{"id":"https://openalex.org/W1483942228","doi":"https://doi.org/10.1186/1471-2148-3-2","title":"Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes","display_name":"Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes","publication_year":2003,"publication_date":"2003-01-06","ids":{"openalex":"https://openalex.org/W1483942228","doi":"https://doi.org/10.1186/1471-2148-3-2","mag":"1483942228","pmid":"https://pubmed.ncbi.nlm.nih.gov/12515582","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/149225"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2148-3-2","doi":"https://doi.org/10.1186/1471-2148-3-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2148-3-2","pdf_url":"https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-3-2","source":{"id":"https://openalex.org/S64097828","display_name":"BMC Evolutionary Biology","issn_l":"1471-2148","issn":["1471-2148"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","ki-jl-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Evolutionary Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-3-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075542475","display_name":"Boris Mirkin","orcid":"https://orcid.org/0000-0001-5470-8635","observed_orcids":["https://orcid.org/0000-0001-5470-8635"]},"institutions":[{"id":"https://openalex.org/I124357947","display_name":"University of London","ror":"https://ror.org/04cw6st05","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947"]},{"id":"https://openalex.org/I98259816","display_name":"Birkbeck, University of London","ror":"https://ror.org/02mb95055","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Boris G Mirkin","raw_affiliation_strings":["School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK. mirkin@dcs.bbk.ac.uk","School of Information Systems and Computer Science, Birkbeck College, University of London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK. mirkin@dcs.bbk.ac.uk","institution_ids":["https://openalex.org/I98259816"]},{"raw_affiliation_string":"School of Information Systems and Computer Science, Birkbeck College, University of London, London, UK","institution_ids":["https://openalex.org/I124357947","https://openalex.org/I98259816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014473920","display_name":"Trevor I. Fenner","orcid":"https://orcid.org/0000-0002-4239-7574","observed_orcids":["https://orcid.org/0000-0002-4239-7574"]},"institutions":[{"id":"https://openalex.org/I124357947","display_name":"University of London","ror":"https://ror.org/04cw6st05","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947"]},{"id":"https://openalex.org/I98259816","display_name":"Birkbeck, University of London","ror":"https://ror.org/02mb95055","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Trevor I Fenner","raw_affiliation_strings":["School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK","School of Information Systems and Computer Science, Birkbeck College, University of London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK","institution_ids":["https://openalex.org/I98259816"]},{"raw_affiliation_string":"School of Information Systems and Computer Science, Birkbeck College, University of London, London, UK","institution_ids":["https://openalex.org/I124357947","https://openalex.org/I98259816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077552473","display_name":"Michael Y. Galperin","orcid":"https://orcid.org/0000-0002-2265-5572","observed_orcids":["https://orcid.org/0000-0002-2265-5572"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Y Galperin","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","National Center for Biotechnology Information, National Library of Medicine National Institutes of Health, Bethesda, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]},{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine National Institutes of Health, Bethesda, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035240489","display_name":"Eugene V. Koonin","orcid":"https://orcid.org/0000-0003-3943-8299","observed_orcids":["https://orcid.org/0000-0003-3943-8299"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eugene V Koonin","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","National Center for Biotechnology Information, National Library of Medicine National Institutes of Health, Bethesda, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]},{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine National Institutes of