{"id":"https://openalex.org/W7213626558","doi":"https://doi.org/10.64898/2026.09.17.752369","title":"Testing for Shared Molecular-Evolutionary Signatures of Diurnality and Nocturnality in Mammalian Circadian Clock Genes","display_name":"Testing for Shared Molecular-Evolutionary Signatures of Diurnality and Nocturnality in Mammalian Circadian Clock Genes","publication_year":2026,"publication_date":"2026-09-18","ids":{"openalex":"https://openalex.org/W7213626558","doi":"https://doi.org/10.64898/2026.09.17.752369"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.17.752369","doi":"https://doi.org/10.64898/2026.09.17.752369","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.17.752369","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.17.752369.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.17.752369.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093446959","display_name":"Alper Kaan Sel\u00e7uko\u011flu","orcid":"https://orcid.org/0009-0003-6480-0111","observed_orcids":["https://orcid.org/0009-0003-6480-0111"]},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Alper Kaan Sel\u00e7uko\u011flu","raw_affiliation_strings":["School of Medicine and Surgery, University of Padua, Padua, Italy"],"raw_orcid":"https://orcid.org/0009-0003-6480-0111","affiliations":[{"raw_affiliation_string":"School of Medicine and Surgery, University of Padua, Padua, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5140042121","display_name":"Ali Koray Ko\u00e7","orcid":"https://orcid.org/0009-0006-2488-1043","observed_orcids":["https://orcid.org/0009-0006-2488-1043"]},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ali Koray Ko\u00e7","raw_affiliation_strings":["Department of Molecular Biology and Genetics, Graduate School of Science and Engineering, Ko\u00e7 University, Istanbul, T\u00fcrkiye"],"raw_orcid":"https://orcid.org/0009-0006-2488-1043","affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Graduate School of Science and Engineering, Ko\u00e7 University, Istanbul, T\u00fcrkiye","institution_ids":["https://openalex.org/I1351752"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5093446959"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"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/T10342","display_name":"Circadian rhythm and melatonin","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2807","display_name":"Endocrine and Autonomic Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10342","display_name":"Circadian rhythm and melatonin","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2807","display_name":"Endocrine and Autonomic Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.0015999999595806003,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.00039999998989515007,"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/diurnal-activity","display_name":"diurnal activity","score":0.9160000085830688},{"id":"https://openalex.org/keywords/nocturnal-activity","display_name":"nocturnal activity","score":0.9980000257492065},{"id":"https://openalex.org/keywords/clock-genes","display_name":"clock genes","score":0.972000002861023},{"id":"https://openalex.org/keywords/circadian-clock","display_name":"circadian clock","score":0.5509999990463257},{"id":"https://openalex.org/keywords/cretaceous-paleogene-boundary","display_name":"Cretaceous-Paleogene boundary","score":0.6990000009536743},{"id":"https://openalex.org/keywords/selective-pressure","display_name":"selection pressure","score":0.3720000088214874},{"id":"https://openalex.org/keywords/evolutionary-rate-shifts","display_name":"evolutionary rate shifts","score":0.699999988079071}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7853999733924866},{"id":"https://openalex.org/C38606739","wikidata":"https://www.wikidata.org/wiki/Q5121352","display_name":"Circadian clock","level":3,"score":0.6726999878883362},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6678000092506409},{"id":"https://openalex.org/C62142553","wikidata":"https://www.wikidata.org/wiki/Q200312","display_name":"Convergent evolution","level":4,"score":0.6536999940872192},{"id":"https://openalex.org/C196662502","wikidata":"https://www.wikidata.org/wiki/Q827541","display_name":"Molecular clock","level":4,"score":0.5748999714851379},{"id":"https://openalex.org/C121446783","wikidata":"https://www.wikidata.org/wiki/Q208353","display_name":"Circadian rhythm","level":2,"score":0.5543000102043152},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4941999912261963},{"id":"https://openalex.org/C2777334680","wikidata":"https://www.wikidata.org/wiki/Q1607611","display_name":"Nocturnal","level":2,"score":0.4763999879360199},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.445499986410141},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43950000405311584},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.43130001425743103},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38420000672340393},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.3813000023365021},{"id":"https://openalex.org/C166393388","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Molecular evolution","level":4,"score":0.36469998955726624},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.32199999690055847},{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.3188999891281128},{"id":"https://openalex.org/C112212490","wikidata":"https://www.wikidata.org/wiki/Q471134","display_name":"Gene conversion","level":4,"score":0.31150001287460327},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.28029999136924744},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.2799000144004822},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.2773999869823456},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.2712000012397766},{"id":"https://openalex.org/C2909880533","wikidata":"https://www.wikidata.org/wiki/Q25420","display_name":"Lampyridae","level":3,"score":0.26759999990463257},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.25380000472068787},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.25040000677108765}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.17.752369","doi":"https://doi.org/10.64898/2026.09.17.752369","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.17.752369","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.17.752369.