**ABSTRACT NOT FOR CITATION WITHOUT AUTHOR PERMISSION. The title, authors, and abstract for this completion report are provided below.  For a copy of the full completion report, please contact the author via e-mail at wstott@usgs.gov. Questions? Contact the GLFC via email at frp@glfc.org or via telephone at 734-662-3209.**

Development and testing of genomic markers for Coregonus species identification and population assessment

Wendylee Stott¹, R. Scott Cornman², Cheryl Morrison², Edward Roseman³, Kevin Donner⁴

¹ Michigan State University, c/o Great Lakes Science Center 1451 Green Rd. Ann Arbor MI 48105

² Leetown Science Center, USGS, 11649 Leetown Rd, Kearneysville, WV 25430

³ Great Lakes Science Center USGS, 1451 Green Rd. Ann Arbor MI 48105

⁴ Little Traverse Bay Bands of Odawa Indians, 7500 Odawa Circle, Harbor Springs, MI 49740

April 2018

ABSTRACT:

High-throughput sequencing methods can be used to identify species diagnostic markers in groups of closely-related species. Members of the coregonine species flock in the Laurentian Great Lakes display variation in habitat use and morphology. While commonly used markers and sequences (e.g., microsatellite DNA loci and mitochondrial cytochrome oxidase I) can be used to distinguish among Lake Whitefish, Cisco, and deepwater Ciscoes (Bloater, Kiyi, Shortjaw Cisco, and Blackfin Cisco) it is difficult to accurately distinguish among the deepwater Ciscoes. In this project, we used restriction site-associated DNA sequencing (RAD-seq) to identify species diagnostic SNPs in Cisco and deepwater Cisco from lakes Superior, Michigan, Huron, and Ontario. The markers were then used to determine the identity of larval coregonids captured in the Detroit and St. Clair rivers. Seven candidate loci with good alignment to genes in other fish species were identified for Cisco, Bloater, Kiyi, and Shortjaw Cisco. These SNPs could be used to distinguish among these four species with greater accuracy than microsatellite DNA markers, although mis-classification rates of Kiyi remained high, possibly due to mis-identification of samples in the field, small sample sizes during marker discovery, or because significant differences do not exist. Most of the larval coregonids from the Detroit and St. Clair rivers were classified as Bloater. Classifications of larval coregonids based on the genomic markers were consistent with those derived using microsatellite DNA loci. Based on these results, it appears that SNPs have the potential to distinguish among deepwater Ciscoes in the Great Lakes. If these markers could be developed into a panel using an approach such as Rapture or GT-Seq, it would provide an accurate and cost-effective way to identify larval and juvenile coregonids capture in monitoring and assessment programs.