Power analysis for detecting trends in juvenile spotted seatrout abundance in Florida Bay

The spotted seatrout (Cynoscion nebulosus) is considered a key species relative to the implementation of the Comprehensive Everglades Restoration Plan (CERP). One of the goals of the CERP is to increase freshwater flows to Florida Bay. Increased freshwater flows can have potential positive and negative impacts on spotted seatrout populations. At low salinities, the planktonic eggs of spotted seatrout sink to the bottom and are not viable (Alshuth and Gilmore, 1994; Holt and Holt, 2002). On the other hand, increased freshwater flows can alleviate hypersaline conditions that could result in an expansion of the distribution of the early life stages of spotted seatrout (Thayer et al., 1999; Florida Department of Environmental Protection1). Thus it would be useful to develop a monitoring program that can detect changes in seatrout abundance on time scales short enough to be useful to resource managers. The NOAA Center for Coastal Fisheries and Habitat Research (NOAA) has made sporadic collections of juvenile seatrout using otter trawls since 1984 (see Powell et al, 2004). The results suggest that it might be useful to sample for seatrout in as many as eight different areas or basins (Figure 1): Bradley Key, Sandy Key, Johnson Key, Palm Key, Snake Bight, Central, Whipray and Crocodile Dragover. Unfortunately, logistical constraints are likely to limit the number of tows to about 40 per month over a period of six months each year. Inasmuch as few seatrout are caught in any given tow and the proportion of tows with zero seatrout is often high, it is important to determine how best to allocate this limited sampling effort among the various basins so that any trends in abundance may be detected with sufficient statistical confidence. (PDF contains 16 pages

A catch-free stock assessment model with application to goliath grouper (Epinephelus itajara) off southern Florida

Many modern stock assessment methods provide the machinery for determining the status of a stock in relation to certain reference points and for estimating how quickly a stock can be rebuilt. However, these methods typically require catch data, which are not always available. We introduce a model-based framework for estimating reference points, stock status, and recovery times in situations where catch data and other measures of absolute abundance are unavailable. The specif ic estimator developed is essentially an age-structured production model recast in terms relative to pre-exploitation levels. A Bayesian estimation scheme is adopted to allow the incorporation of pertinent auxiliary information such as might be obtained from meta-analyses of similar stocks or anecdotal observations. The approach is applied to the population of goliath grouper (Epinephelus itajara) off southern Florida, for which there are three indices of relative abundance but no reliable catch data. The results confirm anecdotal accounts of a marked decline in abundance during the 1980s followed by a substantial increase after the harvest of goliath grouper was banned in 1990. The ban appears to have reduced fishing pressure to between 10% and 50% of the levels observed during the 1980s. Nevertheless, the predicted fishing mortality rate under the ban appears to remain substantial, perhaps owing to illegal harvest and depth-related release mortality. As a result, the base model predicts that there is less than a 40% chance that the spawning biomass will recover to a level that would produce a 50% spawning potential ratio

Standardized Visual Counts of Goliath Grouper off South Florida and Their Possible Use as Indices of Abundance

Two visual surveys are examined for evidence that the number of goliath grouper has increased in the waters off South Florida since a harvest moratorium was imposed in 1990. Both surveys are standardized to account for the unbalanced design of the sampling procedure. The first survey is effectively a census of the number of goliath grouper at five artificial reef sites in the Gulf of Mexico about 90 miles north of Key West, Florida. It is standardized by use of the canonical log-linear model. The second survey includes the observations of many different SCUBA divers at 32 sites scattered along the Atlantic coast of Florida from the Dry Tortugas to Jupiter. The canonical log-linear model is not appropriate for standardizing this data set because observations of 2-10 fish are recorded only as two or more. To accommodate this feature, we developed a standardization procedure based on a censored Poisson distribution. The most important factors in standardizing the two surveys were the year and location. Seasonal effects were also statistically significant but had little effect on the results because most of the dives in any given year were conducted during the warm season. Both the standardized series indicate a substantial increase in abundance since the 1990 moratorium

A new growth model for red drum (Sciaenops ocellatus) that accommodates seasonal and ontogenic changes in growth rates

The red drum (Sciaenops ocellatus) is a popular gamefish found throughout the coastal waters of the Gulf of Mexico and along the eastern seaboard as far north as Massachusetts. Juvenile red drum grow extremely rapidly, especially during the warmer months, but adults grow very little. In fact, the change in growth with age is so abrupt that the standard von Bertalanffy curve has proven inadequate— the predicted lengths of younger fish are generally too large and the predicted lengths of older fish too small (see Beckman et al., 1988; Murphy and Taylor, 1990)

Modeling terminal-year fishing mortality rates in western Atlantic bluefin tuna virtual population analyses

