DOI: 10.5061/dryad.g79cnp5x1
title: Data from: Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance

description: 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.
description: # Fossil evidence for marine dispersal in osteoglossid fishes, a classic
 example of continental vicariance
 [https://doi.org/10.5061/dryad.g79cnp5x1](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.