Tropical origin, global diversification and dispersal in the pond damselflies (Coenagrionoidea) revealed by a new molecular phylogeny
Data files
Sep 15, 2023 version files 785.53 MB
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data_R1.1.zip
785.43 MB
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README.md
99.99 KB
Jan 31, 2024 version files 785.54 MB
Abstract
The processes responsible for the formation of Earth’s most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely-sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea), and investigate the role of time, macroevolutionary processes and biome-shift dynamics in shaping the LDG in this ancient insect superfamily. We used process-based biogeographic models to jointly infer ancestral ranges and speciation times, and to characterise within-biome dispersal and biome-shift dynamics across the cosmopolitan distribution of Coenagrionoidea. We also investigated temporal and biome-dependent variation in diversification rates. Our results uncover a tropical origin of pond damselflies and featherlegs ~ 105 Ma, while highligthing uncertainty of ancestral ranges within the tropics in deep time. Even though diversification rates have declined since the origin of this clade, global climate change and biome-shifts have slowly increased diversity in warm- and cold-temperate areas, where lineage turnover rates have been relatively higher. This study underscores the importance of biogeographic origin and time to diversify as important drivers of the LDG in pond damselflies and their relatives, while diversification dynamics have instead resulted in the formation of ephemeral species in temperate regions. Biome-shifts, although limited by tropical niche conservatism, have been the main factor reducing the steepness of the LDG in the last 30 Myr. With ongoing climate change and increasing northward range expansions of many damselfly taxa, the LDG may become less pronounced. Our results support recent calls to unify biogeographic and macroevolutionary approaches to increase our understanding of how latitudinal diversity gradients are formed and why they vary across time and among taxa.
README: Tropical origin, global diversification and dispersal in the pond damselflies (Coenagrionoidea) revealed by a new molecular phylogeny
This README file was generated on 2024-01-29 by Beatriz Willink.
GENERAL INFORMATION
Title of Dataset: Tropical origin, global diversification and dispersal in the pond damselflies (Coenagrionoidea) revealed by a new molecular phylogeny
Author Information
A. Principal Investigator Contact Information
Name: Beatriz Willink
Institution: Stockholm University
Address: Stockholm, Sweden
Email: bwillink@gmail.comB. Associate or Co-investigator Contact Information
Name: Jessica L. Ware
Institution: American Museum of Natural History
Address: NY, NY USA
Email: jware@amnh.orgC. Associate or Co-investigator Contact Information
Name: Erik I. Svensson
Institution: Lund University
Address: Lund, Sweden
Email: erik.svensson@biologi.lu.seDate of data collection (single date, range, approximate date): 2014-2021
Geographic location of data collection:
A. Field sites
Sweden: Lund Municipality
Guyana: CEIBA Biological Center, Karanambu Lodge, Iwokrama River Lodge and Research Centre
Argentina: Iguazu National Park, Ibera Wetlands
Cameroon: Mefou Park, Nyasoso Village, Mount Kupe, Mount Mbam Minkom, Afamba River, Doume River, Nyong River, Mbakaou Village, Dja Faunal ReserveB. Specimen collections
Florida State Collection of Arthropods (FSCA), Smithsonian Institute (SI), Brigham Young University (BYU)
New Zealand: New Zealand Arthropod Collection (NZAC)
Japan: National Institute of Advanced Industrial Science and Technology (AIST)
Singapore: National University of Singapore (NUS)
Netherlands: National Museum of Natural History Naturalis(RMNH)Information about funding sources that supported the collection of the data:
A. Swedish Research Council (VR: grant no. 2016-03356)
B. Swedish Foundation for International Cooperation in Research and Higher Education
C. Erik Philip Sörensens Stiftelse
D. Royal Physiographic Society of Lund
E. Jörgen Lindströms Fund
F. Lunds Djurskyddsfond
SHARING/ACCESS INFORMATION
Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
Links to publications that cite or use the data:
Willink, B., Ware, J., & Svensson, E. I. (2023). Tropical origin, global diversification and dispersal in the pond damselflies (Coenagrionoidea) revealed by a new molecular phylogeny. bioRxiv. https://doi.org/10.1101/2022.01.21.477207Links to other publicly accessible locations of the data: https://github.com/bwillink/Damsel_Phylo
Links/relationships to ancillary data sets: None
Was data derived from another source? Yes, part of the data was derived from literature searches and online resources
A. If yes, list source(s):
DNA sequences: National Center for Biotechnology Information (NCBI) GenBank
Map files: Global Administrative areas (GADM)
Species distribution data: See complete list of sources in data files Table_S4.csv and Table_S4.BibTeXRecommended citation for this dataset:
Willink, B., Ware, J., & Svensson, E. I. (2023). Data from: Tropical origin, global diversification and dispersal in the pond damselflies (Coenagrionoidea) revealed by a new molecular phylogeny. Dryad Digital Repository. https://doi.org/10.5061/dryad.h18931znp
DATA & FILE OVERVIEW
raw
A. 16S_allspp_unaligned.fst
B. COI_allspp_unaligned.fst
C. D7_allspp_unaligned.fst
D. H3_allspp_unaligned.fst
E. PMTR_allspp_unaligned.fst
F. biome_amb.nex
G. biome.nex
H. present_states.csv
I. Table_S2.csv
J. Table_S4.csv
K. Table_S4.BibTeX
processed
A. mol
- 16S_allspp.fst
- 16S_allspp_sorted.fs
- 16S_allspp_corrected.fst
- 16S_allspp_trim.fst
- 16S_spp.fst
- 16S_spp_sorted.fst
- 16S.nex
- COI_allspp.fst
- COI_allspp_trim.fst
- COI_spp.fst
- COI_spp_sorted.fst
- COI.nex
- D7_allspp.fst
- D7_allspp_corrected.fst
- D7_allspp_trim.fst
- D7_spp.fst
- D7_spp_sorted.fst
- D7.nex
- H3_allspp.fst
- H3_allspp_trim.fst
- H3_spp.fst
- H3_spp_sorted.fst
- H3.nex
- PMTR_allspp.best.fas
- PMTR_allspp_trim.fst
- PMTR_spp.fst
- PMTR_spp_sorted.fst
- PMTR_exon_pruned.fst
- PMTR.nex
- Coen.mol.namecheck.nex
- Coen.mol.final.nexB. nxs
- Coen.mol.no_parts.nex
- M1.mol.nex
- M1.partitions.nex
- M2.mol.nex
- M2.partitions.nex
- M3.mol.nex
- M3.partitions.nex
- M4.mol.nex
- M4.partitions.nex
- M5.mol.nex
- M5.partitions.nex
- M6.mol.nex
- M6.partitions.nexC. bg_dating
- atlas
* earth25.short.atlas.matrix.1.txt
* earth25.short.atlas.matrix.2.txt
* earth25.short.atlas.matrix.3.txt
* earth25.short.atlas.matrix.4.txt
* earth25.short.atlas.matrix.5.txt
* earth25.short.atlas.matrix.6\.txt
* earth25.short.atlas.matrix.7.txt
* earth25.short.atlas.matrix.8.txt
* earth25.short.atlas.matrix.9.txt
* earth25.short.atlas.matrix.10.txt
* earth25.short.atlas.matrix.11.txt
* earth25.short.atlas.matrix.12.txt
* earth25.short.atlas.matrix.13.txt
* earth25.short.atlas.matrix.14.txt
* earth25.short.atlas.matrix.15.txt
* earth25.short.atlas.matrix.16.txt
* earth25.short.atlas.matrix.17.txt
* earth25.short.atlas.matrix.18.txt
* earth25.short.atlas.matrix.19.txt
* earth25.short.atlas.matrix.20.txt
* earth25.med.atlas.matrix.1.txt
* earth25.med.atlas.matrix.2.txt
* earth25.med.atlas.matrix.3.txt
* earth25.med.atlas.matrix.4.txt
* earth25.med.atlas.matrix.5.txt
* earth25.med.atlas.matrix.6.txt
* earth25.med.atlas.matrix.7.txt
* earth25.med.atlas.matrix.8.txt
* earth25.med.atlas.matrix.9.txt
* earth25.med.atlas.matrix.10.txt
* earth25.med.atlas.matrix.11.txt
* earth25.med.atlas.matrix.12.txt
* earth25.med.atlas.matrix.13.txt
* earth25.med.atlas.matrix.14.txt
* earth25.med.atlas.matrix.15.txt
* earth25.med.atlas.matrix.16.txt
* earth25.med.atlas.matrix.17.txt
* earth25.med.atlas.matrix.18.txt
* earth25.med.atlas.matrix.19.txt
* earth25.med.atlas.matrix.20.txt
* earth25.short.times.txt
* earth25.med.times.txt
- Coen.bg.nex
- Coen.mol.nex
- Coen.start.treD.adm_map
- merged.shp
- merged.shx
- merged.bdf
- merged.prj
E. compare_tree
- Coenagrionidae.tre
- Core.tre
- Ridge.tre
- Platynemididae.treF. biome_shift
- atlas_damselfly
* tropical
i. 0_tropical.graph.txt
ii. 1_tropical.graph.txt
iii. 2_tropical.graph.txt
iv. 3_tropical.graph.txt
v. 4_tropical.graph.txt
vi. 5_tropical.graph.txt
vii. 6_tropical.graph.txt
viii. 7_tropical.graph.txt
* warm
i. 0_warm.graph.txt
ii. 1_warm.graph.txt
iii. 2_warm.graph.txt
iv. 3_warm.graph.txt
v. 4_warm.graph.txt
vi. 5_warm.graph.txt
vii. 6_warm.graph.txt
viii. 7_warm.graph.txt
