{"id":"https://openalex.org/W2193843371","doi":null,"title":"Genes and Ecology: Accelerated Rates of Replacement Substitutions in the Cytochrome b Gene of Subterranean Rodents","display_name":"Genes and Ecology: Accelerated Rates of Replacement Substitutions in the Cytochrome b Gene of Subterranean Rodents","publication_year":2009,"publication_date":"2009-07-28","ids":{"openalex":"https://openalex.org/W2193843371","mag":"2193843371"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.712.2829","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.712.2829","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://globins.bch.msstate.edu/pubs/DaSilva_et_al_OpenEvol_2009.pdf","raw_type":"text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://benthamopen.com/ABSTRACT/TOEVOLJ-3-17","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018076301","display_name":"Cecilia C. Da Silva","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cecilia C. Da Silva","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008702194","display_name":"Ivanna H. Tomasco","orcid":"https://orcid.org/0000-0002-8288-8618","observed_orcids":["https://orcid.org/0000-0002-8288-8618"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ivanna H. Tomasco","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-8288-8618","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013599203","display_name":"Federico G. Hoffmann","orcid":"https://orcid.org/0000-0001-5056-4929","observed_orcids":["https://orcid.org/0000-0001-5056-4929"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Federico G. Hoffmann","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-5056-4929","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5017664200","display_name":"Enrique Pablo Lessa","orcid":"https://orcid.org/0000-0001-9750-4093","observed_orcids":["https://orcid.org/0000-0001-9750-4093"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Enrique P. Lessa","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-9750-4093","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.7895,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.67581837,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"3","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11926","display_name":"Subterranean biodiversity and taxonomy","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11926","display_name":"Subterranean biodiversity and taxonomy","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.016100000590085983,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.010099999606609344,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cytochrome-b","display_name":"cytochrome b","score":0.8429999947547913},{"id":"https://openalex.org/keywords/subterranean-rodents","display_name":"subterranean rodents","score":0.9380000233650208},{"id":"https://openalex.org/keywords/ctenomys","display_name":"Ctenomys","score":0.8429999947547913},{"id":"https://openalex.org/keywords/pocket-gophers","display_name":"pocket gophers","score":0.9160000085830688},{"id":"https://openalex.org/keywords/bathyergidae","display_name":"Bathyergidae","score":0.9860000014305115},{"id":"https://openalex.org/keywords/mole-rats","display_name":"mole rats","score":0.8429999947547913},{"id":"https://openalex.org/keywords/tuco-tuco","display_name":"tuco-tuco","score":0.7279999852180481},{"id":"https://openalex.org/keywords/positive-selection","display_name":"positive selection","score":0.7559999823570251},{"id":"https://openalex.org/keywords/dn-ds-ratio","display_name":"dN/dS ratio","score":0.7720000147819519},{"id":"https://openalex.org/keywords/oxidative-phosphorylation","display_name":"oxidative phosphorylation","score":0.8299999833106995},{"id":"https://openalex.org/keywords/hypoxia","display_name":"hypoxia","score":0.9340000152587891},{"id":"https://openalex.org/keywords/niche-shift","display_name":"niche shift","score":0.7179999947547913},{"id":"https://openalex.org/keywords/physicochemical-properties-of-amino-acids","display_name":"amino acid physicochemical properties","score":0.734000027179718},{"id":"https://openalex.org/keywords/molecular-adaptation","display_name":"molecular adaptation","score":0.37400001287460327}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8679522275924683},{"id":"https://openalex.org/C149904235","wikidata":"https://www.wikidata.org/wiki/Q7049620","display_name":"Nonsynonymous substitution","level":4,"score":0.8499174118041992},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6453980207443237},{"id":"https://openalex.org/C157369684","wikidata":"https://www.wikidata.org/wiki/Q34740","display_name":"Genus","level":2,"score":0.4657707214355469},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4608994722366333},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.4608219861984253},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.4527395963668823},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.44118013978004456},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4381488561630249},{"id":"https://openalex.org/C75268714","wikidata":"https://www.wikidata.org/wiki/Q43478","display_name":"Natural selection","level":3,"score":0.42805197834968567},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.4100008010864258},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.40681618452072144},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.40666913986206055},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.38829609751701355},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12913566827774048},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.07466462254524231},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.712.2829","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.712.2829","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://globins.bch.msstate.edu/pubs/DaSilva_et_al_OpenEvol_2009.