{"id":"https://openalex.org/W2163199023","doi":"https://doi.org/10.1007/s00239-009-9267-9","title":"The Genetics of Adaptation for Eight Microvirid Bacteriophages","display_name":"The Genetics of Adaptation for Eight Microvirid Bacteriophages","publication_year":2009,"publication_date":"2009-08-19","ids":{"openalex":"https://openalex.org/W2163199023","doi":"https://doi.org/10.1007/s00239-009-9267-9","mag":"2163199023","pmid":"https://pubmed.ncbi.nlm.nih.gov/19693424","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2746890"},"language":"en","primary_location":{"id":"doi:10.1007/s00239-009-9267-9","doi":"https://doi.org/10.1007/s00239-009-9267-9","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00239-009-9267-9","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00239-009-9267-9.pdf","source":{"id":"https://openalex.org/S144184862","display_name":"Journal of Molecular Evolution","issn_l":"0022-2844","issn":["0022-2844","1432-1432"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Molecular Evolution","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s00239-009-9267-9.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089949345","display_name":"Darin R. Rokyta","orcid":"https://orcid.org/0000-0002-0356-2178","observed_orcids":["https://orcid.org/0000-0002-0356-2178"]},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Darin R. Rokyta","raw_affiliation_strings":["Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA","Department of Biological Sciences, University of Idaho, PO 443051, Moscow, ID, 83844-3051, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA","institution_ids":["https://openalex.org/I155093810"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho, PO 443051, Moscow, ID, 83844-3051, USA","institution_ids":["https://openalex.org/I155093810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004870248","display_name":"Zaid Abdo","orcid":"https://orcid.org/0000-0002-8272-7734","observed_orcids":["https://orcid.org/0000-0002-8272-7734"]},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zaid Abdo","raw_affiliation_strings":["Departments of Mathematics and Statistics, University of Idaho, Moscow, ID, USA","Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Mathematics and Statistics, University of Idaho, Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]},{"raw_affiliation_string":"Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054775452","display_name":"Holly A. Wichman","orcid":"https://orcid.org/0009-0007-0705-4465","observed_orcids":["https://orcid.org/0009-0007-0705-4465"]},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Holly A. Wichman","raw_affiliation_strings":["Department of Biological Sciences, University of Idaho, PO 443051, Moscow, ID, 83844-3051, USA","Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho, PO 443051, Moscow, ID, 83844-3051, USA","institution_ids":["https://openalex.org/I155093810"]},{"raw_affiliation_string":"Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054775452"],"corresponding_institution_ids":["https://openalex.org/I155093810"],"apc_list":{"value":4090,"currency":"USD","value_usd":4090},"apc_paid":{"value":4090,"currency":"USD","value_usd":4090},"fwci":3.2682,"has_fulltext":true,"cited_by_count":85,"citation_normalized_percentile":{"value":0.92327097,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"69","issue":"3","first_page":"229","last_page":"239"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":1.0,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":1.0,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10778","display_name":"Philosophy and History of Science","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1207","display_name":"History and Philosophy of Science"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/adaptive-evolution","display_name":"adaptive evolution","score":0.6940000057220459},{"id":"https://openalex.org/keywords/adaptive-walks","display_name":"adaptive walks","score":0.8349999785423279},{"id":"https://openalex.org/keywords/bacteriophage-phix174","display_name":"bacteriophage phiX174","score":0.7870000004768372},{"id":"https://openalex.org/keywords/microviridae","display_name":"Microviridae","score":0.9869999885559082},{"id":"https://openalex.org/keywords/parallel-evolution","display_name":"parallel evolution","score":0.7799999713897705},{"id":"https://openalex.org/keywords/fitness-improvement","display_name":"fitness