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Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.", "doi": "10.1126/science.abn2937", "pmid": "37104612", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1897004"}, {"db": "pmc", "key": "PMC10259825"}], "notes": [], "created": "2026-09-23T07:35:15.983Z", "modified": "2026-09-23T07:35:16.500Z"}, {"entity": "publication", "iuid": "b9fd8cd4df2f4cfd90ea1c40bf40619e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b9fd8cd4df2f4cfd90ea1c40bf40619e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b9fd8cd4df2f4cfd90ea1c40bf40619e"}}, "title": "Evolutionary constraint and innovation across hundreds of placental mammals.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": 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E", "initials": "DE", "orcid": "0000-0003-3608-152X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7f399939ae14daa8c0bd9bf5b92a896.json"}}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9386c16bd7e14ddca60e03e06f6808fe.json"}}, {"family": "Supple", "given": "Megan A", "initials": "MA", "orcid": "0000-0002-0204-7852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/073a9fab924c4e96973f1e23accaa7ae.json"}}, {"family": "Wilder", "given": "Aryn P", "initials": "AP", "orcid": "0000-0003-4970-6891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b080282d4674df1bde072812bf448be.json"}}, {"family": "Wirthlin", "given": "Morgan E", "initials": "ME", "orcid": "0000-0001-7967-7070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b1757207aa24108859d7c116bda19b7.json"}}, {"family": "Xue", "given": "James R", "initials": "JR", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd4a26d78f1547c7865cab2847ab0d6b.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Birren", "given": "Bruce W", "initials": "BW"}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/992edd7528434c7b900b8d531f18b15c.json"}}, {"family": "Hubley", "given": "Robert M", "initials": "RM", "orcid": "0000-0001-9261-3821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86b6fe3c9be54bc58dd8c750dda51aa3.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "KP"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b1fba9de46a4c8c8cbbbec685a9b94c.json"}}, {"family": "Nweeia", "given": "Martin", "initials": "M", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4846b6d146a4a7288db1543583a0158.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6848f42df6b146df8fd953c169193eb4.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": 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"initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1005d0d1f4264b46b1cfe214c7aca246.json"}}, {"family": "Levesque", "given": "Danielle L", "initials": "DL", "orcid": "0000-0003-0132-8094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/291c0db9f1014708bfe1c52a946e1df7.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}, {"family": "Murphy", "given": "William J", "initials": "WJ", "orcid": "0000-0003-3699-0723", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a71bcbcd8a6437ea7c32ce512ebd38c.json"}}, {"family": "Navarro", "given": "Arcadi", "initials": "A", "orcid": "0000-0003-2162-8246", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8360a54a1b447d0b67d85b3f1e40b5a.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c916e24b35f2459480cf87e27bb21ee1.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d080bc9bff548958f0c161612cdc4cf.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6392a5497414b98999823cbafd67d4b.json"}}, {"family": "Ruf", "given": "Irina", "initials": "I", "orcid": "0000-0002-9728-1210", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbc58d9ceb8d490baab61cb6002cecbe.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f7c2be6e32147d19f03c7ff88fb3f80.json"}}, {"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"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabn3943", "issn-l": "0036-8075"}, "abstract": "Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.", "doi": "10.1126/science.abn3943", "pmid": "37104599", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1896905"}, {"db": "pmc", "key": "PMC10250106"}], "notes": [], "created": "2026-09-23T06:39:33.319Z", "modified": "2026-09-23T06:39:34.893Z"}, {"entity": "publication", "iuid": "cfde07a1c67a494b9a5c899e765c8440", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cfde07a1c67a494b9a5c899e765c8440.