{"id":"https://openalex.org/W2098158317","doi":"https://doi.org/10.1162/106454604773563586","title":"Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods","display_name":"Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods","publication_year":2004,"publication_date":"2004-03-01","ids":{"openalex":"https://openalex.org/W2098158317","doi":"https://doi.org/10.1162/106454604773563586","mag":"2098158317","pmid":"https://pubmed.ncbi.nlm.nih.gov/15107228"},"language":"en","primary_location":{"id":"doi:10.1162/106454604773563586","is_oa":false,"landing_page_url":"https://doi.org/10.1162/106454604773563586","pdf_url":null,"source":{"id":"https://openalex.org/S2181302","display_name":"Artificial Life","issn_l":"1064-5462","issn":["1064-5462","1530-9185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718"],"host_organization_lineage_names":["The MIT Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Life","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090614477","display_name":"George I. Hagstrom","orcid":"https://orcid.org/0000-0002-2635-3723"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"George I. Hagstrom","raw_affiliation_strings":["California Institute of Technology, Pasadena, CA 91125"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"California Institute of Technology, Pasadena, CA 91125","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030744460","display_name":"Dehua Hang","orcid":null},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dehua H. Hang","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026353119","display_name":"Charles Ofria","orcid":"https://orcid.org/0000-0003-2924-1732"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles Ofria","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027040066","display_name":"Eric Torng","orcid":"https://orcid.org/0000-0002-1400-0840"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Torng","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.7255,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.73579872,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"10","issue":"2","first_page":"157","last_page":"166"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9970999956130981,"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":0.9922999739646912,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.793738842010498},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.6960452795028687},{"id":"https://openalex.org/keywords/natural-selection","display_name":"Natural selection","score":0.6144536733627319},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6073118448257446},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5946126580238342},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47663626074790955},{"id":"https://openalex.org/keywords/group-selection","display_name":"Group selection","score":0.4607663154602051},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.434799462556839},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39610719680786133},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3741567134857178},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27023831009864807},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23067206144332886},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09591957926750183}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.793738842010498},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.6960452795028687},{"id":"https://openalex.org/C75268714","wikidata":"https://www.wikidata.org/wiki/Q43478","display_name":"Natural selection","level":3,"score":0.6144536733627319},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6073118448257446},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5946126580238342},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47663626074790955},{"id":"https://openalex.org/C51520907","wikidata":"https://www.wikidata.org/wiki/Q874437","display_name":"Group selection","level":3,"score":0.4607663154602051},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.434799462556839},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39610719680786133},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3741567134857178},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27023831009864807},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23067206144332886},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09591957926750183},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1162/106454604773563586","is_oa":false,"landing_page_url":"https://doi.org/10.1162/106454604773563586","pdf_url":null,"source":{"id":"https://openalex.org/S2181302","display_name":"Artificial Life","issn_l":"1064-5462","issn":["1064-5462","1530-9185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718"],"host_organization_lineage_names":["The MIT Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Life","raw_type":"journal-article"},{"id":"pmid:15107228","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15107228","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":"Artificial life","raw_type":null},{"id":"pmh:oai:authors.library.caltech.edu:13452","is_oa":false,"landing_page_url":"https://authors.library.caltech.edu/13452/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402161","display_name":"CaltechAUTHORS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.562.7516","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.562.7516","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://authors.library.caltech.edu/13452/1/HAGal04.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4699999988079071,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1546639740","https://openalex.org/W1579352620","https://openalex.org/W1675572849","https://openalex.org/W2005946215","https://openalex.org/W2036097912","https://openalex.org/W2039592185","https://openalex.org/W2062342894","https://openalex.org/W2078347845","https://openalex.org/W2097706568","https://openalex.org/W2144386534","https://openalex.org/W2144669098","https://openalex.org/W2147276070","https://openalex.org/W2154284350","https://openalex.org/W2159830634","https://openalex.org/W3199943451","https://openalex.org/W3214380909","https://openalex.org/W4205911826","https://openalex.org/W4254987318"],"related_works":["https://openalex.org/W4251446701","https://openalex.org/W4254952213","https://openalex.org/W93658046","https://openalex.org/W2382542130","https://openalex.org/W2362218761","https://openalex.org/W2113708670","https://openalex.org/W2062354928","https://openalex.org/W2088120817","https://openalex.org/W2158340599","https://openalex.org/W2989909607"],"abstract_inverted_index":{"Phylogenetic":[0],"trees":[1,19],"group":[2],"organisms":[3,103],"by":[4],"their":[5],"ancestral":[6],"relationships.":[7],"There":[8],"are":[9,33,39,64],"a":[10,58],"number":[11],"of":[12,46,54,92],"distinct":[13],"algorithms":[14,63,123],"used":[15,41,80],"to":[16,42,56,76,88],"reconstruct":[17],"these":[18,122],"from":[20],"molecular":[21],"sequence":[22],"data,":[23],"but":[24],"different":[25],"methods":[26,111],"sometimes":[27],"give":[28],"conflicting":[29],"results.":[30],"Since":[31],"there":[32],"few":[34],"precisely":[35],"known":[36],"phylogenies,":[37],"simulations":[38,50],"typically":[40],"test":[43,77],"the":[44,62,67,86,90,102,110],"quality":[45],"reconstruction":[47,81],"algorithms.":[48],"These":[49],"randomly":[51],"evolve":[52],"strings":[53],"symbols":[55],"produce":[57],"tree,":[59],"and":[60],"then":[61],"run":[65],"with":[66],"tree":[68,96],"leaves":[69],"as":[70],"inputs.":[71],"Here":[72],"we":[73],"use":[74],"Avida":[75],"two":[78],"widely":[79],"methods,":[82],"which":[83],"gives":[84],"us":[85],"chance":[87],"observe":[89],"effect":[91],"natural":[93,105],"selection":[94,106,127],"on":[95,116],"reconstruction.":[97],"We":[98],"find":[99],"that":[100],"if":[101],"undergo":[104],"between":[107],"branch":[108],"points,":[109],"will":[112],"be":[113],"successful":[114],"even":[115],"very":[117],"large":[118],"time":[119],"scales.":[120],"However,":[121],"often":[124],"falter":[125],"when":[126],"is":[128],"absent.":[129]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}