DOI: 10.5061/dryad.9w0vt4btk
title: Data from: Interaction of sequence data and paleogeographic priors in biogeographic dating: How could biological data inform time-constrained geological models?

description: Biological and geographic patterns and processes are linked such that
 biological data hold information on paleogeographical patterns and
 processes. Here, we aimed to test Biogeographic dating as a methodological
 framework for the integration of biological, paleontological, and
 geological data to test paleogeographic hypotheses. In Biogeographic
 dating, both forms of data are specified and analyzed simultaneously. We
 evaluate how uncertainty and accuracy in both types of datasets affect the
 inference of divergence times used as a proxy for generating or testing
 geological models. We used data simulation to generate a paleogeographic
 scenario and a nuclear sequence dataset for lineages whose evolution is
 correlated with geological patterns. Then, gene flow was simulated across
 landscape units, such that biological patterns inferred from sequence data
 would deviate from simulated times of paleogeographic change. Under those
 two scenarios, we specified broad, incorrect, and accurate geological
 priors. These various scenarios were analyzed through Biogeographic dating
 analyses run in RevBayes and compared with our simulations. In
 doing so, we test the potential for well-calibrated phylogenies and the
 impact of accuracy and uncertainty in geological priors for estimating
 paleogeographic events.
description: # Data from: Interaction of sequence data and paleogeographic priors in
 biogeographic dating: How could biological data inform time-constrained
 geological models? This DRYAD repository contains data, scripts, and
 results for "Interaction of biological and paleogeographic priors in
 Biogeographic dating: How can biological data inform time-constrained
 geological models" published in the Journal of Biogeography.
 Descriptions of the content available in each folder and its generation
 are listed below. #### Scripts (generation of data, Biogeographic dating
 analyses) We link to Zenodo, where code used to generate simulated
 sequence data using Python and the package msprime provided. Additionally,
 scripts and results for running the Biogeographic dating analysis using
 RevBayes are provided. **demographic_simulation.py =** run with msprime to
 generate sequence data without gene flow.
 **demographic_simulation_gene_flow.py =** run with msprime to generate
 sequence data with gene flow. **fill_in_invariant_sites.py =** Python
 script used to add randomly generated base pairs to invariant sites among
 lineages. **model_.rb =** five unique scripts, run in RevBayes, with
 parameters corresponding to the accuracy and correctness of data described
 in the words following model_. Further information on each model is
 described in the publication. **combine.sh =** Unix script used to combine
 the two generated MCMC output files with a burn in. #### Input Data
 Simulated sequence data from the previous steps and resulting phylogenies,
 along with files containing parameters used in Biogeographic dating
 analyses are provided (input_data.zip). **simulated_range.nex =** lineage
 ranges (presence/absence) **simulated_sequences.nex =** previously
 generated sequences from demographic simulations
 **modified_sequences_filled.nex =** simulated_sequences.nex with invariant
 sites filled **simulated.connectivity.txt** **=** connectivity between
 ranges over epoch times **simulated.distances.txt =** distances between
 ranges **_times.txt =** varying epoch times, used to establish priors in
 Biogeographic dating Information regarding the selection of varying
 parameters is described in detail in the publication, and all parameter
 input can be modified in the analysis scripts available on Zenodo. ####
 Results (no migration and gene flow) The output of each individual MCMC
 run are provided in separate folders based on the presence
 (results_gene_flow.zip) or absence (results_no_migration.zip) of gene flow
 in demographic history generated by msprime. Results include the dated
 phylogenies and ancestral state estimations referred to in the
 publication. Within folders, results files ending FR indicates an enforced
 root age for the phylogeny, while runs lacking this did not have a strict
 root age provided in analyses. geo_unknown, incorrect_normal,
 incorrect_uniform, informed_normal, and informed_uniform refer to the
 paleogeographic prior used in the Biogeographic dating analysis. Each zip
 file also contains a combined_results folder, which contains the combined
 result files of the 2 MCMC runs using the same model after applying
 burn-in.