Genomics reveals identity, phenology and population demographics of larval ciscoes (Coregonus artedi, C. hoyi, and C. kiyi) in the Apostle Islands, Lake Superior

We demonstrate, for the first time, the ability to reliably assign an assemblage of larval coregonines [Salmonidae Coregoninae] to shallow and multiple deepwater species. Larval coregonines from the Apostle Islands, Lake Superior, were genotyped using restriction site-associated DNA sequencing (RADseq) and were assigned to species using reference genotypes from adult corgonines from the same region. Of the 193 genotyped larvae, 101 were assigned as Coregonus artedi (average assignment probability = 97.6%), 57 were assigned as C. kiyi (average assignment probability = 95.5%), and 28 were assigned as C. hoyi (average assignment probability = 89.0%). Coregonus artedi were collected earliest in the season, followed by C. kiyi and then C. hoyi. Estimates of genetic diversity within each species provide a baseline for future monitoring in the Apostle Islands. Our success with species assignment indicates the promise of leveraging genomic data for larval coregonine identification, which could enable assessing and evaluating early life history dynamics and recruitment processes at the species level to the benefit of ongoing coregonine restoration and management efforts.