* cold
i. 0_cold.graph.txt
ii. 1_cold.graph.txt
iii. 2_cold.graph.txt
iv. 3_cold.graph.txt
v. 4_cold.graph.txt
vi. 5_cold.graph.txt
vii. 6_cold.graph.txt
viii. 7_cold.graph.txt
* null
i. 0_null.graph.txt
ii. 1_null.graph.txt
iii. 2_null.graph.txt
iv. 3_null.graph.txt
v. 4_null.graph.txt
vi. 5_null.graph.txt
vii. 6_null.graph.txt
viii. 7_null.graph.txt
* land
i. 0_land.graph.txt
ii. 1_land.graph.txt
iii. 2_land.graph.txt
iv. 3_land.graph.txt
v. 4_land.graph.txt
vi. 5_land.graph.txt
vii. 6_land.graph.txt
viii. 7_land.graph.txt
* epoch_names.txt
* epoch_times.txt
* region_names.txt
- biome_dat.csv
- coen_biome.nexG. biogeo
- backbone.tre
- G1.strong.1000.trees
- G1.weak.1000.trees
- Node_data.txt
- Node_data_weak.txt
- Biogeo_data.txt
- Biogeo_data_weak.txtoutput
A. topology
- M3.Uniform.MAP.treeB. bg_dating
- Coen.g0.flat.calib.433570.params.txt
- Coen.g0.flat.calib.433570.states.txt
- Coen.g0.flat.calib.433570.trees
- Coen.g1.beta.calib.strong.673464.params.txt
- Coen.g1.beta.calib.strong.673464.states.txt
- Coen.g1.beta.calib.strong.673464.trees
- Coen.g1.beta.calib.weak.354635.params.txt
- Coen.g1.beta.calib.weak.354635.states.txt
- Coen.g1.beta.calib.weak.354635.trees
- G1_beta_strong.673464_MAP.tree
- G1_beta_weak.354635_MAP.treeC. node_dating
- Coen.g0.fossil.calib.flat.311333.params.txt
- Coen.g0.fossil.calib.flat.311333.trees
- Coen.g0.fossil.calib.flat.311333.burned.trees
- G0_flat_yule.311333_MAP.tree
- Coen.g0.fossil.calib.flat.prior.495364.params.txt
- Coen.g0.fossil.calib.flat.prior.495364.treesD. EBED
- EBED.strong2020_EBD_extinction_rates.log
- EBED.strong2020_EBD_extinction_times.log
- EBED.strong2020_EBD_speciation_rates.log
- EBED.strong2020_EBD_speciation_times.log
- EBED.weak2020_EBD_extinction_rates.log
- EBED.weak2020_EBD_extinction_times.log
- EBED.weak2020_EBD_speciation_rates.log
- EBED.weak2020_EBD_speciation_times.logE. HiSSE
- BiomeHiSSE_strong_r2model.log
- BiomeHiSSE_strong_r2.ase.tre
- BiomeHiSSE_strong_amb_r1model.log
- BiomeHiSSE_strong_amb_r1.ase.tre
- BiomeHiSSE_weakmodel.log
- BiomeHiSSE_weak.ase.tre
- BiomeHiSSE_strong_prior_r1model_combined.log
- Biome_ML
* BiomeHiSSE_strong_ML_r1.out
- Null_ML
* BiomeHiSSE_strong_null_ML_r1.outF. biome_shift
- run2.paleo.model.log
- run2.paleo.ase.tre
- run2.paleo.history.tsvRelationship between files, if important: files in the "raw" directory are required to produced files in the "processed" directory, files in both directories can be used to reproduce files in the "output" directory.
Additional related data collected that was not included in the current data package: None
Are there multiple versions of the dataset? Yes
A. If yes, name of file(s) that was updated: 16S_allspp_unaligned.fst and 16S_allspp.fst
i. Why was the file updated? To remove one unused sequence
ii. When was the file updated? 06-09-2023B. If yes, name of file(s) that was updated: biome.nex and biome_amb.nex
i. Why was the file updated? Files were created as suggested during peer review
ii. When was the file updated? 24-04-2023 and 12-05-2023, respectivelyC. If yes, name of file(s) that was updated: Node_data.txt, Node_data_weak.txt, Biogeo_data.txt, Biogeo_data_weak.txt
i. Why was the file updated? To remove two unused columns
ii. When was the file updated? 07-09-2023, 13-09-2023, 08-09-2023, and 13-09-2023, respectivelyD. If yes, name of file(s) that was updated: all files in output directory
i. Why was the file updated? these intermediate output files were not included in the first data submission, but were added after peer review
ii. When was the file updated? 07-09-2023E. If yes, name of file(s) that was updated: all files in raw directory
i. Why was the file updated? to correct typos in species names and add accession numbers for all sequence data
ii. When was the file updated? 23-01-2024F. If yes, name of file(s) that was updated: G1_beta_strong.673464_MAP.tree, G1_beta_weak.354635_MAP.tree, run2.paleo.ase.tre, BiomeHiSSE_strong_amb_r1.ase.tre, BiomeHiSSE_strong_r2.ase.tre, BiomeHiSSE_weak.ase.tre, BiomeHiSSE_weak.ase.tre, M3.Uniform.MAP.tree
i. Why was the file updated? to correct typos in species names
ii. When was the file updated? 12-01-2024
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 16S_allspp_unaligned.fst
1. File type: fasta
2. Number of sequences: 621
3. Number of taxa: 621
4. Sequence description: third domain of the 16S ribosomal DNA
5. Notes: unaligned sequences
#########################################################################
DATA-SPECIFIC INFORMATION FOR: COI_allspp_unaligned.fst
1. File type: fasta
2. Number of sequences: 573
3. Number of taxa: 573
4. Sequence description: 481 bp fragment of the cytochrome oxidase subunit I
5. Notes: unaligned sequences
#########################################################################
DATA-SPECIFIC INFORMATION FOR: D7_allspp_unaligned.fst
1. File type: fasta
2. Number of sequences: 518
3. Number of taxa: 518
4. Sequence description: seventh hypervariable (divergent) region of the 28S ribosomal DNA
5. Notes: unaligned sequences
#########################################################################
DATA-SPECIFIC INFORMATION FOR: H3_allspp_unaligned.fst
1. File type: fasta
2. Number of sequences: 395
3. Number of taxa: 395
4. Sequence description: 328 bp coding region of the histone 3 gene
5. Notes: unaligned sequences
#########################################################################
DATA-SPECIFIC INFORMATION FOR: PMTR_allspp_unaligned.fst
1. File type: fasta
2. Number of sequences: 260
3. Number of taxa: 260
4. Sequence description: fragment including coding (336 bp) and intronic regions of the arginine phenyl-methyltransferase gene
5. Notes: unaligned sequences
#########################################################################
DATA-SPECIFIC INFORMATION FOR: biome_amb.nex
1. File type: nexus
2. Number of taxa: 669
3. Number of characters: 1
4. Symbols:
0 = tropical
1 = warm
2 = cold
5. Missing data code: -
6. Notes: taxa occupying multiple biome states are coded as ambiguous (e.g. "(0 1)" represent a taxon distributed between tropical and warm biomes)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: biome.nex
1. File type: nexus
2. Number of taxa: 669
3. Number of characters: 1
4. Symbols:
0 = tropical
1 = warm
2 = cold
5. Missing data code: -
6. Notes: taxa occupying multiple biome states are assigned to the coldest biome they inhabit (e.g. a taxon distributed between tropical and warm biomes is coded as "1")
#########################################################################
DATA-SPECIFIC INFORMATION FOR: present_states.csv
1. File type: csv
2. Number of variables: 11
3. Number of cases/rows: 669
4. Variable List:
* Taxon: species name coded as Genus_species
* area1: first biogeographic area inhabited by taxon
* area2: second biogeographic area inhabited by taxon
* area3: third biogeographic area inhabited by taxon
* area4: fourth biogeographic area inhabited by taxon
* area5: fifth biogeographic area inhabited by taxon
* area6: sixth biogeographic area inhabited by taxon
* area7: seventh biogeographic area inhabited by taxon
* area8: eighth biogeographic area inhabited by taxon
* area9: nineth biogeographic area inhabited by taxon
* area10: tenth biogeographic area inhabited by taxon
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S5 for area abbreviations
7. Notes: area2 - area10 fields used only for taxa inhabiting more than one biogeographic area
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Table_S2.csv
Molecular sequence data used in this study.
1. File type: csv
2. Number of variables: 9
3. Number of cases/rows: 669
4. Variable List:
* Family: family within Coenagrionoidea (Platycnemididae or Coenagrionidae)
* Taxon: species name coded as Genus_species
* 16S: sequence identifier for the 16S marker (third domain of the 16S ribosomal DNA)
* COI: sequence identifier for the COI marker (481 bp fragment of the cytochrome oxidase subunit I)
* H3: sequence identifier for the H3 marker (328 bp coding region of the histone 3 gene)
* D7: sequence identifier for the D7 marker (seventh hypervariable (divergent) region of the 28S ribosomal DNA)
* PMTR: sequence identifier for the PMTR marker (fragment including coding (336 bp) and intronic regions of the arginine phenyl-methyltransferase gene)
* Collection: museum or other academic collection hosting the specimens used for sequencing, or the sequence data if previously available (see 6.)
* Identification: initials of researcher who identified the specimen (see 6.)
