Nick Tolimieri

Assemblage Structure of Eastern Pacific Groundfishes on the U.S. Continental Slope in Relation to Physical and Environmental Variables

Abstract We analyzed data from the National Marine Fisheries Service continental slope trawl surveys (1999–2002) to examine patterns in eastern Pacific groundfish assemblage structure in relation to longitude, latitude, depth, temperature, and interannual variation. The slope surveys spanned approximately 32–48°N and 200–1,200-m depths. We focused on the 26 most abundant species, which made up more than 95% of the catch in terms of biomass. Assemblage structure was strongly correlated with depth and latitude. For the most part, changes in assemblage structure appeared to be fairly continuous, although there were more-abrupt changes at approximately 500–600 m and in the vicinity of Point Conception and Cape Mendocino, California, and Cape Blanco, Oregon. There was also an interaction between depth and latitude; more northerly sites had deeper scores on the canonical axes than did more southerly sites of comparable depth. Shallower sites also showed more variation in assemblage structure with latitude than ...

Taxonomic Distinctness of Demersal Fishes of the California Current: Moving Beyond Simple Measures of Diversity for Marine Ecosystem-Based Management

Background Large-scale patterns or trends in species diversity have long interested ecologists. The classic pattern is for diversity (e.g., species richness) to decrease with increasing latitude. Taxonomic distinctness is a diversity measure based on the relatedness of the species within a sample. Here we examined patterns of taxonomic distinctness in relation to latitude (ca. 32–48 °N) and depth (ca. 50–1220 m) for demersal fishes on the continental shelf and slope of the US Pacific coast. Methodology/Principal Findings Both average taxonomic distinctness (AvTD) and variation in taxonomic distinctness (VarTD) changed with latitude and depth. AvTD was highest at approximately 500 m and lowest at around 200 m bottom depth. Latitudinal trends in AvTD were somewhat weaker and were depth-specific. AvTD increased with latitude on the shelf (50–150 m) but tended to decrease with latitude at deeper depths. Variation in taxonomic distinctness (VarTD) was highest around 300 m. As with AvTD, latitudinal trends in VarTD were depth-specific. On the shelf (50–150 m), VarTD increased with latitude, while in deeper areas the patterns were more complex. Closer inspection of the data showed that the number and distribution of species within the class Chondrichthyes were the primary drivers of the overall patterns seen in AvTD and VarTD, while the relatedness and distribution of species in the order Scorpaeniformes appeared to cause the relatively low observed values of AvTD at around 200 m. Conclusions/Significance These trends contrast to some extent the patterns seen in earlier studies for species richness and evenness in demersal fishes along this coast and add to our understanding of diversity of the demersal fishes of the California Current.

CHANGES IN BODY SIZE, ABUNDANCE, AND ENERGY ALLOCATION IN ROCKFISH ASSEMBLAGES OF THE NORTHEAST PACIFIC

Fish body size, a key driver of many aspects of fish population biology and ecology, is affected by fisheries that deplete the largest individuals. Rockfish (genus Sebastes) are a diverse group that has been heavily fished on the U.S. West Coast in recent decades. We examined trawl survey data from 1980 to 2001 to determine spatial and temporal trends in body size and density of 16 shelf rockfish species, including six that are considered overfished. Mean individual mass and maximum observed mass declined in the majority of species in one or more zoogeographic regions between central California and Washington. Density changes were far more variable in time and space, but in all regions, density declines were most often associated with large-bodied rockfish. We next estimated the impact of size and density changes on energy consumption and fecundity in a five-species rockfish assemblage that includes bocaccio (S. paucispinis), a large-bodied, overfished species. Indexes of both consumption and fecundity by the assemblage increased in the southern portion of the study area between 1980 and 2001 but decreased in the northern portion. Allocation of energy and reproductive potential within the assemblage shifted dramatically: relative to bocaccio, total energy consumption and fecundity indexes for the other four species increased by orders of magnitude from 1980 to 2001. These changes in community structure may affect the ability of bocaccio and other large rockfish species to recover from overfishing, especially in light of long-term declines in zooplankton production that may also be affecting rockfish size and production. Addressing these issues may require a regional, multispecies management approach.

Much ado about nothings: using zero similarity points in distance-decay curves

Distance decay is used to describe the (usually exponential) decay in ecological similarity of assemblages between two sites as a function of their distance apart along an environmental gradient. Exponential distance-decay curves are routinely fitted by calculating the ecological similarity between each pair of sites, and fitting a linear regression to the points on a scatter plot of log-similarity vs. distance (x-axis). However, pairs of sites where the assemblages have no species in common pose a problem, because the similarity is zero, and the log transformation cannot be applied. Common fixes to this problem (i.e., either removing or transforming the zero values) are shown to have undesirable consequences and to give widely disparate estimates. A new method is presented as a special case of a generalized dissimilarity model. It is fitted very quickly and easily using existing software, and it does not require removal or transformation of the zero similarity points. Its simplicity makes it convenient for use in conjunction with the resampling methods that are routinely employed to test hypotheses, to obtain standard errors of estimated parameters, or to compare distance-decay curves. A word of caution about standard application of the bootstrap is noted, and modified bootstrap and jackknife alternatives are demonstrated.

