LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.

Genetic Data Analysis

As well as serving valuable biodiversity conservation roles, functioning no-take fishery reserves protect a portion of the fishery stock as insurance against future overfishing. So long as there is adequate compliance by the fishing community, it is likely that they will also sustain and even enhance fishery yields in the surrounding area. However, there are significant gaps in scientific knowledge that must be filled if no-take reserves are to be used effectively as fishery management tools. Unfortunately, these gaps are being glossed over by some uncritical advocacy. Here, we review the science, identify the most crucial gaps, and suggest ways to fill them, so that a promising management tool can help meet the growing challenges faced by coastal marine fisheries.

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Critical science gaps impede use of no-take fishery reserves

Current global fisheries production of ≈160 million tons is rising as a result of increases in aquaculture production. A number of climate-related threats to both capture fisheries and aquaculture are identified, but we have low confidence in predictions of future fisheries production because of uncertainty over future global aquatic net primary production and the transfer of this production through the food chain to human consumption. Recent changes in the distribution and productivity of a number of fish species can be ascribed with high confidence to regional climate variability, such as the El Nino–Southern Oscillation. Future production may increase in some high-latitude regions because of warming and decreased ice cover, but the dynamics in low-latitude regions are governed by different processes, and production may decline as a result of reduced vertical mixing of the water column and, hence, reduced recycling of nutrients. There are strong interactions between the effects of fishing and the effects of climate because fishing reduces the age, size, and geographic diversity of populations and the biodiversity of marine ecosystems, making both more sensitive to additional stresses such as climate change. Inland fisheries are additionally threatened by changes in precipitation and water management. The frequency and intensity of extreme climate events is likely to have a major impact on future fisheries production in both inland and marine systems. Reducing fishing mortality in the majority of fisheries, which are currently fully exploited or overexploited, is the principal feasible means of reducing the impacts of climate change.

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Global fish production and climate change.

Early in the 20 th century, Johan Hjort developed compelling arguments and hypotheses to explain recruitment variability that became dominant for more than 75 years. A cautious emergence from Hjort’s shadow began late in the 20 th century. Hjort’s “Critical Period” hypothesis, i.e., failure of first-feeding larvae to find food, and a second hypothesis, “Aberrant Drift” of eggs and larvae, were proposed to explain causes of recruitment variability. Tests of the Critical Period hypothesis became an obsession, although support for it was inconsistent and equivocal. Single-minded research on the Critical Period hypothesis gave way to realization that recruitment variability was the outcome of complex trophodynamic and physical processes acting over many temporal and spatial scales and throughout pre-recruit life. A complex mix of main effects and interacting factors can easily generate order-ofmagnitude variability in recruitment via small effects on mortality and growth rates during the abundant egg and larval stages, or via cumulative effects during the pre-recruit juvenile stage. New considerations of compensatory mechanisms that can dampen variability and stabilize recruitment emerged. A little density dependence, especially in the relatively long juvenile stage, can regulate recruitment. Multidisciplinary programs instituted in the 1990s and successful development of statistical models and coupled bio-physical models, offered new insights into mechanisms generating recruitment variability. Despite progress, forecasting recruitment remains a formidable challenge. “Solving the recruitment problem” is no longer the Holy Grail of fishery science. Appreciating recruitment variability, explain ing its probable causes, considering implications for management, and understanding it in the context of broader variability in marine ecosystems, are all worthy goals.

Emerging from Hjort's Shadow

It is now clear that fished populations can fluctuate more than unharvested stocks. However, it is not clear why. Here we distinguish among three major competing mechanisms for this phenomenon, by using the 50-year California Cooperative Oceanic Fisheries Investigations (CalCOFI) larval fish record. First, variable fishing pressure directly increases variability in exploited populations. Second, commercial fishing can decrease the average body size and age of a stock, causing the truncated population to track environmental fluctuations directly. Third, age-truncated or juvenescent populations have increasingly unstable population dynamics because of changing demographic parameters such as intrinsic growth rates. We find no evidence for the first hypothesis, limited evidence for the second and strong evidence for the third. Therefore, in California Current fisheries, increased temporal variability in the population does not arise from variable exploitation, nor does it reflect direct environmental tracking. More fundamentally, it arises from increased instability in dynamics. This finding has implications for resource management as an empirical example of how selective harvesting can alter the basic dynamics of exploited populations, and lead to unstable booms and busts that can precede systematic declines in stock levels.

Why fishing magnifies fluctuations in fish abundance

Numerous groundfish stocks in both the Atlantic and Pacific are considered overfished, resulting in large-scale fishery closures. Fishing, in addition to simply removing biomass, also truncates the age and size structure of fish populations and often results in localized depletions. We summarize recent research suggesting that an old-growth age structure, combined with a broad spatial distribution of spawning and recruitment, is at least as important as spawning biomass in maintaining long-term sustainable population levels. In particular, there is evidence that older, larger female rockfishes produce larvae that withstand starvation longer and grow faster than the offspring of younger fish, that stocks may actually consist of several reproductively isolated units, and that recruitment may come from only a small and different fraction of the spawning population each year. None of these phenomena is accounted for in current management programs. We examine alternative management measures that addre...