5. Missing data codes: --
6. Specialized formats or other abbreviations used:
AIST = National Institute of Advanced Industrial Science and Technology, Japan
BYU = Brigham Young University, USA
FSCA = Florida State Collection of Arthropods, USA
LBEE = Laboratory of Biometry and Evolutionary Biology, S. Charlat Lab, France
LU = Lund University, E. I. Svensson, Sweden
NUS = National University of Singapore, R. Meier, Singapore
NCBI = National Center for Biotechnology Information(Genbank), USA
NZAC = New Zealand Arthropod Collection, New Zealand
RMNH = National Museum of Natural History Naturalis, The Netherlands
Rutgers = Rutgers University, J. Ware Lab, USA
USDA = United States Department of Agriculture, N. Von Ellenrieder, USA
AM = Antonia Monteiro
BW = Beatriz Willink
EIS = Erik I. Svensson
IS = Issah Seidu
JB = Jackie Brown
JN = Julio Neto
KDD = Klaas D. Dijkstra
KK = Kawsar Khan
MSH = Melissa Sanchez-Herrera
NVE = Nathalia von Ellenrieder
OK = Oleg Kosterin
RF = Ryo Futahashi
RM = Rudolf Meier
SB = Seth Bybee
SC = Sylvain Charlat
SF = Sonia Ferreira
SR = Samuel Renner
VNO = Viktor Nilsson-Ortman
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Table_S4.csv
Geographic distribution data for the species included in this study.
1. File type: csv
2. Number of variables: 7
3. Number of cases/rows: 669
4. Variable List:
* Family: Family within Coenagrionoidea (Platycnemididae or Coenagrionidae)
* Taxon: Species name coded as Genus_species
* Countries: 3-letter country codes following ISO 3166
* Province/Region/States: names of provinces, states or regions for countries two span two or more biogeographic areas (Australia, Brazil,
Canada, China, India, Indonesia, Malaysia, Russia, USA)
* Areas: biogeographic areas used for dating analysis
* Biome_region: biome regions used for biome shift and dispersal analysis
* Sources: literature and online sources of distribution data (for full references see Table_S4.BibTeX)
5. Missing data codes: NA
6. Specialized formats or other abbreviations used: See Table S5 for Areas and Table S7 for Biome_region in the Supporting Material
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Table_S4.BibTeX
Literature and online sources of distribution data for the species included in this study.
1. File type: BibTeX
2. Number of references: 395
3. Notes: file is complementary to Table_S4.csv
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 16S_allspp.fst
1. File type: fasta
2. Number of sequences: 621
3. Number of taxa: 621
4. Sequence description: third domain of the 16S ribosomal DNA
5. Notes: sequences aligned using MUSCLE (github.com/rcedgar/muscle/releases/tag/v5.1)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 16S_allspp_sorted.fst
1. File type: fasta
2. Number of sequences: 621
3. Number of taxa: 621
4. Sequence description: third domain of the 16S ribosomal DNA
5. Notes: sequences aligned and sorted alphabetically for clarity
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 16S_allspp_corrected.fst
1. File type: fasta
2. Number of sequences: 621
3. Number of taxa: 621
4. Sequence description: third domain of the 16S ribosomal DNA
5. Notes: sequence alignment corrected after visual verification of secondary structure
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 16S_allspp_trim.fst
1. File type: fasta
2. Number of sequences: 621
3. Number of taxa: 621
4. Sequence description: third domain of the 16S ribosomal DNA
5. Notes: sequence alignment after trimming primers and long sequences downloaded from NCBI
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 16S_spp.fst
1. File type: fasta
2. Number of sequences: 621
3. Number of taxa: 621
4. Sequence description: third domain of the 16S ribosomal DNA
5. Notes: trimmed sequence alignment after removing sequence identifier (for concatetation by taxon name)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 16S_spp_sorted.fst
1. File type: fasta
2. Number of sequences: 621
3. Number of taxa: 621
4. Sequence description: third domain of the 16S ribosomal DNA
5. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 16S.nex
1. File type: nexus
2. Number of sequences: 621
3. Number of taxa: 621
4. Number of characters: 317
5. Number of partitions: 1
6. Sequence description: third domain of the 16S ribosomal DNA
7. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: COI_allspp.fst
1. File type: fasta
2. Number of sequences: 573
3. Number of taxa: 573
4. Sequence description: 481 bp fragment of the cytochrome oxidase subunit I
5. Notes: sequences aligned using MUSCLE (github.com/rcedgar/muscle/releases/tag/v5.1)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: COI_allspp_trim.fst
1. File type: fasta
2. Number of sequences: 573
3. Number of taxa: 573
4. Sequence description: 481 bp fragment of the cytochrome oxidase subunit I
5. Notes: sequence alignment after trimming primers and long sequences downloaded from NCBI
#########################################################################
DATA-SPECIFIC INFORMATION FOR: COI_spp.fst
1. File type: fasta
2. Number of sequences: 573
3. Number of taxa: 573
4. Sequence description: 481 bp fragment of the cytochrome oxidase subunit I
5. Notes: trimmed sequence alignment after removing sequence identifier (for concatetation by taxon name)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: COI_spp_sorted.fst
1. File type: fasta
2. Number of sequences: 573
3. Number of taxa: 573
4. Sequence description: 481 bp fragment of the cytochrome oxidase subunit I
5. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: COI.nex
1. File type: nexus
2. Number of sequences: 573
3. Number of taxa: 573
4. Number of characters: 481
5. Number of partitions: 1
6. Sequence description: 481 bp fragment of the cytochrome oxidase subunit I
7. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: D7_allspp.fst
1. File type: fasta
2. Number of sequences: 518
3. Number of taxa: 518
4. Sequence description: seventh hypervariable (divergent) region of the 28S ribosomal DNA
5. Notes: sequences aligned using MUSCLE (github.com/rcedgar/muscle/releases/tag/v5.1)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: D7_allspp_corrected.fst
1. File type: fasta
2. Number of sequences: 518
3. Number of taxa: 518
4. Sequence description: seventh hypervariable (divergent) region of the 28S ribosomal DNA
5. Notes: sequence alignment corrected after visual verification of secondary structure
#########################################################################
DATA-SPECIFIC INFORMATION FOR: D7_allspp_trim.fst
1. File type: fasta
2. Number of sequences: 518
3. Number of taxa: 518
4. Sequence description: seventh hypervariable (divergent) region of the 28S ribosomal DNA
5. Notes: sequence alignment after trimming primers and long sequences downloaded from NCBI
#########################################################################
DATA-SPECIFIC INFORMATION FOR: D7_spp.fst
1. File type: fasta
2. Number of sequences: 518
3. Number of taxa: 518
4. Sequence description: seventh hypervariable (divergent) region of the 28S ribosomal DNA
5. Notes: trimmed sequence alignment after removing sequence identifier (for concatetation by taxon name)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: D7_spp_sorted.fst
1. File type: fasta
2. Number of sequences: 518
3. Number of taxa: 518
4. Sequence description: seventh hypervariable (divergent) region of the 28S ribosomal DNA
5. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: D7.nex
1. File type: nexus
2. Number of sequences: 518
3. Number of taxa: 518
4. Number of characters: 591
5. Number of partitions: 1
6. Sequence description: seventh hypervariable (divergent) region of the 28S ribosomal DNA
7. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: H3_allspp.fst
1. File type: fasta
2. Number of sequences: 395
3. Number of taxa: 395
4. Sequence description: 328 bp coding region of the histone 3 gene
5. Notes: sequences aligned using MUSCLE (github.com/rcedgar/muscle/releases/tag/v5.1)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: H3_allspp_trim.fst
1. File type: fasta
2. Number of sequences: 395
3. Number of taxa: 395
4. Sequence description: 328 bp coding region of the histone 3 gene
5. Notes: sequence alignment after trimming primers and long sequences downloaded from NCBI
#########################################################################
DATA-SPECIFIC INFORMATION FOR: H3_spp.fst
1. File type: fasta
2. Number of sequences: 395
3. Number of taxa: 395
4. Sequence description: 328 bp coding region of the histone 3 gene
5. Notes: trimmed sequence alignment after removing sequence identifier (for concatetation by taxon name)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: H3_spp_sorted.fst
1. File type: fasta
2. Number of sequences: 395
3. Number of taxa: 395
4. Sequence description: 328 bp coding region of the histone 3 gene
5. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: H3.nex
1. File type: nexus
2. Number of sequences: 395
3. Number of taxa: 395
4. Number of characters: 328
5. Number of partitions: 1
6. Sequence description: 328 bp coding region of the histone 3 gene
7. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: PMTR_allspp_best.fas
1. File type: fasta
2. Number of sequences: 260
3. Number of taxa: 260
4. Sequence description: fragment including coding (336 bp) and intronic regions of the arginine phenyl-methyltransferase gene
5. Notes: sequences aligned using PRANK (http://wasabiapp.org/software/prank/)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: PMTR_allspp_trim.fst
1. File type: fasta
2. Number of sequences: 260
3. Number of taxa: 260
4. Sequence description: fragment including coding (336 bp) and intronic regions of the arginine phenyl-methyltransferase gene
5. Notes: sequence alignment after trimming primers and long sequences downloaded from NCBI
#########################################################################
DATA-SPECIFIC INFORMATION FOR: PMTR_spp.fst
1. File type: fasta
2. Number of sequences: 260
3. Number of taxa: 260
4. Sequence description: fragment including coding (336 bp) and intronic regions of the arginine phenyl-methyltransferase gene
5. Notes: trimmed sequence alignment after removing sequence identifier (for concatetation by taxon name)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: PMTR_spp_sorted.fst
1. File type: fasta
2. Number of sequences: 260
3. Number of taxa: 260
4. Sequence description: fragment including coding (336 bp) and intronic regions of the arginine phenyl-methyltransferase gene
5. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: PMTR_spp_exon_pruned.fst
1. File type: fasta
2. Number of sequences: 260
3. Number of taxa: 260
4. Sequence description: fragment including coding (336 bp) regions of the arginine phenyl-methyltransferase gene
5. Notes: trimmed and sorted sequence alignment without introns to test for codon saturation
#########################################################################
DATA-SPECIFIC INFORMATION FOR: PMTR.nex
1. File type: nexus
2. Number of sequences: 260
3. Number of taxa: 260
4. Number of characters: 750
5. Number of partitions: 1
