{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T01:33:34Z","timestamp":1790300014194,"version":"4.1.0"},"reference-count":91,"publisher":"Wiley","issue":"17","license":[{"start":{"date-parts":[[2021,7,10]],"date-time":"2021-07-10T00:00:00Z","timestamp":1625875200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology"],"published-print":{"date-parts":[[2021,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus <jats:italic>Sebastes<\/jats:italic>) providing a potentially informative study system. <jats:italic>Sebastes<\/jats:italic> rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation\u2010driving adaptations, particularly along a depth gradient. A reduced\u2010representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six <jats:italic>Sebastes<\/jats:italic> species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of <jats:italic>S. chrysomelas<\/jats:italic> (black\u2010and\u2010yellow rockfish) and <jats:italic>S. carnatus<\/jats:italic> (gopher rockfish) <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub> values revealed three major regions of elevated genomic divergence, two of which were also present in the <jats:italic>S. miniatus<\/jats:italic> (vermilion rockfish) and <jats:italic>S. crocotulus<\/jats:italic> (sunset rockfish) comparison. These corresponded with regions of both elevated <jats:italic>D<\/jats:italic><jats:sub>XY<\/jats:sub> values and reduced nucleotide diversity in two cases, suggesting a speciation\u2010with\u2010gene\u2010flow evolutionary model followed by post\u2010speciation selective sweeps within each species. Limited whole\u2010genome resequencing was also performed to identify mutations with predicted effects between <jats:italic>S. chrysomelas<\/jats:italic> and <jats:italic>S. carnatus<\/jats:italic>. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports their potential role in speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how <jats:italic>S. chrysomelas<\/jats:italic> and <jats:italic>S. carnatus<\/jats:italic> may have become reproductively isolated.<\/jats:p>","DOI":"10.1111\/mec.16046","type":"journal-article","created":{"date-parts":[[2021,6,28]],"date-time":"2021-06-28T18:01:15Z","timestamp":1624903275000},"page":"4259-4275","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Regions of genetic divergence in depth\u2010separated <i>Sebastes<\/i> rockfish species pairs: Depth as a potential driver of speciation"],"prefix":"10.1111","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1895-3523","authenticated-orcid":false,"given":"Kristen A.","family":"Behrens","sequence":"first","affiliation":[{"name":"Department of Biology Juniata College Huntingdon Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quinn L.","family":"Girasek","sequence":"additional","affiliation":[{"name":"Department of Biology Juniata College Huntingdon Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Sickler","sequence":"additional","affiliation":[{"name":"Center for Data Driven Discovery in Biomedicine Children's Hospital of Philadelphia Philadelphia Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Hyde","sequence":"additional","affiliation":[{"name":"Fisheries Resources Division Southwest Fisheries Science Center NOAA Fisheries La Jolla California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent P.","family":"Buonaccorsi","sequence":"additional","affiliation":[{"name":"Department of Biology Juniata College Huntingdon Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,7,10]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ceb.2007.09.010"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030523"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/ddrr.1113"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2011.05119.x"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pharmthera.2012.07.010"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00227-008-0963-6"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003940"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.semcdb.2020.04.015"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12354"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0169-5347(00)88957-0"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.5670\/oceanog.2018.201"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2008.10.010"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12796"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13312"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.01.013"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558-5646.2009.00736.x"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002899"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1111\/jeb.13756"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2012.03.009"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558-5646.2009.00943.x"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13594"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-11-643"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.212522.116"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13034"},{"issue":"8","key":"e_1_2_9_27_1","first-page":"1","article-title":"Better prediction of functional effects for sequence variants From VarI\u2010SIG 2014: Identification and annotation of genetic variants in the context of structure, function and disease","volume":"16","author":"Hecht M.","year":"2016","journal-title":"BMC Genomics"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.2307\/1444084"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esy070"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15605"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000862"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.200910095"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mce.2016.01.018"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2007.03653.x"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2006.12.026"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2010.1127"},{"issue":"1","key":"e_1_2_9_37_1","article-title":"Genetics and evidence for balancing selection of a sex\u2010linked colour polymorphism in a songbird","volume":"10","author":"Kim K. W.","year":"2019","journal-title":"Nature