improvement","score":0.5299999713897705},{"id":"https://openalex.org/keywords/long-term-adaptation","display_name":"long-term adaptation","score":0.6830000281333923}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9527373313903809},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.7715432643890381},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.639495313167572},{"id":"https://openalex.org/C87590526","wikidata":"https://www.wikidata.org/wiki/Q3592884","display_name":"Experimental evolution","level":3,"score":0.5757154226303101},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5599079132080078},{"id":"https://openalex.org/C167683757","wikidata":"https://www.wikidata.org/wiki/Q5937774","display_name":"Human evolutionary genetics","level":4,"score":0.44100522994995117},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33681488037109375},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.29252761602401733},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1838037073612213},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017914","descriptor_name":"Microviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017914","descriptor_name":"Microviridae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s00239-009-9267-9","doi":"https://doi.org/10.1007/s00239-009-9267-9","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00239-009-9267-9","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00239-009-9267-9.pdf","source":{"id":"https://openalex.org/S144184862","display_name":"Journal of Molecular Evolution","issn_l":"0022-2844","issn":["0022-2844","1432-1432"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Molecular Evolution","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2746890","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2746890","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Mol Evol","raw_type":"Text"},{"id":"pmid:19693424","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19693424","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":"Journal of molecular evolution","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1007/s00239-009-9267-9","doi":"https://doi.org/10.1007/s00239-009-9267-9","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00239-009-9267-9","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00239-009-9267-9.pdf","source":{"id":"https://openalex.org/S144184862","display_name":"Journal of Molecular Evolution","issn_l":"0022-2844","issn":["0022-2844","1432-1432"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Molecular Evolution","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3193252090","display_name":"Idaho INBRE Program","funder_award_id":"P20RR016454","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G4723518113","display_name":"Center for Research on Processes in Evolution","funder_award_id":"P20RR016448","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320319804","display_name":"Badan Riset dan Inovasi Nasional","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2163199023.pdf","grobid_xml":"https://content.openalex.org/works/W2163199023.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W130472221","https://openalex.org/W1480307447","https://openalex.org/W1576953632","https://openalex.org/W1857653616","https://openalex.org/W1913859964","https://openalex.org/W1964170829","https://openalex.org/W1967600116","https://openalex.org/W1969857637","https://openalex.org/W1983026914","https://openalex.org/W1988724016","https://openalex.org/W1992613346","https://openalex.org/W1993418368","https://openalex.org/W1995039292","https://openalex.org/W1996460711","https://openalex.org/W1998756227","https://openalex.org/W2003393395","https://openalex.org/W2004671976","https://openalex.org/W2004778468","https://openalex.org/W2004915469","https://openalex.org/W2005702974","https://openalex.org/W2006492954","https://openalex.org/W2011882432","https://openalex.org/W2012766690","https://openalex.org/W2017555968","https://openalex.org/W2022730625","https://openalex.org/W2023379882","https://openalex.org/W2036005222","https://openalex.org/W2053450368","https://openalex.org/W2054439085","https://openalex.org/W2057239104","https://openalex.org/W2062650320","https://openalex.org/W2064164319","https://openalex.org/W2068712558","https://openalex.org/W2077613383","https://openalex.org/W2078782530","https://openalex.org/W2086036641","https://openalex.org/W2087808706","https://openalex.org/W2090437685","https://openalex.org/W2099181962","https://openalex