Freshwater fish and the Cretaceous/Palaeogene boundary: A critical assessment of survivorship patterns
Data files
Jul 24, 2024 version files 3.97 GB
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Data_Acanthomorpha.zip
101.70 MB
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Data.zip
3.87 GB
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README.md
4.21 KB
Abstract
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.
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).