Robert Wildermuth, Southwest Fisheries Science Center/UC Santa Cruz

Climate-driven changes in ocean temperatures, currents, or plankton dynamics may disrupt pelagic forage fish recruitment. Being responsive to such impacts enables fisheries management to ensure continued sustainable harvest of forage species. We conducted a management strategy evaluation to assess the robustness of current and alternative Pacific sardine harvest control rules under a variety of recruitment scenarios representing potential projections of future climate conditions in the California Current. The current environmentally-informed control rule modifies the harvest rate for the northern sardine subpopulation based on average sea surface temperatures measured during California Cooperative Oceanic Fisheries Investigations (CalCOFI) field cruises. This rule prioritizes catch at intermediate biomass levels but may increase variability in catch and closure frequency compared to alternative control rules, especially if recruitment is unrelated to ocean temperatures. Fishing at maximum sustainable yield and using dynamically estimated reference points reduced the frequency of biomass falling below 150,000 mt by up to 17%, while using survey index-based biomass estimates resulted in a 14% higher risk of delayed fishery closure during stock declines than when using assessment-based estimates.

Hands-on demonstration for phylogenetic comparative methods using R-package phylosem: improving
stock assessment (natural mortality) and ecosystem modelling (consumption over biomass)

James Thorson, Alaska Fisheries Science Center

Comparative study across species are foundational to many topics in fisheries science, including to justify biological reference point proxies, predict natural mortality rates, or parameterize ecosystem models. Surprisingly, however, fisheries science has largely missed the research interest in phylogenetic comparative methods (PCM), which were pioneered by Joe Felsenstein at University of Washington in
the 1970s and remain a well-published topic in ecology and evolutionary biology. This is unfortunate, because PCM offers many improvements over conventional nested-taxonomic methods used in fisheries science.
In this workshop, I provide a hands-on introduction to the R-package phylosem available on CRAN. Attendees are encouraged to bring a laptop with package-install privileges, or pre-install phylosem. I will walk through vignettes which show how phylosem generalizes existing packages for phylogenetic linear models (phylolm), structural equation models (sem), phylogenetic trait imputation (Rphylopars), and phylogenetic path analysis (phylopath).
I will then provide a quick overview of results using two fisheries case studies. The first applies phylosem to the Then et al. natural mortality database, where phylosem reduces variance for out-of-sample prediction of natural mortality rates. The second replicates Palomeres and Pauly (1998), and confirms that consumption over biomass (a parameter in Ecopath with Ecosim models) is elevated for small-bodied with a high caudal-fin aspect ratio in warmer waters. I hope to demonstrate that PCM is broadly applicable for routine use throughout fisheries science.