{"id":"https://openalex.org/W2952455712","doi":"https://doi.org/10.1371/journal.pcbi.1006493","title":"Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion","display_name":"Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion","publication_year":2019,"publication_date":"2019-02-15","ids":{"openalex":"https://openalex.org/W2952455712","doi":"https://doi.org/10.1371/journal.pcbi.1006493","mag":"2952455712","pmid":"https://pubmed.ncbi.nlm.nih.gov/30768597"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006493","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006493","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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 Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1006493","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036050137","display_name":"Nico M. Franz","orcid":"https://orcid.org/0000-0001-7089-7018"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nico M. Franz","raw_affiliation_strings":["School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7089-7018","affiliations":[{"raw_affiliation_string":"School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057269298","display_name":"Lukas J. Musher","orcid":"https://orcid.org/0000-0003-3490-0341"},"institutions":[{"id":"https://openalex.org/I1338124936","display_name":"American Museum of Natural History","ror":"https://ror.org/03thb3e06","country_code":"US","type":"archive","lineage":["https://openalex.org/I1338124936"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lukas J. Musher","raw_affiliation_strings":["Richard Gilder Graduate School and Department of Ornithology, American Museum of Natural History, New York, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-3490-0341","affiliations":[{"raw_affiliation_string":"Richard Gilder Graduate School and Department of Ornithology, American Museum of Natural History, New York, New York, United States of America","institution_ids":["https://openalex.org/I1338124936"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031689741","display_name":"Joseph W. Brown","orcid":"https://orcid.org/0000-0002-3835-8062"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Joseph W. Brown","raw_affiliation_strings":["Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-3835-8062","affiliations":[{"raw_affiliation_string":"Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100759694","display_name":"Shizhuo Yu","orcid":"https://orcid.org/0009-0008-5147-7251"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shizhuo Yu","raw_affiliation_strings":["Department of Computer Science, University of California at Davis, Davis, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California at Davis, Davis, California, United States of America","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057600294","display_name":"Bertram Lud\u00e4scher","orcid":"https://orcid.org/0000-0001-9140-936X"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bertram Lud\u00e4scher","raw_affiliation_strings":["School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5036050137"],"corresponding_institution_ids":["https://openalex.org/I55732556"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.9061,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.85968904,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"15","issue":"2","first_page":"e1006493","last_page":"e1006493"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10955","display_name":"Paleontology and Evolutionary Biology","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10955","display_name":"Paleontology and Evolutionary Biology","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.9930999875068665,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11387","display_name":"Ichthyology and Marine Biology","score":0.987500011920929,"subfield":{"id":"https://openalex.org/subfields/2309","display_name":"Nature and Landscape Conservation"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/congruence","display_name":"Congruence (geometry)","score":0.7016021013259888},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6281849145889282},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.4883120059967041},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41619962453842163},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3389541804790497},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3349054455757141},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3222770392894745},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24010390043258667},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13936734199523926},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.06617307662963867}],"concepts":[{"id":"https://openalex.org/C132074034","wikidata":"https://www.wikidata.org/wiki/Q154210","display_name":"Congruence (geometry)","level":2,"score":0.7016021013259888},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6281849145889282},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.4883120059967041},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41619962453842163},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3389541804790497},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3349054455757141},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3222770392894745},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24010390043258667},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13936734199523926},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.06617307662963867},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001717","descriptor_name":"Birds","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001717","descriptor_name":"Birds","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001717","descriptor_name":"Birds","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1006493","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006493","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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 Computational Biology","raw_type":"journal-article"},{"id":"pmid:30768597","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30768597","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,"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 computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1006493","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006493","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:490a1ffc3e1d47f989fba6f149621ba8","is_oa":true,"landing_page_url":"https://doaj.org/article/490a1ffc3e1d47f989fba6f149621ba8","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,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 15, Iss 2, p e1006493 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5394801","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6395011","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/7727855","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Verbalizing_phylogenomic_conflict_Representation_of_node_congruence_across_competing_reconstructions_of_the_neoavian_explosion/7727855","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006493","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006493","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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 Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1473721797","display_name":"CAREER: Systematics of eustyline and geonemine weevils: Connecting and contrasting Caribbean and Neotropical mainland radiations","funder_award_id":"1155984","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1919092838","display_name":null,"funder_award_id":"DBI-1147273","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"},{"id":"https://openalex.org/G2157009985","display_name":null,"funder_award_id":"DEB-1155984","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"},{"id":"https://openalex.org/G4762368576","display_name":"Collaborative research:   Automated and community-driven synthesis of the tree of life","funder_award_id":"1207915","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5311962964","display_name":"Collaborative Research: ABI: Innovation: The Global Names Architecture, an infrastructure for unifying taxonomic databases and services for managers of biological information.","funder_award_id":"1342595","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5454034950","display_name":"BCSP:   Collaborative Research:   ABI Development: Exploring Taxon Concepts (ETC) through analysing fine-grained semantic markup of descriptive literature","funder_award_id":"1147273","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5581497425","display_name":null,"funder_award_id":"DEB-1155984","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G691159008","display_name":null,"funder_award_id":"DEB-1207915","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"},{"id":"https://openalex.org/G8706959937","display_name":null,"funder_award_id":"DEB-1207915","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8764659264","display_name":"III:Small: A Logic-Based, Provenance-Aware System for Merging Scientific Data under Context and Classification Constraints","funder_award_id":"1118088","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8996879502","display_name":null,"funder_award_id":"DBI-1342595","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320332169","display_name":"Directorate for Computer and Information Science and Engineering","ror":"https://ror.org/025kzpk63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W852874","https://openalex.org/W173754285","https://openalex.org/W372138008","https://openalex.org/W1501566751","https://openalex.org/W1501678631","https://openalex.org/W1527612193","https://openalex.org/W1601677923","https://openalex.org/W1745539279","https://openalex.org/W1806326109","https://openalex.org/W1836492352","https://openalex.org/W1869002246","https://openalex.org/W1886547141","https://openalex.org/W1887892324","https://openalex.org/W1920304345","https://openalex.org/W1932287049","https://openalex.org/W1946807837","https://openalex.org/W1982803741","https://openalex.org/W1990628530","https://openalex.org/W1992732214","https://openalex.org/W1997396781","https://openalex.org/W2016163216","https://openalex.org/W2028407198","https://openalex.org/W2054952488","https://openalex.org/W2079335886","https://openalex.org/W2081037582","https://openalex.org/W2081545011","https://openalex.org/W2088688477","https://openalex.org/W2099352568","https://openalex.org/W2100152398","https://openalex.org/W2105897284","https://openalex.org/W2106482