6. Sequence description: fragment including coding (336 bp) and intronic regions of the arginine phenyl-methyltransferase gene
7. Notes: trimmed and sorted sequence alignment
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.mol.namecheck.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 5
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.mol.final.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 5
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: updated taxon names in Coen.mol.nex to match current taxonomy
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.mol.no_parts.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 1
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: removed partition block for model comparison
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M1.mol.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 6
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: different partitions for exons and introns in PMTR.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M1.partitions.nex
1. File type: nexus
2. Number of partitions: 6
3. Notes: partition block for M1.mol.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M2.mol.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 9
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: different partitions for exons and introns in PMTR.nex, different partitions for codon positions 1 and 2 vs 3 in all coding sequences
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M2.partitions.nex
1. File type: nexus
2. Number of partitions: 9
3. Notes: partition block for M2.mol.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M3.mol.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 10
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: different partitions for exons and introns in PMTR.nex, different partitions for codon positions 1 and 2 vs 3 in H3.nex and PMTR.nex, different partitions for all codon positions in COI.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M3.partitions.nex
1. File type: nexus
2. Number of partitions: 10
3. Notes: partition block for M3.mol.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M4.mol.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 11
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: different partitions for exons and introns in PMTR.nex, different partitions for codon positions 1 and 2 vs 3 in PMTR.nex, different partitions for all codon positions in COI.nex and H3.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M4.partitions.nex
1. File type: nexus
2. Number of partitions: 11
3. Notes: partition block for M4.mol.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M5.mol.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 11
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: different partitions for exons and introns in PMTR.nex, different partitions for codon positions 1 and 2 vs 3 in H3.nex, different partitions for all codon positions in COI.nex and PMTR.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M5.partitions.nex
1. File type: nexus
2. Number of partitions: 11
3. Notes: partition block for M5.mol.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M6.mol.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 12
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: different partitions for exons and introns in PMTR.nex, different partitions for all codon positions in all coding sequences
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M6.partitions.nex
1. File type: nexus
2. Number of partitions: 12
3. Notes: partition block for M6.mol.nex
#########################################################################
DATA-SPECIFIC INFORMATION FOR: earth25.short.atlas.matrix.1.txt - earth25.short.atlas.matrix.20.txt
1. File type: plain text
2. Description: 25 x 25 adjacency matrices for short-distance dispersal routes. Each file represents a time epoch between 240 Ma (matrix.1) and 0 Ma (matrix.20)
3. Symbols:
0 = not adjacent
1 = adjacent
4. Notes: data created by Landis, 2017 Syst Biol (https://doi.org/10.1093/sysbio/syw040) and renamed for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: earth25.med.atlas.matrix.1.txt - earth25.med.atlas.matrix.20.txt
1. File type: plain text
2. Description: 25 x 25 adjacency matrices for medium-distance dispersal routes. Each file represents a time epoch between 240 Ma (matrix.1) and 0 Ma (matrix.20)
3. Symbols:
0 = not adjacent
1 = adjacent
4. Notes: data created by Landis, 2017 Syst Biol (https://doi.org/10.1093/sysbio/syw040) and renamed for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: earth25.short.times.txt
1. File type: plain text
2. Description: comma-separated vector of times defining 20 epochs between 240 Ma and 0 Ma
3. Notes: data created by Landis, 2017 Syst Biol (https://doi.org/10.1093/sysbio/syw040) and modified for this study. File is complementary to earth25.short.atlas.matrix.1.txt - earth25.short.atlas.matrix.20.txt
#########################################################################
DATA-SPECIFIC INFORMATION FOR: earth25.med.times.txt
1. File type: plain text
2. Description: comma-separated vector of times defining 20 epochs between 240 Ma and 0 Ma
3. Notes: data created by Landis, 2017 Syst Biol (https://doi.org/10.1093/sysbio/syw040) and modified for this study. File is complementary to earth25.med.atlas.matrix.1.txt - earth25.med.atlas.matrix.20.txt
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.bg.nex
1. File type: nexus
2. Number of taxa: 669
3. Number of characters: 1
4. Symbols:
0 = SAm_N
1 = SAm_E
2 = SAm_S
3 = NAm_NW
4 = NAm_NE
5 = NAm_SE
6 = NAm_SW
7 = Grn
8 = Eur
9 = As_C
A = As_E
B = As_SE
C = As_NE
D = Afr_W
E = Afr_S
F = Afr_E
G = Afr_N
H = Aus_W
I = Aus_E
J = Ind
K = Mdg
L = Ant_W
M = Ant_E
N = Mly
O = NZ
5. Missing data code: -
6. Specialized formats or other abbreviations used: see Table S5 in the Supporting Material
7. Notes: taxa occupying multiple biogeographic areas are coded as ambiguous (e.g. "(0 1)" represent a taxon distributed between SAm_N and SAm_E)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.mol.nex
1. File type: nexus
2. Number of sequences: 669
3. Number of taxa: 669
4. Number of characters: 2467
5. Number of partitions: 10
6. Sequence description: concatenation of COI.nex, H3.nex, PMTR.nex, 16S.nex, and D7.nex
7. Notes: different partitions for exons and introns in PMTR.nex, different partitions for codon positions 1 and 2 vs 3 in H3.nex and PMTR.nex, different partitions for all codon positions in COI.nex. File used in bigeographic and node dating analyses
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.start.tre
1. File type: newick
2. Number of trees: 1
3. Number of taxa: 669
4. Notes: starting tree for biogeographic and node dating analyses
#########################################################################
DATA-SPECIFIC INFORMATION FOR: merged.shp
1. File type: shape
2. Number of features: 528
3. Description: map of administrative areas used to record distribution ranges and biogeographic areas in this study
4. Notes: data downloaded from https://gadm.org/ and edited for this study. File complementary to merged.shx, merged.bdf, and merged.prj
#########################################################################
DATA-SPECIFIC INFORMATION FOR: merged.shx
1. File type: shape index
2. Number of features: 528
3. Description: map of administrative areas used to record distribution ranges and biogeographic areas in this study
4. Notes: data downloaded from https://gadm.org/ and edited for this study. File complementary to merged.shp, merged.bdf, and merged.prj
#########################################################################
DATA-SPECIFIC INFORMATION FOR: merged.dbf
1. File type: attribute
2. Number of attributes: 12
3. Number of cases/rows: 527
4. Attribute List:
* ENGTYPE_1: Type of administrative boundary associated to the second level of subdivision (e.g. region, departament, province, etc)
* HASC_1: Index compounded by the initials of the first and second level of subdivision (e.g. "AF.BD" for country = Afghanistan and province = Badakhshan)
* ID_0: unique country-level ID (first level of subdivision)
* ID_1: unique ID at the second level of subdivision (e.g. region, departament, province, etc)
* ISO: ISO-Alpha 3 code for countries
* NAME_0: Name of feature at first level of subdivision (i.e. country name)
* NAME_1: Name of feature at second level of subdivision (i.e. name of region, department, province, etc)
* OBJECTID: unique identifier
* SHAPE_AREA: feature area in square kilometers * 10^-1
* SHAPE_LENG: always 0, as all features are polygons
* TYPE_1: Alternative type of administrative boundary associated to the second level of subdivision (e.g. region, departament, province, etc)
* Area: Biogeographic area assing in this study
5. Description: attributes of administrative areas used to record distribution ranges and biogeographic areas in this study
6. Specialized formats or other abbreviations used: see Table S5 in the Supporting Material
7. Notes: data downloaded from https://gadm.org/ and edited for this study. File complementary to merged.shp, merged.shx, and merged.prj
#########################################################################
DATA-SPECIFIC INFORMATION FOR: merged.prj
1. File type: projection description
2. Description: map of administrative areas used to record distribution ranges and biogeographic areas in this study
3. Notes: data downloaded from https://gadm.org/ and edited for this study. File complementary to merged.shp, merged.bdf, and merged.shx
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coenagrionidae.tre
1. File type: nexus
2. Number of trees: 4
3. Number of taxa: 4
4. Notes: alternative topologies for the main clades within Coenagrionidae
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Core.tre
1. File type: nexus
2. Number of trees: 4
3. Number of taxa: 9
4. Notes: alternative topologies for the main clades within 'core' pond damselflies (family Coenagrionidae)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Ridge.tre
1. File type: nexus
2. Number of trees: 4
3. Number of taxa: 9
4. Notes: alternative topologies for the main clades within 'ridge-face' pond damselflies (family Coenagrionidae)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Platynemididae.tre
1. File type: nexus
2. Number of trees: 4
3. Number of taxa: 5
4. Notes: alternative topologies for the main clades within featherleg damselflies (family Platycnemididae)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 0_tropical.graph.txt - 7_tropical.graph.txt
1. File type: plain text
2. Description: 9 x 9 availability and connectivity matrices for tropical paleobiomes. Each file represents a time epoch between 106 Ma (0_tropical.graph) and 0 Ma (7_tropical.graph)
3. Symbols:
0 = biome regional coverage less than 1%, not connected between regions
1 = biome regional coverage between 1-25%, weakly connected between regions
2 = biome regional coverage greater than 25%, strongly connected between regions
4. Notes: data created by Landis et al., 2021 Syst Biol (https://doi.org/10.1093/sysbio/syaa045), edited and expanded for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 0_warm.graph.txt - 7_warm.graph.txt
