{"entity": "researcher", "timestamp": "2026-08-20T21:03:44.704Z", "family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "affiliations": ["The Genome Center, University of California, Davis, CA 95616; Lewin@ucdavis.edu.", "Department of Evolution and Ecology, University of California, Davis, CA 95616.", "John Muir Institute for the Environment, University of California, Davis, CA 95616."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759"}}, "publications": [{"entity": "publication", "iuid": "b09c06812d9246c6941dc437ba05b1e1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b09c06812d9246c6941dc437ba05b1e1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b09c06812d9246c6941dc437ba05b1e1"}}, "title": "Evolution of the ancestral mammalian karyotype and syntenic regions.", "authors": [{"family": "Damas", "given": "Joana", "initials": "J", "orcid": "0000-0003-4857-2510", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f60eb6afeabc435ea1e6378786162fa8.json"}}, {"family": "Corbo", "given": "Marco", "initials": "M"}, {"family": "Kim", "given": "Jaebum", "initials": "J"}, {"family": "Turner-Maier", "given": "Jason", "initials": "J"}, {"family": "Farr\u00e9", "given": "Marta", "initials": "M"}, {"family": "Larkin", "given": "Denis M", "initials": "DM"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Steiner", "given": "Cynthia", "initials": "C"}, {"family": "Houck", "given": "Marlys L", "initials": "ML"}, {"family": "Hall", "given": "Shaune", "initials": "S"}, {"family": "Shiue", "given": "Lily", "initials": "L"}, {"family": "Thomas", "given": "Stephen", "initials": "S"}, {"family": "Swale", "given": "Thomas", "initials": "T"}, {"family": "Daly", "given": "Mark", "initials": "M"}, {"family": "Korlach", "given": "Jonas", "initials": "J"}, {"family": "Uliano-Silva", "given": "Marcela", "initials": "M"}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ"}, {"family": "Birren", "given": "Bruce W", "initials": "BW"}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Nweeia", "given": "Martin T", "initials": "MT", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4846b6d146a4a7288db1543583a0158.json"}}, {"family": "Johnson", "given": "Rebecca N", "initials": "RN", "orcid": "0000-0003-3035-2827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5486418f837c4e9199e31f61b20887cd.json"}}, {"family": "Zoonomia Consortium", "given": "", "initials": ""}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}], "type": "journal article", "published": "2022-10-04", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "40", "pages": "e2209139119", "issn-l": "0027-8424"}, "abstract": "Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for \u223c320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.", "doi": "10.1073/pnas.2209139119", "pmid": "36161960", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9550189"}], "notes": [], "created": "2026-08-20T09:31:15.877Z", "modified": "2026-08-20T09:31:15.982Z"}, {"entity": "publication", "iuid": "3841603fbf9e43e6a1460db8f686ef9e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3841603fbf9e43e6a1460db8f686ef9e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3841603fbf9e43e6a1460db8f686ef9e"}}, "title": "Why sequence all eukaryotes?", "authors": [{"family": "Blaxter", "given": "Mark", "initials": "M", "orcid": "0000-0003-2861-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b785bc131a241c4815ab5ef1576709b.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM", "orcid": "0000-0001-7255-780X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9381e61c33164dca82411b18b9fcc0d3.json"}}, {"family": "Childers", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-0747-8539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b04257eed5dd48a7b631d8c8e78c2df1.json"}}, {"family": "Coddington", "given": "Jonathan A", "initials": "JA", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efae0bfdf0c64e86a175c8921b1af0b4.json"}}, {"family": "Crandall", "given": "Keith A", "initials": "KA", "orcid": "0000-0002-0836-3389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853c5da68a5a4c96bd2248b21bd15ba7.json"}}, {"family": "Di Palma", "given": "Federica", "initials": "F", "orcid": "0000-0002-4394-0102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf0785a103c45368f4e1cca6e5cb5f7.json"}}, {"family": "Durbin", "given": "Richard", "initials": "R", "orcid": "0000-0002-9130-1006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8972546b724b0d9c6ed69a766cc41b.json"}}, {"family": "Edwards", "given": "Scott V", "initials": "SV", "orcid": "0000-0003-2535-6217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/249a83cc8fb240609cd7bd76c6c79e2c.json"}}, {"family": "Graves", "given": "Jennifer A M", "initials": "JAM", "orcid": "0000-0001-6480-7856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48044e7f378c41e28b58ae92e1102efb.json"}}, {"family": "Hackett", "given": "Kevin J", "initials": "KJ", "orcid": "0000-0002-7459-7175", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc72dad2a31b443db715bf82966f44f4.json"}}, {"family": "Hall", "given": "Neil", "initials": "N", "orcid": "0000-0003-2808-0009", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc8087425525426994b690f1ae2637e0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Johnson", "given": "Rebecca N", "initials": "RN", "orcid": "0000-0003-3035-2827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5486418f837c4e9199e31f61b20887cd.