248","https://openalex.org/W2106581684","https://openalex.org/W2119837484","https://openalex.org/W2125793391","https://openalex.org/W2143597777","https://openalex.org/W2153165351","https://openalex.org/W2155132113","https://openalex.org/W2162050818","https://openalex.org/W2168931216","https://openalex.org/W2171435063","https://openalex.org/W2227270210","https://openalex.org/W2256663809","https://openalex.org/W2282513479","https://openalex.org/W2288882354","https://openalex.org/W2310479359","https://openalex.org/W2314422014","https://openalex.org/W2525250298","https://openalex.org/W2526744222","https://openalex.org/W2533812722","https://openalex.org/W2555309594","https://openalex.org/W2575463631","https://openalex.org/W2588097571","https://openalex.org/W2601425645","https://openalex.org/W2615929478","https://openalex.org/W2751414096","https://openalex.org/W2766582063","https://openalex.org/W2786568953","https://openalex.org/W2949664887","https://openalex.org/W2950241835","https://openalex.org/W2951002538","https://openalex.org/W2951975758","https://openalex.org/W2953087319","https://openalex.org/W2963514194","https://openalex.org/W3124821131","https://openalex.org/W4231106801","https://openalex.org/W4231969088","https://openalex.org/W4392188009","https://openalex.org/W4394081945","https://openalex.org/W6631540646","https://openalex.org/W6637796522","https://openalex.org/W6744969987","https://openalex.org/W6763404483","https://openalex.org/W6832949185"],"related_works":["https://openalex.org/W2388471861","https://openalex.org/W2997603844","https://openalex.org/W2354789018","https://openalex.org/W4380684998","https://openalex.org/W2391316944","https://openalex.org/W2065462305","https://openalex.org/W4399230304","https://openalex.org/W4293665628","https://openalex.org/W3171917333","https://openalex.org/W1588041347"],"abstract_inverted_index":{"Phylogenomic":[0],"research":[1],"is":[2,56,196],"accelerating":[3],"the":[4,25,39,82,96,145,166,186,212,223,236,241,262],"publication":[5],"of":[6,15,27,98,107,137,148,159,168,177,201,245,264],"landmark":[7],"studies":[8],"that":[9,94,181],"aim":[10],"to":[11,41,81,103,121,154,191,228,254],"resolve":[12],"deep":[13],"divergences":[14],"major":[16],"organismal":[17],"groups.":[18],"Meanwhile,":[19],"systems":[20],"for":[21,59,64,250],"identifying":[22],"and":[23,46,67,91,216,225,271],"integrating":[24],"products":[26],"phylogenomic":[28,54,113,175,232],"inference-such":[29],"as":[30,218],"newly":[31],"supported":[32],"clade":[33,118],"concepts-have":[34],"not":[35,276],"kept":[36],"pace.":[37],"However,":[38],"ability":[40],"verbalize":[42],"node":[43,108,140,265],"concept":[44,119,141],"congruence":[45,156],"conflict":[47,83,184,195],"across":[48],"multiple,":[49],"in":[50,157,185,211,277],"effect":[51],"simultaneously":[52],"endorsed":[53,110],"hypotheses,":[55],"a":[57,78,88,256],"prerequisite":[58],"building":[60],"synthetic":[61,231],"data":[62,233],"environments":[63,252],"biological":[65],"systematics":[66],"other":[68],"domains":[69],"impacted":[70],"by":[71,111,125,144,198,268],"these":[72,130],"conflicting":[73],"inferences.":[74],"Here":[75],"we":[76,171,274],"develop":[77],"novel":[79],"solution":[80],"verbalization":[84],"challenge,":[85],"based":[86],"on":[87],"logic":[89],"representation":[90],"reasoning":[92],"approach":[93,116],"utilizes":[95],"language":[97],"Region":[99],"Connection":[100],"Calculus":[101],"(RCC-5)":[102],"produce":[104],"consistent":[105],"alignments":[106,238],"concepts":[109,123,153,266],"incongruent":[112],"studies.":[114],"The":[115],"employs":[117],"labels":[120,224],"individuate":[122],"used":[124],"each":[126,280],"source,":[127],"even":[128],"if":[129],"carry":[131],"identical":[132],"names.":[133],"Indirect":[134],"RCC-5":[135,237],"modeling":[136],"intensional":[138],"(property-based)":[139],"definitions,":[142],"facilitated":[143],"local":[146],"relaxation":[147],"coverage":[149],"constraints,":[150],"allows":[151],"parent":[152],"attain":[155],"spite":[158],"their":[160],"differentially":[161],"sampled":[162],"children.":[163],"To":[164],"demonstrate":[165],"feasibility":[167],"this":[169,194],"approach,":[170],"align":[172],"two":[173],"recent":[174],"reconstructions":[176],"higher-level":[178],"avian":[179],"groups":[180],"entail":[182],"strong":[183],"\"neoavian":[187],"explosion\"":[188],"region.":[189],"According":[190],"our":[192,269],"representations,":[193],"constituted":[197],"26":[199],"instances":[200,207],"input":[202],"\"whole":[203],"concept\"":[204],"overlap.":[205],"These":[206],"are":[208,275],"further":[209],"resolvable":[210],"output":[213],"labeling":[214],"schemes":[215],"visualizations":[217],"\"split":[219],"concepts\",":[220],"which":[221],"provide":[222],"relations":[226],"needed":[227],"build":[229],"truly":[230],"environments.":[234],"Because":[235],"fundamentally":[239],"reflect":[240],"trained,":[242],"logic-enabled":[243],"judgments":[244],"systematic":[246],"experts,":[247],"future":[248],"designs":[249],"such":[251],"need":[253],"promote":[255],"culture":[257],"where":[258],"experts":[259],"routinely":[260],"assess":[261],"intensionalities":[263],"published":[267],"peers-even":[270],"especially":[272],"when":[273],"agreement":[278],"with":[279],"other.":[281]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
