DOI: 10.5061/dryad.76hdr7t48
title: Data for: Reliable biogeography requires fossils: Insights from a new species-level phylogeny of extinct and living carnivores

description: A central objective of historical biogeography is to understand where
 clades originated and how they moved across space and over time. However,
 given the dynamic history of ecosystem changes in response to climate
 change and geologic events, the manifold long-distance dispersals over
 evolutionary timescales, and regional and global extinctions, it remains
 uncertain how reliable inferences based solely on extant taxa can be
 achieved. Using a novel species-level phylogeny of all known extant and
 extinct species of the mammalian order Carnivora and related extinct
 groups, we show that far more precise and accurate  ancestral
 areas can be estimated by fully integrating extinct species into the
 analyses, rather than solely relying on extant species or identifying
 ancestral areas only based on the geography of the oldest fossils. Through
 a series of simulations, we further show that this conclusion is robust
 under realistic scenarios in which the unknown extinct taxa represent a
 biased subset of all extinct species. Our results highlight the importance
 of integrating fossil taxa into a phylogenetic framework to further
 improve our understanding of historical biogeography and reveal the
 dynamic dispersal and diversification history of carnivores.
description: Appendix 1 contains the produced phylogeny of all carnivores.
 Appendix 2 contains all the R codes for the analyses. Appendix 3 contains
 a description of our treatment of all the individual fossil records.
 Appendix 4 shows topological variation across trees plotted as 18 separate
 subtrees focusing on smaller clades. Appendix 5 contains morphological
 character coding for the newly coded taxa and the MrBayes input
 files
description: # Data for: Reliable biogeography requires fossils: Insights from a new
 species-level phylogeny of extinct and living carnivores
 [https://doi.org/10.5061/dryad.76hdr7t48](https://doi.org/10.5061/dryad.76hdr7t48) Appendix 1 contains the produced phylogeny of all carnivores. Appendix 2 contains all the R codes for the analyses. Appendix 3 contains a description of our treatment of all the individual fossil records. Appendix 4 shows topological variation across trees plotted as 18 separate subtrees focusing on smaller clades. Appendix 5 contains morphological character coding for the newly coded taxa and the MrBayes input files ## Description of the data and file structure Appendix 1 is the resulting phylogeny Appendix 2 contains commented R codes for all analyses published in the paper. The total script is divided into 18 separate files with titles describing the overall theme of each script file. To fully replicate all analyses in the paper the scripts needs to be run in order based on the numbers listed as the first two letters of the names. An ultrashort description of of what each script is doing is noted in the first lines of each file. Appendix 3 shows the taxonomic assignment of all fossils for this paper, i.e. the name the fossil is listed under in PBDB or NoW and the name we assign it to. The first sheet of the file serves as a read.me file describing the data-structure of the following sheets. Appendix 4 contains a partial visualization of the phylogeny produced in appendix 1 Appendix 5 contains input information being used to build the phylogeny.  ## Sharing/Access information Data was derived from the following sources: * All fossil data were originally downloaded from PBDB ([https://paleobiodb.org/](https://paleobiodb.org/) and NOW ([http://www.helsinki.fi/science/now/](http://www.helsinki.fi/science/now/) ## Code/Software Appendix 1 is in Nexus format Appendix 2 are all R codes. Appendix 3 is an excel file Appendix 4 is a PDF Appendix 5 contains coding information on selected fossils in a txt files and a number of input files for MrBayes 3.2