{"id":"https://openalex.org/W7225734075","doi":"https://doi.org/10.3390/oceans7060094","title":"Leveraging Transcriptomic Data to Expand Mitogenome Knowledge and Phylogenetic Inference in Cartilaginous Fishes","display_name":"Leveraging Transcriptomic Data to Expand Mitogenome Knowledge and Phylogenetic Inference in Cartilaginous Fishes","publication_year":2026,"publication_date":"2026-11-10","ids":{"openalex":"https://openalex.org/W7225734075","doi":"https://doi.org/10.3390/oceans7060094"},"language":"en","primary_location":{"id":"doi:10.3390/oceans7060094","doi":"https://doi.org/10.3390/oceans7060094","is_oa":true,"landing_page_url":"https://doi.org/10.3390/oceans7060094","pdf_url":null,"source":{"id":"https://openalex.org/S4210240591","display_name":"Oceans","issn_l":"2673-1924","issn":["2673-1924"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Oceans","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3390/oceans7060094","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062204164","display_name":"Manuel J. Seixas","orcid":"https://orcid.org/0000-0001-5555-843X","observed_orcids":["https://orcid.org/0000-0001-5555-843X"]},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4387153601","display_name":"Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental","ror":"https://ror.org/05p7z7s64","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4387153601"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Manuel J. Seixas","raw_affiliation_strings":["CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, 4450-208 Porto, Portugal","Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, 4450-208 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4387153601"]},{"raw_affiliation_string":"Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088870719","display_name":"Luana Ramos","orcid":"https://orcid.org/0000-0002-9617-2741","observed_orcids":["https://orcid.org/0000-0002-9617-2741"]},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4387153601","display_name":"Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental","ror":"https://ror.org/05p7z7s64","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4387153601"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Luana Ramos","raw_affiliation_strings":["CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, 4450-208 Porto, Portugal","Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":"https://orcid.org/0000-0002-9617-2741","affiliations":[{"raw_affiliation_string":"CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, 4450-208 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4387153601"]},{"raw_affiliation_string":"Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078431100","display_name":"Rodrigo Rodrigues Domingues","orcid":"https://orcid.org/0000-0002-8979-645X","observed_orcids":["https://orcid.org/0000-0002-8979-645X"]},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4387153601","display_name":"Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental","ror":"https://ror.org/05p7z7s64","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4387153601"]},{"id":"https://openalex.org/I879563668","display_name":"Universidade Estadual Paulista (Unesp)","ror":"https://ror.org/00987cb86","country_code":"BR","type":"education","lineage":["https://openalex.org/I879563668"]}],"countries":["BR","PT"],"is_corresponding":false,"raw_author_name":"Rodrigo R. Domingues","raw_affiliation_strings":["Biological Science and Environmental Department, Bioscience Institute, S\u00e3o Paulo State University (UNESP), S\u00e3o Vicente 11330-900, SP, Brazil","CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, 4450-208 Porto, Portugal","Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Science and Environmental Department, Bioscience Institute, S\u00e3o Paulo State University (UNESP), S\u00e3o Vicente 11330-900, SP, Brazil","institution_ids":["https://openalex.org/I879563668"]},{"raw_affiliation_string":"CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, 4450-208 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4387153601"]},{"raw_affiliation_string":"Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017842519","display_name":"Agostinho Antunes","orcid":"https://orcid.org/0000-0002-1328-1732","observed_orcids":["https://orcid.org/0000-0002-1328-1732"]},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4387153601","display_name":"Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental","ror":"https://ror.org/05p7z7s64","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4387153601"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Agostinho Antunes","raw_affiliation_strings":["CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, 4450-208 Porto, Portugal","Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":"https://orcid.org/0000-0002-1328-1732","affiliations":[{"raw_affiliation_string":"CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, 4450-208 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4387153601"]},{"raw_affiliation_string":"Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1600,"currency":"CHF","value_usd":1930},"apc_paid":{"value":1600,"currency":"CHF","value_usd":1930},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":"6","first_page":"94","last_page":"94"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11387","display_name":"Ichthyology and Marine Biology","score":0.6484000086784363,"subfield":{"id":"https://openalex.org/subfields/2309","display_name":"Nature and Landscape Conservation"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11387","display_name":"Ichthyology and Marine Biology","score":0.6484000086784363,"subfield":{"id":"https://openalex.org/subfields/2309","display_name":"Nature