1. File type: plain text
2. Description: 9 x 9 availability and connectivity matrices for warm-temperate paleobiomes. Each file represents a time epoch between 106 Ma (0_warm.graph) and 0 Ma (7_warm.graph)
3. Symbols:
0 = biome regional coverage less than 1%, not connected between regions
1 = biome regional coverage between 1-25%, weakly connected between regions
2 = biome regional coverage greater than 25%, strongly connected between regions
4. Notes: data created by Landis et al., 2021 Syst Biol (https://doi.org/10.1093/sysbio/syaa045), edited and expanded for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 0_cold.graph.txt - 7_cold.graph.txt
1. File type: plain text
2. Description: 9 x 9 availability and connectivity matrices for cold-temperate paleobiomes. Each file represents a time epoch between 106 Ma (0_cold.graph) and 0 Ma (7_cold.graph)
3. Symbols:
0 = biome regional coverage less than 1%, not connected between regions
1 = biome regional coverage between 1-25%, weakly connected between regions
2 = biome regional coverage greater than 25%, strongly connected between regions
4. Notes: data created by Landis et al., 2021 Syst Biol (https://doi.org/10.1093/sysbio/syaa045), edited and expanded for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 0_null.graph.txt - 7_null.graph.txt
1. File type: plain text
2. Description: 9 x 9 availability and connectivity matrices for null features. Each file represents a time epoch between 106 Ma (0_null.graph) and 0 Ma (7_null.graph)
3. Symbols:
2 = null features always have regional coverage greater than 25% and are strongly connected between regions
4. Notes: data created by Landis et al., 2021 Syst Biol (https://doi.org/10.1093/sysbio/syaa045), edited and expanded for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: 0_land.graph.txt - 7_land.graph.txt
1. File type: plain text
2. Description: 9 x 9 connectivity matrices for land regions. Each file represents a time epoch between 106 Ma (0_land.graph) and 0 Ma (7_land.graph)
3. Symbols:
0 = regions not connected by land
1 = regions weakly connected by land
2 = regions connected by land
4. Notes: data created by Landis et al., 2021 Syst Biol (https://doi.org/10.1093/sysbio/syaa045), edited and expanded for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: epoch_names.txt
1. File type: csv
2. Number of variables: 4
3. Number of cases/rows: 8
4. Variable List:
* index: epoch indices as integers from 0 to 7
* start_age: start time of each epoch in Ma
* end_age: end time of each epoch in Ma
* name: epoch names
5. Missing data codes: None
6. Notes: data created by Landis et al., 2021 Syst Biol (https://doi.org/10.1093/sysbio/syaa045), edited for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: epoch_times.txt
1. File type: plain text
2. Description: line-separated vector of end times defining 8 epochs between 66 Ma and 0 Ma
3. Notes: data created by Landis et al., 2021 Syst Biol (https://doi.org/10.1093/sysbio/syaa045)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: region_names.txt
1. File type: csv
2. Number of variables: 3
3. Number of cases/rows: 9
4. Variable List:
* index: region indices as integers from 1 to 9
* region_code: abbreviations used for regions
* region_name: full region names
5. Missing data codes: None
6. Notes: data created by Landis et al., 2021 Syst Biol (https://doi.org/10.1093/sysbio/syaa045), edited for this study
#########################################################################
DATA-SPECIFIC INFORMATION FOR: biome_dat.csv
1. File type: csv
2. Number of variables: 8
3. Number of cases/rows: 669
4. Variable List:
* Taxon: Species name coded as Genus_species
* Region_1: first region inhabited by taxon
* Region_2: second region inhabited by taxon
* Region_3: third region inhabited by taxon
* Region_4: fourth region inhabited by taxon
* Biome_1: first biome inhabited by taxon
* Biome_2: second biome inhabited by taxon
* Biome_3: third biome inhabited by taxon
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S7 in the Supporting Material for region abbreviations
T = Tropical
W = Warm-Temperate
C = Cold-Temperate
7. Notes: Region_2 - Region_4 fields used only for taxa inhabiting more than one region, Biome_2 - Biome_3 fields used only for taxa inhabiting more than one biome
#########################################################################
DATA-SPECIFIC INFORMATION FOR: coen_biome.nex
1. File type: nexus
2. Number of taxa: 669
3. Number of characters: 1
4. Symbols:
A = Tropical+Aus
B = Tropical+SEAs
C = Tropical+EAs
D = Tropical+Eur
E = Tropical+Ind
F = Tropical+Afr
G = Tropical+NAm
H = Tropical+CAm
I = Tropical+SAm
J = Warm+Aus
K = Warm+SEAs
L = Warm+EAs
M = Warm+Eur
N = Warm+Ind
O = Warm+Afr
P = Warm+NAm
Q = Warm+CAm
R = Warm+SAm
S = Cold+Aus
T = Cold+SEAs
U = Cold+EAs
V = Cold+Eur
W = Cold+Ind
X = Cold+Afr
Y = Cold+NAm
0 = Cold+CAm
Z = Cold+SAm
5. Missing data code: -
6. Specialized formats or other abbreviations used: see Table S7 in the Supporting Material
7. Notes: taxa occupying multiple biome-region states are coded as ambiguous (e.g. "(A B)" represent a taxon distributed between Tropical+Aus and Tropical+SEAs)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: backbone.tre
1. File type: newick
2. Number of trees: 1
3. Number of taxa: 3
4. Description: backbone topology for Coeangrionoidea
#########################################################################
DATA-SPECIFIC INFORMATION FOR: G1.strong.1000.trees
1. File type: newick
2. Number of trees: 1000
3. Number of taxa: 669
4. Description: randomly sampled posterior trees from the strongly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: G1.weak.1000.trees
1. File type: newick
2. Number of trees: 1000
3. Number of taxa: 669
4. Description: randomly sampled posterior trees from the weakly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Node_dat.txt
1. File type: space separated value
2. Number of variables: 4
3. Number of cases/rows: 2674000
4. Variable List:
* tree: posterior tree index (1-1000)
* node: node index in R (1-1337)
* age: node age in Ma
* index: node index in RevBayes (1-1337)
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: used to match node indices from R and Revbayes in a posterior sample of trees from the strongly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Node_dat_weak.txt
1. File type: space separated value
2. Number of variables: 4
3. Number of cases/rows: 2674000
4. Variable List:
* tree: posterior tree index (1-1000)
* node: node index in R (1-1337)
* age: node age in Ma
* index: node index in RevBayes (1-1337)
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: used to match node indices from R and Revbayes in a posterior sample of trees from the weakly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Biogeo_dat.txt
1. File type: space separated value
2. Number of variables: 6
3. Number of cases/rows: 1337001
4. Variable List:
* tree: posterior tree index (1-1000)
* node: node index in R (1-1337)
* age: node age in Ma
* index: node index in RevBayes (1-1337)
* start: start state of branch before node (biogeographic region)
* end: end state of branch before node (biogeographic region)
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S5 in the Supporting Material for start and end state codes
7. Notes: ancestral states sampled from the strongly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Biogeo_dat_weak.txt
1. File type: space separated value
2. Number of variables: 6
3. Number of cases/rows: 1337001
4. Variable List:
* tree: posterior tree index (1-1000)
* node: node index in R (1-1337)
* age: node age in Ma
* index: node index in RevBayes (1-1337)
* start: start state of branch before node (biogeographic region)
* end: end state of branch before node (biogeographic region)
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S5 in the Supporting Material for start and end state symbols
7. Notes: ancestral states sampled from the strongly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: M3.Uniform.MAP.tree
1. File type: nexus
2. Number of trees: 1
3. Number of taxa: 669
4. Description: maximum a posteriori (MAP) tree of the topology inference
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g0.flat.calib.433570.params.txt
1. File type: tsv
2. Number of variables: 10
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* b_long: relative weight of long-distance dispersal
* b_med: relative weight of medium-distance dispersal
* b_short: relative weight of short-distance dispersal
* height_bg: expected number of disperal events (biogeographic clock * root age)
* height_mol: expected number of substitutions per site (molecular clock * root age)
* root_age: age (in Ma) of the most recent common ancestor of Coenagrionoidea
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the biogeographic dating analysis ignoring empirical paleogeography
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g0.flat.calib.433570.states.txt
1. File type: tsv
2. Number of variables: 2675
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* start_i: starting state (biogeographic area) of branch "i" of a total of 1337 branches
* end_i: ending state (biogeographic area) of branch "i" of a total of 1337 branches
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S5 in the Supporting Material for start and end state codes
7. Notes: ancestral states sampled at the start and end of each branch from the biogeographic dating analysis ignoring empirical paleogeography
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g0.flat.calib.433570.trees
1. File type: tsv
2. Number of variables: 5
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* tau: newick-formatted posterior tree sampled
5. Missing data codes: None
6. Specialized formats or other abbreviations used: none
7. Notes: parameters sampled from the biogeographic dating analysis ignoring empirical paleogeography
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g1.beta.calib.strong.673464.params.txt
1. File type: tsv
2. Number of variables: 10
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* b_long: relative weight of long-distance dispersal
* b_med: relative weight of medium-distance dispersal
* b_short: relative weight of short-distance dispersal
* height_bg: expected number of disperal events (biogeographic clock * root age)
* height_mol: expected number of substitutions per site (molecular clock * root age)
* root_age: age (in Ma) of the most recent common ancestor of Coenagrionoidea
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the strongly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g1.beta.calib.strong.673464.states.txt
1. File type: tsv
2. Number of variables: 2675
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* start_i: starting state (biogeographic area) of branch "i" of a total of 1337 branches
* end_i: ending state (biogeographic area) of branch "i" of a total of 1337 branches
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S5 in the Supporting Material for start and end state codes