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cfde07a1c67a494b9a5c899e765c8440"}}, "title": "\u200bComparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs.", "authors": [{"family": "Moon", "given": "Katherine L", "initials": "KL", "orcid": "0000-0002-0795-3096", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb9238e381a9411eb9b291e42b20e082.json"}}, {"family": "Huson", "given": "Heather J", "initials": "HJ", "orcid": "0000-0001-8299-0447", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e51686ecd3a4ee19c848c0224536c3b.json"}}, {"family": "Morrill", "given": "Kathleen", "initials": "K", "orcid": "0000-0002-9139-453X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5176e46101684ebf9f1b906efc570261.json"}}, {"family": "Wang", "given": "Ming-Shan", "initials": "MS", "orcid": "0000-0003-4663-2735", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c6d44821db14858a82c031153184edd.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5766930b7e3946e5a3f2e268605ab97b.json"}}, {"family": "Srikanth", "given": "Krishnamoorthy", "initials": "K", "orcid": "0000-0002-5205-193X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d5594661b8840a5b5397ec30f367ce0.json"}}, {"family": "Zoonomia Consortium", "given": "", "initials": ""}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Svenson", "given": "Gavin J", "initials": "GJ", "orcid": "0000-0003-0207-6458", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3e34cce40440ac822049000cf16cca.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f15a636469944ddb56489a74a75591b.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabn5887", "issn-l": "0036-8075"}, "abstract": "We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.", "doi": "10.1126/science.abn5887", "pmid": "37104591", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1893725"}, {"db": "pmc", "key": "PMC10184777"}], "notes": [], "created": "2026-09-23T11:18:01.178Z", "modified": "2026-09-23T11:18:01.487Z"}, {"entity": "publication", "iuid": "ed052a37c9034e419dc4c750334f158e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ed052a37c9034e419dc4c750334f158e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ed052a37c9034e419dc4c750334f158e"}}, "title": "The functional and evolutionary impacts of human-specific deletions in conserved elements.", "authors": [{"family": "Xue", "given": "James R", "initials": "JR", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd4a26d78f1547c7865cab2847ab0d6b.json"}}, {"family": "Mackay-Smith", "given": "Ava", "initials": "A", "orcid": "0000-0003-0404-0563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85549bb8898d430794cfb2d99c4aece2.json"}}, {"family": "Mouri", "given": "Kousuke", "initials": "K", "orcid": "0000-0003-1712-6833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/364a8a27d3994f58b67f4e2ec5523d5b.json"}}, {"family": "Garcia", "given": "Meilin Fernandez", "initials": "MF", "orcid": "0000-0002-8745-9775", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efbb665201e44b7a9782008b5df38e0a.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acaddec22cd64c8aaec92764cd4adf08.json"}}, {"family": "Akers", "given": "Jared F", "initials": "JF", "orcid": "0000-0002-9270-0017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf559e00336c49819e1a24dfbd7c07d9.json"}}, {"family": "Noble", "given": "Mark", "initials": "M", "orcid": "0000-0002-9618-120X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b133520a1d2342b38928324d5ba6948b.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5766930b7e3946e5a3f2e268605ab97b.json"}}, {"family": "Zoonomia Consortium\u2020", "given": "", "initials": ""}, {"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": "Noonan", "given": "James P", "initials": "JP", "orcid": "0000-0001-9632-5835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c505baaf8dc4ab0b3a11c253a46fc08.json"}}, {"family": "Capellini", "given": "Terence D", "initials": "TD", "orcid": "0000-0003-3842-8478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2287620d2b164320a1002b3ba2a9aad8.json"}}, {"family": "Brennand", "given": "Kristen J", "initials": "KJ", "orcid": "0000-0003-0993-5956", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/296ba82dabed45a6b7b78d1ad9e14da4.json"}}, {"family": "Tewhey", "given": "Ryan", "initials": "R", "orcid": "0000-0002-4607-8001", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cee2dc254fc42289d2c55c8f8b37472.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6848f42df6b146df8fd953c169193eb4.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dea3d4ff8a9643d196e3f3fd1ded79d4.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabn2253", "issn-l": "0036-8075"}, "abstract": "Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.", "doi": "10.1126/science.abn2253", "pmid": "37104592", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1897409"}, {"db": "pmc", "key": "PMC10202372"}], "notes": [], "created": "2026-09-23T08:28:45.123Z", "modified": "2026-09-23T08:28:47.819Z"}]}