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Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.

Autor: Wirthlin ME; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Schmid TA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA., Elie JE; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94708, USA., Zhang X; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Kowalczyk A; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Redlich R; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Shvareva VA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA., Rakuljic A; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA., Ji MB; Department of Psychology, University of California, Berkeley, Berkeley, CA 94708, USA., Bhat NS; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA., Kaplow IM; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA., Schäffer DE; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Lawler AJ; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Wang AZ; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Phan BN; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Annaldasula S; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Brown AR; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Lu T; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Lim BK; Neurobiology section, Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA., Azim E; Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA., Clark NL; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA., Meyer WK; Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA., Pond SLK; Department of Biology, Temple University, Philadelphia, PA 19122, USA., Chikina M; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA., Yartsev MM; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94708, USA., Pfenning AR; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X

Publikováno v: Science (New York, N.Y.) [Science] 2024 Mar 29; Vol. 383 (6690), pp. eabn3263. Date of Electronic Publication: 2024 Mar 29.

Evolutionary constraint and innovation across hundreds of placental mammals.

Autor: Christmas MJ; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden., Kaplow IM; Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Genereux DP; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Dong MX; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden., Hughes GM; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland., Li X; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.; Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA.; Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA., Sullivan PF; Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA.; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden., Hindle AG; School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA., Andrews G; Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA., Armstrong JC; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Bianchi M; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden., Breit AM; School of Biology and Ecology, University of Maine, Orono, ME 04469, USA., Diekhans M; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Fanter C; School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA., Foley NM; Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA., Goodman DB; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA., Goodman L; Fauna Bio, Inc., Emeryville, CA 94608, USA., Keough KC; Fauna Bio, Inc., Emeryville, CA 94608, USA.; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA.; Gladstone Institutes, San Francisco, CA 94158, USA., Kirilenko B; Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany.; LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany.; Senckenberg Research Institute, 60325 Frankfurt, Germany., Kowalczyk A; Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Lawless C; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland., Lind AL; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA.; Gladstone Institutes, San Francisco, CA 94158, USA., Meadows JRS; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden., Moreira LR; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.; Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA., Redlich RW; Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Ryan L; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland., Swofford R; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Valenzuela A; Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain., Wagner F; Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany., Wallerman O; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden., Brown AR; Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Damas J; The Genome Center, University of California Davis, Davis, CA 95616, USA., Fan K; Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA., Gatesy J; Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA., Grimshaw J; Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA., Johnson J; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Kozyrev SV; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden., Lawler AJ; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.; Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Marinescu VD; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden., Morrill KM; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.; Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA.; Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA., Osmanski A; Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA., Paulat NS; Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA., Phan BN; Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA., Reilly SK; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA., Schäffer DE; Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Steiner C; Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA., Supple MA; Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Wilder AP; Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA., Wirthlin ME; Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Allen Institute for Brain Science, Seattle, WA 98109, USA., Xue JR; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA., Birren BW; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Gazal S; Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA., Hubley RM; Institute for Systems Biology, Seattle, WA 98109, USA., Koepfli KP; Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC 20008, USA.; Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia.; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA., Marques-Bonet T; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain.; Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain.; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain., Meyer WK; Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA., Nweeia M; Department of Comprehensive Care, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.; Department of Vertebrate Zoology, Canadian Museum of Nature, Ottawa, Ontario K2P 2R1, Canada.; Department of Vertebrate Zoology, Smithsonian Institution, Washington, DC 20002, USA.; Narwhal Genome Initiative, Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA., Sabeti PC; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA., Shapiro B; Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA.; Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Smit AFA; Institute for Systems Biology, Seattle, WA 98109, USA., Springer MS; Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA., Teeling EC; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland., Weng Z; Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA., Hiller M; Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany.; LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany.; Senckenberg Research Institute, 60325 Frankfurt, Germany., Levesque DL; School of Biology and Ecology, University of Maine, Orono, ME 04469, USA., Lewin HA; The Genome Center, University of California Davis, Davis, CA 95616, USA.; Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA.; John Muir Institute for the Environment, University of California Davis, Davis, CA 95616, USA., Murphy WJ; Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA., Navarro A; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.; Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain.; BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 08005 Barcelona, Spain.; CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain., Paten B; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Pollard KS; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA.; Gladstone Institutes, San Francisco, CA 94158, USA.; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Ray DA; Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA., Ruf I; Division of Messel Research and Mammalogy, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany., Ryder OA; Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.; Department of Evolution, Behavior and Ecology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92039, USA., Pfenning AR; Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA., Lindblad-Toh K; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden.; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Karlsson EK; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.; Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA.; Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA.

Publikováno v: Science (New York, N.Y.) [Science] 2023 Apr 28; Vol. 380 (6643), pp. eabn3943. Date of Electronic Publication: 2023 Apr 28.

Genome-Wide Analyses for Osteosarcoma in Leonberger Dogs Reveal the CDKN2A/B Gene Locus as a Major Risk Locus.

Autor: Letko A; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.; Institut de Génétique et Développement de Rennes (IGDR)-UMR6290, University Rennes, CNRS, 35000 Rennes, France., Minor KM; Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA., Norton EM; Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA., Marinescu VD; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75105 Uppsala, Sweden., Drögemüller M; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland., Ivansson E; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75105 Uppsala, Sweden., Megquier K; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75105 Uppsala, Sweden.; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Noh HJ; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Starkey M; Animal Health Trust, Newmarket CB8 7UU, UK., Friedenberg SG; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55113, USA., Lindblad-Toh K; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75105 Uppsala, Sweden.; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Mickelson JR; Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA., Drögemüller C; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.

Publikováno v: Genes [Genes (Basel)] 2021 Dec 09; Vol. 12 (12). Date of Electronic Publication: 2021 Dec 09.