genetics

The objective of this work was to begin the process of describing Lake Superior larval ciscoe population dynamics at the species level, something which was not possible prior to 2019 (Ackiss et al. 2020) and use this information to develop standard collection protocols. From 2014-2023, larval fish were sampled at 163 and collected at 159 locations across Lake Superior. Due to COVID restrictions, no sampling occurred in 2020 and sampling in 2021 was limited to USA waters. Across all years, this sampling yielded 90,618 ciscoe larvae of which 11,751 individuals were identified based on genomics. The 4,369 larval ciscoes collected in 2023 have not yet but will be genomically identified. Genomic identifications yielded 78 Bloater, 8,671 Cisco, 75 Lake Whitefish, 1,969 Kiyi, and 958 putative hybrids. Principal findings include the widespread distribution of all species across the lake by July; high annual variation in hatching dates, sequential species hatch dates that match chronological spawning periods; Cisco first, Kiyi second, and Bloater third, and the occurrence of a genetically unique stock of Cisco along the north shore of the lake.

In 2022, unprecedented larval ciscoe survival past July provided an opportunity to collect young age-0 ciscoes in August, September, and October and evaluate their population dynamics. This effort resulted in the collection and genomic identification of 79 Bloater, 456 Cisco, 1,086 Kiyi, and 77 putative hybrids. A principal finding to date was documenting the late-summer movement of these fish from the surface, their preferred habitat in May-July, to 10-15 m below the surface in early August at around 25 mm in total length. This discovery has implications for when and how these fish can be collected. 

A third outgrowth of this study was the opportunity to compare morphological-based species identifications to genomic-based species identifications for age-0 and near age-1 fish. This work could lead to a better understanding of which species, and at which size they can be reliably identified aboard the ship based on morphological characteristics. Dual identifications to date include 503 Bloater, 81 Cisco, 75 Kiyi, 3 Shortnose Cisco, 4 Pygmy Whitefish, and 89 putative hybrids, with an additional 2,292 age-1 ciscoes collected in 2023 remaining to be genomically identified. Preliminary analyses show rates of accurate morphological identification as compared to genomics to be highest for Cisco and lowest for Bloater, with the overall identification accuracy exceeding 90% for all three ciscoes when total length exceeds 140 mm.