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Kress", "given": "W John", "initials": "WJ", "orcid": "0000-0002-0140-5267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25477498e7dd41e7891088988a40713e.json"}}, {"family": "Kuraku", "given": "Shigehiro", "initials": "S", "orcid": "0000-0003-1464-8388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be2fb1e4a3e548498f5590365dedc81e.json"}}, {"family": "Lawniczak", "given": "Mara K N", "initials": "MKN"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Lopez", "given": "Jose V", "initials": "JV", "orcid": "0000-0002-1637-4125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d60d31a72bb64d6894367a3ffc1785e7.json"}}, {"family": "Moran", "given": "Nancy A", "initials": "NA", "orcid": "0000-0003-2983-9769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c685964435471096e5dbc580505cb8.json"}}, {"family": "Robinson", "given": "Gene E", "initials": "GE", "orcid": "0000-0003-4828-4068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86d1dc6e76694345ba735e5612bff820.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Soltis", "given": "Pamela S", "initials": "PS", "orcid": "0000-0001-9310-8659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c4308f7e0e84bbfaad58eac840db765.json"}}, {"family": "Warnow", "given": "Tandy", "initials": "T", "orcid": "0000-0001-7717-3514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/072c8f6823984406aedb974d6a97f7dc.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}], "type": "journal article", "published": "2022-01-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "4", "issn-l": "0027-8424"}, "abstract": "Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.", "doi": "10.1073/pnas.2115636118", "pmid": "35042801", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8795522"}, {"db": "pii", "key": "2115636118"}], "notes": [], "created": "2026-08-20T09:31:06.931Z", "modified": "2026-08-20T09:31:07.517Z"}, {"entity": "publication", "iuid": "626310cbddb14ff48c80c0f9372c585b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/626310cbddb14ff48c80c0f9372c585b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/626310cbddb14ff48c80c0f9372c585b"}}, "title": "The Earth BioGenome Project 2020: Starting the clock.", "authors": [{"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}, {"family": "Richards", "given": "Stephen", "initials": "S", "orcid": "0000-0001-8959-5466", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8005cf3b343461388e2b82a2c61c293.json"}}, {"family": "Lieberman Aiden", "given": "Erez", "initials": "E"}, {"family": "Allende", "given": "Miguel L", "initials": "ML", "orcid": "0000-0002-2783-2152", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27d6fdda2e7b4487b651c852c3f3cd11.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM"}, {"family": "B\u00e1lint", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Barker", "given": "Katharine B", "initials": "KB"}, {"family": "Baumgartner", "given": "Bridget", "initials": "B"}, {"family": "Belov", "given": "Katherine", "initials": "K"}, {"family": "Bertorelle", "given": "Giorgio", "initials": "G"}, {"family": "Blaxter", "given": "Mark L", "initials": "ML", "orcid": "0000-0003-2861-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b785bc131a241c4815ab5ef1576709b.json"}}, {"family": "Cai", "given": "Jing", "initials": "J"}, {"family": "Caperello", "given": "Nicolette D", "initials": "ND"}, {"family": "Carlson", "given": "Keith", "initials": "K"}, {"family": "Castilla-Rubio", "given": "Juan Carlos", "initials": "JC"}, {"family": "Chaw", "given": "Shu-Miaw", "initials": "SM"}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "Childers", "given": "Anna K", "initials": "AK"}, {"family": "Coddington", "given": "Jonathan A", "initials": "JA", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efae0bfdf0c64e86a175c8921b1af0b4.json"}}, {"family": "Conde", "given": "Dalia A", "initials": "DA", "orcid": "0000-0002-7923-8163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b73243e2df04c5a8d771456b262a4bf.json"}}, {"family": "Corominas", "given": "Montserrat", "initials": "M", "orcid": "0000-0002-0724-8346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0805b84e0e824c93a51262f4fdc8f8e2.json"}}, {"family": "Crandall", "given": "Keith A", "initials": "KA", "orcid": "0000-0002-0836-3389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853c5da68a5a4c96bd2248b21bd15ba7.json"}}, {"family": "Crawford", "given": "Andrew J", "initials": "AJ"}, {"family": "DiPalma", "given": "Federica", "initials": "F"}, {"family": "Durbin", "given": "Richard", "initials": "R", "orcid": "0000-0002-9130-1006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8972546b724b0d9c6ed69a766cc41b.json"}}, {"family": "Ebenezer", "given": "ThankGod E", "initials": "TE"}, {"family": "Edwards", "given": "Scott V", "initials": "SV", "orcid": "0000-0003-2535-6217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/249a83cc8fb240609cd7bd76c6c79e2c.