.org/W2105291362","https://openalex.org/W2106882534","https://openalex.org/W2110455575","https://openalex.org/W2111403860","https://openalex.org/W2112945902","https://openalex.org/W2116963188","https://openalex.org/W2117980283","https://openalex.org/W2122534488","https://openalex.org/W2123171772","https://openalex.org/W2124200870","https://openalex.org/W2126682991","https://openalex.org/W2128327734","https://openalex.org/W2130823594","https://openalex.org/W2132337479","https://openalex.org/W2134766930","https://openalex.org/W2142251166","https://openalex.org/W2142391696","https://openalex.org/W2143271868","https://openalex.org/W2152885981","https://openalex.org/W2161367161","https://openalex.org/W2161444534","https://openalex.org/W2161647617","https://openalex.org/W2165105171","https://openalex.org/W2166980082","https://openalex.org/W2168268382","https://openalex.org/W2169973249","https://openalex.org/W2174908239","https://openalex.org/W2295005065","https://openalex.org/W2499097944","https://openalex.org/W2994240441","https://openalex.org/W4241088457","https://openalex.org/W4245550089","https://openalex.org/W4246887724","https://openalex.org/W4285719527","https://openalex.org/W4388244982"],"related_works":["https://openalex.org/W1857653616","https://openalex.org/W2128327734","https://openalex.org/W2295005065","https://openalex.org/W2167653189","https://openalex.org/W2090437685","https://openalex.org/W2003393395","https://openalex.org/W2117980283","https://openalex.org/W2121998750","https://openalex.org/W2125836280","https://openalex.org/W7112892077"],"abstract_inverted_index":{"Theories":[0],"of":[1,39,68,75,91,102,125,156,168,177,201,211,220],"adaptive":[2,35,69,104,215],"molecular":[3],"evolution":[4,150],"have":[5,15],"recently":[6,72],"experienced":[7],"significant":[8,131],"expansion,":[9],"and":[10,13,110,139,217,230],"their":[11],"predictions":[12],"assumptions":[14],"begun":[16],"to":[17,20,51,86],"be":[18],"subjected":[19],"rigorous":[21],"empirical":[22,56,237],"testing.":[23],"However,":[24,135],"these":[25],"theories":[26],"focus":[27],"largely":[28],"on":[29,147],"predicting":[30],"the":[31,37,65,76,92,112,116,126,157,173,209,218],"first":[32],"event":[33],"in":[34,97,133,213],"evolution,":[36],"fixation":[38],"a":[40,100,130],"single":[41],"beneficial":[42],"mutation.":[43],"To":[44,62],"address":[45],"long-term":[46],"adaptation":[47,140,167,241],"it":[48],"is":[49],"necessary":[50],"include":[52],"new":[53],"assumptions,":[54],"but":[55,196,223],"data":[57],"are":[58],"needed":[59],"for":[60,99,239],"guidance.":[61],"empirically":[63],"characterize":[64],"general":[66],"properties":[67],"walks,":[70],"eight":[71,93],"isolated":[73],"relatives":[74],"single-stranded":[77],"DNA":[78],"(ssDNA)":[79],"bacteriophage":[80],"phiX174":[81],"(family":[82],"Microviridae)":[83],"were":[84,95,122],"adapted":[85,96],"identical":[87],"selective":[88],"conditions.":[89],"Three":[90],"genotypes":[94,195],"replicate,":[98],"total":[101],"11":[103,127],"walks.":[105],"We":[106],"measured":[107],"fitness":[108,136,221],"improvement":[109],"identified":[111],"genetic":[113],"changes":[114],"underlying":[115],"observed":[117],"adaptation.":[118],"Nearly":[119],"all":[120],"phages":[121],"evolvable;":[123],"nine":[124],"lineages":[128],"showed":[129],"increase":[132],"fitness.":[134,232],"plateaued":[137],"quickly,":[138],"was":[141,151,206,226],"achieved":[142],"through":[143,172],"only":[144],"three":[145],"substitutions":[146,212],"average.":[148],"Parallel":[149],"rampant,":[152],"both":[153],"across":[154,163,194,198],"replicates":[155,169],"same":[158,175],"genotype":[159],"as":[160,162],"well":[161],"different":[164],"genotypes,":[165],"yet":[166],"never":[170],"proceeded":[171],"exact":[174],"set":[176],"mutations.":[178],"Despite":[179],"this,":[180],"final":[181],"fitnesses":[182,190],"did":[183,191],"not":[184,197],"vary":[185,192],"significantly":[186,193],"among":[187],"replicates.":[188],"Final":[189],"phylogenetic":[199],"groupings":[200],"genotypes.":[202],"A":[203],"positive":[204],"correlation":[205,225],"found":[207,227],"between":[208,228],"number":[210],"an":[214,236],"walk":[216],"magnitude":[219],"improvement,":[222],"no":[224],"starting":[229],"ending":[231],"These":[233],"results":[234],"provide":[235],"framework":[238],"future":[240],"theory.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":6}],"updated_date":"2026-11-01T11:40:01.658920","created_date":"2016-06-24T00:00:00"}
