Shifts in nearshore fish assemblages following reintroduction of an apex predator

Enclosed data and code are an archive for submitted manuscript "Shifts in nearshore fish assemblages following reintroduction of an apex predator". We include two scripts, one for each objective in the manuscript and the corresponding required datasets to run those analyses and generate figures and tables for the manuscript. Manuscript abstract Ecosystem structure and function is modulated by complex food web interactions driven by the presence of apex predators. The loss of apex predators can drastically alter ecosystems leading to abrupt phase shifts. Infrequently can we study the recolonization of a previously extirpated apex predator. The reintroduction and expansion of sea otters (Enhydra lutris) in Southeast Alaska provides an opportunity to explore the role of an apex predator on biodiversity and species composition post previous extirpation. We employed a before-after-control-impact framework to quantify changes associated with sea otter presence while accounting for changes across time in the richness, diversity, evenness, and species composition of nearshore fish communities in eelgrass (Zostera marina) and understory kelp habitats. The impacts of sea otters differed among eelgrass and understory kelp habitats. Fish species richness in eelgrass meadows increased over time where sea otters recolonized but remained stable in areas without sea otter recolonization. Occurrence of flatfish (Pleuronectidae and Paralicthyidae), greenlings (Hexagrammidae), and rockfish (Sebastidae) increased after sea otters recolonized and contributed to the observed increase in richness in eelgrass. In contrast, understory kelp beds fish community composition shifted in areas where sea otters recolonized, characterized by declines in bay pipefish (Syngnathus leptorhynchus), rockfish, and juvenile greenling. We did not detect a change in species composition in eelgrass meadows nor a change in species richness, diversity, or evenness in understory kelp beds. Through trophic connections and indirect impacts, we posit sea otters may be facilitating prey availability changes, habitat alterations including modifying the presence of algal species, increased niche diversity or a combination thereof allowing new species to establish themselves in nearshore habitats. Our results demonstrate the strong indirect effects of apex predators on nearshore food webs through shifts in fish assemblages.