Genomic Distortion of Jawed Vertebrate Phylogeny

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Brownstein, Chase, 2026, "Genomic Distortion of Jawed Vertebrate Phylogeny", https://doi.org/10.60600/YU/YL2LSZ, Yale Dataverse, V1, UNF:6:WwN5lD3oH1D4Pb4ov2ov+A== [fileUNF]
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Description
Description of the data and file structure Data analyzed in this paper were exon sequences extracted from published genomes on GenBank or from the exonic dataset provided in the following paper: Hughes, L.C., Ortí, G., Huang, Y., Sun, Y., Baldwin, C.C., Thompson, A.W., Arcila, D., Betancur-R, R., Li, C., Becker, L. and Bellora, N., 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences, 115(24), pp.6249-6254. Files and variables File: Clade_Support_IQ_TREE.zip Description: Csv files contain clade support values for lineages of interest found across different maximum likelihood and ASTRAL-III multispecies coalescent analyses. File: gene_concordance_through_time.zip Description: Csv files contain clade support values for lineages found across different maximum likelihood and ASTRAL-III multispecies coalescent analyses, and paired with the corresponding clade ages found via BEAST Bayesian time-calibration analyses. File: Scripts.zip Description: Scripts associated with this manuscript. File: 75_(662).zip Description: Results of the IQ-TREE and ASTRAL analyses of the 75% complete matrix. File: 1105.zip Description: Results of the IQ-TREE and ASTRAL analyses of the whole matrix. File: FASTA_input.zip Description: Input FASTA files for exons. File: Living_Fossil_Time_Test.zip Description: Output tree and log files from the rate test analyses in BEAST. File: run_1_logs.tar.gz Description: Output log files from the calibration test analyses (run 1) in BEAST. File: run_2_logs.tar.gz Description: Output log files from the calibration test analyses (run 2) in BEAST. File: run_3_logs.tar.gz Description: Output log files from the calibration test analyses (run 3) in BEAST. File: Mammal_123SUM.trees Description: Output combined posterior trees from the calibration test analyses in BEAST. File: BEAST_Main.zip Description: Output tree and log files from the main analyses in BEAST. Code/software Scripts are all in R and python: Branching events through time.R - branching events through time plottng concordance_Factors.R -plotting concordance factors, after https://www.robertlanfear.com/blog/files/concordance_factors.html dendrogram.R - dendrogram plotting Heatmap.R - heatmap of support values for select clades ltt.R - lineage through time plots Plot_Ages.R - plot age comparison in Extended Data Figure 6 rateplotting.R - plot rate values in Figure 5 Support_through_time.R - plot curves in Figure 3 tree_pruner.R -prune target phylogeny for fixing BEAST tree Access information Other publicly accessible locations of the data: Genbank, NCBI Data was derived from the following sources: n/a
Subject Medicine, Health and Life Sciences
Keyword Phylogenetics
License/Data Use Agreement

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Mammal_123SUM.trees
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run_1_logs.tar.gz
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run_2_logs.tar.gz
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run_3_logs.tar.gz
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1105/Anomaly_Zone/ASTRAL_anomaly/Unknown - 6.6 KB
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anomaly_tree.tree
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anomaly_concat.tre
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ASTRAL_TREE_ALL.tree
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Tree_Problem_List.pages
1105/ASTRAL/initial_Tree_set_problems/Unknown - 380.0 KB
Published Jun 8, 2026
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Tree_Problem_List.pdf
1105/ASTRAL/initial_Tree_set_problems/Adobe PDF - 65.2 KB
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