{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T19:17:34Z","timestamp":1792005454737,"version":"4.4.0"},"reference-count":94,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2021,8,19]],"date-time":"2021-08-19T00:00:00Z","timestamp":1629331200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2022,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high\u2010throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid\u2010preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target\u2010capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae:\n                    <jats:italic>Gyrinophilus porphyriticus<\/jats:italic>\n                    ) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin\u2010fixed tissues. We designed capture probes based on double\u2010digest restriction\u2010site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture\u2010based samples clustered together, but RADseq samples did not cluster with corresponding capture\u2010based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous\/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin\u2010fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.13481","type":"journal-article","created":{"date-parts":[[2021,7,30]],"date-time":"2021-07-30T14:51:01Z","timestamp":1627656661000},"page":"487-502","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Genomic library preparation and hybridization capture of formalin\u2010fixed tissues and allozyme supernatant for population genomics and considerations for combining capture\u2010 and RADseq\u2010based single nucleotide polymorphism data sets"],"prefix":"10.1111","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0464-9259","authenticated-orcid":false,"given":"Kyle A.","family":"O\u2019Connell","sequence":"first","affiliation":[{"name":"Global Genome Initiative National Museum of Natural History Smithsonian Institution Washington District of Columbia USA"},{"name":"Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA"},{"name":"Department of Biological Sciences The George Washington University Washington District of Columbia USA"},{"name":"Biomedical Data Science Lab Deloitte Consulting LLP Arlington Virginia USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6688-8848","authenticated-orcid":false,"given":"Kevin P.","family":"Mulder","sequence":"additional","affiliation":[{"name":"Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA"},{"name":"CIBIO\/InBIO Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos Universidade do Porto Vair\u00e3o Portugal"},{"name":"Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park Washington District of Columbia USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3444-2814","authenticated-orcid":false,"given":"Addison","family":"Wynn","sequence":"additional","affiliation":[{"name":"Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9165-3522","authenticated-orcid":false,"given":"Kevin","family":"de Queiroz","sequence":"additional","affiliation":[{"name":"Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0123-8833","authenticated-orcid":false,"given":"Rayna C.","family":"Bell","sequence":"additional","affiliation":[{"name":"Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA"},{"name":"Department of Herpetology California Academy of Sciences San Francisco California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,8,19]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.115.183665"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.5175"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esr096"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mss223"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msn163"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.3389\/fevo.2020.603948"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.14260"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1008119"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12516"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0161531"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhevol.2014.10.015"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-61779-516-9_11"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12862\u2010016\u20100791\u20100"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/gcb.12550"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12354"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.4236\/fmar.2015.31001"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0223953"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx100"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.5089"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13072"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v022.i04"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz966"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1601066113"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13082"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv646"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13167"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12089"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.yexmp.2012.07.002"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010018\u201019946\u20102"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.3389\/fevo.2018.00151"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13324"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.119.400556"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12566"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13529"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0141579"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt193"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-59745-251-9_3"},{"key":"e_1_2_9_40_1","unstructured":"Krueger F.(2015).Trim galore. A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files 516 517."},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2018.0248"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13168"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.2478\/pfs\u20102019\u20100020"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13245"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.119792.110"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1093\/zoolinnean\/zlaa033"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz268"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.12538"},{"key":"e_1_2_9_50_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.12466"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.4470"},{"key":"e_1_2_9_52_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0103728"},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15541"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.86.6.1939"},{"key":"e_1_2_9_56_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ab.2013.04.006"},{"key":"e_1_2_9_57_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0037135"},{"key":"e_1_2_9_58_1","doi-asserted-by":"publisher","DOI":"10.1670\/19\u2010012"},{"key":"e_1_2_9_59_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12965"},{"key":"e_1_2_9_60_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"e_1_2_9_61_1","volume-title":"R: A language and environment for statistical computing","author":"R Core Team","year":"2020"},{"key":"e_1_2_9_62_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1755\u20100998.2011.03052.x"},{"key":"e_1_2_9_63_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.12655"},{"key":"e_1_2_9_64_1","volume-title":"Molecular cloning: A laboratory manual","author":"Sambrook J.","year":"2001"},{"key":"e_1_2_9_65_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12610"},{"key":"e_1_2_9_66_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0034131"},{"key":"e_1_2_9_67_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1249"},{"key":"e_1_2_9_68_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12785"},{"key":"e_1_2_9_69_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.3699"},{"key":"e_1_2_9_70_1","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2017.0387"},{"key":"e_1_2_9_71_1","doi-asserted-by":"publisher","DOI":"10.1111\/eva.13045"},{"key":"e_1_2_9_72_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.089532.108"},{"key":"e_1_2_9_73_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa113"},{"key":"e_1_2_9_74_1","first-page":"1","volume-title":"Collection forum","author":"S\u00f8rensen M.","year":"2016"},{"key":"e_1_2_9_75_1","doi-asserted-by":"publisher","DOI":"10.1111\/jfb.13307"},{"key":"e_1_2_9_76_1","doi-asserted-by":"publisher","DOI":"10.1111\/syen.12301"},{"key":"e_1_2_9_77_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0069189"},{"key":"e_1_2_9_78_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12686\u2010018\u20101036\u2010x"},{"key":"e_1_2_9_79_1","doi-asserted-by":"publisher","DOI":"10.1017\/S1477200005001891"},{"key":"e_1_2_9_80_1","doi-asserted-by":"publisher","DOI":"10.1641\/0006-3568(2004)054[0066:TVOMCF]2.0.CO;2"},{"key":"e_1_2_9_81_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0151651"},{"key":"e_1_2_9_82_1","doi-asserted-by":"publisher","DOI":"10.1101\/pdb.prot5138"},{"key":"e_1_2_9_83_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0096793"},{"key":"e_1_2_9_84_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2009.05.009"},{"key":"e_1_2_9_85_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0225807"},{"key":"e_1_2_9_86_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13077"},{"key":"e_1_2_9_87_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.5257"},{"key":"e_1_2_9_88_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2018.11.055"},{"key":"e_1_2_9_89_1","first-page":"1","article-title":"The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections","volume":"2020","author":"Vershinina A. O.","year":"2019","journal-title":"Molecular Ecology Resources"},{"key":"e_1_2_9_90_1","doi-asserted-by":"publisher","DOI":"10.3897\/zookeys.457.6822"},{"key":"e_1_2_9_91_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2007.08.017"},{"key":"e_1_2_9_92_1","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.15931.1"},{"key":"e_1_2_9_93_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2018.06.038"},{"key":"e_1_2_9_94_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cois.2016.09.009"},{"key":"e_1_2_9_95_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12686\u2010017\u20100811\u20104"}],"container-title":["Molecular Ecology Resources"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.13481","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/1755-0998.13481","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.13481","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,25]],"date-time":"2023-08-25T17:56:13Z","timestamp":1692986173000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1755-0998.13481"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,19]]},"references-count":94,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,2]]}},"alternative-id":["10.1111\/1755-0998.13481"],"URL":"https:\/\/doi.org\/10.1111\/1755-0998.13481","archive":["Portico"],"relation":{},"ISSN":["1755-098X","1755-0998"],"issn-type":[{"value":"1755-098X","type":"print"},{"value":"1755-0998","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,19]]},"assertion":[{"value":"2021-02-25","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-07-14","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-08-19","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}