{"id":"https://openalex.org/W197156525","doi":null,"title":"The evolutionary analysis of the vertebrate two-round whole genome duplications","display_name":"The evolutionary analysis of the vertebrate two-round whole genome duplications","publication_year":2012,"publication_date":"2012-03-23","ids":{"openalex":"https://openalex.org/W197156525","mag":"197156525"},"language":"en","primary_location":{"id":"pmh:oai:ir.soken.ac.jp:00003149","doi":null,"is_oa":true,"landing_page_url":"https://ir.soken.ac.jp/records/3149","pdf_url":"https://ir.soken.ac.jp/record/3149/files/\u677e\u6ce2\u96c5\u4fca\uff08\u8ad6\u6587\u3001\u8981\u65e8\uff09.pdf","source":{"id":"https://openalex.org/S4306401394","display_name":"SOKENDAI (Graduate University for Advanced Studies)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I200475212","host_organization_name":"The Graduate University for Advanced Studies, SOKENDAI","host_organization_lineage":["https://openalex.org/I200475212"],"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":"thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://ir.soken.ac.jp/record/3149/files/\u677e\u6ce2\u96c5\u4fca\uff08\u8ad6\u6587\u3001\u8981\u65e8\uff09.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056383586","display_name":"\u96c5\u4fca \u677e\u6ce2","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"\u96c5\u4fca \u677e\u6ce2","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083958075","display_name":"\u30de\u30b5\u30c8\u30b7 \u30de\u30c4\u30ca\u30df","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"\u30de\u30b5\u30c8\u30b7 \u30de\u30c4\u30ca\u30df","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5070334771","display_name":"Masatoshi Matsunami","orcid":"https://orcid.org/0000-0003-4109-2493","observed_orcids":["https://orcid.org/0000-0003-4109-2493"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Masatoshi Matsunami","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-4109-2493","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9613999724388123,"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"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9613999724388123,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.014299999922513962,"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":0.013500000350177288,"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/vertebrate-evolution","display_name":"vertebrate evolution","score":0.9580000042915344},{"id":"https://openalex.org/keywords/conserved-non-coding-sequences","display_name":"conserved non-coding elements","score":0.8989999890327454},{"id":"https://openalex.org/keywords/hox-clusters","display_name":"Hox gene clusters","score":0.8510000109672546},{"id":"https://openalex.org/keywords/cis-regulatory-elements","display_name":"cis-regulatory elements","score":0.8270000219345093},{"id":"https://openalex.org/keywords/gene-regulatory-elements","display_name":"gene regulatory elements","score":0.597000002861023},{"id":"https://openalex.org/keywords/vertebrate-diversification","display_name":"vertebrate diversification","score":0.640999972820282}],"concepts":[{"id":"https://openalex.org/C2778961482","wikidata":"https://www.wikidata.org/wiki/Q25241","display_name":"Vertebrate","level":3,"score":0.6973783373832703},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5615794658660889},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5207414627075195},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5039064288139343},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4104241728782654},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3273715376853943},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17229992151260376}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:ir.soken.ac.jp:00003149","doi":null,"is_oa":true,"landing_page_url":"https://ir.soken.ac.jp/records/3149","pdf_url":"https://ir.soken.ac.jp/record/3149/files/\u677e\u6ce2\u96c5\u4fca\uff08\u8ad6\u6587\u3001\u8981\u65e8\uff09.pdf","source":{"id":"https://openalex.org/S4306401394","display_name":"SOKENDAI (Graduate University for Advanced Studies)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I200475212","host_organization_name":"The Graduate University for Advanced Studies, SOKENDAI","host_organization_lineage":["https://openalex.org/I200475212"],"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":"thesis"},{"id":"pmh:oai:irdb.nii.ac.jp:00947:0001442360","doi":null,"is_oa":true,"landing_page_url":"https://ir.soken.ac.jp/records/3149","pdf_url":"https://ir.soken.ac.jp/record/3149/files/%E6%9D%BE%E6%B3%A2%E9%9B%85%E4%BF%8A%EF%BC%88%E8%AB%96%E6%96%87%E3%80%81%E8%A6%81%E6%97%A8%EF%BC%89.pdf","source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"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":null,"raw_type":"thesis"},{"id":"mag:197156525","doi":null,"is_oa":false,"landing_page_url":"https://ir.soken.ac.jp/index.php?action=pages_view_main&active_action=repository_action_common_download&item_id=3149&item_no=1&attribute_id=19&file_no=1&page_id=29&block_id=155","pdf_url":null,"source":{"id":"https://openalex.org/S4306502617","display_name":"application/pdf","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":"other"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"application/pdf","raw_type":null}],"best_oa_location":{"id":"pmh:oai:ir.soken.ac.jp:00003149","doi":null,"is_oa":true,"landing_page_url":"https://ir.soken.ac.jp/records/3149","pdf_url":"https://ir.soken.ac.jp/record/3149/files/\u677e\u6ce2\u96c5\u4fca\uff08\u8ad6\u6587\u3001\u8981\u65e8\uff09.pdf","source":{"id":"https://openalex.org/S4306401394","display_name":"SOKENDAI (Graduate University for Advanced Studies)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I200475212","host_organization_name":"The Graduate University for Advanced Studies, SOKENDAI","host_organization_lineage":["https://openalex.org/I200475212"],"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":"thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W197156525.pdf","grobid_xml":"https://content.openalex.org/works/W197156525.grobid-xml"},"referenced_works_count":162,"referenced_works":["https://openalex.org/W29317256","https://openalex.org/W209659943","https://openalex.org/W585830581","https://openalex.org/W594174739","https://openalex.org/W599917843","https://openalex.org/W791550880","https://openalex.org/W1493919779","https://openalex.org/W1530022729","https://openalex.org/W1537144074","https://openalex.org/W1539836938","https://openalex.org/W1565800544","https://openalex.org/W1576915419","https://openalex.org/W1603219094","https://openalex.org/W1847545559","https://openalex.org/W1854399242","https://openalex.org/W1923477899","https://openalex.org/W1965178844","https://openalex.org/W1965403600","https://openalex.org/W1968577980","https://openalex.org/W1970007988","https://openalex.org/W1974367156","https://openalex.org/W1974430330","https://openalex.org/W1978896959","https://openalex.org/W1985348819","https://openalex.org/W1987331600","https://openalex.org/W1987414043","https://openalex.org/W1989681239","https://openalex.org/W1991170638","https://openalex.org/W1992140809","https://openalex.org/W1994615404","https://openalex.org/W1996760543","https://openalex.org/W1997340752","https://openalex.org/W1999960938","https://openalex