Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography
Cite this dataset
Olivar, Jay Edneil (2024). Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography [Dataset]. Dryad. https://doi.org/10.5061/dryad.pk0p2ngtf
Abstract
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.
README: 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
muellner-riehl@uni-leipzig.de
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 numbersOther 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
Usage notes
Software requirements: R, MrBayes and BEAST.
Funding
German Academic Exchange Service, Award: 91690870
Federal Ministry of Education and Research, Award: 16GW0120K