Health, Bethesda, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5035240489"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":8.1487,"has_fulltext":true,"cited_by_count":365,"citation_normalized_percentile":{"value":0.98713435,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"3","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9901999831199646,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9901999831199646,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.002300000051036477,"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"}},{"id":"https://openalex.org/T11879","display_name":"Protist diversity and phylogeny","score":0.0013000000035390258,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/horizontal-gene-transfer","display_name":"horizontal gene transfer","score":0.9409999847412109},{"id":"https://openalex.org/keywords/gene-loss","display_name":"gene loss","score":0.9190000295639038},{"id":"https://openalex.org/keywords/last-universal-common-ancestor","display_name":"last universal common ancestor","score":0.8519999980926514},{"id":"https://openalex.org/keywords/ancestral-genome-reconstruction","display_name":"ancestral genome reconstruction","score":0.7639999985694885},{"id":"https://openalex.org/keywords/orthologs","display_name":"orthologs","score":0.6600000262260437},{"id":"https://openalex.org/keywords/clusters-of-orthologous-groups","display_name":"clusters of orthologous groups","score":0.902999997138977},{"id":"https://openalex.org/keywords/prokaryotic-evolution","display_name":"prokaryotic evolution","score":0.8889999985694885},{"id":"https://openalex.org/keywords/genome-evolution","display_name":"genome evolution","score":0.382999986410141}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.799346923828125},{"id":"https://openalex.org/C92938381","wikidata":"https://www.wikidata.org/wiki/Q83185","display_name":"Horizontal gene transfer","level":4,"score":0.7969279885292053},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.653594970703125},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5671724081039429},{"id":"https://openalex.org/C197583594","wikidata":"https://www.wikidata.org/wiki/Q1052390","display_name":"Most recent common ancestor","level":4,"score":0.559468686580658},{"id":"https://openalex.org/C151913843","wikidata":"https://www.wikidata.org/wiki/Q3454555","display_name":"Dominance (genetics)","level":3,"score":0.5414817929267883},{"id":"https://openalex.org/C167683757","wikidata":"https://www.wikidata.org/wiki/Q5937774","display_name":"Human evolutionary genetics","level":4,"score":0.5094760060310364},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4748407006263733},{"id":"https://openalex.org/C2780422015","wikidata":"https://www.wikidata.org/wiki/Q402152","display_name":"Ancestor","level":2,"score":0.4304538369178772},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.4233914613723755},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3714565634727478},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3372088670730591},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008432","descriptor_name":"Mathematical Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":true},{"descriptor_ui":"D019843","descriptor_name":"Archaeal Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019843","descriptor_name":"Archaeal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2148-3-2","doi":"https://doi.org/10.1186/1471-2148-3-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2148-3-2","pdf_url":"https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-3-2","source":{"id":"https://openalex.org/S64097828","display_name":"BMC Evolutionary Biology","issn_l":"1471-2148","issn":["1471-2148"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","ki-jl-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Evolutionary Biology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:149225","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/149225","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Evol Biol","raw_type":"Text"},{"id":"pmid:12515582","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12515582","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":"BMC evolutionary biology","raw_type":"Comparative Study"},{"id":"pmh:oai:doaj.org/article:c0e363cf55dd4c4ba71a397715a47e61","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/c0e363cf55dd4c4ba71a397715a47e61","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Evolutionary Biology, Vol 3, Iss 1, p 2 (2003)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2148-3-2","doi":"https://doi.org/10.1186/1471-2148-3-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2148-3-2","pdf_url":"https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-3-2","source":{"id":"https://openalex.org/S64097828","display_name":"BMC Evolutionary Biology","issn_l":"1471-2148","issn":["1471-2148"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","ki-jl-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Evolutionary Biology","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/W1483942228.pdf","grobid_xml":"https://content.openalex.org/works/W1483942228.grobid-xml"},"referenced_works_count":87,"referenced_works":["https://openalex.org/W156146614","https://openalex.org/W174663226","https://openalex.org/W1487781539","https://openalex.org/W1497618653","https://openalex.org/W1501400124","https://openalex.org/W1507860313","https://openalex.org/W1519987066","https://openalex.org/W1544293646","https://openalex.org/W1571205912","https://openalex.org/W1587558271","https://openalex.org/W1669459870","https://openalex.org/W1872722587","https://openalex.org/W1891018726","https://openalex.org/W1952540142","https://openalex.org/W1968248848","https://openalex.org/W1972189965","https://openalex.org/W1978858440","https://openalex.org/W1979558568","https://openalex.org/W1979899435","https://openalex.org/W1981888730","https://openalex.org/W1990453950","https://openalex.org/W1991207390","https://openalex.org/W2006834210","https://openalex.org/W2009219904","https://openalex.org/W2010908637","https://openalex.org/W2015225927","https://openalex.org/W2018024025","https://openalex.org/W2018305380","https://openalex.org/W2018756788","https://openalex.org/W2023218781","https://openalex.org/W2024174659","https://openalex.org/W2032603188","https://openalex.org/W2036224124","https://openalex.org/W2036847531","https://openalex.org/W2039158827","https://openalex.org/W2039706474","https://openalex.org/W2041303239","https://openalex.org/W2042354418","https://openalex.org/W2042773270","https://openalex.org/W2044145517","https://openalex.org/W2044610621","https://openalex.org/W2046039468","https://openalex.org/W2053708801","https://openalex.org/W2054457669","https://openalex.org/W2059676405","https://openalex.org/W2064794187","https://openalex.org/W2065973977","https://openalex.org/W2073977194","https://openalex.org/W2076115496","https://openalex.org/W2077167882","https://openalex.org/W2079115652","https://openalex.org/W2086184240","https://openalex.org/W2089675753","https://openalex.org/W2097117583","https://openalex.org/W2098558111","https://openalex.org/W2099369372","https://openalex.org/W2104399271","https://openalex.org/W2104454769","https://openalex.org/W2107424557","https://openalex.org/W2110105435","https://openalex.org/W2112606377","https://openalex.org/W2113653809","https://openalex.org/W2118427672","https://openalex.org/W2121166240","https://openalex.org/W2122451246","https://openalex.org/W2126161931","https://openalex.org/W2127596034","https://openalex.org/W2129538546","https://openalex.org/W2141857686","https://openalex.org/W2143276497","https://openalex.org/W2146754116","https://openalex.org/W2151101886","https://openalex.org/W2154565942","https://openalex.org/W2155754759","https://openalex.org/W2158350566","https://openalex.org/W2159892619","https://openalex.org/W2161257056","https://openalex.org/W2163892779","https://openalex.org/W2166865790","https://openalex.org/W2169929748","https://openalex.org/W2169950947","https://openalex.org/W2317317577","https://openalex.org/W4211022623","https://openalex.org/W4241196009","https://openalex.org/W4242816210","https://openalex.org/W4301131015","https://openalex.org/W7095857204"],"related_works":["https://openalex.org/W2582263979","https://openalex.org/W2020184108","https://openalex.org/W7097109094","https://openalex.org/W7099143255","https://openalex.org/W2121562498","https://openalex.org/W2737296825","https://openalex.org/W3200845947","https://openalex.org/W1617795814","https://openalex.org/W7152522764","https://openalex.org/W2009219904"],"abstract_inverted_index":{"BACKGROUND:":[0],"Comparative":[1],"analysis":[2,406,445],"of":[3,9,37,56,61,72,79,94,96,99,109,115,118,152,164,178,189,203,248,259,268,285,301,314,336,355,364,378,386,399,407,410,414,453,462,472,480,492,497,517],"sequenced":[4,113,501],"genomes":[5,63,502],"reveals":[6],"numerous":[7],"instances":[8],"apparent":[10],"horizontal":[11,337,509],"gene":[12,23,142,158,212,227,236,250,274,338,341,381,392,431,438,473,498],"transfer":[13,339,510],"(HGT),":[14],"at":[15],"least":[16],"in":[17,31,111,270,383,500,528],"prokaryotes,":[18],"and":[19,58,146,180,244,309,340,359,380,394