.org/W2000947836","https://openalex.org/W2003953346","https://openalex.org/W2005350877","https://openalex.org/W2006788765","https://openalex.org/W2009851083","https://openalex.org/W2011647003","https://openalex.org/W2011925831","https://openalex.org/W2015633789","https://openalex.org/W2021987019","https://openalex.org/W2023635398","https://openalex.org/W2023653962","https://openalex.org/W2025425734","https://openalex.org/W2025665146","https://openalex.org/W2026665158","https://openalex.org/W2028037783","https://openalex.org/W2031112533","https://openalex.org/W2034193485","https://openalex.org/W2034718537","https://openalex.org/W2035174793","https://openalex.org/W2040308393","https://openalex.org/W2040636723","https://openalex.org/W2042673698","https://openalex.org/W2044718587","https://openalex.org/W2047405437","https://openalex.org/W2047483387","https://openalex.org/W2049896656","https://openalex.org/W2054755820","https://openalex.org/W2055298722","https://openalex.org/W2055666215","https://openalex.org/W2056169004","https://openalex.org/W2060842569","https://openalex.org/W2061008107","https://openalex.org/W2061507735","https://openalex.org/W2064473863","https://openalex.org/W2064627444","https://openalex.org/W2065375138","https://openalex.org/W2066519709","https://openalex.org/W2073442331","https://openalex.org/W2075746068","https://openalex.org/W2075895263","https://openalex.org/W2077615221","https://openalex.org/W2079868048","https://openalex.org/W2080200696","https://openalex.org/W2081850624","https://openalex.org/W2081933515","https://openalex.org/W2083895892","https://openalex.org/W2087878206","https://openalex.org/W2088316383","https://openalex.org/W2094746228","https://openalex.org/W2095005830","https://openalex.org/W2095186604","https://openalex.org/W2096860411","https://openalex.org/W2097205777","https://openalex.org/W2097706568","https://openalex.org/W2099934240","https://openalex.org/W2100152398","https://openalex.org/W2100703845","https://openalex.org/W2100990361","https://openalex.org/W2101581842","https://openalex.org/W2101723071","https://openalex.org/W2102208272","https://openalex.org/W2103087497","https://openalex.org/W2104152293","https://openalex.org/W2104383145","https://openalex.org/W2106882534","https://openalex.org/W2107449113","https://openalex.org/W2107545174","https://openalex.org/W2110335151","https://openalex.org/W2112555386","https://openalex.org/W2112765255","https://openalex.org/W2116236561","https://openalex.org/W2116251070","https://openalex.org/W2116847895","https://openalex.org/W2118526609","https://openalex.org/W2119822826","https://openalex.org/W2120868323","https://openalex.org/W2120960764","https://openalex.org/W2122368655","https://openalex.org/W2124341273","https://openalex.org/W2125013165","https://openalex.org/W2125125955","https://openalex.org/W2125539728","https://openalex.org/W2127677836","https://openalex.org/W2127774996","https://openalex.org/W2128114769","https://openalex.org/W2128983351","https://openalex.org/W2129509542","https://openalex.org/W2129532057","https://openalex.org/W2129765989","https://openalex.org/W2130128304","https://openalex.org/W2131871062","https://openalex.org/W2131918846","https://openalex.org/W2132632499","https://openalex.org/W2132955602","https://openalex.org/W2134033103","https://openalex.org/W2134797741","https://openalex.org/W2134910771","https://openalex.org/W2135123683","https://openalex.org/W2138477565","https://openalex.org/W2139391993","https://openalex.org/W2140463176","https://openalex.org/W2140628921","https://openalex.org/W2143228020","https://openalex.org/W2144893438","https://openalex.org/W2146810839