Salmon Life Histories and Fisheries Management

Thesis (Ph.D.)--University of Washington, 2020Understanding the life histories of exploited aquatic taxa is important to sustainable fisheries management. Life history diversity has been shown to stabilize population dynamics through ‘portfolio effects’ which can maintain robust fishery yields despite environmental variability. Moreover, the reproductive life histories of fishes can be important to shaping management-relevant properties such as the steepness of the stock-recruit relationship, genetic diversity, age and size structure, and stock rebuilding potential. Despite the importance of life history information to conservation and management, achieving a practical understanding of the evolutionary and ecological factors that maintain particular life histories can be challenging. This difficulty is exemplified by widespread declines in size-and-age-at-maturity of many commercially valuable fish stocks, the causes of which are seldom be reliably discerned. In this dissertation, I seek to better understand the factors that control the frequencies of alternative maturation and reproductive life histories in sockeye salmon (Oncorhynchus nerka) populations. In chapter 1, I used Bayesian hierarchical modelling to identify the basis of variation in early maturation rates among sockeye salmon populations in Bristol Bay, Alaska. In my second chapter, I developed an age-structured Bayesian state space model to assess the causes of elevated early maturation rates in Kodiak sockeye salmon. Finally, in my third chapter I developed an individual-based population dynamics framework to explore the ecological and evolutionary factors that regulate frequencies of alternative maturation and reproductive life histories in age-structured populations. Collectively, my results demonstrate that the maintenance of alternative life histories within populations may be more complex than existing evolutionary frameworks suggest, and reveal a novel role of population dynamics in the evolution and maintenance of complex mating systems

A Bayesian hierarchical approach to integrating historical and in-season genetic data for real-time assessment of a mixed stock fishery

With advances in molecular genetics, it is becoming increasingly feasible to conduct genetic stock identification (GSI) to inform management actions that occur within a fishing season. While applications of in-season GSI are becoming widespread, such programs seldom integrate data from previous years, underutilizing the full breadth of information available for real-time inference. In this study, we developed a Bayesian hierarchical model that integrates historical and in-season GSI data to estimate temporal changes in the composition of a mixed stock of sockeye salmon (Oncorhynchus nerka) returning to Alaska’s Chignik watershed across the fishing season. Simulations showed that even after accounting for time constraints of transporting and analyzing genetic samples, a hierarchical approach can rapidly achieve accurate in-season stock allocation, outperforming alternative methods that rely solely on historical or in-season data by themselves. As the distribution and phenology of fish populations becomes more variable and difficult to predict under climate change, in-season management tools will likely be increasingly relied upon to protect biocomplexity while maximizing harvest opportunity in mixed stock fisheries.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Assessing the potential for demographic restoration and assisted evolution to build climate resilience in coral reefs.

Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral colonies ex situ and transplant them to degraded reef areas to augment habitat for reef-dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such demographic restoration efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such assisted evolution strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco-evolutionary simulation model. We found that supplementing reefs with pre-existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long-term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat-tolerant genotypes

Workshop on Unavoidable Survey Effort Reduction 2 (WKUSER2)

The Workshop on Unavoidable Survey Effort Reduction 2 (WKUSER2) focused on best-available approaches that can minimize information loss and ensure continuity in survey time series when unavoidable changes to survey effort occur. WKUSER2 recognised that reductions, reallocations, or increases in survey effort present similar set of problems, and therefore concentrated on all aspects of survey effort changes. The workshop reviewed available research, current practices, and recommended future directions on four key topics: (i) key elements of flexibility of a survey, (ii) why and how to combine data from different sources (e.g. surveys, fishery sampling) and deal with survey gaps, (iii) how to configure estimation and simulation models, and (iv) review existing tools and technology to evaluate consequences of survey effort changes.Road maps were developed for the key topic areas i, ii, iii, and iv, whenever possible, to assist scientists and survey managers in making decisions on how to evaluate and mitigate the impact of survey effort changes on data and advice quality. Many tools are available or are being developed for that purpose, but the group recognized two important needs during the workshop: i) defining clear objectives and priorities of a survey, which are essential to properly evaluate con- sequences of survey changes; and ii) making all tools accessible, reproducible, and transparent to benefit the whole community. This requires organisational and cultural shift to create support systems that ensure the development and sustainability of such tools in the future