{"id":"https://openalex.org/W7203671222","doi":"https://doi.org/10.1371/journal.pone.0360852","title":"Assessing the impact of phylogenetic reconstruction error on genetic reassortment inference in segmented viruses","display_name":"Assessing the impact of phylogenetic reconstruction error on genetic reassortment inference in segmented viruses","publication_year":2026,"publication_date":"2026-10-22","ids":{"openalex":"https://openalex.org/W7203671222","doi":"https://doi.org/10.1371/journal.pone.0360852","pmid":"https://pubmed.ncbi.nlm.nih.gov/42911973","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13690219"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pone.0360852","doi":"https://doi.org/10.1371/journal.pone.0360852","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0360852","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0360852&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS One","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0360852&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083697243","display_name":"Hugo Gildardo Castel\u00e1n-S\u00e1nchez","orcid":"https://orcid.org/0000-0002-4763-0267","observed_orcids":["https://orcid.org/0000-0002-4763-0267"]},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Hugo G. Castel\u00e1n-S\u00e1nchez","raw_affiliation_strings":["Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 201, London, Ontario N6A 5C1, Canada"],"raw_orcid":"https://orcid.org/0000-0002-4763-0267","affiliations":[{"raw_affiliation_string":"Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 201, London, Ontario N6A 5C1, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004110504","display_name":"Art F. Y. Poon","orcid":"https://orcid.org/0000-0003-3779-154X","observed_orcids":["https://orcid.org/0000-0003-3779-154X"]},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Art F. Y. Poon","raw_affiliation_strings":["Department of Computer Science, Western University, Rm. 355, Middlesex College, London N6A 5B7, Canada","Department of Microbiology & Immunology, Western University, 1151 Richmond Street, London, Ontario N6A 3K7, Canada","Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 201, London, Ontario N6A 5C1, Canada"],"raw_orcid":"https://orcid.org/0000-0003-3779-154X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western University, Rm. 355, Middlesex College, London N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Microbiology & Immunology, Western University, 1151 Richmond Street, London, Ontario N6A 3K7, Canada","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 201, London, Ontario N6A 5C1, Canada","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5004110504"],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":{"value":2382,"currency":"USD","value_usd":2382},"apc_paid":{"value":2382,"currency":"USD","value_usd":2382},"fwci":3.7643,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.94222247,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"21","issue":"10","first_page":"e0360852","last_page":"e0360852"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.8525000214576721,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.8525000214576721,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.10209999978542328,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.029600000008940697,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/reassortment","display_name":"reassortment","score":0.6169999837875366},{"id":"https://openalex.org/keywords/influenza-a-virus","display_name":"influenza A virus","score":0.8799999952316284},{"id":"https://openalex.org/keywords/phylogenetic-incongruence","display_name":"phylogenetic incongruence","score":0.9359999895095825},{"id":"https://openalex.org/keywords/antigenic-shift","display_name":"antigenic shift","score":0.7319999933242798},{"id":"https://openalex.org/keywords/hemagglutinin","display_name":"hemagglutinin","score":0.859000027179718},{"id":"https://openalex.org/keywords/sampling-design","display_name":"sampling design","score":0.5899999737739563},{"id":"https://openalex.org/keywords/false-positive-rate","display_name":"false positive rate","score":0.5329999923706055},{"id":"https://openalex.org/keywords/false-negative-rate","display_name":"false negative rate","score":0.5519999861717224},{"id":"https://openalex.org/keywords/phylogenetic-uncertainty","display_name":"phylogenetic