","https://openalex.org/W2151659916","https://openalex.org/W2152075687","https://openalex.org/W2152545090","https://openalex.org/W2152876917","https://openalex.org/W2153646569","https://openalex.org/W2154035365","https://openalex.org/W2156392314","https://openalex.org/W2158714788","https://openalex.org/W2159433765","https://openalex.org/W2160969485","https://openalex.org/W2163892779","https://openalex.org/W2166212839","https://openalex.org/W2168253026","https://openalex.org/W2169236261","https://openalex.org/W2171498188","https://openalex.org/W2264544043","https://openalex.org/W2332066232","https://openalex.org/W2346628768","https://openalex.org/W2346870455","https://openalex.org/W3149996897","https://openalex.org/W4255893942","https://openalex.org/W4317676575","https://openalex.org/W6991233648","https://openalex.org/W7019119777"],"related_works":["https://openalex.org/W3004066512","https://openalex.org/W183718135","https://openalex.org/W7096830187","https://openalex.org/W2157245632","https://openalex.org/W2008956020","https://openalex.org/W2299837029","https://openalex.org/W2047405437","https://openalex.org/W6987922845","https://openalex.org/W3008714670","https://openalex.org/W7096630534"],"abstract_inverted_index":{"Two-rounds":[0],"whole":[1],"genome":[2,902,916,958],"duplications":[3,903,990,1048],"(2R":[4],"WGD)":[5],"occurred":[6,658,905,1062],"in":[7,60,99,226,237,356,368,410,517,525,612,766,819,919,1037,1041],"the":[8,29,35,39,61,67,100,107,123,163,169,203,216,231,238,258,319,332,357,402,411,422,435,438,484,526,530,550,605,651,660,663,668,682,685,692,732,743,747,767,777,793,813,820,847,852,856,860,898,907,911,920,929,992,995,1004,1008,1013,1023,1038,1045,1053],"vertebrate":[9,124,227,285,295,396,429,478,508,534,592,712],"ancestors,":[10],"and":[11,20,56,80,102,119,201,208,297,336,361,405,413,510,543,583,614,700,714,726,741,760,782,841,882,954,968,977,1012,1017,1044],"they":[12,521,640,826],"generated":[13,65,501],"large":[14],"numbers":[15],"of":[16,31,38,104,109,116,122,132,155,162,194,230,251,261,293,345,363,372,428,437,442,467,476,533,558,568,575,619,644,662,670,684,694,711,735,746,779,795,855,866,895,936,964,1047],"duplicated":[17,78],"protein-coding":[18,55,79,118,165],"genes":[19,166,178,236,475,492,512,536,1034],"their":[21,143],"regulatory":[22,82,134,157,183,247,387],"elements.":[23,158],"These":[24,380],"events":[25,881],"could":[26],"contribute":[27,649],"to":[28,76,91,138,142,189,212,472,625,650,829,846,850],"emergence":[30],"vertebrate-specific":[32],"features.":[33],"However,":[34,264,450,675,872],"evolutionary":[36,85],"impact":[37],"2R":[40,68,170,217,232,423,439,656,686,748,857,1060],"WGD":[41,171,657,687,749,1061],"is":[42,210,554,623,677,688,706],"still":[43,274],"unclear.":[44],"To":[45,702],"address":[46],"this":[47,110,279,369,457,704],"issue,":[48],"I":[49,112,281,288,303,324,393,460,482,562,594,730,799,810,837,874,926,960,1002,1056],"conducted":[50],"comprehensive":[51],"studies":[52,255,453],"on":[53,114,807,833],"both":[54,117,904],"non-coding":[57,120,148],"sequences":[58,121,149,633,734,844,917],"found":[59,298,325,367,406,1018],"conserved":[62,71,140,147,301,310,330,341,587],"synteny":[63,72,577],"blocks":[64,73,93],"by":[66,493,502,539,627,750,785,940],"WGD.":[69,218,233,424,858],"Such":[70],"are":[74,136,273,329,340,382,432,602,720,870],"expected":[75,137],"retain":[77,416],"gene":[81,133,156,181,207,271,385,444,646,718,862,868,932,966],"sequences.":[83],"Consequently,":[84],"changes":[86],"or":[87,220,690],"some":[88,451],"constraints":[89],"relating":[90],"these":[92,252,269,373,620,632,834,942],"would":[94],"have":[95,187,513,634,883],"played":[96],