Salmonid Selection, Evolution, and Historical Abundance Patterns

233 Pages·2015·8.07 MB·English

Salmonid Selection, Evolution, and Historical
Abundance Patterns

Curry James Cunningham

A dissertation
submitted in partial fulfillment of the
requirements for the degree of

Doctor of Philosophy

University of Washington
2015

Reading Committee:
Ray Hilborn, Chair
Thomas P. Quinn
Trevor Branch

Program Authorized to Offer Degree:
School of Aquatic and Fishery Sciences
University of Washington

Abstract

Salmonid Selection, Evolution, and Historical Abundance Patterns

Curry J. Cunningham

Chair of the Supervisory Committee:
Dr. Ray Hilborn
School of Aquatic and Fishery Sciences

Pacific salmon represent an important group of species both from both cultural and
economic perspectives. Given the importance of salmonids in marine and freshwater ecosystems,
as a component of human food security, it is important to understand what natural and
anthropogenic factors influence the evolutionary and demographic dynamics of population
across their range, and develop quantitative tools to aid in the implementation of sustainable
management practices. This dissertation is focused upon: (i) evaluating whether selective
predation by brown bears (Ursus arctos) depends upon the density of their sockeye salmon
(Oncorhynchus nerka) prey, (ii) quantifying strength and direction of natural and anthropogenic
selection forces and life history tradeoffs that shaping optimal phenotypic distributions for
populations of sockeye in Bristol Bay, Alaska, (iii) development of methods for reconstructing
salmon run size by partitioning mixed-stock catches while accounting for differences in
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availability to harvest within common fishing areas and interception in spatially proximate
terminal fishing districts using both age and genetic composition of catch data, (iv) simulation
testing of a stage-structured statistical life cycle model for evaluating the natural and
anthropogenic drivers of Chinook salmon (O. tshawytscha), and (v) an application for the
statistical life cycle model to seven populations of fall and spring-run Chinook in the Sacramento
River watershed of California.

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©Copyright 2015
Curry J. Cunningham

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CHAPTER 1: SIZE-SELECTIVITY OF PREDATION BY BROWN BEARS

DEPENDS ON THE DENSITY OF THEIR SOCKEYE SALMON PREY ....... 1
ABSTRACT .................................................................................................................................. 1

INTRODUCTION .......................................................................................................................... 3

METHODS ................................................................................................................................... 7

RESULTS .................................................................................................................................. 10

DISCUSSION .............................................................................................................................. 12

ACKNOWLEDGEMENTS ............................................................................................................ 17

FIGURES ................................................................................................................................... 18

TABLES .................................................................................................................................... 21

CHAPTER 2: SELECTING FOR THE PHENOTYPIC OPTIMUM: SIZE-
RELATED TRADEOFFS BETWEEN MORTALITY RISK AND
REPRODUCTIVE OUTPUT IN FEMALE SOCKEYE SALMON ............... 22
ABSTRACT ................................................................................................................................ 22

INTRODUCTION ........................................................................................................................ 24

METHODS ................................................................................................................................. 28

STUDY SITE AND SURVEY METHODS ................................................................................................................... 28

ANALYTICAL METHODS ...................................................................................................................................... 32

RESULTS .................................................................................................................................. 35

DISCUSSION .............................................................................................................................. 38

ACKNOWLEDGEMENTS ............................................................................................................ 45

FIGURES ................................................................................................................................... 47

TABLES .................................................................................................................................... 51

CHAPTER 3: A GENERAL MODEL FOR SALMON RUN RECONSTRUCTION
ACCOUNTING FOR INTERCEPTION AND DIFFERENTIAL AVAILABILITY
TO HARVEST ................................................................................... 54
ABSTRACT ................................................................................................................................ 54

INTRODUCTION ........................................................................................................................ 55

METHODS ................................................................................................................................. 59

GENERAL MODEL DESCRIPTION .......................................................................................................................... 59

BRISTOL BAY ...................................................................................................................................................... 61

Catch data .................................................................................................................. 62

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Escapement data ........................................................................................................ 62

Age composition data ............................................................................................... 63

Genetic stock identification data ............................................................................... 64

MODEL STRUCTURE ............................................................................................................................................ 65

LIKELIHOODS AND PENALTIES ............................................................................................................................ 68

ESTIMATION PROCEDURE .................................................................................................................................... 72

SPECIAL HARVEST AREA, SOUTH PENINSULA, AND HIGH SEAS CATCH ALLOCATION .......................................... 73

RESULTS .................................................................................................................................. 75

MODEL FITS TO DATA .......................................................................................................................................... 75

PARAMETER ESTIMATES ...................................................................................................................................... 76

APPORTIONED CATCH ......................................................................................................................................... 78

COMPARISON OF RECONSTRUCTION METHODS ................................................................................................... 79

DISCUSSION .............................................................................................................................. 80

FIGURES ................................................................................................................................... 85

TABLES .................................................................................................................................. 105

CHAPTER 4: A STATISTICAL LIFE CYCLE MODEL FOR CENTRAL
VALLEY CHINOOK SALMON: A SIMULATION STUDY ................... 114
ABSTRACT .............................................................................................................................. 114

INTRODUCTION ...................................................................................................................... 116

METHODS ............................................................................................................................... 123

