Department of Aquatic and Fishery Sciences Faculty Papers

Permanent URI for this collectionhttps://digital.lib.washington.edu/handle/1773/19720

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Shoaling Behavior as a Tool to Understand Microhabitat Use by Juvenile Chum Salmon, Oncorhynchus keta
(2009) Young, Carl Douglas
Density is most often used to compare estuarine microhabitats to determine if they are nurseries for juvenile marine fishes and invertebrates. But using only density fails to determine how organisms are using, or meeting life requirements, each microhabitat. Measuring in situ behavior of organisms is a tool that can complement density to better clarify how organisms are using estuarine microhabitats. Juvenile chum salmon, Oncorhynchus keta, is an example of an organism where behavior in nearshore estuarine microhabitats can be used to understand how they are using these microhabitats. Two estuarine microhabitats where juvenile chum salmon are found are the cobble/gravel beaches of the upper intertidal and eelgrass beds, Zostera marina, in the lower intertidal. The upper intertidal is about 2 – 3 times steeper than the lower intertidal. Eelgrass beds have long been thought to be particularly important because prey preferred by juvenile chum salmon are often found in higher densities in lower intertidal eelgrass beds. This study developed an in situ method of observing juvenile chum salmon shoaling behavior in nearshore microhabitats by video recording a 0.25 m2 quadrat nested inside a larger 8-m x 6-m rope grid divided into 2-m x 2-m squares. Shoaling behavior was used as a method to examine microhabitat use because predation and foraging are the two main factors that structure fish shoals. A number of quantitative metrics of shoal cohesiveness were developed and 4 of the 7 of these metrics produced significant results that indicated shoals were more cohesive in the lower intertidal than in the upper intertidal. From shoal movements and the depth distribution of fish in the upper and lower intertidal microhabitats it was discovered that there is a “stay shallow” mandate for juvenile chum salmon that likely developed as a way to avoid predators. This stay shallow mandate possibly limits microhabitat availability of the lower intertidal microhabitats when the tidal level is high. Also, because of the combination of differences in slope between upper and lower intertidal microhabitats and the stay shallow mandate, any interpretations of only density are likely to be flawed because fish concentrate in areas with the steeper beach slope. Possible explanations are increased predation in the lower intertidal or decreased foraging in the lower intertidal. One site, Tabook Point, in Dabob Bay had the lowest indices of shoal cohesiveness for both years as well as higher than expected density in the lower intertidal. This indicates that this site may be an important potential foraging ground during low tides.
BUILDING EFFECTIVE FISHERY ECOSYSTEM PLANS
(2016-11) Essington, Timothy; Levin, Phillip; Anderson, Lee; Bundy, Alida; Carothers, Courtney; Coleman, Felicia; Gerber, Leah; Grabowski, Jonathan; Houde, Edward; Jensen, Olaf; Mollmann, Christian; Rose, Kenneth; Sanchirico, James; Smith, Tony
Connections matter. That is the unifying principle of ecosystem-based fisheries management (EBFM). Ecological connections matter because fishing affects target species, predators, prey, competitors, bycatch species, and habitat. Economic connections matter because management affects fishermen, wholesalers, retailers, and recreational fishing guides. And social connections matter because fishing supports families and communities. U.S. fisheries management has made tremendous strides under the current management framework, which centers on single stocks or stock complexes rather than ecosystems. In addition, fishermen, managers, and many others have cooperated to reduce bycatch, conserve habitats, and improve the equity and safety of fisheries. However, conventional management has certain limitations. It generally focuses on one fishing sector at a time, which may unexpectedly lead to worse outcomes in another sector. It often considers a narrow range of issues, potentially overlooking other factors that shape fishery systems, such as loss of habitat and the behavior of people and markets. And fundamentally, the current system is atomized into individual fishery management plans (FMPs), often leaving little opportunity to consider overarching management goals or the trade-offs across fisheries that attend almost every decision. EBFM provides mechanisms to address these issues and many others. Yet despite this, and despite many other reports and studies that have made the case for EBFM, it has not been widely adopted. The Task Force believes a major reason is that there is no clear way to put its principles into practice.
Adult low pH exposure influences larval abundance in Pacific oysters (Crassostrea gigas)
(2019-01) Venkataraman, Yaamini R.; Spencer, Laura H.; Roberts, Steven B.
As negative effects of ocean acidification are experienced by coastal ecosystems, there is a growing trend to investigate the effect ocean acidification has on multiple generations. Parental exposure to ocean acidification has been shown to induce larval carryover effects, but whether or not an acute exposure to a stressor as an adult can influence the larval generation long after the stress has been removed has yet to be tested. To assess how a temporary exposure to experimental ocean acidification affects the ecologically and commercially relevant Pacific oyster (Crassostrea gigas), adult oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for seven weeks. Oysters were then held for eight weeks in ambient conditions, and subsequently reproductively conditioned for four weeks at ambient pH. After conditioning, oysters were strip-spawned to create four families based on maternal and paternal ocean acidification exposure. The number of D-hinge larvae were counted eighteen hours post fertilization. A sex-specific broodstock response was observed, where female exposure to low pH conditions resulted in fewer D-hinge larvae. This study demonstrates that the effects of ocean acidification can last beyond the time from when the environmental perturbation is experienced. Broadening the understanding of environmental memory will be valuable when considering an organism’s ability to persist in the face of environmental change.
Genetic and epigenetic insight into morphospecies in a reef coral
(2017-08) Dimond, James L; Gamblewood, Sanoosh K; Roberts, Steven B