"important":[97,211,708],"roles":[98],"evolution":[101,115,214,713],"diversification":[103,669],"vertebrates.":[105],"On":[106],"basis":[108],"view,":[111],"focused":[113],"genomes,":[125],"especially":[126],"Hox":[127,223,239,262,286,291,322,348,359,391,403,430,443,469,479,491,496,519,535,559],"clusters.":[128,287,323,349,392,981],"Because":[129,507,631],"a":[130,377,447],"part":[131],"elements":[135,266],"be":[139,152,642],"according":[141],"functional":[144],"importance,":[145],"evolutionarily":[146],"(CNSs)":[150],"might":[151,179,641],"good":[153],"candidates":[154,383],"In":[159,350],"addition,":[160],"portion":[161],"paralogous":[164,177,199,206,222,235,270,321,347,358,390,569,585,598,621,645,842],"retained":[167],"after":[168,215,659,691,1052],"show":[172,241,446],"overlapping":[173,191],"expression":[174,182,192,243,250,259,272,386,611,647],"pattern.":[175],"Therefore,":[176],"share":[180],"mechanisms.":[184],"Paralogous":[185],"CNSs":[186,200,209,283,307,353,381,397,400,409,420,582,586,622],"possibility":[188,930],"control":[190,268],"patterns":[193],"those":[195],"paralogs.":[196,654],"Thus,":[197,729],"detecting":[198],"inferring":[202],"relation":[204],"between":[205,313,342,653],"understand":[213],"Four":[219],"more":[221],"clusters":[224,240,292,315,335,415,431],"exist":[225],"genomes":[228],"because":[229],"The":[234,425,617,655,716,769,892],"similar":[242],"patterns,":[244],"implying":[245],"shared":[246],"mechanisms":[248,260],"for":[249,306,384,709,723],"genes.":[253,263,470,497,925],"Previous":[254],"partly":[256],"revealed":[257,579],"cis-regulatory":[265],"that":[267,308,328,339,407,549,900,931,1019,1032,1059],"poorly":[275],"understood.":[276],"Toward":[277],"solving":[278],"problem,":[280],"searched":[282,305],"within":[284,401],"compared":[289,395,1003],"orthologous":[290,314,581,840],"19":[294],"species,":[296],"208":[299],"intergenic":[300,343],"regions.":[302],"then":[304,563],"were":[309,354,365,500,522,537,774,783,827,890,970,1035],"not":[311,455],"only":[312,887],"but":[316,666],"also":[317,394,721,811,927],"among":[318,331,389,488,588],"four":[320,334],"three":[326],"regions":[327,338,344,375,388,609],"all":[333],"eight":[337],"two":[346,408,879,901,978,989],"total,":[351],"28":[352],"identified":[355],"clusters,":[360],"nine":[362],"them":[364,896],"newly":[366,595,752,943],"study.":[370],"One":[371],"novel":[374],"bears":[376],"RARE":[378],"motif.":[379],"with":[398,418,803,951,973],"amphioxus":[399,419,503,518,527],"cluster,":[404],"HoxA":[412],"HoxB":[414],"homology":[417],"through":[421],"duplication":[426,531,629,880],"histories":[427,532],"controversial.":[433],"Under":[434],"assumption":[436],"WGD,":[440],"phylogenies":[441],"should":[445],"symmetrical":[448,458],"topology.":[449,459],"previous":[452,628],"did":[454],"support":[456],"thus":[461,1057],"carried":[462,564],"out":[463,565],"exhaustive":[464],"phylogenetic":[465,541,544,864,962],"analysis":[466,547],"deuterostome":[468,489],"First,":[471],"identify":[473],"outgroup":[474],"each":[477,576],"paralog":[480],"group,":[481],"inferred":[483,538],"correct":[485],"ortholog/paralog":[486,938],"relationships":[487,939],"posterior":[490],"comparing":[494],"available":[495],"Amphioxus":[498],"Hox9-11":[499],"specific":[504],"tandem":[505],"duplications.":[506,561],"Hox10-12,":[509],"Hox14-15":[511],"no":[514,678],"counter":[515],"parts":[516],"genes,":[520],"probably":[523],"lost":[524,1036],"lineage.":[528],"Secondly,":[529],"constructing":[540],"trees":[542,865,876,889,963,972,984,998,1021],"networks.":[545],"My":[546],"suggested":[548],"((A,B),":[551],"(C,D))":[552],"topology":[553,986,1000],"most