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O"}, {"family": "Flicek", "given": "Paul", "initials": "P"}, {"family": "Formenti", "given": "Giulio", "initials": "G"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93cbe282154844588f63bc7cc6983b30.json"}}, {"family": "Goldstein", "given": "Melissa M", "initials": "MM"}, {"family": "Graves", "given": "Jennifer Marshall", "initials": "JM", "orcid": "0000-0001-6480-7856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48044e7f378c41e28b58ae92e1102efb.json"}}, {"family": "Greely", "given": "Henry T", "initials": "HT", "orcid": "0000-0002-1105-6734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea9e4bfb13764d13b4418be1ecc2d27d.json"}}, {"family": "Grigoriev", "given": "Igor V", "initials": "IV", "orcid": "0000-0002-3136-8903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cb43708257842149fbbeed91293d400.json"}}, {"family": "Hackett", "given": "Kevin J", "initials": "KJ"}, {"family": "Hall", "given": "Neil", "initials": "N"}, {"family": "Haussler", "given": "David", "initials": "D"}, {"family": "Helgen", "given": "Kristofer M", "initials": "KM"}, {"family": "Hogg", "given": "Carolyn J", "initials": "CJ", "orcid": "0000-0002-6328-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faf4b7a234c84bdbac97cf9b0e8f5531.json"}}, {"family": "Isobe", "given": "Sachiko", "initials": "S"}, {"family": "Jakobsen", "given": "Kjetill Sigurd", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}, {"family": "Janke", "given": "Axel", "initials": "A", "orcid": "0000-0002-9394-1904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ef0f0bab20e45cca4e726c84b8645f2.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Johnson", "given": "Warren E", "initials": "WE", "orcid": "0000-0002-5954-186X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa69a0b1643541b0b490e0c1186c8307.json"}}, {"family": "Jones", "given": "Steven J M", "initials": "SJM"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Kersey", "given": "Paul J", "initials": "PJ"}, {"family": "Kim", "given": "Jin-Hyoung", "initials": "JH"}, {"family": "Kress", "given": "W John", "initials": "WJ", "orcid": "0000-0002-0140-5267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25477498e7dd41e7891088988a40713e.json"}}, {"family": "Kuraku", "given": "Shigehiro", "initials": "S"}, {"family": "Lawniczak", "given": "Mara K N", "initials": "MKN"}, {"family": "Leebens-Mack", "given": "James H", "initials": "JH", "orcid": "0000-0003-4811-2231", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b52ac9ce6dba4bee8dae7b594242c49b.json"}}, {"family": "Li", "given": "Xueyan", "initials": "X"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Liu", "given": "Xin", "initials": "X"}, {"family": "Lopez", "given": "Jose V", "initials": "JV"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Mazard", "given": "Sophie", "initials": "S"}, {"family": "Mazet", "given": "Jonna A K", "initials": "JAK", "orcid": "0000-0002-8712-5951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9daa6d747c704145a06420aa76ce3426.json"}}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ"}, {"family": "Myers", "given": "Eugene W", "initials": "EW", "orcid": "0000-0002-6580-7839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf74ba4bae3546eca812b29793341604.json"}}, {"family": "O'Neill", "given": "Rachel J", "initials": "RJ"}, {"family": "Paez", "given": "Sadye", "initials": "S"}, {"family": "Park", "given": "Hyun", "initials": "H"}, {"family": "Robinson", "given": "Gene E", "initials": "GE", "orcid": "0000-0003-4828-4068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86d1dc6e76694345ba735e5612bff820.json"}}, {"family": "Roquet", "given": "Cristina", "initials": "C", "orcid": "0000-0001-8748-3743", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82e0bb00dab543318861f81cb3569541.