Data from: Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance
Data files
Jun 26, 2024 version files 5.52 GB
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README.md
5.59 KB
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SupplementaryDatasetForSubmission.zip
5.52 GB
Abstract
The separation of closely-related terrestrial or freshwater species by vast marine barriers represents a biogeographic riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographic ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here we present a new total-evidence hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographic pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day.
https://doi.org/10.5061/dryad.g79cnp5x1
This compressed file archive contains all data and scripts used for the phylogenetic, biogeographic, and ancestral habitat estimation analyses included in the paper, as well as all raw output files.
Description of the data and file structure
data folder: contains data files used for all analyses and data sources
AccessionNumbersMolecularData.xlsx: Genbank accession numbers, BOLD accession numbers, and literature references for molecular data used in the phylogenetic analysisAllConcatRAxML.phy: Concatenated alignment of molecular data in Newick format, used as input data for PartitionFinder 2FossilTipAges.xlsx: Minimum and maximum ages associated to fossil tips for the phylogenetic analysis, with literature referencesMolecularData.nex: Concatenated alignment of molecular data in Nexus format, used in the phylogenetic analysisMorphologicalCharactersList.docx: List of morphological characters and character statesMorphologicalData.nex: Morphological data in Nexus format, used in the phylogenetic analysisOsteo_SpeciesList_Classification.csv: List of valid species of extant Osteoglossomorpha, with taxonomic classificationTotalEvidenceAlignment.nex: Combinated molecular and morphological data in Nexus format, used in the phylogenetic analysisBioGeoBEARSsubfolder:Osteo_Analysis1Long_PosteriorTrees_ForBio.t: List of time-calibrated phylogenetic trees forming Bayesian posterior distribution of trees, obtained by combining the tree output files from the two MrBayes runs, removing 10% burn-in, pruning outgroup (non-Osteoglossomorpha) taxa, and subsampling every 10 trees to reduce computational burdenOsteoGeographyWithMarine_ForBSM.txt: Geography input file for biogeographic stochastic mapping (BSM) analyses (BSM in BioGeoBEARS requires geographic areas to be defined by a single character)OsteoGeographyWithMarine_OnlyExtant.txt: Geography input file with only extant taxaOsteoGeographyWithMarine.txt: Geography input fileOsteoGeographyNoMarine.txt: Geography input file with alternative biogeography coding schemeOsteoTree_ForBiogeography.tree: 'Allcompat' summary consensus tree of OsteoglossomorphaOsteoTree_OnlyExtant.tree: 'Allcompat' summary consensus tree of Osteoglossomorpha, with fossil tips pruned (only extant taxa included)
AncestralHabitatEstimationsubfolder:Osteo_Analysis1Long_PosteriorTrees_ForBio.t: List of time-calibrated phylogenetic trees forming Bayesian posterior distribution of trees, obtained by combining the tree output files from the two MrBayes runs, removing 10% burn-in, pruning outgroup (non-Osteoglossomorpha) taxa, and subsampling every 10 trees to reduce computational burdenOsteoTree_ForBiogeography.tree: 'Allcompat' summary consensus tree of OsteoglossomorphaTrait.nex: Habitat data ('0' = freshwater, '1' = marine)
scripts folder: contains scripts for all analyses
MolecularDatasetBuild_regPhylo.R: R script to source molecular data from GenBank and BOLD and align itpartition_finder.cfg: Script for running PartitionFinder 2RoguePlot_Analysis1Long.R: R script to run the RoguePlots functions to determine the phylogenetic position of fossil taxa in respect to extant taxa across the Bayesian posterior distribution of treesRoguePlots_KlopfsteinSpasojevic2019.R: R script including all RoguePlots functions, as downloaded from the supplementary material of Klopfstein & Spasojevic (2019)SFBD_TotalEvidenceAnalysis_MrBayes.nex: MrBayes script to run tip-dated, total-evidence phylogenetic analysis under the Skyline Fossilized Birth Death (SFBD) modelUnrootedTotalEvidenceAnalysis_MrBayes.nex: MrBayes script to run unrooted, non-time-calibrated, total-evidence phylogenetic analysisBioGeoBEARSsubfolder:BGB_BiogeographicStochasticMapping_WithPhyloUncertainty.R: BioGeoBEARS R script to run biogeographic stochastic mapping (BSM) on a sample of 200 phylogenies from the Bayesian posterior distribution of trees, thus accounting for phylogenetic uncertaintyBGB_BiogeographicStochasticMapping.R: BioGeoBEARS R script to run biogeographic stochastic mapping (BSM) on the 'AllCompat' summary consensus treeBGB_MarineAsArea_ExtantOnly_Script.R: BioGeoBEARS R script for biogeographic analyses on the 'Allcompat' summary consensus tree with fossil tips pruned (only extant taxa included)BGB_MarineAsArea_Script.R: BioGeoBEARS R script for biogeographic analyses on the 'Allcompat' summary consensus treeBGB_MarineAsArea_WithPhyloUncertainty.R: BioGeoBEARS R script for biogeographic analyses on a sample of 200 phylogenies from the Bayesian posterior distribution of trees, thus accounting for phylogenetic uncertaintyBGB_MarineNotArea_Script.R: BioGeoBEARS R script for biogeographic analyses on the 'Allcompat' summary consensus tree with alternative biogeography scoring scheme
AncestralHabitatEstimationsubfolder:ASR_ADRmodel_SIMMAP.R: R script for ancestral habitat estimation, including script for stochastic character mapping
output folder: contains output files as generated by the scripts included in the scripts folder using the data files included in the data folder.
- Capobianco, Alessio; Friedman, Matt (2024), Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance, Proceedings of the Royal Society B: Biological Sciences, Journal-article, https://doi.org/10.1098/rspb.2024.1293