":[555],"suitable":[556],"explanation":[557],"cluster":[560],"genome-wide":[566],"identification":[567],"CNSs.":[570,599],"A":[571],"sensitive":[572],"BLAST":[573],"search":[574],"block":[578],"7,924":[580],"309":[584],"8":[589],"high":[590,884],"quality":[591],"genomes.":[593],"detected":[596],"194":[597],"Their":[600],"locations":[601],"biased":[603],"nearby":[604],"transcription":[606,636],"factors":[607],"coding":[608],"shown":[610],"brain":[613],"neural":[615],"system.":[616,791],"existence":[618],"difficult":[624],"explain":[626],"models.":[630],"same":[635],"factor":[637],"binding":[638],"motifs,":[639],"backup":[643],"and/or":[648],"interaction":[652],"split":[661,693],"urochordate":[664],"ancestors":[665],"before":[667,689,906,991,1063],"extant":[671],"gnathostomes":[672,953,979],"(jawed":[673],"vertebrates).":[674],"there":[676,969],"clear":[679],"evidence":[680],"whether":[681],"timing":[683,745,854],"agnathans":[695],"(jawless":[696],"vertebrates":[697],"including":[698,923],"lamprey)":[699],"gnathostomes.":[701],"clarify":[703],"problem":[705],"highly":[707],"study":[710],"development.":[715],"lamprey":[717,738,759,762,772,815,835,848,908,913,946,1039],"data":[719,755,765,818],"useful":[722],"molecular":[724],"function":[725],"developmental":[727],"studies.":[728],"analyzed":[731,812,838],"mRNA":[733,816],"Japanese":[736,757,770],"brook":[737,758,771],"(Lethenteron":[739],"reissneri)":[740],"estimated":[742],"relative":[744,853],"combining":[751],"obtained":[753,800],"sequence":[754,797],"from":[756,776],"sea":[761,814,912,945],"(Petromyzon":[763,914],"marinus)":[764,915],"database.":[768,822],"cDNAs":[773],"synthesized":[775],"mRNAs":[778],"ammocoetes":[780],"larva":[781],"sequenced":[784],"Roche":[786],"454":[787],"GS":[788],"FLX":[789],"titanium":[790],"After":[792],"assembly":[794],"426,476":[796],"reads,":[798,825],"7,708":[801],"contigs":[802,849],"336":[804],"bp":[805],"length":[806],"average.":[808],"Additionally,":[809],"sequencing":[817],"SRA":[821],"Including":[823],"119,412,170":[824],"assembled":[828],"78,947":[830],"contigs.":[831],"Based":[832],"data,":[836,947],"putative":[839],"gnathostome":[843],"corresponding":[845],"estimate":[851],"From":[859],"homologous":[861],"clustering,":[863],"358":[867],"families":[869],"reconstructed.":[871],"if":[873],"restrict":[875],"which":[877],"contain":[878],"statistical":[885],"supports,":[886],"55":[888],"left.":[891],"majority":[893],"(49)":[894],"showed":[897,985],"pattern":[899],"divergence":[909],"Recently,":[910],"appeared":[918],"public":[921],"database":[922],"11,429":[924],"investigated":[928],"losses":[933],"caused":[934],"misunderstanding":[935],"true":[937],"using":[941],"released":[944],"as":[948,950],"well":[949],"13":[952],"6":[955],"nonvertebrate":[956],"species":[957],"data.":[959],"reconstructed":[961],"545":[965],"families,":[967],"127":[971],"one":[974],"agnathan":[975,1033],"(A)":[976],"(G)":[980],"Although":[982],"69":[983],"((A,G),G)":[987],"suggesting":[988],"agnathans/gnathostomes":[993,1054,1064],"divergence,":[994],"remaining":[996],"58":[997],"had":[999,1022],"((G,G),A).":[1001],"branch":[1005,1026],"lengths":[1006],"connecting":[1007],"gnathan":[1009],"common":[1010,1015],"ancestor":[1011],"agnathan/gnathostomes":[1014],"ancestor,":[1016],"((G,G),A)-topology":[1020,1042],"significantly":[1024],"longer":[1025],"than":[1027],"((A,G),G)-topology":[1028],"trees.":[1029],"This":[1030],"suggests":[1031],"lineage":[1040],"trees,":[1043],"occurrence":[1046],"erroneously":[1049],"looked":[1050],"like":[1051],"divergence.":[1055,1065],"conclude":[1058]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
