DOI: 10.5061/dryad.v6wwpzh4d
title: Freshwater fish and the Cretaceous/Palaeogene boundary: A critical assessment of survivorship patterns

description: Mass extinctions are major influences on both the phylogenetic structure
 of the modern biota and our ability to reconstruct broad-based patterns of
 evolutionary history. The most recent mass extinction is also the most
 famous—that which implicates a bolide impact in defining the
 Cretaceous/Palaeogene boundary (K/Pg). Although the biotic effects of this
 event receive intensive scrutiny, certain ecologically important and
 diverse groups remain woefully understudied. One such group is the
 freshwater ray-finned fishes (Actinopterygii). These fish represent 25% of
 modern vertebrate diversity, yet the isolated and fragmentary nature of
 their K/Pg fossil record limits our understanding of their diversity
 dynamics across this event. Here, we address this problem using
 diversification analysis of molecular-based phylogenies alongside a
 morphotype analysis of fossils recovered from a unique site in the Denver
 Basin of western North America that provides unprecedented K/Pg
 resolution. Our results reveal previously unrecognized signals of
 post-K/Pg diversification in freshwater clades, and suggest the change was
 driven by localized and sporadic patterns of extinction. Supported
 inferences regarding the effects of the K/Pg event on freshwater fish also
 inform our expectations of how freshwater faunas might recover from the
 current biodiversity crisis.
description: FRESHWATER FISH AND THE CRETACEOUS/PALAEOGENE BOUNDARY: A CRITICAL
 ASSESSMENT OF SURVIVORSHIP PATTERNS This study analyzed diversity dynamics
 of freshwater actinopterygians across the K/Pg boundary using
 diversification rate analyses in extant phylogenies and morphotype
 analysis of fossil specimens. Data are in two folders. Data.zip includes
 the majority of data from this study. Data_Acanthomorpha.zip includes only
 the BAMM data for the Acanthomorpha analysis. In Data.zip, data are
 divided into BAMM analyses and morphotype analyses. All code (.rmd, .r,
 and .py) includes comments that describe the purpose and action of each
 section.   **BAMM folder** *speciesnamechanges.csv* Spreadsheet with all
 name changes made to the original Rabosky et al. (2018) trees *bamm runs*
 For all BAMM analyses, each analyzed clade has a folder further subdivided
 by analyses that excluded taxa (if applicable) and then by expected number
 of shifts. The .R script in each clade folder includes code to run
 analyses for all expected shift scenarios. In each expected shift folder,
 the files needed to run the original BAMM analysis (control, sample, and
 tree files) and the output files required for processing (mcmc_out files
 and event_data files) are included alongside output files in .pdf form. If
 an analysis was used in a figure, an additional r script is included in
 the folder for that specific analysis. *making sampling doc* This folder
 contains the r code used to make each sampling file for all BAMM runs, as
 well as the python script used to produce exact cover solutions.
 'sampling matrices' includes all matrices input into the exact
 cover script and 'dictionary files' includes the dictionary
 files for making each sampling file. The workflow for this was to first
 use the r code to make a boolean matrix with genus trees as rows and
 species as columns. If a genus tree contained a species, it puts a 1 in
 the common cell. We took this matrix, sorted it by the number of species
 each genus tree contained (decreasing order), and made a dictionary file
 identifying how lines in the sorted and unsorted matrices correspond. We
 input the sorted matrix into the python script, then took the resulting
 list of trees and input that list into the second part of the r code to
 get the sampling file. Then, we added the global sampling probability by
 dividing the number of taxa in the tree by the total number of taxa in
 each focal clade from FishBase. *making figure 4* This folder includes an
 r script that was used to produce the trees for figure 4   **Morphotype
 Analysis** *morphotypeanalysis.Rmd* Contains all code used to set  up and
 run an anonymized morphotype analysis. In this markdown file are also
 instructions for how to use the code in a morphotype analysis.
 Essentially, images of each specimen are grouped by folder, then all
 specimen folders are grouped in folders by site. Running the first part of
 the markdown file in the directory containing the site folders produces
 anonymized, combined image files, a .csv for the user to input morphotype
 identities, and a .csv that contains the original specimen identities.
 After the user has input morphotypes, they can use the second part of the
 r code to output the final results and pupulate the specimen identity csv
 with the morphotype identities. *anonymized analysis* For the original
 anonymized analysis, we include the finalresults.csv and specidentity.csv
 alongside an additional folder with data and code used to produce the
 figures and run Hutcheson and Levene's tests for the morphotype
 results. *retrospective analysis* For the retrospective analysis, we
 include a final results file and a specidentity file. Then, we include an
 R script and data files for running Hutcheson and Levene's tests and
 building the figures. The retrospective folder further contains a
 retro_additional analyses folder with data files and R scripts for all
 additional analyses (e.g., retrospective without unique specimens)
 *photos* This folder contains processing images of all specimens used in
 constructing morphotype groups. The images are arranged in subfolders by
 specimen (with DMNH EPV number) and locality (DMNH 3648 or 2560).