uncertainty","score":0.6330000162124634}],"concepts":[{"id":"https://openalex.org/C16154277","wikidata":"https://www.wikidata.org/wiki/Q2004399","display_name":"Reassortment","level":5,"score":0.9157999753952026},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7541999816894531},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6818000078201294},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6689000129699707},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.5034000277519226},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47029998898506165},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.45500001311302185},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4341000020503998},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.4097000062465668},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4049000144004822},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36980000138282776},{"id":"https://openalex.org/C21833749","wikidata":"https://www.wikidata.org/wiki/Q7189431","display_name":"Viral phylodynamics","level":4,"score":0.29490000009536743},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.27250000834465027},{"id":"https://openalex.org/C166733315","wikidata":"https://www.wikidata.org/wiki/Q6934831","display_name":"Multipartite","level":4,"score":0.26249998807907104}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001717","descriptor_name":"Birds","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016865","descriptor_name":"Reassortant Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pone.0360852","doi":"https://doi.org/10.1371/journal.pone.0360852","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0360852","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0360852&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS One","raw_type":"journal-article"},{"id":"doi:10.1101/2025.02.24.639875","doi":"https://doi.org/10.1101/2025.02.24.639875","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.02.24.639875","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:13690219","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13690219/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13690219/pdf/pone.0360852.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS One","raw_type":"Text"},{"id":"pmid:42911973","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42911973","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PloS one","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:a856913f5c264805b75db48d2d6e796f","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/a856913f5c264805b75db48d2d6e796f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS ONE, Vol 21, Iss 10, p e0360852 (2026)","raw_type":"article"},{"id":"doi:10.5281/zenodo.21985669","doi":"https://doi.org/10.5281/zenodo.21985669","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.21985669","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.5281/zenodo.21985671","doi":"https://doi.org/10.5281/zenodo.21985671","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.21985671","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.5281/zenodo.22083393","doi":"https://doi.org/10.5281/zenodo.22083393","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22083393","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pone.0360852","doi":"https://doi.org/10.1371/journal.pone.0360852","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0360852","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0360852&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS One","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7203671222.pdf","grobid_xml":"https://content.openalex.org/works/W7203671222.grobid-xml"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W1445990149","https://openalex.org/W1492465290","https://openalex.org/W1538145326","https://openalex.org/W1594683133","https://openalex.org/W1969955142","https://openalex.org/W1977233594","https://openalex.org/W1986146966","https://openalex.org/W1987071374","https://openalex.org/W1990545448","https://openalex.org/W2025033471","https://openalex.org/W2041753380","https://openalex.org/W2043951993","https://openalex.org/W2046757585","https://openalex.org/W2061737786","https://openalex.org/W2068225247","https://openalex.org/W2075588026","https://openalex.org/W2092339835","https://openalex.org/W2097879530","https://openalex.org/W2110322110","https://openalex.org/W2111414304","https://openalex.org/W2115888213","https://openalex.org/W2119226701","https://openalex.org/W2129706873","https://openalex.org/W2130597146","https://openalex.org/W2140700622","https://openalex.org/W2143794041","https://openalex.org/W2145171033","https://openalex.org/W2151057382","https://openalex.org/W2151596939","https://openalex.org/W2157322272","https://openalex.org/W2160378127","https://openalex.org/W2169702034","https://openalex.org/W2272078433","https://openalex.org/W2344862355","https://openalex.org/W2408328645","https://openalex.org/W2550705160","https://openalex.org/W2613579550","https://openalex.org/W2620210735","https://openalex.org/W2888871909","https://openalex.org/W2889900726","https://openalex.org/W2942537438","https://openalex.org/W2951126701","https://openalex.org/W3005235420","https://openalex.org/W3021001696","https://openalex.org/W3038874609","https://openalex.org/W3044633967","https://openalex.org/W3046018393","https://openalex.org/W3089454776","https://openalex.org/W3104455460","https://openalex.org/W3164565349","https://openalex.org/W3185344063","https://openalex.org/W4205930168","https://openalex.org/W4214665998","https://openalex.org/W4280623137","https://openalex.org/W4291016578","https://openalex.org/W4292362068","https://openalex.org/W4299167275","https://openalex.org/W4322720367","https://openalex.org/W4382248980","https://openalex.org/W4384616649","https://openalex.org/W4390608966","https://openalex.org/W4390970843","https://openalex.org/W4395012819","https://openalex.org/W4396579454","https://openalex.org/W4400676996","https://openalex.org/W4404852258","https://openalex.org/W4413109575"],"related_works":["https://openalex.org/W4408057918","https://openalex.org/W2151057382","https://openalex.org/W4292362068","https://openalex.org/W4395012819","https://openalex.org/W1969955142","https://openalex.org/W4386946153","https://openalex.org/W6948279096","https://openalex.org/W3022711289","https://openalex.org/W2061737786","https://openalex.org/W1996189748"],"abstract_inverted_index":{"Recombination":[0],"is":[1,48],"an":[2],"important":[3],"process":[4,26],"in":[5,32,79],"the":[6,33,54,94,101,145,162,177,216,226,243,262],"evolution":[7,143,155],"of":[8,21,37,56,88,96,103,119,129,136,154,221,238,245],"RNA":[9],"viruses.":[10],"For":[11],"viruses":[12,39],"with":[13,40,132,229,242],"segmented":[14],"genomes,":[15],"recombination":[16],"can":[17,74,254],"occur":[18],"by":[19,51,183],"reassortment":[20,104,253],"entire":[22],"genomic":[23,42,61,164],"segments.":[24,165],"This":[25,204],"has":[27],"played":[28],"a":[29,117,234],"significant":[30],"role":[31],"adaptation":[34],"and":[35,66,126,156,269],"spread":[36],"influenza":[38,107],"novel":[41],"combinations,":[43],"i.e.,":[44],"antigenic":[45],"shifts.":[46],"Reassortment":[47],"usually":[49],"identified":[50,175],"discrepancies":[52],"between":[53],"topologies":[55],"trees":[57,146,179,214,228],"reconstructed":[58,147],"from":[59,77,106,112,148,176,190,201,215,258],"different":[60,133],"segments,":[62],"e.g.,":[63],"subtree":[64],"prune":[65],"regraft":[67],"(SPR)":[68],"rearrangements.":[69],"However,":[70],"this":[71,89],"phylogenetic":[72,97,173,259,267],"discordance":[73,174],"also":[75],"result":[76],"errors":[78],"tree":[80],"reconstruction":[81,98,137,184],"due":[82],"to":[83,92,100,159,161,210,264],"insufficient":[84],"information.":[85],"The":[86],"objective":[87],"study":[90],"was":[91,208],"evaluate":[93],"contribution":[95],"error":[99],"inference":[102],"events":[105],"A":[108],"virus":[109],"(IAV)":[110],"genomes":[111,125],"avian":[113,122],"hosts.":[114],"We":[115,186],"curated":[116],"dataset":[118],"11,795":[120],"complete":[121],"H5Nx":[123],"IAV":[124,274],"sampled":[127],"subsets":[128],"HA":[130,150,222],"sequences":[131],"expected":[134],"levels":[135],"error.":[138,185],"Next,":[139],"we":[140,232,250],"simulated":[141,227],"molecular":[142],"along":[144],"these":[149,167],"samples,":[151],"varying":[152],"rates":[153],"sequence":[157],"lengths":[158],"correspond":[160],"other":[163],"Because":[166],"simulations":[168,189],"had":[169],"no":[170],"reassortment,":[171],"any":[172],"resulting":[178],"must":[180],"be":[181,255],"caused":[182],"found":[187,251],"that":[188,252],"random":[191],"samples":[192],"yielded":[193],"about":[194],"32%":[195],"as":[196,199],"many":[197],"SPRs":[198,246],"obtained":[200],"real":[202],"data.":[203],"false":[205,235],"positive":[206],"rate":[207,237],"reduced":[209],"4%":[211],"when":[212,272],"simulating":[213],"most":[217],"genetically":[218],"divergent":[219],"subset":[220],"sequences.":[223],"By":[224],"modifying":[225],"SPR":[230],"rearrangements,":[231],"observed":[233],"negative":[236],"8.5%,":[239],"which":[240],"increased":[241],"number":[244],"per":[247],"tree.":[248],"Overall,":[249],"substantially":[256],"overestimated":[257],"discordance,":[260],"underscoring":[261],"need":[263],"account":[265],"for":[266,276],"uncertainty":[268],"sampling":[270],"design":[271],"analyzing":[273],"datasets":[275],"reassortment.":[277]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-08-19T00:00:00"}
