{"id":"https://openalex.org/W2035571812","doi":"https://doi.org/10.1093/bib/bbu015","title":"Causes, consequences and solutions of phylogenetic incongruence","display_name":"Causes, consequences and solutions of phylogenetic incongruence","publication_year":2014,"publication_date":"2014-05-27","ids":{"openalex":"https://openalex.org/W2035571812","doi":"https://doi.org/10.1093/bib/bbu015","mag":"2035571812","pmid":"https://pubmed.ncbi.nlm.nih.gov/24872401"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbu015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu015","pdf_url":"https://academic.oup.com/bib/article-pdf/16/3/536/670898/bbu015.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/16/3/536/670898/bbu015.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056692897","display_name":"Anup Som","orcid":"https://orcid.org/0000-0003-1857-2368"},"institutions":[{"id":"https://openalex.org/I168893459","display_name":"University of Allahabad","ror":"https://ror.org/03vrx7m55","country_code":"IN","type":"education","lineage":["https://openalex.org/I168893459"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"A. Som","raw_affiliation_strings":["Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, India","Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Allahabad 211002, India"],"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, India","institution_ids":["https://openalex.org/I168893459"]},{"raw_affiliation_string":"Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Allahabad 211002, India","institution_ids":["https://openalex.org/I168893459"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5056692897"],"corresponding_institution_ids":["https://openalex.org/I168893459"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.9966,"has_fulltext":true,"cited_by_count":189,"citation_normalized_percentile":{"value":0.86202258,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"16","issue":"3","first_page":"536","last_page":"548"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9952999949455261,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8937807083129883},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.6713746190071106},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6692352294921875},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.634672224521637},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.44370564818382263},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.43430617451667786},{"id":"https://openalex.org/keywords/phylogenetic-comparative-methods","display_name":"Phylogenetic comparative methods","score":0.4194175899028778},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3577110469341278},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2659243941307068}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8937807083129883},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6713746190071106},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6692352294921875},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.634672224521637},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.44370564818382263},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.43430617451667786},{"id":"https://openalex.org/C176771619","wikidata":"https://www.wikidata.org/wiki/Q7189434","display_name":"Phylogenetic comparative methods","level":4,"score":0.4194175899028778},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3577110469341278},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2659243941307068}],"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbu015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu015","pdf_url":"https://academic.oup.com/bib/article-pdf/16/3/536/670898/bbu015.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24872401","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24872401","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbu015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu015","pdf_url":"https://academic.oup.com/bib/article-pdf/16/3/536/670898/bbu015.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5799999833106995,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309835","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2035571812.pdf","grobid_xml":"https://content.openalex.org/works/W2035571812.grobid-xml"},"referenced_works_count":115,"referenced_works":["https://openalex.org/W93965243","https://openalex.org/W1566572727","https://openalex.org/W1581881067","https://openalex.org/W1656398202","https://openalex.org/W1664439142","https://openalex.org/W1844951369","https://openalex.org/W1846926012","https://openalex.org/W1964356973","https://openalex.org/W1965084611","https://openalex.org/W1965612692","https://openalex.org/W1966972227","https://openalex.org/W1971827346","https://openalex.org/W1974437146","https://openalex.org/W1974477108","https://openalex.org/W1974883772","https://openalex.org/W1975041634","https://openalex.org/W1975829042","https://openalex.org/W1977169047","https://openalex.org/W1984178787","https://openalex.org/W1984647070","https://openalex.org/W1990263013","https://openalex.org/W1991821268","https://openalex.org/W1994332522","https://openalex.org/W1994465420","https://openalex.org/W1996019265","https://openalex.org/W2010879590","https://openalex.org/W2017051353","https://openalex.org/W2019316513","https://openalex.org/W2021588961","https://openalex.org/W2027347467","https://openalex.org/W2036272181","https://openalex.org