 distribution.txt * equal_rates_manual_dispersal_multipliers.txt *
 ML_tree.cut1000 * nearest_neighbour_manual_dispersal_multipliers.txt *
 no_out_tree.newick * phil_nexus_manual_dispersal_multipliers.txt *
 sahul_nexus_manual_dispersal_multipliers.txt * summary_counts_BSMs.txt *
 wallacea_nexus_manual_dispersal_multipliers.txt ## File/Folder Details ##
 Details for: BAMM\_control\_diversification.txt * Description: control
 file containing all settings necessary to run the BAMM analysis. *
 Format(s): .txt * Size: 9 KB * Other encoding details:
 globalSamplingFraction was adjusted to represent sampling rate in the
 study. ## Details for: BAMM\_myPriors.txt * Description: priors block for
 the BAMM analysis. * Format(s): .txt * Size: 284 bytes * Other encoding
 details: output file generated by BAMMtools in R. ## Details for:
 BAYES\_tree.tre * Description: Bayesian inference consensus tree of
 Cyrtandra based on ITS, psbA-trnH, and rpl32 regions * Format(s): .tre *
 Size: 85 KB * Other encoding details: Numbers on nodes are posterior
 probabilities. ## Details for: BEAST\_bdi\_input.xml * Description: input
 file for BEAST analysis with birth-death prior. * Format(s): .xml * Size:
 705 KB ## Details for: BEAST\_tree.tre * Description: Maximum clade
 credibility tree of Cyrtandra based on BEAST analysis. * Format(s): .tre *
 Size: 309 KB ## Details for: BEAST\_yule\_input.xml * Description: input
 file for BEAST analysis with yule prior. * Format(s): .xml * Size: 678 KB
 ## Details for: complete\_BioGeoBeaRs\_script.R * Description: R script
 for running the BioGeoBeaRs analysis * Format(s): .R * Size: 66 KB ##
 Details for: continental\_source\_manual\_dispersal\_multipliers.txt *
 Description: a tab-delimited input file for the ancestral area estimation
 in 'BioGeoBEARS'. See manuscript for the description of the
 Continental source model. * Format(s): .txt * Size: 77 bytes * Dimensions:
 4 columns x 5 rows ## Details for: cyr\_alignment.nex * Description:
 alignment file for Bayesian analysis. * Format(s): .nex * Size: 860 KB *
 Other encoding details: This is a combined dataset of ITS, psbA-trnH, and
 rpL32. following the alignment are the coded indels, then followed by the
 Bayes block. ## Details for: DEC + J\_100BSMs\_v1.pdf * Description: a
 image file displaying the 100 simulated Biogeographic Stochastics Mapping
 (BSM), based on the ancestral area estimation with the best fitting model,
 DEC+J. * Format(s): .pdf * Size: 4 MB * Dimensions: 100 pages * Other
 encoding details: Output file created by 'BioGeoBEARS' in R. ##
 Details for: DEC + J\_single\_stochastic\_map\_n1.pdf * Description: a
 image file averaging results of 100 simulated iogeographic Stochastics
 Map. * Format(s): .pdf * Size: 47 KB * Dimensions: 1 page ## Details for:
 distribution.txt * Description: tab-delimited input file for the ancestral
 area estimation in 'BioGeoBEARS'. * Format(s): .txt * Size: 4 KB
 * Dimensions: 202 rows x 2 columns * Other encoding details: distribution
 is based on the four areas of delimitation (Su=Sunda; P=Philippines;
 W=Wallacea; Sa=Sahul including PAcific) ## Details for:
 equal\_rates\_manual\_dispersal\_multipliers.txt * Description: a
 tab-delimited input file for the ancestral area estimation in
 'BioGeoBEARS'. See manuscript for the description of the Equal
 Rates model. * Format(s): .txt * Size: 59 bytes * Dimensions: 4 columns x
 5 rows ## Details for: ML\_tree.cut1000 * Description: Maximum Likehood
 tree of Cyrtandra based on ITS, psbA-trnH, and rpl32 regions. * Format(s):
 .cut1000 * Size: 16 KB * Other encoding details: numbers on node are
 Bootstrap support values ## Details for:
 nearest\_neighbour\_manual\_dispersal\_multipliers.txt * Description: a
 tab-delimited input file for the ancestral area estimation in
 'BioGeoBEARS'. See manuscript for the description of the Nearest
 Neighbour model. * Format(s): .txt * Size: 63 bytes * Dimensions: 4
 columns x 5 rows ## Details for: no\_out\_tree.newick * Description: tree
 file used for BioGeoBeaRs analysis excluding the outgroup. * Format(s): *
 Size: 9 KB * Other encoding details: generated using drop.tip function of
 the R package ape. ## Details for:
 phil\_nexus\_manual\_dispersal\_multipliers.txt * Description: a
 tab-delimited input file for the ancestral area estimation in
 'BioGeoBEARS'. See manuscript for the description of the
 Philippines Nexus model. * Format(s): .txt * Size: 71 bytes * Dimensions:
 4 columns x 5 rows ## Details for:
 sahul\_nexus\_manual\_dispersal\_multipliers.txt * Description: a
 tab-delimited input file for the ancestral area estimation in
 'BioGeoBEARS'. See manuscript for the description of the Sahul
 Nexus model. * Format(s): .txt * Size: 71 bytes * Dimensions: 4 columns x
 5 rows ## Details for: summary\_counts\_BSMs.txt * Description: a
 tab-delimited file displaying a summary of biogeographic events calculated
 in the Biogeographic Stochastic Mapping (BSM). The file contains the means
 and standard deviations of all event types. * Format(s): .txt * Size: 266
 bytes * Dimensions:4 rows x 13 columns * Variables: founder:
 founder-event/jump dispersal a: range-switching dispersal d:
 range-expansion dispersal e: extinction subset: speciation in subsets
 (allopatric) vicariance: vicariance ebvents sympatry: sympatric speciation
 ALL_disp: sum of all dispersal events ana_disp: anagenetic dispersal
 events (a+d) all_ana: sum of all anagenetic events all_clado: sum of all
 cladogenetic events total_events: total event numbers * Other encoding
 details: Output file created by 'BioGeoBEARS' in R. ## Details
 for: wallacea\_nexus\_manual\_dispersal\_multipliers.txt * Description: a
 tab-delimited input file for the ancestral area estimation in
 'BioGeoBEARS'. See manuscript for the description of the
 Wallacea Nexus model. * Format(s): .txt * Size: 71 bytes * Dimensions: 4
 columns x 5 rows