{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T20:28:22Z","timestamp":1784406502022,"version":"3.55.0"},"reference-count":66,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2021,8,14]],"date-time":"2021-08-14T00:00:00Z","timestamp":1628899200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010404","name":"Forest Genetics Council of British Columbia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010404","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010404","name":"Forest Genetics Council of British Columbia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010404","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010404","name":"Forest Genetics Council of British Columbia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010404","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005247","name":"University of British Columbia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005247","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005247","name":"University of British Columbia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005247","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008459","name":"University of Calgary","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008459","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2022,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Despite their suitability for studying evolution, many conifer species have large and repetitive giga\u2010genomes (16\u201331\u00a0Gbp) that create hurdles to producing high coverage SNP data sets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within\n                    <jats:italic>Pinaceae<\/jats:italic>\n                    , false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost\u2010saving benefits of pool\u2010seq and exome\u2010capture to discover SNPs in two conifer species, Douglas\u2010fir (\n                    <jats:italic>Pseudotsuga menziesii<\/jats:italic>\n                    var.\n                    <jats:italic>menziesii<\/jats:italic>\n                    (Mirb.) Franco,\n                    <jats:italic>Pinaceae<\/jats:italic>\n                    ) and jack pine (\n                    <jats:italic>Pinus banksiana<\/jats:italic>\n                    Lamb.,\n                    <jats:italic>Pinaceae<\/jats:italic>\n                    ). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong, positive correlation with those estimated by sequencing the same population as individuals (\n                    <jats:italic>r<\/jats:italic>\n                    \u00a0&gt;\u00a0.948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are probably due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (\n                    <jats:italic>r<\/jats:italic>\n                    \u00a0&gt;\u00a0.973). Our work addresses bioinformatic challenges in non\u2010model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralogous artefacts, and suggests the combination of pool\u2010seq and exome capture to be robust for further evolutionary hypothesis testing in these systems.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.13474","type":"journal-article","created":{"date-parts":[[2021,7,16]],"date-time":"2021-07-16T14:32:14Z","timestamp":1626445934000},"page":"225-238","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non\u2010model tree species"],"prefix":"10.1111","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8560-5417","authenticated-orcid":false,"given":"Brandon M.","family":"Lind","sequence":"first","affiliation":[{"name":"Department of Forest and Conservation Sciences Centre for Forest Conservation Genetics University of British Columbia  Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5023-3759","authenticated-orcid":false,"given":"Mengmeng","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences University of Calgary  Calgary AB Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1529-3347","authenticated-orcid":false,"given":"Dragana","family":"Obreht Vidakovic","sequence":"additional","affiliation":[{"name":"Department of Forest and Conservation Sciences Centre for Forest Conservation Genetics University of British Columbia  Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6576-400X","authenticated-orcid":false,"given":"Pooja","family":"Singh","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences University of Calgary  Calgary AB Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8403-6219","authenticated-orcid":false,"given":"Tom R.","family":"Booker","sequence":"additional","affiliation":[{"name":"Department of Forest and Conservation Sciences Centre for Forest Conservation Genetics University of British Columbia  Vancouver BC Canada"},{"name":"Biodiversity Research Centre University of British Columbia  Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2228-3625","authenticated-orcid":false,"given":"Sally N.","family":"Aitken","sequence":"additional","affiliation":[{"name":"Department of Forest and Conservation Sciences Centre for Forest Conservation Genetics University of British Columbia  Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1706-8699","authenticated-orcid":false,"given":"Sam","family":"Yeaman","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences University of Calgary  Calgary AB Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,8,14]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1752\u20104571.2007.00013.x"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/gcb.12181"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esv015"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2015.28"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.13994"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12354"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.114.169052"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_2_9_10_1","volume-title":"3B24_fc1136_ln7_GTGGCC","author":"Cronn R.","year":"2017"},{"key":"e_1_2_9_11_1","volume-title":"Multi\u2010genotype #2 (MG2_I)","author":"Cronn R.","year":"2017"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1214\/aoms\/1177731363"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/1745\u20106150\u20107\u201017"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12581"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0140462"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.110.114397"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12360"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1883"},{"key":"e_1_2_9_20_1","volume-title":"GSM1893337: LA9S7; 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