7. Notes: ancestral states sampled at the start and end of each branch from the strongly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g1.beta.calib.strong.673464.trees
1. File type: tsv
2. Number of variables: 5
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* tau: newick-formatted posterior tree sampled
5. Missing data codes: None
6. Specialized formats or other abbreviations used: none
7. Notes: parameters sampled from the strongly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g1.beta.calib.weak.354635.params.txt
1. File type: tsv
2. Number of variables: 10
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* b_long: relative weight of long-distance dispersal
* b_med: relative weight of medium-distance dispersal
* b_short: relative weight of short-distance dispersal
* height_bg: expected number of disperal events (biogeographic clock * root age)
* height_mol: expected number of substitutions per site (molecular clock * root age)
* root_age: age (in Ma) of the most recent common ancestor of Coenagrionoidea
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the weakly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g1.beta.calib.weak.354635.states.txt
1. File type: tsv
2. Number of variables: 2675
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* start_i: starting state (biogeographic area) of branch "i" of a total of 1337 branches
* end_i: ending state (biogeographic area) of branch "i" of a total of 1337 branches
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S5 in the Supporting Material for start and end state codes
7. Notes: ancestral states sampled at the start and end of each branch from the weakly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g1.beta.calib.weak.354635.trees
1. File type: tsv
2. Number of variables: 5
3. Number of cases/rows: 3001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* tau: newick-formatted posterior tree sampled
5. Missing data codes: None
6. Specialized formats or other abbreviations used: none
7. Notes: parameters sampled from the weakly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: G1_beta_strong.673464_MAP.tree
1. File type: nexus
2. Number of trees: 1
3. Number of taxa: 669
4. Description: maximum a posteriori (MAP) tree of the strongly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: G1_beta_weak.354635_MAP.tree
1. File type: nexus
2. Number of trees: 1
3. Number of taxa: 669
4. Description: maximum a posteriori (MAP) tree of the weakly informed biogeographic dating analysis
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g0.fossil.calib.flat.311333.params.txt
1. File type: tsv
2. Number of variables: 12
3. Number of cases/rows: 60001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* age_Argia: age (in Ma) of the most recent ancestor of the genus Argia
* age_Ischnura: age (in Ma) of the most recent ancestor of the genus Ischnura
* age_Nehalennia: age (in Ma) of the most recent ancestor of the genus Nehalennia
* age_Platycnemididae: age (in Ma) of the most recent ancestor of featherlegs (family Platycnemididae)
* extinction_rate: extinction rate of the pure-birth process (always 0)
* height_mol: expected number of substitutions per site (molecular clock * root age)
* root_age: age (in Ma) of the most recent common ancestor of Coenagrionoidea
* speciation_rate: speciation rate of the pure-birth process
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the node dating analysis using fossil calibrations
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g0.fossil.calib.flat.311333.trees
1. File type: tsv
2. Number of variables: 5
3. Number of cases/rows: 12001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* tau: newick-formatted posterior tree sampled
5. Missing data codes: None
6. Specialized formats or other abbreviations used: none
7. Notes: parameters sampled from the node dating analysis using fossil calibrations
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g0.fossil.calib.flat.311333.burned.trees
1. File type: tsv
2. Number of variables: 5
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* tau: newick-formatted posterior tree sampled
5. Missing data codes: None
6. Specialized formats or other abbreviations used: none
7. Notes: parameters sampled from the node dating analysis using fossil calibrations after discarding the first 2000 trees
#########################################################################
DATA-SPECIFIC INFORMATION FOR: G0_flat_yule.311333_MAP.tree
1. File type: nexus
2. Number of trees: 1
3. Number of taxa: 669
4. Description: maximum a posteriori (MAP) tree of the node dating analysis using fossil calibrations
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g0.fossil.calib.flat.prior.495364.params.txt
1. File type: tsv
2. Number of variables: 11
3. Number of cases/rows: 30001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* age_Argia: age (in Ma) of the most recent ancestor of the genus Argia
* age_Ischnura: age (in Ma) of the most recent ancestor of the genus Ischnura
* age_Nehalennia: age (in Ma) of the most recent ancestor of the genus Nehalennia
* extinction_rate: extinction rate of the pure-birth process (always 0)
* height_mol: expected number of substitutions per site (molecular clock * root age)
* root_age: age (in Ma) of the most recent common ancestor of Coenagrionoidea
* speciation_rate: speciation rate of the pure-birth process
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the node dating analysis using fossil calibrations and ran under the prior (i.e. without data)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Coen.g0.fossil.calib.flat.prior.495364.trees
1. File type: tsv
2. Number of variables: 5
3. Number of cases/rows: 6001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* tau: newick-formatted posterior tree sampled
5. Missing data codes: None
6. Specialized formats or other abbreviations used: none
7. Notes: parameters sampled from the node dating analysis using fossil calibrations and ran under the prior (i.e. without data)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: EBED.strong2020_EBD_extinction_rates.log
1. File type: tsv
2. Number of variables: 24
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* extinction[i]: extinction rate of the episodic birth-death process during time interval "i" of a total of 20 time intervals
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the episodic birth-death model over 20 time intervals and using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input
#########################################################################
DATA-SPECIFIC INFORMATION FOR: EBED.strong2020_EBD_extinction_times.log
1. File type: tsv
2. Number of variables: 23
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* interval_times[i]: end times (in Ma) of time interval "i" of a total of 19 time intervals before the present time interval
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the episodic birth-death model over 20 time intervals and using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input
#########################################################################
DATA-SPECIFIC INFORMATION FOR: EBED.strong2020_EBD_speciation_rates.log
1. File type: tsv
2. Number of variables: 24
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* speciation[i]: speciation rate of the episodic birth-death process during time interval "i" of a total of 20 time intervals
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the episodic birth-death model over 20 time intervals and using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input
#########################################################################
DATA-SPECIFIC INFORMATION FOR: EBED.strong2020_EBD_speciation_times.log
1. File type: tsv
2. Number of variables: 23
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* interval_times[i]: end times (in Ma) of time interval "i" of a total of 19 time intervals before the present time interval
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the episodic birth-death model over 20 time intervals and using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input
#########################################################################
DATA-SPECIFIC INFORMATION FOR: EBED.weak2020_EBD_extinction_rates.log
1. File type: tsv
2. Number of variables: 24
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* extinction[i]: extinction rate of the episodic birth-death process during time interval "i" of a total of 20 time intervals
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the episodic birth-death model over 20 time intervals and using the maximum a posteriori tree of the weakly informed biogeographic dating analysis as input
#########################################################################
DATA-SPECIFIC INFORMATION FOR: EBED.weak2020_EBD_extinction_times.log
1. File type: tsv
2. Number of variables: 23
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* interval_times[i]: end times (in Ma) of time interval "i" of a total of 19 time intervals before the present time interval
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the episodic birth-death model over 20 time intervals and using the maximum a posteriori tree of the weakly informed biogeographic dating analysis as input
#########################################################################
DATA-SPECIFIC INFORMATION FOR: EBED.weak2020_EBD_speciation_rates.log
1. File type: tsv
2. Number of variables: 24
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* speciation[i]: speciation rate of the episodic birth-death process during time interval "i" of a total of 20 time intervals
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the episodic birth-death model over 20 time intervals and using the maximum a posteriori tree of the weakly informed biogeographic dating analysis as input
#########################################################################
DATA-SPECIFIC INFORMATION FOR: EBED.weak2020_EBD_speciation_times.log
1. File type: tsv
2. Number of variables: 23
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* interval_times[i]: end times (in Ma) of time interval "i" of a total of 19 time intervals before the present time interval
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from the episodic birth-death model over 20 time intervals and using the maximum a posteriori tree of the weakly informed biogeographic dating analysis as input
#########################################################################
DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_strong_r2model.log
1. File type: tsv
2. Number of variables: 46
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Replicate_ID: index for independent MCMC run (0 or 1)
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* extinction[1]: extinction rate for Tropical biome in hidden state 1
* extinction[2]: extinction rate for Warm-Temperate biome in hidden state 1
* extinction[3]: extinction rate for Cold-Temperate biome in hidden state 1
* extinction[4]: extinction rate for Tropical biome in hidden state 2
* extinction[5]: extinction rate for Warm-Temperate biome in hidden state 2
