1 Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada.
2 Rubenstein Ecosystem Science Laboratory, University of Vermont, 3 College St., Burlington, VT, 05401, USA.
3 Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada. julie.gibelli@concordia.ca.
4 Honam National Institute of Biological Resources, 99 Gohadoan-Gil, Mokpo, 58762, Republic of Korea.
5 National Institute of Biological Resources, 42 Hwangyeong-Ro, Seo-Gu, Incheon, 22689, Republic of Korea.
6 Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, MB, R3T 2N6, Canada.

Intraspecific variation is important for species' long-term persistence in changing environments. Conservation strategies targeting intraspecific variation often rely on the identification of management or policy units below the species level based on biological differences among populations. To identify management units, this paper examines intraspecific divergence of Lake Trout (Salvelinus namaycush) in Great Slave Lake (GSL), Canada, using low-coverage whole-genome sequencing data. Specifically, we evaluate genetic differentiation and assess the relationship with morphological, mitochondrial, and putatively adaptive divergence. We show that at least three and up to five genetically distinct Lake Trout populations co-occur in GSL and exhibit differences in spatial distribution and body size, with signatures of selection. However, admixture was widespread (60% of the fish) and population structure was shallow (average F_ST = 0.022). These findings highlight that, even in the era of whole genome sequencing, identifying discrete management units to implement conservation efforts and policy can remain challenging in systems where gene flow among genetically and ecologically distinct populations is ubiquitous. To give more recognition to this complexity, management efforts should also focus on the area where adaptive variation is evident, and evolutionary acts are at play, to better protect species' resilience and adaptive potential in some natural systems.