ESTIMATION MODEL .......................................................................................................................................... 123

OPERATING MODEL ........................................................................................................................................... 131

SIMULATION STUDY CASES ............................................................................................................................... 134

RESULTS ................................................................................................................................ 136

DISCUSSION ............................................................................................................................ 142

FIGURES ................................................................................................................................. 147

CHAPTER 5: EVALUATION OF FRESHWATER AND MARINE INFLUENCES
ON THE SURVIVAL OF SPRING AND FALL-RUN SACRAMENTO RIVER
CHINOOK ...................................................................................... 156
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ABSTRACT .............................................................................................................................. 156

INTRODUCTION ...................................................................................................................... 158

METHODS ............................................................................................................................... 161

THE DATA ......................................................................................................................................................... 161

Estimation model structure ..................................................................................... 166

UNCERTAINTY – AICC SELECTION AND MCMC METHODS .............................................................................. 168

STEPWISE AICC MODEL SELECTION ................................................................................................................. 169

MARKOV CHAIN MONTE-CARLO ESTIMATION METHODS ................................................................................ 171

TRANSLATING COEFFICIENTS INTO SURVIVAL DIFFERENCES ........................................................................... 173

RESULTS ................................................................................................................................ 174

MODEL SELECTION RESULTS ............................................................................................................................ 174

Estimation Results .................................................................................................. 179

DISCUSSION ............................................................................................................................ 185

FIGURES ................................................................................................................................. 194

TABLES .................................................................................................................................. 201

REFERENCES .......................................................................................................................... 209

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Introduction

Pacific salmon are culturally and economically important species, forming the foundation
of valuable commercial, sport, and subsistence fisheries in many regions. In addition to their
importance to humans, salmon are also important sources of nutrients for terrestrial ecosystems
(Moore and Schindler 2004) and critical prey items for maintaining sustainable predator
populations. Despite the importance of salmon in the United States and globally, many questions
still remain regarding their evolutionary ecology, interactions with terrestrial predators, and the
natural and anthropogenic factors that influence their survival and abundance over time.
Furthermore, there is a need to develop quantitative tools for addressing conservation concerns
and aiding in the efficient operation of sustainable fisheries, if the sustainability of salmon
populations and the communities relying on them is to be ensured in the future.
Within their range, Pacific salmon traverse a gradient both in latitude and the level of
anthropogenic influence exerted on their freshwater spawning habitats. Sockeye salmon
(Oncorhynchus nerka) spawning in Bristol Bay, Alaska represent one end of this continuum,
with minimal human development on, or alterations to, freshwater habitats. The only direct
anthropogenic impacts originate from a carefully managed commercial fishery in the region.
Chinook salmon (O. tshawytscha) native to the Central Valley of California represent the other
end of that continuum, with a long history of severely altered freshwater and estuarine habitats,
lost access to traditional spawning grounds, and direct impacts from water management
(Williams 2006). Contrasting in many ways, salmon populations in these two regions provide an
opportunity to understand the ecology of salmon in differing habitats, subject to diverse factors
influencing their evolutionary and demographic histories.
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This dissertation has a dual focus on: (i) understanding the evolutionary forces shaping
the evolutionary trajectory of salmon in habitats which remain unaltered by anthropogenic
influence, and (ii) developing quantitative tools to aid in effective management of commercial
fisheries and improve understanding regarding the environmental forces driving the demographic
trajectory of salmon in heavily altered habitats. The first chapter of my dissertation, Size-
selectivity of Brown Bears Depends on the Density of their Sockeye Salmon Prey, examines how
the size selective nature of predation by brown bears (Ursus arctos) on sockeye salmon in a
tributary of Bristol Bay is directly influenced by interannual variation in prey abundance. The
second chapter of my dissertation, Selecting for the Phenotypic Optimum: Size-related Tradeoffs
Between Mortality Risk and Reproductive Output in Female Sockeye Salmon, expands upon the
first chapter placing the influence of predatory selection within the context of other forms of
selection shaping the morphology of sockeye salmon, including fishery selection, the mortality
cost of prolonged marine residence required for growth, and physiological relationships between
body size and reproductive output. The third chapter of my dissertation, A General Model for
Salmon Run Reconstruction Accounting for Interception and Differential Availability to Harvest,
describes a flexible model for reconstructing salmon brood tables by partition catches in mixed
stock salmon fisheries and accounting for interception harvest in proximate terminal fishing
districts, using age and genetic composition of catch data. This chapter reports results from an
application of this model to data from the commercial sockeye salmon fishery in Bristol Bay.
Chapter four, A Statistical Life Cycle Model for Central Valley Chinook Salmon: A Simulation
Study, describes a stage-structured model for testing hypotheses regarding the strength and
direction of influence natural and anthropogenic factors have on the survival of multiple
populations of Chinook in the Central Valley of California. This chapter details results of a
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simulation study evaluating the level bias and precision in model estimates for parameters of
interest, and the influence of observation uncertainty in model predictions. The fifth and final
chapter of my dissertation, Evaluation of Freshwater and Marine Influences on The Survival of
Spring and Fall-run Sacramento River Chinook, presents findings from an application of the
statistical model described and tested in Chapter 4, to seven populations of wild and hatchery-
reared, spring and fall-run Chinook in the Sacramento River watershed of California.

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