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Sabir", "given": "Jamal S M", "initials": "JSM", "orcid": "0000-0003-4785-9894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b644127a1d8740bba24dc2fef3c23c81.json"}}, {"family": "Shaffer", "given": "H Bradley", "initials": "HB", "orcid": "0000-0002-5795-9242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/910008f9a77840e5ada4302460516dec.json"}}, {"family": "Shank", "given": "Timothy M", "initials": "TM"}, {"family": "Sherkow", "given": "Jacob S", "initials": "JS", "orcid": "0000-0002-9724-9261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ac5a78ced4f490499d8ea3358a73741.json"}}, {"family": "Soltis", "given": "Pamela S", "initials": "PS", "orcid": "0000-0001-9310-8659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c4308f7e0e84bbfaad58eac840db765.json"}}, {"family": "Tang", "given": "Boping", "initials": "B", "orcid": "0000-0002-3241-7914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab99aedf62e948c5839d1912180fc2b9.json"}}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Uliano-Silva", "given": "Marcela", "initials": "M"}, {"family": "Wang", "given": "Kun", "initials": "K"}, {"family": "Wei", "given": "Xiaofeng", "initials": "X"}, {"family": "Wetzer", "given": "Regina", "initials": "R"}, {"family": "Wilson", "given": "Julia L", "initials": "JL"}, {"family": "Xu", "given": "Xun", "initials": "X"}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Yoder", "given": "Anne D", "initials": "AD", "orcid": "0000-0002-1781-9552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f4e827f5db545de84e8ae91e7603fc1.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}], "type": "introductory journal article", "published": "2022-01-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "4", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.2115635118", "pmid": "35042800", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8795548"}, {"db": "pii", "key": "2115635118"}], "notes": [], "created": "2026-08-20T09:31:03.855Z", "modified": "2026-08-20T09:31:05.035Z"}, {"entity": "publication", "iuid": "b8f68b45bcd643d784b9cf62a589160d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b8f68b45bcd643d784b9cf62a589160d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b8f68b45bcd643d784b9cf62a589160d"}}, "title": "Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.", "authors": [{"family": "Damas", "given": "Joana", "initials": "J", "orcid": "0000-0003-4857-2510", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f60eb6afeabc435ea1e6378786162fa8.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9785e94b95a3466dbb70ad8eb9b34ccd.json"}}, {"family": "Keough", "given": "Kathleen C", "initials": "KC", "orcid": "0000-0002-7481-0511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27ba6707b77e4d0eb914e71063dab333.json"}}, {"family": "Painter", "given": "Corrie A", "initials": "CA", "orcid": "0000-0001-6174-1548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8344bb3d42144f98f550aa8f83e42d7.json"}}, {"family": "Persky", "given": "Nicole S", "initials": "NS", "orcid": "0000-0002-9948-2761", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed0fc24668b242f1ab1c772856f17d24.json"}}, {"family": "Corbo", "given": "Marco", "initials": "M", "orcid": "0000-0002-4566-2724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8133d835c1ec4fe4937748d71a6794e8.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1005d0d1f4264b46b1cfe214c7aca246.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "KP", "orcid": "0000-0001-7281-0676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90e8966ff0e04ca391070664d52cdf04.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f7c2be6e32147d19f03c7ff88fb3f80.json"}}, {"family": "Zhao", "given": "Huabin", "initials": "H", "orcid": "0000-0002-7848-6392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce72657ddbab4665991d934bf3ccfdbe.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Swofford", "given": "Ross", "initials": "R", "orcid": "0000-0003-3676-8479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85b0174c633b417b933092763175bb1c.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d080bc9bff548958f0c161612cdc4cf.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Nweeia", "given": "Martin T", "initials": "MT", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4846b6d146a4a7288db1543583a0158.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Teeling", "given": "Emma C", "initials": "EC", "orcid": "0000-0002-3309-1346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28069443db794cb596e58aea060d9dea.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}], "type": "comparative study", "published": "2020-09-08", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "117", "issue": "36", "pages": "22311-22322", "issn-l": "0027-8424"}, "abstract": "The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.", "doi": "10.1073/pnas.2010146117", "pmid": "32826334", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7486773"}, {"db": "pii", "key": "2010146117"}], "notes": [], "created": "2026-08-20T09:30:48.684Z", "modified": "2026-08-20T09:30:49.333Z"}]}