/W2036325355","https://openalex.org/W2039980955","https://openalex.org/W2054908644","https://openalex.org/W2055298722","https://openalex.org/W2056568233","https://openalex.org/W2057303159","https://openalex.org/W2062931377","https://openalex.org/W2063479108","https://openalex.org/W2068225247","https://openalex.org/W2071465766","https://openalex.org/W2075894544","https://openalex.org/W2076514478","https://openalex.org/W2078969200","https://openalex.org/W2079213755","https://openalex.org/W2082473664","https://openalex.org/W2083690910","https://openalex.org/W2084536447","https://openalex.org/W2086569686","https://openalex.org/W2090995971","https://openalex.org/W2092882875","https://openalex.org/W2094434786","https://openalex.org/W2095824228","https://openalex.org/W2097412226","https://openalex.org/W2099411299","https://openalex.org/W2099459260","https://openalex.org/W2101546326","https://openalex.org/W2101891826","https://openalex.org/W2104891575","https://openalex.org/W2104988583","https://openalex.org/W2105006906","https://openalex.org/W2108061158","https://openalex.org/W2108187446","https://openalex.org/W2108923274","https://openalex.org/W2109258478","https://openalex.org/W2111414304","https://openalex.org/W2114179999","https://openalex.org/W2117681388","https://openalex.org/W2121677860","https://openalex.org/W2123770356","https://openalex.org/W2125121305","https://openalex.org/W2126487146","https://openalex.org/W2126799735","https://openalex.org/W2127320825","https://openalex.org/W2127322768","https://openalex.org/W2127860913","https://openalex.org/W2129204745","https://openalex.org/W2129711736","https://openalex.org/W2131985618","https://openalex.org/W2132926880","https://openalex.org/W2134038527","https://openalex.org/W2134572315","https://openalex.org/W2135713257","https://openalex.org/W2138910980","https://openalex.org/W2140099453","https://openalex.org/W2142718629","https://openalex.org/W2144377499","https://openalex.org/W2144778969","https://openalex.org/W2145608399","https://openalex.org/W2147307434","https://openalex.org/W2148723086","https://openalex.org/W2149680071","https://openalex.org/W2150178057","https://openalex.org/W2150815933","https://openalex.org/W2152529266","https://openalex.org/W2153631698","https://openalex.org/W2153800802","https://openalex.org/W2155320525","https://openalex.org/W2157311267","https://openalex.org/W2157797619","https://openalex.org/W2159957100","https://openalex.org/W2160844444","https://openalex.org/W2163087581","https://openalex.org/W2163373465","https://openalex.org/W2163970999","https://openalex.org/W2164652663","https://openalex.org/W2165910410","https://openalex.org/W2168198916","https://openalex.org/W2169444195","https://openalex.org/W2170991287","https://openalex.org/W2332869178","https://openalex.org/W2477408078","https://openalex.org/W3143110774","https://openalex.org/W4205911826","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1578457637","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2135713257","https://openalex.org/W2057191541","https://openalex.org/W2057244434","https://openalex.org/W2624272545","https://openalex.org/W1966811458","https://openalex.org/W1972621850","https://openalex.org/W2992186163"],"abstract_inverted_index":{"Phylogenetic":[0],"analysis":[1],"is":[2,19,40,100],"used":[3],"to":[4,61,83],"recover":[5],"the":[6,59,84,89,96,101,138,149,152],"evolutionary":[7,25,86,125],"history":[8,34],"of":[9,22,43,88,95,104,118,124,129,140],"species,":[10],"genes":[11,60,92,112],"or":[12,91,113],"proteins.":[13],"Understanding":[14],"phylogenetic":[15,73,130],"relationships":[16,87,126],"between":[17],"organisms":[18],"a":[20,32],"prerequisite":[21],"almost":[23],"any":[24],"study,":[26],"as":[27],"contemporary":[28],"species":[29,90],"all":[30],"share":[31],"common":[33],"through":[35],"their":[36],"ancestry.":[37],"Moreover,":[38],"it":[39],"important":[41],"because":[42],"its":[44],"wide":[45],"applications":[46,128],"that":[47,78,143,154,162],"include":[48],"understanding":[49],"genome":[50],"organization,":[51],"epidemiological":[52],"investigations,":[53],"predicting":[54],"protein":[55],"functions,":[56],"and":[57,108,127,158],"deciding":[58],"be":[62],"analyzed":[63],"in":[64,70,146,151],"comparative":[65],"studies.":[66],"Despite":[67],"immense":[68],"progress":[69],"recent":[71],"years,":[72],"reconstruction":[74],"involves":[75],"many":[76],"challenges":[77],"create":[79],"uncertainty":[80],"with":[81,166],"respect":[82],"true":[85],"analyzed.":[93],"One":[94],"most":[97],"notable":[98],"difficulties":[99],"widespread":[102,119],"occurrence":[103],"incongruence":[105,120,145,164],"among":[106,110],"methods":[107],"also":[109],"individual":[111],"different":[114],"genomic":[115],"regions.":[116],"Presence":[117],"inhibits":[121],"successful":[122],"revealing":[123],"analysis.":[131],"In":[132],"this":[133],"article,":[134],"I":[135],"concisely":[136],"review":[137],"effect":[139],"various":[141],"factors":[142,161],"cause":[144,163],"molecular":[147],"phylogenies,":[148],"advances":[150],"field":[153],"resolved":[155],"some":[156],"factors,":[157],"explore":[159],"unresolved":[160],"along":[165],"possible":[167],"ways":[168],"for":[169],"tackling":[170],"them.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":27},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":25},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-24T08:23:43.765630","created_date":"2025-10-10T00:00:00"}
