University of Vermont Burlington, Vermont, United States
Anthropogenic habitat fragmentation can isolate segments of populations and lead to genetic differentiation. Fragmentation is common in terrestrial systems (e.g., by roads) and rivers (by dams), but rare in lakes. Lake Champlain is naturally structured by several large islands, and construction of several causeways in the 1800s isolated three large basins from the Main Lake. Our objective was to determine whether the causeways have contributed to genetic differentiation of fish species within and among the lake basins. We focused on burbot (Lota lota), a circumpolar freshwater cod species that occupies deep lakes and rivers; populations have declined throughout much of their range due to commercial harvest and dams. Burbot were collected from a tributary, two regions of the Main Lake separated by approximately 12 km, and the Inland Sea, an isolated basin connected to the Main Lake only through narrow, shallow openings. Because burbot are a coldwater species, they would not have access to the causeway openings except in winter. We used low-coverage whole-genome sequencing and principle components analysis to assess genome-wide differences among samples.
Observed variation in nuclear DNA indicated isolation by distance between fish captured in the two regions of the Main Lake, and genetic separation among fish captured in the Main Lake, its tributary, and the Inland Sea. Mitochondrial DNA data indicated at least three maternal lineages, all of which are shared between the Main Lake and Inland Sea. Lack of differentiation in the much smaller mitochondrial genome supports the hypothesis that isolation between the lake basins is a recent phenomenon. The river population apparently arose from one Main Lake maternal lineage and has diverged from the lake population since colonization of the tributary. The presence of genetic structure suggests that human activities have fundamentally altered the population dynamics of this top predator, with implications for both burbot conservation and the larger food web.