{"doi":"10.1126/science.abn3943","title":"Evolutionary constraint and innovation across hundreds of placental mammals","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.","journal":"Science","year":2023,"id":314963,"datarank":3.0435210647838646,"base_score":5.605802066295998,"endowment":5.605802066295998,"self_citation_contribution":0.8408703099443998,"citation_network_contribution":2.202650754839465,"self_endowment_contribution":0.8408703099443998,"citer_contribution":2.202650754839465,"corpus_percentile":92.72839792681984,"corpus_rank":941,"citation_count":271,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7872,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":25.0,"fair_percentile":40.966065423417916,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":53198,"name":"Irene M. 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Christmas","orcid":"0000-0002-6355-7581","position":0,"is_corresponding":true}],"reference_count":319,"raw_metadata":null,"created_at":"2026-07-19T01:06:02.898877Z","pmid":"37104599","pmcid":"PMC10250106","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":22.2222,"fair_a":25.0,"fair_i":0.0,"fair_r":33.3333,"fair_zscore":-0.374,"fair_rationale":{"fair_score":25.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":22.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The Cactus alignment and constraint scores are available at https://cglgenomics.ucsc.edu/data/cactus/ and at https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons241way.","grounded":false,"rationale":"The data have web addresses, not persistent identifiers. 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No licence is attached to the data.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"We used PhyloFit from Phast v1.5 to estimate branch lengths.","grounded":true,"rationale":"A named software tool is given for data production. 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[majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper gives no version token or date for the data snapshot. [majority verdict 'no' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Scripts are archived at Zenodo (180).","grounded":false,"rationale":"A machine-resolvable locator (Zenodo DOI) is given for the study's own code, as indicated in the data-availability statement. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"This work was funded by National Institutes of Health (NIH) grant R37CA218570; NIH grant R01HG008742; NIH grant R01HG010485; NIH grant RO1HG002939; NIH grant U01HG010961; NIH grant U24-HG010136; NIH grant U24HG009446; NIH grant U41HG002371; NIH grant U41HG007234; NIH grant U19AG057377; NIH grant DP1DA046585; NIH grant F30DA053020; NIH grant R24OD018250; National Science Foundation (NSF) grant DEB-1753760; NSF grant DEB2150664; NSF grant DBI-2046550; NSF grant DEB 1838283; NSF grant DEB-1457735; NSF grant DGE-1252522; NSF grant DGE1745016; NSF grant IOS-2032006; NSF grant IOS-1929592; NSF grant IOS-2022007; NSF grant IOS-2029774; NSF grant TGBIO200055; NSF grant ACI-1548562; NSF Postdoctoral Fellowship in Biology 2011038 (C.F.); European Research Council under the European Union’s Horizon 2020 research and innovation program grant 864203 (T.M.-B.); MINECO/FEDER, UE grant PID2021126004NB-100 (T.M.-B.); FEDER/UE grant AEI-PGC2018-101927BI00 704 (A.N.C.), AEI grant CEX2018-000792-M (A.N.C. and T.M.-B.), Science Foundation Ireland 19/FFP/6790 (E.C.T.); Irish Research Council Laureate grant (E.C.T.); Distinguished professorship from the Swedish Research Council (K.L.-T.); Swedish Research Council Vetenskapsrådet grant D0886501 (P.F.S.); Carnegie Mellon University Computational Biology Department Lane Postdoctoral Fellowship (I.M.K.); Carnegie Mellon University SURF grant (D.E.S.); Gift from Ed and Pam Taft, Roddenberry Foundation, Gladstone Institutes (K.S.P.); LOEWECentre for Translational Biodiversity Genomics (M.H.); Robert and Rosabel Osborne Endowment, UC Davis (H.A.L.); SFI Centre for Research Training in Genomics Data Science grant 18/CRT/6214 (L.R.); Sloan Foundation grant (A.R.P.); UMaine Institute of Medicine Seed Grant (D.L.L.); University College Dublin Ad Astra Fellowship (G.M.H.); Knut and Alice Wallenberg Foundation (K.L.-T.); NSF grant 2019035 (Lehigh University Research Computing Infrastructure); NSF grant TG-BIO200055 [The Extreme Science and Engineering Discovery Environment (XSEDE)]; and Swedish Research Council grant 2018-05973 [Swedish National Infrastructure for Computing (SNIC) at UPPMAX].","grounded":true,"rationale":"Multiple award numbers are given with funder names. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The Cactus alignment and constraint scores are available at https://cglgenomics.ucsc.edu/data/cactus/ and at https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons241way.","why":"The data have web addresses, not persistent identifiers. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 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For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The Cactus alignment and constraint scores are available at https://cglgenomics.ucsc.edu/data/cactus/ and at https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons241way.","why":"UCSC Genome Browser is a named repository. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The Cactus alignment and constraint scores are available at https://cglgenomics.ucsc.edu/data/cactus/ and at https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons241way.","why":"The data are stated to be available at URLs with no precondition. [downgraded to 'partial' — no verifiable quote from the paper]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The Cactus alignment and constraint scores are available at https://cglgenomics.ucsc.edu/data/cactus/ and at https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons241way.","why":"The dataset identifier appears only in body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. 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[downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper gives no version token or date for the data snapshot. [majority verdict 'no' (4/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data and materials availability: Scripts are archived at Zenodo (180 ). The Cactus alignment and constraint scores are available at https://cglgenomics.ucsc.edu/data/cactus/ and at https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons241way. The protein-coding sequence alignment is at http://genome.senckenberg.de/download/TOGA/. Information regarding genome assemblies and specimen biosamples is provided in (4) and at https://zoonomiaproject.org/.","why":"The statement points to repositories with URLs. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Zoonomia is the largest comparative genomics resource for mammals produced to date, with whole genomes aligned for 240 diverse species [2.3- fold more families and 3.9fold more species than the mammals included in the earlier 100 Vertebrates alignment (5)] and protein-coding sequences aligned for 427 species ( 6).","why":"The dataset is described in running prose, not an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The Cactus alignment and constraint scores are available at https://cglgenomics.ucsc.edu/data/cactus/ and at https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons241way.","why":"The paper describes the action of downloading from URLs without labeling the access level. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard is named for the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No documentation object is named as accompanying the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sensitive data or gatekeeper mentioned.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not provide identifiers for external resources it builds on; it only cites other papers. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No retention period or availability timing stated.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. 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Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:52:29.766540Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}