* extinction[6]: extinction rate for Cold-Temperate biome in hidden state 2
* extinction_alpha[1]: turnover rate for Tropical biome in hidden state 1
* extinction_alpha[2]: turnover rate for Warm-Temperate biome in hidden state 1
* extinction_alpha[3]: turnover rate for Cold-Temperate biome in hidden state 1
* extinction_beta: additive effect of hidden state 2 on turnover rate
* hidden_rate: transition rate between hidden states
* Q[1]: transition rate from Tropical to Warm-Temperate biome
* Q[2]: transition rate from Tropical to Cold-Temperate biome
* Q[3]: transition rate from Warm-Temperate to Tropical biome
* Q[4]: transition rate from Warm-Temperate to Cold-Temperate biome
* Q[5]: transition rate from Cold-Temperate to Tropical biome
* Q[6]: transition rate from Cold-Temperate to Warm-Temperate biome
* R[1]: transition rate from hidden state 1 to hidden state 2
* R[2]: transition rate from hidden state 1 to hidden state 2
* rate_01: transition rate from Tropical to Warm-Temperate biome
* rate_02: transition rate from Tropical to Cold-Temperate biome
* rate_10: transition rate from Warm-Temperate to Tropical biome
* rate_12: transition rate from Warm-Temperate to Cold-Temperate biome
* rate_02: transition rate from Cold-Temperate to Tropical biome
* rate_21: transition rate from Cold-Temperate to Warm-Temperate biome
* rate_category_prior[1]: root frequency of Tropical-hidden state 1
* rate_category_prior[2]: root frequency of Warm-Temperate-hidden state 1
* rate_category_prior[3]: root frequency of Cold-Temperate-hidden state 1
* rate_category_prior[4]: root frequency of Tropical-hidden state 2
* rate_category_prior[5]: root frequency of Warm-Temperate-hidden state 2
* rate_category_prior[6]: root frequency of Cold-Temperate-hidden state 2
* speciation[1]: speciation rate for Tropical biome in hidden state 1
* speciation[2]: speciation rate for Warm-Temperate biome in hidden state 1
* speciation[3]: speciation rate for Cold-Temperate biome in hidden state 1
* speciation[4]: speciation rate for Tropical biome in hidden state 2
* speciation[5]: speciation rate for Warm-Temperate biome in hidden state 2
* speciation[6]: speciation rate for Cold-Temperate biome in hidden state 2
* speciation_alpha[1]: diversification rate for Tropical biome in hidden state 1
* speciation_alpha[2]: diversification rate for Warm-Temperate biome in hidden state 1
* speciation_alpha[3]: diversification rate for Cold-Temperate biome in hidden state 1
* speciation_beta: multiplicative effect of hidden state 2 on diversification rate
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from a Hidden State Speciation and Extinction model, using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input, and assigning taxa occupying multiple biome states to the coldest biome they inhabit
#########################################################################
DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_strong_r2.ase.tre
1. File type: nexus
2. Number of trees: 1
3. Number of taxa: 669
4. Description: tree annotated with ancestral state reconstructions from Hidden State Speciation and Extinction model, using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input, and assigning taxa occupying multiple biome states to the coldest biome they inhabit
#########################################################################
DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_strong_amb_r1model.log
1. File type: tsv
2. Number of variables: 46
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Replicate_ID: index for independent MCMC run (0 or 1)
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* extinction[1]: extinction rate for Tropical biome in hidden state 1
* extinction[2]: extinction rate for Warm-Temperate biome in hidden state 1
* extinction[3]: extinction rate for Cold-Temperate biome in hidden state 1
* extinction[4]: extinction rate for Tropical biome in hidden state 2
* extinction[5]: extinction rate for Warm-Temperate biome in hidden state 2
* extinction[6]: extinction rate for Cold-Temperate biome in hidden state 2
* extinction_alpha[1]: turnover rate for Tropical biome in hidden state 1
* extinction_alpha[2]: turnover rate for Warm-Temperate biome in hidden state 1
* extinction_alpha[3]: turnover rate for Cold-Temperate biome in hidden state 1
* extinction_beta: additive effect of hidden state 2 on turnover rate
* hidden_rate: transition rate between hidden states
* Q[1]: transition rate from Tropical to Warm-Temperate biome
* Q[2]: transition rate from Tropical to Cold-Temperate biome
* Q[3]: transition rate from Warm-Temperate to Tropical biome
* Q[4]: transition rate from Warm-Temperate to Cold-Temperate biome
* Q[5]: transition rate from Cold-Temperate to Tropical biome
* Q[6]: transition rate from Cold-Temperate to Warm-Temperate biome
* R[1]: transition rate from hidden state 1 to hidden state 2
* R[2]: transition rate from hidden state 1 to hidden state 2
* rate_01: transition rate from Tropical to Warm-Temperate biome
* rate_02: transition rate from Tropical to Cold-Temperate biome
* rate_10: transition rate from Warm-Temperate to Tropical biome
* rate_12: transition rate from Warm-Temperate to Cold-Temperate biome
* rate_02: transition rate from Cold-Temperate to Tropical biome
* rate_21: transition rate from Cold-Temperate to Warm-Temperate biome
* rate_category_prior[1]: root frequency of Tropical-hidden state 1
* rate_category_prior[2]: root frequency of Warm-Temperate-hidden state 1
* rate_category_prior[3]: root frequency of Cold-Temperate-hidden state 1
* rate_category_prior[4]: root frequency of Tropical-hidden state 2
* rate_category_prior[5]: root frequency of Warm-Temperate-hidden state 2
* rate_category_prior[6]: root frequency of Cold-Temperate-hidden state 2
* speciation[1]: speciation rate for Tropical biome in hidden state 1
* speciation[2]: speciation rate for Warm-Temperate biome in hidden state 1
* speciation[3]: speciation rate for Cold-Temperate biome in hidden state 1
* speciation[4]: speciation rate for Tropical biome in hidden state 2
* speciation[5]: speciation rate for Warm-Temperate biome in hidden state 2
* speciation[6]: speciation rate for Cold-Temperate biome in hidden state 2
* speciation_alpha[1]: diversification rate for Tropical biome in hidden state 1
* speciation_alpha[2]: diversification rate for Warm-Temperate biome in hidden state 1
* speciation_alpha[3]: diversification rate for Cold-Temperate biome in hidden state 1
* speciation_beta: multiplicative effect of hidden state 2 on diversification rate
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from a Hidden State Speciation and Extinction model, using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input, and coding taxa occupying multiple biome states as ambiguous (e.g. "(0 1)" represent a taxon distributed between tropical and warm biomes)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_strong_amb_r1.ase.tre
1. File type: nexus
2. Number of trees: 1
3. Number of taxa: 669
4. Description: tree annotated with ancestral state reconstructions from Hidden State Speciation and Extinction model, using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input, and coding taxa occupying multiple biome states as ambiguous (e.g. "(0 1)" represent a taxon distributed between tropical and warm biomes)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_weakmodel.log
1. File type: tsv
2. Number of variables: 46
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Replicate_ID: index for independent MCMC run (0 or 1)
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* extinction[1]: extinction rate for Tropical biome in hidden state 1
* extinction[2]: extinction rate for Warm-Temperate biome in hidden state 1
* extinction[3]: extinction rate for Cold-Temperate biome in hidden state 1
* extinction[4]: extinction rate for Tropical biome in hidden state 2
* extinction[5]: extinction rate for Warm-Temperate biome in hidden state 2
* extinction[6]: extinction rate for Cold-Temperate biome in hidden state 2
* extinction_alpha[1]: turnover rate for Tropical biome in hidden state 1
* extinction_alpha[2]: turnover rate for Warm-Temperate biome in hidden state 1
* extinction_alpha[3]: turnover rate for Cold-Temperate biome in hidden state 1
* extinction_beta: additive effect of hidden state 2 on turnover rate
* hidden_rate: transition rate between hidden states
* Q[1]: transition rate from Tropical to Warm-Temperate biome
* Q[2]: transition rate from Tropical to Cold-Temperate biome
* Q[3]: transition rate from Warm-Temperate to Tropical biome
* Q[4]: transition rate from Warm-Temperate to Cold-Temperate biome
* Q[5]: transition rate from Cold-Temperate to Tropical biome
* Q[6]: transition rate from Cold-Temperate to Warm-Temperate biome
* R[1]: transition rate from hidden state 1 to hidden state 2
* R[2]: transition rate from hidden state 1 to hidden state 2
* rate_01: transition rate from Tropical to Warm-Temperate biome
* rate_02: transition rate from Tropical to Cold-Temperate biome
* rate_10: transition rate from Warm-Temperate to Tropical biome
* rate_12: transition rate from Warm-Temperate to Cold-Temperate biome
* rate_02: transition rate from Cold-Temperate to Tropical biome
* rate_21: transition rate from Cold-Temperate to Warm-Temperate biome
* rate_category_prior[1]: root frequency of Tropical-hidden state 1
* rate_category_prior[2]: root frequency of Warm-Temperate-hidden state 1
* rate_category_prior[3]: root frequency of Cold-Temperate-hidden state 1
* rate_category_prior[4]: root frequency of Tropical-hidden state 2
* rate_category_prior[5]: root frequency of Warm-Temperate-hidden state 2
* rate_category_prior[6]: root frequency of Cold-Temperate-hidden state 2
* speciation[1]: speciation rate for Tropical biome in hidden state 1
* speciation[2]: speciation rate for Warm-Temperate biome in hidden state 1
* speciation[3]: speciation rate for Cold-Temperate biome in hidden state 1
* speciation[4]: speciation rate for Tropical biome in hidden state 2
* speciation[5]: speciation rate for Warm-Temperate biome in hidden state 2
* speciation[6]: speciation rate for Cold-Temperate biome in hidden state 2
* speciation_alpha[1]: diversification rate for Tropical biome in hidden state 1
* speciation_alpha[2]: diversification rate for Warm-Temperate biome in hidden state 1
* speciation_alpha[3]: diversification rate for Cold-Temperate biome in hidden state 1
* speciation_beta: multiplicative effect of hidden state 2 on diversification rate
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from a Hidden State Speciation and Extinction model, using the maximum a posteriori tree of the weakly informed biogeographic dating analysis as input, and assigning taxa occupying multiple biome states to the coldest biome they inhabit
#########################################################################
DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_weak.ase.tre
1. File type: nexus
2. Number of trees: 1
3. Number of taxa: 669