Scale and pattern of broadnose sevengill shark Notorynchus cepedianus movement in estuarine embayments

The detailed movements of 32 acoustically tagged broadnose sevengill shark Notorynchus cepedianus were documented in and around north-east Pacific Ocean estuarine embayments from 2005 to 2007. Arrangements of passive acoustic receivers allowed analysis of movement at several spatial scales, with sex and size examined as possible factors influencing the pattern and timing of these movements. Notorynchus cepedianus exhibited a distinctly seasonal pattern of estuary use over three consecutive years, entering Willapa Bay in the spring, residing therein for extended periods of time during the summer and dispersing into nearshore coastal habitats and over the continental shelf during the autumn. Notorynchus cepedianus within Willapa Bay showed spatio-temporal patterns of segregation by size and sex, with males and small females using peripheral southern estuary channels early in the season before joining large females, who remained concentrated in central estuary channels for the entire season. Individuals displayed a high degree of fidelity not only to Willapa Bay (63% were documented returning over three consecutive seasons), but also to specific areas within the estuary, showing consistent patterns of site use from year to year. Cross-estuary movement was common during the summer, with most fish also moving into an adjacent estuarine embayment for some extent of time. Most winter and autumn coastal detections of N. cepedianus were made over the continental shelf near Oregon and Washington, U.S.A., but there were also examples of individuals moving into nearshore coastal habitats further south into California, suggesting the feasibility of broad-scale coastal movements to known birthing and nursery grounds for the species. These findings contribute to a better understanding of N. cepedianus movement ecology, which can be used to improve the holistic management of this highly mobile apex predator in regional ecosystems.

Beta diversity of demersal fish assemblages in the North-Eastern Pacific: interactions of latitude and depth.

Knowledge of broad-scale global patterns in beta diversity (i.e., variation or turnover in identities of species) for marine systems is in its infancy. We analysed the beta diversity of groundfish communities along the North American Pacific coast, from trawl data spanning 32.57°N to 48.52°N and 51 m to 1200 m depth. Analyses were based on both the Jaccard measure and the probabilistic Raup-Crick measure, which accounts for variation in alpha diversity. Overall, beta diversity decreased with depth, and this effect was strongest at lower latitudes. Superimposed on this trend were peaks in beta diversity at around 400–600 m and also around 1000–1200 m, which may indicate high turnover around the edges of the oxygen minimum zone. Beta diversity was also observed to decrease with latitude, but this effect was only observed in shallower waters (<200 m); latitudinal turnover began to disappear at depths >800 m. At shallower depths (<200 m), peaks in latitudinal turnover were observed at ∼43°N, 39°N, 35°N and 31°N, which corresponded well with several classically observed oceanographic boundaries. Turnover with depth was stronger than latitudinal turnover, and is likely to reflect strong environmental filtering over relatively short distances. Patterns in beta diversity, including latitude-by-depth interactions, should be integrated with other biodiversity measures in ecosystem-based management and conservation of groundfish communities.

Linking the Trophic Fingerprint of Groundfishes to Ecosystem Structure and Function in the California Current

Mean trophic level (MTL) is one of the most widely used indicators of marine ecosystem health. It usually represents the relative abundance of fished species across a spectrum of TLs. The reality, ubiquity, and causes of a general decline in the MTL of fisheries catch through time, and whether fisheries catch tracks ecosystem level changes, have engendered much attention. However, the consequences of such patterns for broader ecosystem structure and function remain virtually unexplored. Along the Pacific U.S. Coast, previous work has documented fluctuations and a slow increase in ecosystem MTL from 1977 to 2004. Here, we document a decline in the ecosystem MTL of groundfishes in the same ecosystem from 2003 to 2011, the proximate cause of which was a decrease in the biomass of higher TL groundfishes. Using a food web model, we illustrate how these shifts in ecosystem structure may have resulted in short term, positive responses by many lower TL species in the broader ecosystem. In the longer term, the model predicts that initial patterns of prey release may be tempered in part by lagged responses of other higher TL species, such as salmon and seabirds. Although ecosystem functions related to specific groups like piscivores (excluding high-TL groundfishes) changed, aggregate ecosystem functions altered little following the initial reorganization of biomass, probably due to functional redundancy within the predator guild. Efforts to manage and conserve marine ecosystems will benefit from a fuller consideration of the information content contained within, and implied by, fisheries-independent TL indicators.