Communications"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.129684.111"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12387"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.2307\/1942480"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1242\/jeb.201.2.165"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1124\/jpet.111.184671"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1152\/ajprenal.00029.2004"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1175\/1520-0485(2002)032<2171:TISRTW>2.0.CO;2"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1713288114"},{"key":"e_1_2_9_48_1","volume-title":"Randomization, bootstrap and Monte Carlo methods in biology","author":"Manly B. F.","year":"2006"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0277-3791(00)00113-X"},{"key":"e_1_2_9_50_1","doi-asserted-by":"publisher","DOI":"10.1643\/CG-02-061R2"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2006.02908.x"},{"key":"e_1_2_9_52_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.76.10.5269"},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-pharmtox-010617-052713"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.1152\/physrev.00025.2013"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncb3028"},{"key":"e_1_2_9_56_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07750-5"},{"key":"e_1_2_9_57_1","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2011.0263"},{"key":"e_1_2_9_58_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2008.10.011"},{"key":"e_1_2_9_59_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.18.7.4324"},{"issue":"2","key":"e_1_2_9_60_1","first-page":"328","article-title":"The dusky rockfishes (Teleostei: Socrpaeniformes) of the North Pacific Ocean: resurrection of Sebastes variabilis (Pallas, 1814) and a redescription of Sebastes ciliatus (Tilesius, 1813)","volume":"102","author":"Orr J. W.","year":"2004","journal-title":"Fishery Bulletin"},{"key":"e_1_2_9_61_1","volume-title":"Guide to rockfishes (Scorpaenidae) of the genera Sebastes, Sebastolobus, and Adelosebastes of the Northeast Pacific Ocean","author":"Orr J. W.","year":"2000"},{"key":"e_1_2_9_62_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M208352200"},{"key":"e_1_2_9_63_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0037135"},{"key":"e_1_2_9_64_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0211399"},{"key":"e_1_2_9_65_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/155.2.945"},{"key":"e_1_2_9_66_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.13324"},{"key":"e_1_2_9_67_1","volume-title":"R: A language and environment for statistical computing","author":"R Core Development Team","year":"2019"},{"key":"e_1_2_9_68_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005008"},{"key":"e_1_2_9_69_1","doi-asserted-by":"publisher","DOI":"10.1111\/jeb.13664"},{"key":"e_1_2_9_70_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007358"},{"key":"e_1_2_9_71_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2000234"},{"key":"e_1_2_9_72_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbamcr.2006.09.006"},{"key":"e_1_2_9_73_1","doi-asserted-by":"publisher","DOI":"10.1002\/evl3.204"},{"key":"e_1_2_9_74_1","doi-asserted-by":"publisher","DOI":"10.1002\/bies.950180109"},{"key":"e_1_2_9_75_1","doi-asserted-by":"publisher","DOI":"10.1021\/tx400305w"},{"key":"e_1_2_9_76_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF02296872"},{"issue":"1","key":"e_1_2_9_77_1","first-page":"1","article-title":"Divergence by depth in an oceanic fish","volume":"2014","author":"Shum P.","year":"2014","journal-title":"PeerJ"},{"key":"e_1_2_9_78_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1420-9101.2010.01977.x"},{"key":"e_1_2_9_79_1","doi-asserted-by":"publisher","DOI":"10.1029\/2011JC007183"},{"key":"e_1_2_9_80_1","doi-asserted-by":"publisher","DOI":"10.1111\/evo.14215"},{"key":"e_1_2_9_81_1","doi-asserted-by":"publisher","DOI":"10.1093\/icesjms\/fsp059"},{"key":"e_1_2_9_82_1","article-title":"qqman: An R package for visualizing GWAS results using Q\u2010Q and manhattan plots","author":"Turner S. D.","year":"2018","journal-title":"Journal of Open Source Software"},{"key":"e_1_2_9_83_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0030285"},{"key":"e_1_2_9_84_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-017-1035-7"},{"key":"e_1_2_9_85_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0901397106"},{"key":"e_1_2_9_86_1","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2011.0260"},{"key":"e_1_2_9_87_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2008.03921.x"},{"key":"e_1_2_9_88_1","doi-asserted-by":"publisher","DOI":"10.21105\/joss.01686"},{"key":"e_1_2_9_89_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.iy.06.040188.002121"},{"key":"e_1_2_9_90_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1420-9101.2001.00335.x"},{"key":"e_1_2_9_91_1","doi-asserted-by":"publisher","DOI":"10.1124\/mol.110.070607"},{"key":"e_1_2_9_92_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbagen.2014.04.016"}],"container-title":["Molecular Ecology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mec.16046","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/mec.16046","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/am-pdf\/10.1111\/mec.16046","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mec.16046","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,25]],"date-time":"2023-08-25T21:10:39Z","timestamp":1692997839000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/mec.16046"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,10]]},"references-count":91,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2021,9]]}},"alternative-id":["10.1111\/mec.16046"],"URL":"https:\/\/doi.org\/10.1111\/mec.16046","archive":["Portico"],"relation":{},"ISSN":["0962-1083","1365-294X"],"issn-type":[{"value":"0962-1083","type":"print"},{"value":"1365-294X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,7,10]]},"assertion":[{"value":"2021-03-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-06-24","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-07-10","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}