Incongruence between conventional and molecular systematics has left the delineation of many species unresolved. Reef-building corals are no exception, with phenotypic plasticity among the most plausible explanations for alternative morphospecies. As potential molecular signatures of phenotypic plasticity, epigenetic processes may contribute to our understanding of morphospecies. We compared genetic and epigenetic variation in Caribbean branching Porites spp., testing the hypothesis that epigenetics—specifically, differential patterns of DNA methylation—play a role in alternative morphotypes of a group whose taxonomic status has been questioned. We used reduced representation genome sequencing to analyze over 1,000 single nucleotide polymorphisms and CpG sites in 27 samples of Porites spp. exhibiting a range of morphotypes from a variety of habitats in Belize. We found stronger evidence for genetic rather than epigenetic structuring, identifying three well-defined genetic groups. One of these groups exhibited significantly thicker branches, and branch thickness was a better predictor of genetic groups than depth, habitat, or symbiont type. In contrast, no clear epigenetic patterns emerged with respect to phenotypic or habitat variables. While there was a weak positive correlation between pairwise genetic and epigenetic distance, two pairs of putative clones exhibited substantial epigenetic differences, suggesting a strong environmental effect. We speculate that epigenetic patterns are a complex mosaic reflecting diverse environmental histories superimposed over a relatively small heritable component. Given the role of genetics in branching Porites spp. morphospecies we were able to detect with genome-wide sequencing, use of such techniques throughout the geographic range of these corals may help settle their phylogeny.
Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change
(Epigenetic Studies in Ecology and Evolution, 2015-10-01) Dimond, James L.; Roberts, Steven B.
DNA methylation is an epigenetic mark that plays an inadequately understood role in gene regulation, particularly in non-model species. Because it can be influenced by the environment, DNA methylation may contribute to the ability of organisms to acclimatize and adapt to environmental change. We evaluated the distribution of gene body methylation in reef-building corals, a group of organisms facing significant environmental threats. Gene body methylation in six species of corals was inferred from in silico transcriptome analysis of CpG O/E, an estimate of germline DNA methylation that is highly correlated with patterns of methylation enrichment. Consistent with what has been documented in most other invertebrates, all corals exhibited bimodal distributions of germline methylation suggestive of distinct fractions of genes with high and low levels of methylation. The hypermethylated fractions were enriched with genes with housekeeping functions, while genes with inducible functions were highly represented in the hypomethylated fractions. High transcript abundance was associated with intermediate levels of methylation. In three of the coral species, we found that genes differentially expressed in response to thermal stress and ocean acidification exhibited significantly lower levels of methylation. These results support a link between gene body hypomethylation and transcriptional plasticity that may point to a role of DNA methylation in the response of corals to environmental change.
Local adaptation limits lifetime reproductive success of dispersers in a wild salmon metapopulation
(University of Washington School of Aquatic & Fishery Sciences, 2014-10) Peterson, Daniel A.; Hilborn, Ray; Hauser, Lorenz;
Demographic and evolutionary dynamics in wild metapopulations are critically affected by the balance between dispersal and local adaptation. Where populations are demographically interconnected by migration, gene flow is often assumed to prevent local adaptation. However, reduced fitness of immigrants may limit gene flow between populations adapted to distinct habitat types, although direct quantification of the lifetime reproductive success of immigrants in the wild is lacking. Here, we show that dispersers between stream-spawning populations of sockeye salmon (Oncorhynchus nerka) had similar reproductive success to those that spawned in their natal stream, 2while dispersers from a different habitat (nearby lake beaches) produced half as many offspring. The stream- and beach-spawning ecotypes exhibited striking morphological differences despite their close spatial proximity, yet dispersal from the beach to the streams was more common than dispersal between streams, presenting empirical evidence that variation in immigrant reproductive success is important for the maintenance of intraspecific biodiversity.
Electronic Journal of Applied Multivariate Statistics
(FISH 560, 2008-01-01)
The ecological sciences have experienced immense growth over the course of this century, and chances are that they will continue to grow well on into the next millennium. There are some good reasons for this – ecology encompasses some of the most pressing concerns facing humanity. With recent advances in data collection technology and ambitious field research, ecologists are increasingly calling upon multivariate statistics to explore and test for patterns in their data. The goal of FISH 560 (Applied Multivariate Statistics for Ecologists) at the University of Washington is to introduce graduate students to the multivariate statistical techniques necessary to carry out sophisticated analyses and to critically evaluate scientific papers using these approaches. It is a practical, hands-on course emphasizing the analysis and interpretation of multivariate analysis, and covers the majority of approaches in common use by ecologists. To celebrate the hard work of past students, I am pleased to announce the creation of the Electronic Journal of Applied Multivariate Statistics (EJAMS). Each year, students in FISH 560 are required to write a final paper consisting of a statistical analysis of their own multivariate data set. These papers are submitted to EJAMS at the end of quarter and are peer reviewed by two other class members. A decision on publication is based on the reviewers’ recommendations and my own reading the paper. In closing, there is a need for the rapid dissemination of ecological research using multivariate statistics at the University of Washington. EJAMS is committed to this challenge.

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