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Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography

Olivar, Jay Edneil1

Research facility: Leipzig University
Published Jan 15, 2024 on Dryad. https://doi.org/10.5061/dryad.pk0p2ngtf

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 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

Usage notes

Software requirements: R, MrBayes and BEAST.

Funding

German Academic Exchange Service, Award: 91690870

Federal Ministry of Education and Research, Award: 16GW0120K