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When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early\u2010life ecology questions can be studied. Genotyping\u2010in\u2010thousands by sequencing (GT\u2010seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT\u2010seq panel capable of differentiating the members of the\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Coregonus artedi<\/jats:italic>\n                    <\/jats:styled-content>\n                    complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi\u2010national conservation initiatives. Our panel of 494 loci was able to assign fishes in the\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C. artedi<\/jats:italic>\n                    <\/jats:styled-content>\n                    complex to species and lake. We examined cross\u2010amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C. clupeaformis<\/jats:italic>\n                    <\/jats:styled-content>\n                    ) cross\u2010amplified at 94% of loci and confamilial Round and Pygmy Whitefish (\n                    <jats:italic>Prosopium<\/jats:italic>\n                    spp.) cross\u2010amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for\n                    <jats:italic>Prosopium<\/jats:italic>\n                    \u2010specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3066 coregonine larvae and juveniles collected in spring 2019\u20132021 from Lake Superior. These results hold promise for future insights into the species\u2010specific ecology of early life coregonines and demonstrate the flexibility of GT\u2010seq panels, which may cross\u2010amplify hundreds of informative genome\u2010wide loci in related taxa.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.70203","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T12:39:15Z","timestamp":1790253555000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Genomic Tool to Tackle Cryptic Diversity Demonstrates the Potential for Off\u2010Target Use of\n                    <scp>GT<\/scp>\n                    \u2010Seq Panels"],"prefix":"10.1111","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8726-7423","authenticated-orcid":false,"given":"Amanda S.","family":"Ackiss","sequence":"first","affiliation":[{"name":"U.S. Geological Survey Great Lakes Science Center  Ann Arbor Michigan USA"},{"name":"Wisconsin Cooperative Fishery Research Unit, College of Natural Resources University of Wisconsin\u2010Stevens Point  Stevens Point Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark R.","family":"Vinson","sequence":"additional","affiliation":[{"name":"U.S. Geological Survey Great Lakes Science Center, Lake Superior Biological Station  Ashland Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7934-6471","authenticated-orcid":false,"given":"Ann J.","family":"Ropp","sequence":"additional","affiliation":[{"name":"U.S. Geological Survey Great Lakes Science Center  Ann Arbor Michigan USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1985-5071","authenticated-orcid":false,"given":"Kristen M.","family":"Gruenthal","sequence":"additional","affiliation":[{"name":"Alaska Department of Fish and Game, Division of Commercial Fisheries Gene Conservation Laboratory  Juneau Alaska USA"},{"name":"Wisconsin Department of Natural Resources, Office of Applied Science College of Natural Resources, University of Wisconsin\u2010Stevens Point  Stevens Point Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7680-5169","authenticated-orcid":false,"given":"Trevor J.","family":"Krabbenhoft","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences University at Buffalo  Buffalo New York USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4343-3439","authenticated-orcid":false,"given":"Joseph V.","family":"Siegel","sequence":"additional","affiliation":[{"name":"Biological Sciences Department SUNY Oswego  Oswego New York USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5252-4901","authenticated-orcid":false,"given":"Wendylee","family":"Stott","sequence":"additional","affiliation":[{"name":"Fisheries &amp; Oceans Canada P\u00eaches et Oc\u00e9ans Canada  Winnipeg Manitoba Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0117-5115","authenticated-orcid":false,"given":"Daniel L.","family":"Yule","sequence":"additional","affiliation":[{"name":"U.S. Geological Survey Great Lakes Science Center, Lake Superior Biological Station  Ashland Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4473-3401","authenticated-orcid":false,"given":"Wesley A.","family":"Larson","sequence":"additional","affiliation":[{"name":"National Oceanographic and Atmospheric Administration National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories  Juneau Alaska USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/eva.12919"},{"key":"e_1_2_12_3_1","volume-title":"Identification of Larval Fishes of the Great Lakes Basin With Emphasis on the Lake Michigan Drainage","author":"Auer N. 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