and Landscape Conservation"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.28780001401901245,"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/T12319","display_name":"Fish Biology and Ecology Studies","score":0.029899999499320984,"subfield":{"id":"https://openalex.org/subfields/1104","display_name":"Aquatic Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7871999740600586},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.7432000041007996},{"id":"https://openalex.org/C162100973","wikidata":"https://www.wikidata.org/wiki/Q217743","display_name":"Polyphyly","level":5,"score":0.7289999723434448},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6886000037193298},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.664900004863739},{"id":"https://openalex.org/C24586158","wikidata":"https://www.wikidata.org/wiki/Q27075","display_name":"Mitochondrial DNA","level":3,"score":0.527400016784668},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.45750001072883606},{"id":"https://openalex.org/C160798450","wikidata":"https://www.wikidata.org/wiki/Q4230870","display_name":"Concordance","level":2,"score":0.450300008058548},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.39239999651908875},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.36579999327659607},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.3361000120639801},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.3239000141620636},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.32100000977516174},{"id":"https://openalex.org/C2993807623","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genetic data","level":3,"score":0.31459999084472656},{"id":"https://openalex.org/C41806617","wikidata":"https://www.wikidata.org/wiki/Q3516404","display_name":"Systematics","level":3,"score":0.3124000132083893},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.30550000071525574},{"id":"https://openalex.org/C33009525","wikidata":"https://www.wikidata.org/wiki/Q208841","display_name":"Coevolution","level":2,"score":0.29980000853538513},{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.2994999885559082},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2915000021457672},{"id":"https://openalex.org/C196662502","wikidata":"https://www.wikidata.org/wiki/Q827541","display_name":"Molecular clock","level":4,"score":0.2702000141143799},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.27000001072883606},{"id":"https://openalex.org/C2778961482","wikidata":"https://www.wikidata.org/wiki/Q25241","display_name":"Vertebrate","level":3,"score":0.26179999113082886},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2556000053882599}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3390/oceans7060094","doi":"https://doi.org/10.3390/oceans7060094","is_oa":true,"landing_page_url":"https://doi.org/10.3390/oceans7060094","pdf_url":null,"source":{"id":"https://openalex.org/S4210240591","display_name":"Oceans","issn_l":"2673-1924","issn":["2673-1924"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Oceans","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.3390/oceans7060094","doi":"https://doi.org/10.3390/oceans7060094","is_oa":true,"landing_page_url":"https://doi.org/10.3390/oceans7060094","pdf_url":null,"source":{"id":"https://openalex.org/S4210240591","display_name":"Oceans","issn_l":"2673-1924","issn":["2673-1924"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Oceans","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Despite":[0],"their":[1],"ecological":[2],"and":[3,60,81,129,142],"evolutionary":[4,138],"importance,":[5],"genetic":[6],"data":[7,20],"for":[8,33],"chondrichthyans":[9,141],"remains":[10],"scarce.":[11],"To":[12],"address":[13],"this,":[14],"we":[15],"assembled":[16],"mitogenomes":[17,47],"from":[18,36],"RNA-seq":[19],"of":[21,53,71,97,140,146],"eight":[22],"elasmobranchs,":[23],"including":[24],"Urobatis":[25],"jamaicensis,":[26],"representing":[27],"the":[28,64,77,88,95,109,137,144],"first":[29],"preliminary":[30],"mitogenome":[31],"assembly":[32],"Urotrygonidae":[34],"derived":[35],"transcriptomic":[37],"data.":[38],"We":[39],"integrated":[40],"these":[41],"sequences":[42],"with":[43],"230":[44],"publicly":[45],"available":[46],"to":[48],"form":[49],"a":[50,122],"final":[51],"dataset":[52],"238":[54],"taxa":[55],"(11":[56],"chimaeras,":[57],"109":[58],"batoids,":[59],"118":[61],"selachians),":[62],"generating":[63],"most":[65],"comprehensive":[66],"chondrichthyan":[67],"mitogenomic":[68],"phylogeny":[69,120],"as":[70,107],"May":[72],"2024.":[73],"Our":[74],"analyses":[75],"reinforced":[76],"fundamental":[78],"elasmobranch\u2013chimaera":[79],"split":[80],"resolved":[82],"key":[83],"taxonomic":[84],"conflicts:":[85],"they":[86],"supported":[87],"newly":[89],"proposed":[90],"family":[91],"Dichichthyidae":[92],"while":[93],"revealing":[94],"polyphyly":[96],"Odontaspididae.":[98],"Furthermore,":[99],"gene":[100],"concordance":[101,113],"factor":[102],"(gCF)":[103],"analysis":[104],"identified":[105],"ND5":[106],"exhibiting":[108],"highest":[110],"relative":[111],"topological":[112],"among":[114],"mitochondrial":[115,148],"genes.":[116],"Finally,":[117],"our":[118,134],"time-calibrated":[119],"demonstrated":[121],"temporal":[123],"correspondence":[124],"between":[125],"major":[126],"divergence":[127],"events":[128],"historical":[130],"mass":[131],"extinctions.":[132],"Overall,":[133],"findings":[135],"refine":[136],"framework":[139],"clarify":[143],"utility":[145],"individual":[147],"genes":[149],"in":[150],"phylogenetic":[151],"inference.":[152]},"counts_by_year":[],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2026-11-11T00:00:00"}