Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages.

"raw rna-seq data are available through national center for biotechnology information (ncbi) bioproject number prjna908888. a copy of precomputed genome assembly-derived intermediate inputs (including whole-genome alignment chains) for generating the final candidate list has been deposited at https://doi org/10 5281/zenodo 7140838 .; a copy of the files underlying the japanese medaka assembly hub is available at https://doi org/10 5281/zenodo 7909719 ."

"a code repository with instructions for replicating the computational screen starting with flat-text genome assembly fasta files is available at https://github com/bejerano-lab/percomorphcondels . lastz-based pairwise whole-genome alignment chains ( ) were generated using the doblastzchainnet pl tool ( https://github com/encode-dcc/kentutils/ last accessed 12 sep 2022) and the parameters listed in supplementary spreadsheet 1 supplementary material online."

"Conflict of interest statement. H.I.C., Y.T., G.B., and D.M.K. have no conflicts of interest to declare."

"We acknowledge the Ohlone, Dena’ina, and Semiahmoo Nations, from whose traditional territories the Threespine Stickleback used in this study were derived. We are grateful to the following people for providing nonstickleback tissue and/or DNA samples used in this study: Leo Smith (KUBI Ichthyology), Andrew Bentley (KUBI Ichthyology), Pierre-Alexandre Gagnaire, François Bonhomme, Jessica Muniz, Angel Seery, Leo Nico, Chris Smith, Scott Collenberg, Carol Cozzi-Schmarr, Xuegeng Wang, Ramji Bhandari, Susan L. Bassham, William A. Cresko, Molly Schumer, Shreya Banerjee, Anne Brunet, Rahul Nagvekar, Leonor Cancela, and Vincent Laizé. We thank the National Center for Biotechnology Information and the numerous researchers who generated and made freely available the genome assemblies used in this study; the UCSC Genome Browser Team and Hiram Clawson for the generously shared wisdom and tools they have developed for visualizing and analyzing genomic data; Dave Catania (California Academy of Sciences) for assistance in obtaining radiographs of various fish species; Julia Wucherpfennig, Abbey Thompson, Ken Thompson, and Dolph Schluter for help collecting sticklebacks from Little Campbell River; Sarah Frail for contributions to initial CRISPR/Cas9 experiments; William Talbot for generously lending imaging equipment; Shannon Brady and the team of fish feeders for critical husbandry support; and all members of the Bejerano and Kingsley Labs (especially Erich Weiler, Mark Berger, Amir Marcovitz, Johannes Birgmeier, Karthik Jagadeesh, Whitney Heavner, Boyoung Yoo, Yosuke Tanigawa, Janet Song, Amy Herbert, Julia Wucherpfennig, and Hiren Banerjee) as well as Michael A. Bell, William Talbot, and Margaret Fuller for their helpful suggestions. This work was supported by a National Science Foundation Graduate Research Fellowship (1656518), NIH training grant (5T32GM007790), and Stanford CEHG Fellowship to H.I.C.; D.M.K. is an investigator of the Howard Hughes Medical Institute."