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.911.9985","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.911.9985","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://benthamopen.com/contents/pdf/TOEVOLJ/TOEVOLJ-3-17.pdf","raw_type":"text"},{"id":"mag:2193843371","doi":null,"is_oa":true,"landing_page_url":"https://benthamopen.com/ABSTRACT/TOEVOLJ-3-17","pdf_url":null,"source":{"id":"https://openalex.org/S85818921","display_name":"The Open Evolution Journal","issn_l":"1874-4044","issn":["1874-4044"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":"https://openalex.org/P4310320079","host_organization_name":"Bentham Science Publishers","host_organization_lineage":["https://openalex.org/P4310320079"],"host_organization_lineage_names":["Bentham Science Publishers"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"The Open Evolution Journal","raw_type":null}],"best_oa_location":{"id":"mag:2193843371","doi":null,"is_oa":true,"landing_page_url":"https://benthamopen.com/ABSTRACT/TOEVOLJ-3-17","pdf_url":null,"source":{"id":"https://openalex.org/S85818921","display_name":"The Open Evolution Journal","issn_l":"1874-4044","issn":["1874-4044"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":"https://openalex.org/P4310320079","host_organization_name":"Bentham Science Publishers","host_organization_lineage":["https://openalex.org/P4310320079"],"host_organization_lineage_names":["Bentham Science Publishers"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"The Open Evolution Journal","raw_type":null},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W791550880","https://openalex.org/W1576953632","https://openalex.org/W1964343732","https://openalex.org/W1967536299","https://openalex.org/W1967733222","https://openalex.org/W1979999628","https://openalex.org/W1984999127","https://openalex.org/W1999402715","https://openalex.org/W2002446259","https://openalex.org/W2002854942","https://openalex.org/W2003734490","https://openalex.org/W2006786379","https://openalex.org/W2010142973","https://openalex.org/W2010279801","https://openalex.org/W2022165859","https://openalex.org/W2026583344","https://openalex.org/W2029353325","https://openalex.org/W2029549914","https://openalex.org/W2029996282","https://openalex.org/W2032725566","https://openalex.org/W2035265126","https://openalex.org/W2042601802","https://openalex.org/W2067207399","https://openalex.org/W2074097929","https://openalex.org/W2079167667","https://openalex.org/W2096390810","https://openalex.org/W2097977090","https://openalex.org/W2114828923","https://openalex.org/W2116111392","https://openalex.org/W2119811919","https://openalex.org/W2133585817","https://openalex.org/W2137426528","https://openalex.org/W2138883346","https://openalex.org/W2144368480","https://openalex.org/W2145032210","https://openalex.org/W2152076818","https://openalex.org/W2153110078","https://openalex.org/W2161444534","https://openalex.org/W2170565120","https://openalex.org/W2179885821","https://openalex.org/W2180985785","https://openalex.org/W2276777345","https://openalex.org/W2283151919","https://openalex.org/W2290183901","https://openalex.org/W2319958421","https://openalex.org/W2330854702","https://openalex.org/W2332913093","https://openalex.org/W2493619585","https://openalex.org/W4388325051"],"related_works":["https://openalex.org/W7099162459","https://openalex.org/W1983732539","https://openalex.org/W2052548833","https://openalex.org/W3163560856","https://openalex.org/W3116728564","https://openalex.org/W2888141452","https://openalex.org/W2737991191","https://openalex.org/W1979999628","https://openalex.org/W2201033899","https://openalex.org/W2804363522"],"abstract_inverted_index":{"Abstract:":[0],"South":[1],"American":[2,12],"tuco-tucos":[3],"(genus":[4,9],"Ctenomys)":[5],"and":[6,17,82,88,97,142,165,198,209],"related":[7],"coruros":[8],"Spalacopus),":[10],"North":[11],"pocket":[13],"gophers":[14],"(family":[15,21],"Geomyidae),":[16],"African":[18],"mole":[19,140],"rats":[20,141],"Bathyergidae)":[22],"are":[23,193],"lineages":[24,81],"of":[25,43,52,67,94,110,168],"rodents":[26],"that":[27,54,124,137],"colonized":[28],"the":[29,39,44,49,64,68,111,157,169,206],"sub-terranean":[30],"niche":[31,210],"independently.":[32],"An":[33],"energetically":[34],"demanding":[35],"lifestyle,":[36],"coupled":[37],"with":[38,114,195],"hypoxic":[40],"atmosphere":[41],"characteristic":[42],"subterranean":[45,112,139,178,184],"environment":[46],"may":[47,151],"change":[48],"selective":[50],"regime":[51],"genes":[53],"encode":[55],"proteins":[56],"involved":[57],"in":[58,76,79,108,156,177],"cellular":[59],"respi-ration.":[60],"Here,":[61],"we":[62,91,135],"examined":[63],"molecular":[65,207],"evolution":[66],"cytochome":[69,158],"b":[70,159],"gene,":[71],"a":[72,103,200],"mitochondrially-encoded":[73],"gene":[74,160],"participating":[75],"oxidative":[77],"phosphorylation,":[78],"these":[80,190],"their":[83,117,162],"above-ground":[84],"relatives.":[85],"Using":[86,120],"maximum-likelihood":[87],"Bayesian":[89],"approaches,":[90],"estimated":[92],"rates":[93],"synonymous":[95],"(dS)":[96],"nonsynonymous":[98],"(dN)":[99],"substitutions.":[100],"We":[101],"found":[102,136],"significantly":[104],"higher":[105],"ratio":[106],"(dN/dS)":[107],"each":[109,196],"groups":[113],"respect":[115],"to":[116,172],"non-subterranean":[118,163],"counterparts.":[119],"an":[121],"al-ternative":[122],"procedure":[123],"tests":[125],"for":[126],"positive":[127,154],"selection":[128,155,175,204],"on":[129],"quantitative":[130],"physicochemical":[131],"amino":[132,148],"acid":[133,149],"properties,":[134],"i)":[138],"tucu-tucus":[143],"showed":[144],"more":[145],"sites":[146,170],"whose":[147],"properties":[150],"be":[152,173],"under":[153,174],"than":[161],"relatives,":[164],"ii)":[166],"some":[167],"identified":[171],"ex-clusively":[176],"taxa":[179],"were":[180],"shared":[181],"among":[182],"all":[183],"taxa.":[185],"The":[186],"results":[187],"given":[188],"by":[189],"two":[191],"approaches":[192],"consistent":[194],"other":[197],"suggest":[199],"link":[201],"between":[202],"directional":[203],"at":[205],"level":[208],"shift.":[211]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2016-06-24T00:00:00"}
