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Data from: Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance

Cite this dataset

Capobianco, Alessio; Friedman, Matt (2024). Data from: Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance [Dataset]. Dryad. https://doi.org/10.5061/dryad.g79cnp5x1

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.

README: Fossil evidence for marine dispersal in osteoglossid fishes, a classic example of continental vicariance

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 analysis
  • AllConcatRAxML.phy : Concatenated alignment of molecular data in Newick format, used as input data for PartitionFinder 2
  • FossilTipAges.xlsx : Minimum and maximum ages associated to fossil tips for the phylogenetic analysis, with literature references
  • MolecularData.nex : Concatenated alignment of molecular data in Nexus format, used in the phylogenetic analysis
  • MorphologicalCharactersList.docx : List of morphological characters and character states
  • MorphologicalData.nex : Morphological data in Nexus format, used in the phylogenetic analysis
  • Osteo_SpeciesList_Classification.csv : List of valid species of extant Osteoglossomorpha, with taxonomic classification
  • TotalEvidenceAlignment.nex : Combinated molecular and morphological data in Nexus format, used in the phylogenetic analysis
  • BioGeoBEARS subfolder:
    • 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 burden
    • OsteoGeographyWithMarine_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 taxa
    • OsteoGeographyWithMarine.txt : Geography input file
    • OsteoGeographyNoMarine.txt : Geography input file with alternative biogeography coding scheme
    • OsteoTree_ForBiogeography.tree : 'Allcompat' summary consensus tree of Osteoglossomorpha
    • OsteoTree_OnlyExtant.tree : 'Allcompat' summary consensus tree of Osteoglossomorpha, with fossil tips pruned (only extant taxa included)
  • AncestralHabitatEstimation subfolder:
    • 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 burden
    • OsteoTree_ForBiogeography.tree : 'Allcompat' summary consensus tree of Osteoglossomorpha
    • Trait.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 it
  • partition_finder.cfg : Script for running PartitionFinder 2
  • RoguePlot_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 trees
  • RoguePlots_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) model
  • UnrootedTotalEvidenceAnalysis_MrBayes.nex : MrBayes script to run unrooted, non-time-calibrated, total-evidence phylogenetic analysis
  • BioGeoBEARS subfolder:
    • 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 uncertainty
    • BGB_BiogeographicStochasticMapping.R : BioGeoBEARS R script to run biogeographic stochastic mapping (BSM) on the 'AllCompat' summary consensus tree
    • BGB_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 tree
    • BGB_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 uncertainty
    • BGB_MarineNotArea_Script.R : BioGeoBEARS R script for biogeographic analyses on the 'Allcompat' summary consensus tree with alternative biogeography scoring scheme
  • AncestralHabitatEstimation subfolder:
    • 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.

Funding

Palaeontological Association, Award: PA-CD202102

National Science Foundation, Award: NSF DEB 2017822

European Research Council, Award: GA 101043187

Society of Systematic Biologists, 2017 SSB Graduate Student Research Award

University of Michigan–Ann Arbor, Rackham Predoctoral Fellowship 2020-2021 and Horace H. Rackham School of Graduate Studies

University of Michigan–Ann Arbor, Scott Turner Student Research Grant Award 2017 under Department of Earth and Environmental Sciences