4. Description: tree annotated with ancestral state reconstructions from Hidden State Speciation and Extinction model, using the maximum a posteriori tree of the weakly informed biogeographic dating analysis as input, and assigning taxa occupying multiple biome states to the coldest biome they inhabit
#########################################################################
DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_strong_prior_r1model_combined.log
1. File type: tsv
2. Number of variables: 46
3. Number of cases/rows: 10001
4. Variable List:
* Iteration: MCMC iteration index
* Replicate_ID: index for independent MCMC run (0 or 1)
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* extinction[1]: extinction rate for Tropical biome in hidden state 1
* extinction[2]: extinction rate for Warm-Temperate biome in hidden state 1
* extinction[3]: extinction rate for Cold-Temperate biome in hidden state 1
* extinction[4]: extinction rate for Tropical biome in hidden state 2
* extinction[5]: extinction rate for Warm-Temperate biome in hidden state 2
* extinction[6]: extinction rate for Cold-Temperate biome in hidden state 2
* extinction_alpha[1]: turnover rate for Tropical biome in hidden state 1
* extinction_alpha[2]: turnover rate for Warm-Temperate biome in hidden state 1
* extinction_alpha[3]: turnover rate for Cold-Temperate biome in hidden state 1
* extinction_beta: additive effect of hidden state 2 on turnover rate
* hidden_rate: transition rate between hidden states
* Q[1]: transition rate from Tropical to Warm-Temperate biome
* Q[2]: transition rate from Tropical to Cold-Temperate biome
* Q[3]: transition rate from Warm-Temperate to Tropical biome
* Q[4]: transition rate from Warm-Temperate to Cold-Temperate biome
* Q[5]: transition rate from Cold-Temperate to Tropical biome
* Q[6]: transition rate from Cold-Temperate to Warm-Temperate biome
* R[1]: transition rate from hidden state 1 to hidden state 2
* R[2]: transition rate from hidden state 1 to hidden state 2
* rate_01: transition rate from Tropical to Warm-Temperate biome
* rate_02: transition rate from Tropical to Cold-Temperate biome
* rate_10: transition rate from Warm-Temperate to Tropical biome
* rate_12: transition rate from Warm-Temperate to Cold-Temperate biome
* rate_02: transition rate from Cold-Temperate to Tropical biome
* rate_21: transition rate from Cold-Temperate to Warm-Temperate biome
* rate_category_prior[1]: root frequency of Tropical-hidden state 1
* rate_category_prior[2]: root frequency of Warm-Temperate-hidden state 1
* rate_category_prior[3]: root frequency of Cold-Temperate-hidden state 1
* rate_category_prior[4]: root frequency of Tropical-hidden state 2
* rate_category_prior[5]: root frequency of Warm-Temperate-hidden state 2
* rate_category_prior[6]: root frequency of Cold-Temperate-hidden state 2
* speciation[1]: speciation rate for Tropical biome in hidden state 1
* speciation[2]: speciation rate for Warm-Temperate biome in hidden state 1
* speciation[3]: speciation rate for Cold-Temperate biome in hidden state 1
* speciation[4]: speciation rate for Tropical biome in hidden state 2
* speciation[5]: speciation rate for Warm-Temperate biome in hidden state 2
* speciation[6]: speciation rate for Cold-Temperate biome in hidden state 2
* speciation_alpha[1]: diversification rate for Tropical biome in hidden state 1
* speciation_alpha[2]: diversification rate for Warm-Temperate biome in hidden state 1
* speciation_alpha[3]: diversification rate for Cold-Temperate biome in hidden state 1
* speciation_beta: multiplicative effect of hidden state 2 on diversification rate
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: parameters sampled from a Hidden State Speciation and Extinction model, using the maximum a posteriori tree of the weakly informed biogeographic dating analysis as input, and ran under the prior (i.e. without data)
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DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_strong_ML_r1.out
1. File type: tsv
2. Number of variables: 3
3. Number of cases/rows: 408
4. Variable List:
* state: sampling generation within each stepping stone (300 -
* power: power to which likelihood is raised for sampling model parameters (1 = sampling from the posterior and 0 = sampling from the prior)
* likelihood: likelihood of the data given the sampled model parameters
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: power posterior analysis for Hidden State Speciation and Extinction (HiSSE) model wherein diversification rates vary between biomes (Tropical, Warm-Temperate and Cold-Temperate) and between two states of a hidden trait. This file is used to estimate the marginal likelihood of the HiSSE model
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DATA-SPECIFIC INFORMATION FOR: BiomeHiSSE_strong_null_ML_r1.out
1. File type: tsv
2. Number of variables: 3
3. Number of cases/rows: 408
4. Variable List:
* state: sampling generation within each stepping stone (300 - 1000)
* power: power to which likelihood is raised for sampling model parameters (1 = sampling from the posterior and 0 = sampling from the prior)
* likelihood: likelihood of the data given the sampled model parameters
5. Missing data codes: None
6. Specialized formats or other abbreviations used: None
7. Notes: power posterior analysis for Hidden State Speciation and Extinction (HiSSE) model wherein diversification rates vary between two states of a hidden trait, but are equal across biomes. This file is used to estimate the marginal likelihood of a suitable null model
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DATA-SPECIFIC INFORMATION FOR: run2.paleo.model.log
1. File type: tsv
2. Number of variables: 53
3. Number of cases/rows: 604
4. Variable List:
* Iteration: MCMC iteration index
* Posterior: posterior probability of sampled parameters
* Likelihood: likelihood of sampled parameters
* Prior: prior probability of sampled parameters
* biome_rates[1]: base biome shift rate from Tropical to Warm-Temperate
* biome_rates[2]: base biome shift rate from Warm-Temperate to Tropical
* biome_rates[3]: base biome shift rate from Warm-Temperate to Cold-Temperate
* biome_rates[4]: base biome shift rate from Cold-Temperate to Warm-Temperate
* br_base: expected proportion of biome shift events relative to dispersal events
* br_CW: base biome shift rate from Cold-Temperate to Warm-Temperate
* br_TW: base biome shift rate from Tropical to Warm-Temperate
* br_WC: base biome shift rate from Warm-Temperate to Cold-Temperate
* br_WT: base biome shift rate from Warm-Temperate to Tropical
* dr_base: expected proportion of dispersal events relative to biome shift events (1 - br_base)
* rate_biome: biome shift rate
* rf_simplex[1]: root frequency of biome-region Tropical+Aus
* rf_simplex[2]: root frequency of biome-region Tropical+SE_As
* rf_simplex[3]: root frequency of biome-region Tropical+E_As
* rf_simplex[4]: root frequency of biome-region Tropical+Eur
* rf_simplex[5]: root frequency of biome-region Tropical+Ind
* rf_simplex[6]: root frequency of biome-region Tropical+Afr
* rf_simplex[7]: root frequency of biome-region Tropical+N_Am
* rf_simplex[8]: root frequency of biome-region Tropical+C_Am
* rf_simplex[9]: root frequency of biome-region Tropical+S_Am
* rf_simplex[10]: root frequency of biome-region Warm-Temperate+Aus
* rf_simplex[11]: root frequency of biome-region Warm-Temperate+SE_As
* rf_simplex[12]: root frequency of biome-region Warm-Temperate+E_As
* rf_simplex[13]: root frequency of biome-region Warm-Temperate+Eur
* rf_simplex[14]: root frequency of biome-region Warm-Temperate+Ind
* rf_simplex[15]: root frequency of biome-region Warm-Temperate+Afr
* rf_simplex[16]: root frequency of biome-region Warm-Temperate+N_Am
* rf_simplex[17]: root frequency of biome-region Warm-Temperate+C_Am
* rf_simplex[18]: root frequency of biome-region Warm-Temperate+S_Am
* rf_simplex[19]: root frequency of biome-region Cold-Temperate+Aus
* rf_simplex[20]: root frequency of biome-region Cold-Temperate+SE_As
* rf_simplex[21]: root frequency of biome-region Cold-Temperate+E_As
* rf_simplex[22]: root frequency of biome-region Cold-Temperate+Eur
* rf_simplex[23]: root frequency of biome-region Cold-Temperate+Ind
* rf_simplex[24]: root frequency of biome-region Cold-Temperate+Afr
* rf_simplex[25]: root frequency of biome-region Cold-Temperate+N_Am
* rf_simplex[26]: root frequency of biome-region Cold-Temperate+C_Am
* rf_simplex[27]: root frequency of biome-region Cold-Temperate+S_Am
* w_adj[1]: marginal features for availability/connectivity among biomes/regions (always 0)
* w_adj[2]: weak features for availability/connectivity among biomes/regions (equal to y and between 0 and 1)
* w_adj[3]: strong features for availability/connectivity among biomes/regions (always 1)
* w_B: weight of biome features
* w_G: weight of biome-independent land (geographical) features
* w_graph[1]: weight of null (biome- and land-independent) features
* w_graph[2]: weight of biome-independent land (geographical) features
* w_graph[3]: weight of biome features
* w_not_B: weight of null and land features combined
* w_U: weight of null (biome- and land-independent) features
* y: effect of weak features relative to strong and marginal features
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S7 for biome-region abbreviations
7. Notes: parameters sampled from a joint dispersal and biome shift model, using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input
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DATA-SPECIFIC INFORMATION FOR: run2.paleo.ase.tre
1. File type: nexus
2. Number of trees: 1
3. Number of taxa: 669
4. Description: tree annotated with ancestral state reconstructions from a joint dispersal and biome shift model, using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input
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DATA-SPECIFIC INFORMATION FOR: run2.paleo.history.tsv
1. File type: tsv
2. Number of variables: 11
3. Number of cases/rows: 1470376
4. Variable List:
* iteration: MCMC iteration index
* node_index: RevBayes index for tree node (1-1337)
* branch_start_time: start time of branch (in Ma)
* branch_end_time: end time of branch (in Ma)
* start_state: biome-region state at the start of the branch
* end_state: biome-region state at the end of the branch
* transition_time: time (in Ma) when the transition between biome-region states occurred
* transition_type: always anagenetic (i.e. occuring along branches)
* parent_index: node index of parent node
* child1_index: node index of first child node
* child2_index: node index of second child node
5. Missing data codes: None
6. Specialized formats or other abbreviations used: see Table S7 for biome-region state symbols
7. Notes: stochastic character histories simulated in a joint dispersal and biome shift model, using the maximum a posteriori tree of the strongly informed biogeographic dating analysis as input
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Methods
Data collection processing and analyses are described in full in the Supplementary Material (PhyloSupporting_SysBio_R1.pdf)
Usage notes
All the code used in this study is recorded and described in the file COENPhylo_R1.html