Fisheries Sustainability via Protection of Age Structure and Spatial Distribution of Fish Populations

In temporally variable environments, longevity is generally considered to be a bet- hedging adaptation in which reproductive effort is spread across many years, increasing the proba- bility that favorable conditions for larvae will be encountered at least some time in a female's life span. A long reproductive life span provides the potential for individual females to exhibit inter- annual differences in energy allocation patterns that may be age- or size-dependent. We examine the effects of maternal age and size on larval quality, fecundity, and timing of parturition in 5 species of live-bearing rockfishes in the genus Sebastes (blue, yellowtail, olive, gopher, and kelp rockfish), and compare these maternal effects with previously documented patterns in black rockfish Sebastes melanops. Larval quality was indexed by size (notochord length) and condition (lipid storage in the oil globule). Maternal effects were found for oil globule size in blue, yellowtail and gopher rockfish, for weight-specific fecundity in blue and yellowtail rockfish, and for parturition date in blue, yellow- tail, and kelp rockfish. In all cases the maternal effects were similar to those reported for black rock- fish, with increasing lipid provisioning of larvae, greater weight-specific fecundity, and earlier timing of parturition in the spawning season with increasing maternal age or size. No effect of maternal age or size on larval size was observed. In general, maternal effects were more evident in winter spawn- ing species of the subgenus Sebastosomus (black, blue, olive, and yellowtail rockfish) than the spring spawning species of the subgenus Pteropodus (gopher and kelp rockfish). These results confirm that older and larger females in rockfish populations may contribute disproportionately to larval recruit- ment by producing higher quality larvae and more larvae per unit biomass, and releasing them at a different time than younger and smaller females. A shift in timing of parturition with female age may constitute a diversified bet-hedging strategy, providing a temporal spread of spawning effort within a maternal lineage, whereby successive female progeny release larvae at different times within the same year.

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Maternal effects in rockfishes Sebastes spp.: A comparison among species

Reproductive strategies balancing offspring size and offspring number have been well documented in empirical tests of life-history theory. Here we found an additional trade-off between offspring size and offspring condition. Among 5 species of live-bearing rockfishes (Sebastes spp.) from central Californian populations, we observed a negative relationship between larval length at parturition and the size of their oil globule (a triacylglycerol-rich energy reserve). When compared with a variety of performance variables (resistance to starvation, growth, startle-escape performance and routine activity levels), it appears that this trade-off leads to a conflict when trying to optimize survival potential, with differing benefits to each trait. A large oil globule greatly increases resistance to starvation, whereas larger body size is associated with numerous performance benefits likely to synergistically decrease predation-based mortality and increase success at capturing prey (increased startle speeds and distances, as well as more rapid onset of growth and larger size at age). The tradeoff between energy reserves and body size is further reflected in the seasonal patterns of parturition of the 5 species, with larvae having large oil globules and small body size being released in winter, when productivity in the California Current is low but transport is generally onshore, and those with small oil globule reserves and large body size released in late spring, when productivity is high but transport is generally offshore. These 2 apparent reproductive strategies also reflect subgeneric phylogenetic relationships, suggesting a potential lineage-specific basis for the contrast in larval traits. The results highlight the importance of measuring both physical and performance traits of larvae, as well as considering multiple attributes of both, when evaluating progeny quality.

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Trade-offs between size and energy reserves reflect alternative strategies for optimizing larval survival potential in rockfish

Analysis of multilocus microsatellite genotypes revealed multiple paternity for all of the seven viable broods of larvae produced by kelp rockfish, Sebastes atrovirens (Jordan and Gilbert 1880), held jointly in a large aquarium tank (n = eight females and eight males). Only two of the eight experimental males were identified as fathers, and alleles not found in any of the captive males were present in all seven broods, demonstrating paternity by wild males external to the experiment. Thus, all of the females mated with one or more males prior to capture, confirming that female kelp rockfish are capable of storing sperm and controlling the overall timing of egg fertilization. These results highlight the potential for a paternal influence on larval quality through female mate choice and sperm competition.

Steven A. Berkeley

Papers

Fisheries Sustainability via Protection of Age Structure and Spatial Distribution of Fish Populations

Maternal effects in rockfishes Sebastes spp.: A comparison among species

Trade-offs between size and energy reserves reflect alternative strategies for optimizing larval survival potential in rockfish

Multiple paternity in viviparous kelp rockfish, Sebastes atrovirens

Methods to Reduce Bycatch Mortality in Longline Fisheries