,433],"indicates":[20,294],"that":[21,104,162,391,450,457],"lineage-specific":[22],"loss":[24,179,216,228,342,382,393,432],"might":[25,229,320,464,511],"have":[26,512],"been":[27],"even":[28,296,360],"more":[29,232],"common":[30,256],"evolution.":[32,530],"This":[33,347,444],"complicates":[34],"the":[35,53,70,92,105,119,124,133,137,184,190,194,200,204,245,253,260,271,278,286,312,334,356,365,368,384,408,411,451,460,467,470,478,490,515],"notion":[36,390],"a":[38,47,64,83,168,231,298,307,310,326,417,441,525],"species":[39,84,126,138,185,357,419,442],"tree,":[40],"which":[41,172,429,522],"needs":[42],"to":[43,131,306,318,324,371,448,477,489,514],"be":[44,174,230,321,372,465],"re-interpreted":[45],"as":[46,157,176,277,469],"prevailing":[48],"evolutionary":[49,170,191,427,481],"trend,":[50],"rather":[51],"than":[52,235],"full":[54],"depiction":[55],"evolution,":[57],"makes":[59,523],"reconstruction":[60,479],"ancestral":[62],"non-trivial":[65],"task.":[66],"RESULTS:":[67],"We":[68,102,160],"addressed":[69],"problem":[71],"constructing":[73,425],"parsimonious":[74,169,426],"scenarios":[75,482],"for":[76,252,351,424,436],"individual":[77],"sets":[78,88,251,275],"orthologous":[80,87,437],"genes":[81,269,316,520],"given":[82,440],"tree.":[85,127,186,366,420,443],"The":[86,187,266,389,475],"were":[89,129,154,242,264,422],"taken":[90,504],"from":[91],"database":[93],"Clusters":[95],"Orthologous":[97],"Groups":[98],"proteins":[100],"(COGs).":[101],"show":[103],"phyletic":[106,134,412],"patterns":[107,135,413,496],"(patterns":[108],"presence-absence":[110,499],"completely":[112],"genomes)":[114],"almost":[116],"90%":[117],"COGs":[120,415],"are":[121,219,344,396,503],"inconsistent":[122],"with":[123,136,290,297,374,487],"hypothetical":[125,418],"Algorithms":[128,421],"developed":[130,423],"reconcile":[132],"tree":[139,195,358],"by":[140,404],"postulating":[141],"loss,":[143],"COG":[144],"emergence":[145],"HGT":[147,379,395,455,493],"(the":[148],"latter":[149],"two":[150,352],"classes":[151],"events":[153,182,192,343,456],"collectively":[155],"treated":[156],"gains).":[159],"prove":[161],"each":[163],"these":[165],"algorithms":[166],"produces":[167],"scenario,":[171],"can":[173],"represented":[175],"mapping":[177,409],"gain":[181,240,279,292,299,308,331,434],"on":[183,199,225],"distribution":[188],"among":[193],"nodes":[196],"substantially":[197],"depends":[198],"underlying":[201],"assumptions":[202],"reconciliation":[205],"algorithm,":[206],"e.g.":[207],"whether":[208],"or":[209],"not":[210],"independent":[211],"gains":[213],"(gain":[214],"after":[215,217],"gain)":[218],"permitted.":[220],"Biological":[221],"considerations":[222],"suggest":[223],"that,":[224,295],"average,":[226],"likely":[233],"event":[234],"gain.":[237],"Therefore":[238],"different":[239,291],"penalties":[241,293],"used":[243],"resulting":[246],"series":[247],"reconstructed":[249,272,289],"last":[254],"universal":[255],"ancestor":[257],"(LUCA)":[258],"extant":[261],"life":[262],"forms":[263],"analysed.":[265],"number":[267,452,471],"LUCA":[273,287,319],"grows":[276],"penalty":[280,300,332],"increases.":[281],"However,":[282],"qualitative":[283],"examination":[284],"versions":[288],"1":[302],"(equal":[303],"weights":[304],"assigned":[305,317],"loss),":[311],"set":[313],"572":[315],"nearly":[322,345],"sufficient":[323],"sustain":[325],"functioning":[327],"organism.":[328],"Under":[329],"this":[330],"value,":[333],"numbers":[335],"identical.":[346],"result":[348],"holds":[349],"true":[350],"alternative":[353],"topologies":[354],"under":[361],"random":[362],"shuffling":[363],"Therefore,":[367],"results":[369],"seem":[370],"compatible":[373],"approximately":[375,466],"equal":[376],"likelihoods":[377],"evolution":[385,401,461,516],"prokaryotes.":[387],"CONCLUSIONS:":[388],"major":[397],"aspects":[398],"prokaryotic":[400,529],"was":[402],"supported":[403],"quantitative":[405],"onto":[416],"scenarios,":[428],"include":[430],"events,":[435],"sets,":[439],"shows,":[446],"contrary":[447],"expectations,":[449],"predicted":[454],"occurred":[458],"during":[459],"prokaryotes":[463],"same":[468],"losses.":[474],"approach":[476],"employed":[483],"here":[484],"is":[485],"conservative":[486],"regard":[488],"detection":[491],"because":[494],"only":[495],"into":[505],"account.":[506],"In":[507],"reality,":[508],"contributed":[513],"many":[518],"other":[519],"also,":[521],"it":[524],"dominant":[526],"force":[527]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":16},{"year":2012,"cited_by_count":26}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}