Differences in Responses of Chinook Salmon to Climate Shifts: Implications for Conservation

Understanding how organisms respond to climate is critical for focusing the debate about ways to recover imperiled or manage exploited species. However, efforts to understand climate effects on biota are complicated by differences among species in life history and physiology. Even within a species it is not clear if different populations will react similarly to large-scale climate trends. Climate regimes exhibit basin-wide effects similar to the El Ni no Southern Oscillation but persist for decades. In the North Pacific Ocean, two regime shifts (abrupt changes from one regime to another) occurred in 1976–1977 and 1989–1990 and had wide ranging effects on many species. We examined the response of chinook salmon from 9 evolutionary significant units (ESUs) to the regime shifts. While there was an average decline in spawner numbers associated with the regime shifts, ESUs did not respond in a uniform manner: some ESUs declined, some did not respond and one may have increased. Four ESUs currently listed under the Endangered Species Act may have declined more across regime boundaries than did the five non-listed ones. Interpretation of this result depends on two ESUs: the Snake River spring/summer run and the Central Valley fall run. The Snake River ESU had the largest decline and most sampling effort. If this ESU was excluded from the analysis, there was no evidence that listed and non-listed stocks responded differently to the regimes. The Central Valley ESU is currently a candidate for listing. If this ESU is considered to be a threatened or endangered, then listed ESUs declined more on average than did non-listed ESUs across the regime boundaries regardless of the Snake River ESU. As a whole, these results suggest that long-term climate trends are important to the dynamics of chinook populations and that sub-units of a species (here ESUs) can respond differently to these regimes.

Can we increase our confidence about the locations of biodiversity ‘hotspots' by using multiple diversity indices?

Some have suggested that targeting conservation efforts on biodiversity hotspots—areas of exceptionally high diversity—is the most efficient way to use limited resources to protect the most or rarest species. Moreover, the preservation of biodiversity is a focus for resource management and conservation because of the links between biodiversity and ecosystem function. However, there are many ways to define biodiversity and a plethora of diversity indices. Do these indices agree on where biodiversity hotspots are, and by extension, where conservation should take place? Here we use a habitat modeling approach to map spatial and temporal patterns in five community metrics of the demersal fish community in the California Current Large Marine Ecosystem: species density, species evenness, taxonomic distinctness, functional divergence and total biomass. Depth, bottom temperature, sediment grain size, and distance to hard substratum were included as covariates in the model. All indices showed strong spatial patterns and relationships with depth. Spatial patterns for functional divergence and total biomass varied among years, but other indices did not show temporal variation. We identified hotspots as cells where at least one index was in the top 5% or 10% of its range. There was minimal spatial overlap among 10% hotspots for the five indices. Over 40% of the study area was classified as a biodiversity hotspot by at least one metric. However, no area was identified as a hotspot by all five metrics, and only slightly more than one percent of the coast was identified as within a hotspot for three or more metrics. Since different indices represent various aspects of diversity, our results caution against the uninformed use of these indices in the identification of biodiversity hotspots. Instead, we must define our objectives and then choose the relevant metrics for the problem.

Population assessment using multivariate time-series analysis: A case study of rockfishes in Puget Sound

Abstract Estimating a populations growth rate and year‐to‐year variance is a key component of population viability analysis (PVA). However, standard PVA methods require time series of counts obtained using consistent survey methods over many years. In addition, it can be difficult to separate observation and process variance, which is critical for PVA. Time‐series analysis performed with multivariate autoregressive state‐space (MARSS) models is a flexible statistical framework that allows one to address many of these limitations. MARSS models allow one to combine surveys with different gears and across different sites for estimation of PVA parameters, and to implement replication, which reduces the variance‐separation problem and maximizes informational input for mean trend estimation. Even data that are fragmented with unknown error levels can be accommodated. We present a practical case study that illustrates MARSS analysis steps: data choice, model set‐up, model selection, and parameter estimation. Our case study is an analysis of the long‐term trends of rockfish in Puget Sound, Washington, based on citizen science scuba surveys, a fishery‐independent trawl survey, and recreational fishery surveys affected by bag‐limit reductions. The best‐supported models indicated that the recreational and trawl surveys tracked different, temporally independent assemblages that declined at similar rates (an average of −3.8% to −3.9% per year). The scuba survey tracked a separate increasing and temporally independent assemblage (an average of 4.1% per year). Three rockfishes (bocaccio, canary, and yelloweye) are listed in Puget Sound under the US Endangered Species Act (ESA). These species are associated with deep water, which the recreational and trawl surveys sample better than the scuba survey. All three ESA‐listed rockfishes declined as a proportion of recreational catch between the 1970s and 2010s, suggesting that they experienced similar or more severe reductions in abundance than the 3.8–3.9% per year declines that were estimated for rockfish populations sampled by the recreational and trawl surveys.