Virtual population analysis requires information on the fishing mortality rate (or abundance) for one age group from each cohort. In many cases available data are insufficient to estimate these rates for every age group and structural assumptions must be imposed to reduce the number of effective parameters. Past assessments of western Atlantic bluefin tuna (Thunnus thynnus) have reduced the number of parameters by assuming pre-specified values for the ratios of the fishing mortality rates on adjacent age groups. More recent bluefin tuna assessments have estimated terminal fishing mortality rates (F) on each age with a constraint that restricts change from one year to the next. We explore the implications of these methods of estimating terminal-year F through retrospective analyses of the 2006 bluefin tuna assessment and through stochastic simulations. The use of pre-specified ratios for F created strong retrospective biases and may have led to overly optimistic projections. Constraining annual changes in the terminal-year F appeared to mute retrospective patterns and resulted in abundance projections less prone to spurious initial leaps. Simulation results indicate that the constraint improves estimation, particularly with moderate to low interannual changes in selectivity

On Making Statistical Inferences Regarding the Relationship between Spawners and Recruits and the Irresolute Case of Western Atlantic Bluefin Tuna (Thunnus thynnus).

Forecasts of the future abundance of western Atlantic bluefin tuna (Thunnus thynnus) have, for nearly two decades, been based on two competing views of future recruitment potential: (1) a "low" recruitment scenario based on hockey-stick (two-line) curve where the expected level of recruitment is set equal to the geometric mean of the recruitment estimates for the years after a supposed regime-shift in 1975, and (2) a "high" recruitment scenario based on a Beverton-Holt curve fit to the time series of spawner-recruit pairs beginning in 1970. Several investigators inferred the relative plausibility of these two scenarios based on measures of their ability to fit estimates of spawning biomass and recruitment derived from stock assessment outputs. Typically, these comparisons have assumed the assessment estimates of spawning biomass are known without error. It is shown here that ignoring error in the spawning biomass estimates can predispose model-choice approaches to favor the regime-shift hypothesis over the Beverton-Holt curve with higher recruitment potential. When the variance of the observation error approaches that which is typically estimated for assessment outputs, the same model-choice approaches tend to favor the single Beverton-Holt curve. For this and other reasons, it is argued that standard model-choice approaches are insufficient to make the case for a regime shift in the recruitment dynamics of western Atlantic bluefin tuna. A more fruitful course of action may be to move away from the current high/low recruitment dichotomy and focus instead on adopting biological reference points and management procedures that are robust to these and other sources of uncertainty

Parameter estimates for the Beverton-Holt, three-line regime shift and Beverton-Holt regime shift models fitted to the spawning stock biomass and recruitment estimates from the 2014 assessment of western Atlantic bluefin tuna.

<p>Parameter estimates for the Beverton-Holt, three-line regime shift and Beverton-Holt regime shift models fitted to the spawning stock biomass and recruitment estimates from the 2014 assessment of western Atlantic bluefin tuna.</p

Spawning stock biomass (t) and recruitment estimates (in number) from the 2014 stock assessment (note that results for the last three years were not included in the AICc computations because they were considered to be poorly determined by the assessment working group).

<p>Spawning stock biomass (t) and recruitment estimates (in number) from the 2014 stock assessment (note that results for the last three years were not included in the AICc computations because they were considered to be poorly determined by the assessment working group).</p

The Journey from Overfishing to Sustainability for Atlantic Bluefin Tuna, Thunnus thynnus

The Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758), is the largest of the tunas and among the largest of all bony fish, reaching to 3.3 m and 725 kg (Cort et al. 2013). The species is highly migratory and broadly distributed through most of the Atlantic Ocean and its adjacent seas (Figure 1), thanks in large measure to a highly developed thermoregulatory system that allows it to thrive in waters as cold as 3°C (Carey and Lawson 1973, Block et al. 2001). Their great size and power has captivated fishermen and scientists alike since ancient times. Aristotle, Pliny the Elder, and Oppian wrote of them two thousand years ago, and their bones have been excavated from prehistoric sites dating back to the Stone Age (Aristotelis III BC; Plinius 65 CE; Salvini 1738; Ravier and Fromentin 2001; Di Natale 2012, 2014; Puncher et al. 2016). The fascination with Atlantic bluefin tuna (ABFT) has only grown in modern times. The demand for bluefin tuna for the sashimi market in Japan fuels a lucrative commercial fishery where a single fish can be worth tens of thousands of dollars. Researchers passionately pursue investigations on ABFT, writing dozens of scientific papers every year. Public interest in this charismatic species, fanned by warnings of overfishing, has risen to a level usually reserved for whales (Porch 2005). The story of ABFT has been told in compelling documentaries and popular books such as Safina’s (1998) Song for the Blue Ocean, Maggio’s (2000a,b) Mattanza, and Ellis’s (2008) Tuna: A Love Story. They even have their own reality show in National Geographic’s Wicked Tuna. As Ellis puts it, ABFT just may be “the worlds best-loved fish.”