DOI: 10.5061/dryad.9cnp5hqrb
title: Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean

description: Major ecological transitions are thought to fuel diversification, but
 whether they are contingent on the evolution of certain traits called key
 innovations is unclear. Key innovations are routinely invoked to explain
 how lineages rapidly exploit new ecological opportunities . However,
 investigations of key innovations often focus on single traits rather than
 considering trait combinations that collectively produce effects of
 interest . Here, we investigate the evolution of synergistic trait
 interactions in anglerfishes, which include one of the most species-rich
 vertebrate clades in the bathypelagic, or ‘midnight,’ zone of the deep
 sea: Ceratioidea. Ceratioids are the only vertebrates that possess sexual
 parasitism, wherein males temporarily attach or permanently fuse to
 females to mate. We show that the rapid transition of ancestrally benthic
 anglerfishes into pelagic habitats occurred during a period of major
 global warming 50-35 million years ago. This transition coincided with the
 origins of sexual parasitism, which is thought to increase the probability
 of successful reproduction once a mate is found in the midnight zone,
 Earth’s largest habitat. Our reconstruction of the evolutionary history of
 anglerfishes and the loss of immune genes support that permanently-fusing
 clades have convergently degenerated their adaptive immunity. We find that
 degenerate adaptive immune genes and sexual body size dimorphism, both
 variably present in anglerfishes outside the ceratioid radiation, likely
 promoted their transition into the bathypelagic zone. These results show
 how traits from separate physiological, morphological, and reproductive
 systems can interact synergistically to drive major transitions and
 subsequent diversification in novel environments.
description: The main text of the manuscript describes this.
description: # Reproductive innovation enabled radiation in the deep sea during an
 ecological crisis
 [https://doi.org/10.5061/dryad.9cnp5hqrb](https://doi.org/10.5061/dryad.9cnp5hqrb) This repository contains all data from the article "Reproductive innovation enabled radiation in the deep sea during an ecological crisis" ## Description of the data and file structure Ancestral_States_Phytools.zip ## Contains all data necessary for the phytools ancestral state reconstructions Angler_Reproduction.csv #reproduction trait file Angler_Locomotion.csv #locomotion trait file Immune_data.csv #immunogenetics trait file Angler_Dimorphism.csv #dimorphism trait file Anglerfish_script_R.R ### R code to replicate all analyses in the paper Anomaly_Finder.zip ##Contains all code and data necessary for the anomaly zone analysis anomaly_finder.py #python script to find anomaly zones Anomaly_Finder_Output_ASTRAL.tree #output IQ_TREE_CONCAT_anomaly_finder.tree #input IQTREE file Chaunacidae_test.zip ##Mitochondrial phylogeny and genetic dissimilarity tests for Chaunacidae Chaunax_test.fas #fasta file containing alignments IQ_TREE_Output ##folder containing IQ-TREE output files IQ-Tree_and_Astral.zip ##IQTREE and ASTRAL output iq_tree_concatenated_final ## folder containing output for concatenated IQ-TREE analysis iqtree_final ##folder containing output for iqtree gene trees run partitioned_iqtree_final ## folder containing output for partitioned concatenated IQ-TREE analysis Astral ## folder containing input and output for ASTRAL-III multispecies coalescent tree concordance_factors ## folder containing output for IQ-TREE concordance factor analysis Paralog-ILS-test ##TOAST paralogy input and output really_long_branch ##folder containing gene trees with abnormally long singleton branches but passed TOAST gene_trees_TOAST_fail_ILS_only ##folder containing gene trees that failed TOAST genetrees_TOAST_pass ##folder containing gene trees that passed TOAST and lack odd long branches TOAST_fail_weird_branches ##folder containing gene trees that failed TOAST and have odd long branches tree_trim_sheet.xlsx ##record sheet Singleton_Bad_long_branches ##list of taxa that have odd long branches subtending them in one tree Multiple_bad_long_branches ##list of taxa that have odd long branches subtending them in many trees Desktop\omit_trees.csv ##list of trees to omit SSE.zip ## Data for state dependent diversification rate analyses Angler_MuSSE_reproduction.csv #reproductive traits Angler_BiSSE_locomotion.csv #locomotion traits Angler_BiSSE_reproduction_2.csv #reproduction traits 2 Angler_MuSSE_habitat.csv #MuSSE reproducion xmls_corrected.zip ##XML files for the 15 largest partitions; see main text for prior specs logs.zip ##log file output for the 11 converged BEAST runs Top_11_SUM.trees ##combined posterior trees file for 11 converged BEAST runs IQTREE_Basis.tree ##target tree without branch lengths (partitioned IQ TREE topology) BEAST_Sum.tree ##summary tree from BEAST Individuals_for_BEAST.xlsx ##BEAST individuals file Supplementary_Figures.pdf ##PDF containing Supplementary Figures. Supplementary_Figure_Captions.docx ##Supplementary Figure Captions BioSampleObjects.txt ##Genbank BioObjects File for UCE Data ## Code/Software All code is contained in : Anglerfish_Script_R.R ## Log Changes: Dec 25, 2024: Changed title to match final title of published manuscript