{"doi":"10.1016/j.ajhg.2012.08.025","title":"Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation","abstract":"Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago.","journal":"The American Journal of Human Genetics","year":2012,"id":5657,"datarank":5.1375582322923705,"base_score":4.709530201312334,"endowment":4.709530201312334,"self_citation_contribution":0.7064295301968502,"citation_network_contribution":4.431128702095521,"self_endowment_contribution":0.7064295301968502,"citer_contribution":4.431128702095521,"corpus_percentile":71.27746135069162,"corpus_rank":354,"citation_count":111,"citer_count":86,"citers_with_citation_signal":76,"citers_with_endowment":76,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9271,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2012-10-01","fair_score":31.3333,"fair_percentile":13.390501319261213,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":35177,"name":" Simon Gravel ","orcid":"0000-0002-9183-964X","position":1,"is_corresponding":false},{"id":51081,"name":"Jake Byrnes","orcid":null,"position":2,"is_corresponding":false},{"id":28371,"name":"Andres Moreno-Estrada","orcid":null,"position":3,"is_corresponding":false},{"id":54968,"name":"Shaila Musharoff","orcid":"0000-0002-6958-2366","position":4,"is_corresponding":false},{"id":187,"name":"Katarzyna Bryc","orcid":"0009-0006-7659-1056","position":5,"is_corresponding":false},{"id":54969,"name":"Jeremiah D. Degenhardt","orcid":null,"position":6,"is_corresponding":false},{"id":54970,"name":"Abra Brisbin","orcid":"0000-0002-3723-6194","position":7,"is_corresponding":false},{"id":54971,"name":"Vrunda Sheth","orcid":null,"position":8,"is_corresponding":false},{"id":50,"name":"Rong Chen","orcid":"0000-0001-6322-0340","position":9,"is_corresponding":false},{"id":35122,"name":" Stephen F. McLaughlin","orcid":null,"position":10,"is_corresponding":false},{"id":35124,"name":" Heather E. Peckham","orcid":null,"position":11,"is_corresponding":false},{"id":13888,"name":"Larsson Omberg","orcid":"0000-0002-4719-9120","position":12,"is_corresponding":false},{"id":54972,"name":"Christina A. Bormann Chung","orcid":null,"position":13,"is_corresponding":false},{"id":54973,"name":"Kevin Pearlstein","orcid":null,"position":15,"is_corresponding":false},{"id":54974,"name":"Elizabeth Levandowsky","orcid":null,"position":16,"is_corresponding":false},{"id":54975,"name":"Suehelay Acevedo-Acevedo","orcid":null,"position":17,"is_corresponding":false},{"id":51085,"name":"Joanna M. M. Howson","orcid":"0000-0001-7618-0050","position":18,"is_corresponding":false},{"id":54976,"name":"Alon Keinan","orcid":"0000-0002-9760-1122","position":19,"is_corresponding":false},{"id":54977,"name":"Victor Acuña-Alonzo","orcid":null,"position":20,"is_corresponding":false},{"id":54978,"name":"Rodrigo Barquera-Lozano","orcid":null,"position":21,"is_corresponding":false},{"id":54979,"name":"Samuel Canizales-Quinteros","orcid":null,"position":22,"is_corresponding":false},{"id":54980,"name":"Celeste Eng","orcid":"0000-0001-7968-1862","position":23,"is_corresponding":false},{"id":24949,"name":"Esteban G. 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Bustamante","orcid":"0000-0002-4187-7920","position":32,"is_corresponding":false},{"id":28374,"name":"Andrés Moreno‐Estrada","orcid":"0000-0001-8329-8292","position":33,"is_corresponding":false},{"id":15461,"name":"Sarah A. Stanley","orcid":"0000-0002-0253-2663","position":34,"is_corresponding":false},{"id":54984,"name":"Kevin A. Pearlstein","orcid":null,"position":35,"is_corresponding":false},{"id":54985,"name":"Suehelay Acevedo‐Acevedo","orcid":"0000-0002-8559-6055","position":36,"is_corresponding":false},{"id":54986,"name":"Víctor Acuña-Alonzo","orcid":"0000-0001-6588-7616","position":37,"is_corresponding":false},{"id":54987,"name":"Rodrigo Barquera","orcid":"0000-0003-0518-4518","position":38,"is_corresponding":false},{"id":54988,"name":"Samuel Canizales‐Quinteros","orcid":"0000-0002-4833-6932","position":39,"is_corresponding":false},{"id":19567,"name":"Jeffrey M. Kidd","orcid":"0000-0002-9631-1465","position":0,"is_corresponding":true}],"reference_count":45,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"23040495","pmcid":"PMC3484644","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":64.0,"fair_a":48.0,"fair_i":0.0,"fair_r":13.3333,"fair_zscore":-1.2553,"fair_rationale":{"fair_score":31.33,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":64.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"The text does not mention any metadata, machine-readable or otherwise, for the genomic data."}]},"A":{"name":"Accessible","score":48.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"No data or code access protocol is described; no repository or URL is provided."}]},"I":{"name":"Interoperable","score":0.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"The text does not specify use of standard formats, vocabularies, or identifiers for the genetic variants."}]},"R":{"name":"Reusable","score":13.33,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.0,"signal":null,"rationale":"No data-availability statement, license, or reproducibility information is included in the text."}]}},"suggestions":["Add a data availability statement with a persistent identifier (e.g., DOI) to a public repository such as EGA or dbGaP.","Provide machine-readable metadata describing the dataset, including sample ancestry, coverage, and variant call format.","Use standard file formats (e.g., VCF, BAM) and reference genome identifiers (e.g., GRCh37) to enhance interoperability.","Include a clear license (e.g., CC0 or CC-BY) to specify reuse terms and conditions.","Document the analysis pipeline and software versions to enable reproducibility of the results."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"abstract_only"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"abstract_only","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:39:40.079203Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}