Widespread admixture blurs population structure and confounds Lake Trout (Salvelinus namaycush) conservation even in the genomic era

Intraspecific variation is important for species’ long-term persistence,
and a main conservation target. Units below the species level are often
identified based on evidence for adaptive divergence and reproductive
isolation. For complexchallenging taxa, population genomics has the
potential to improve management strategies by facilitating the
identification of genetic boundaries and adaptive variation between
discrete 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 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). These
findings highlight that, even in the era of whole genome sequencing,
identifying discrete population units can remain challenging in systems
where gene flow among genetically distinct populations is ubiquitous. To
give more recognition to this complexity, shifting the focus of management
efforts from discrete populations (i.e., intraspecific units) to the area
where evolutionary acts are at play could be beneficial to protect
species’ resilience and adaptive potential in some natural systems.