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.17.752369","doi":"https://doi.org/10.64898/2026.09.17.752369","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.17.752369","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.17.752369.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7213626558.pdf","grobid_xml":"https://content.openalex.org/works/W7213626558.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1964145455","https://openalex.org/W1974424793","https://openalex.org/W1992726958","https://openalex.org/W1995080247","https://openalex.org/W2020879271","https://openalex.org/W2028098940","https://openalex.org/W2029669485","https://openalex.org/W2036024950","https://openalex.org/W2046183549","https://openalex.org/W2061305437","https://openalex.org/W2076189890","https://openalex.org/W2110488158","https://openalex.org/W2113790044","https://openalex.org/W2114850508","https://openalex.org/W2115888213","https://openalex.org/W2123307680","https://openalex.org/W2163892779","https://openalex.org/W2277953252","https://openalex.org/W2567503091","https://openalex.org/W2614081736","https://openalex.org/W2791136402","https://openalex.org/W2809827064","https://openalex.org/W2883251903","https://openalex.org/W2914232633","https://openalex.org/W2948406132","https://openalex.org/W2950672567","https://openalex.org/W2950950814","https://openalex.org/W2951422792","https://openalex.org/W2970147901","https://openalex.org/W2991998196","https://openalex.org/W3021936614","https://openalex.org/W3035965352","https://openalex.org/W3093191500","https://openalex.org/W3110394251","https://openalex.org/W3136653930","https://openalex.org/W3208799931","https://openalex.org/W4316926647","https://openalex.org/W4385077611","https://openalex.org/W4390608966","https://openalex.org/W7131618380","https://openalex.org/W7160408120"],"related_works":["https://openalex.org/W2034098043","https://openalex.org/W4387013708","https://openalex.org/W2192367441","https://openalex.org/W2525788982","https://openalex.org/W2950672567","https://openalex.org/W4393308227","https://openalex.org/W4381857296","https://openalex.org/W1984188616","https://openalex.org/W7131618380","https://openalex.org/W4294991445"],"abstract_inverted_index":{"Abstract":[0],"Following":[1],"an":[2],"ancestral":[3],"nocturnal":[4,46],"phase,":[5],"diurnality":[6,53],"evolved":[7],"independently":[8],"in":[9,26,157,169,184],"multiple":[10],"mammalian":[11,170],"lineages":[12,129],"after":[13],"the":[14,27,105,185],"Cretaceous\u2013Palaeogene":[15],"boundary.":[16],"Whether":[17],"these":[18],"recurrent":[19],"temporal-niche":[20],"transitions":[21,168],"drove":[22],"convergent":[23,102],"molecular":[24,83],"evolution":[25],"circadian":[28,187],"oscillator":[29],"remains":[30],"largely":[31],"untested.":[32],"We":[33],"analyzed":[34],"18":[35],"core":[36,186],"clock":[37],"genes":[38],"and":[39,45,54,76,151],"direct":[40],"regulators":[41],"across":[42,127],"60":[43],"diurnal":[44],"mammals,":[47],"identifying":[48],"10":[49],"independent":[50],"gains":[51],"of":[52,123,180],"5":[55],"reversals":[56],"to":[57,114],"nocturnality":[58],"on":[59],"a":[60,177],"fixed":[61],"supertree":[62],"topology.":[63],"Using":[64],"six":[65],"complementary":[66],"evolutionary":[67,77,161],"frameworks":[68],"(spanning":[69],"substitution":[70],"counts,":[71],"profile":[72],"shifts,":[73],"selective":[74,158],"regimes,":[75],"rates)":[78],"we":[79,98],"tested":[80],"for":[81],"shared":[82,117],"adaptations.":[84],"To":[85],"ensure":[86],"that":[87,166],"our":[88],"negative":[89],"findings":[90],"reflected":[91],"biological":[92],"reality":[93],"rather":[94],"than":[95],"methodological":[96],"insensitivity,":[97],"planted":[99,125],"90":[100],"synthetic":[101],"residues":[103],"into":[104],"empirical":[106,133],"alignments.":[107],"While":[108],"this":[109],"benchmark":[110],"demonstrated":[111],"high":[112],"power":[113],"detect":[115],"broadly":[116],"convergence":[118,140],"(e.g.,":[119],"PCOC":[120],"recovered":[121],"35":[122],"36":[124],"sites":[126],"ten":[128],"without":[130],"false":[131],"positives),":[132],"alignments":[134],"showed":[135],"no":[136,152],"credible":[137],"signal.":[138],"Same-residue":[139],"occurred":[141],"at":[142],"expected":[143],"background":[144],"levels":[145],"(0.310":[146],"observed":[147],"vs.":[148],"0.337":[149],"null),":[150],"gene":[153],"displayed":[154],"activity-dependent":[155],"shifts":[156],"pressure":[159],"or":[160],"rate.":[162],"These":[163],"results":[164],"indicate":[165],"repeated":[167],"activity":[171],"patterns":[172],"were":[173],"not":[174],"driven":[175],"by":[176],"common":[178],"set":[179],"detectable":[181],"amino-acid":[182],"changes":[183],"machinery.":[188]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-20T00:00:00"}