Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

10 p.

A probability-based approach to setting annual catch levels.

The requirement of setting annual catch limits to prevent overfishing has been added to the Magnuson-Stevens Fishery Conservation and Management Reauthorization Act of 2006 (MSRA). Because this requirement is new, a body of applied scientific practice for deriving annual catch limits and accompanying targets does not yet exist. This article demonstrates an approach to setting levels of catch that is intended to keep the probability of future overfishing at a preset low level. The proposed framework is based on stochastic projection with uncertainty in population dynamics. The framework extends common projection methodology by including uncertainty in the limit reference point and in management implementation, and by making explicit the risk of overfishing that managers consider acceptable. The approach is illustrated with application to gag (Mycteroperca microlepis), a grouper that inhabits the waters off the southeastern United States. Although devised to satisfy new legislation of the MSRA, the framework has potential application to any fishery where the management goal is to limit the risk of overfishing by controlling catch.

Multi-species and multi-interest management: An ecosystem approach to market squid (Loligo opalescens) harvest in California

Market squid (Loligo opalescens) plays a vital role in the California ecosystem and serves as a major link in the food chain as both a predator and prey species. For over a century, market squid has also been harvested off the California coast from Monterey to San Pedro. Expanding global markets, coupled with a decline in squid product from other parts of the world, in recent years has fueled rapid expansion of the virtually unregulated California fishery. Lack of regulatory management, in combination with dramatic increases in fishing effort and landings, has raised numerous concerns from the scientific, fishing, and regulatory communities. In an effort to address these concerns, the National Oceanic and Atmospheric Administration’s (NOAA) Channel Islands National Marine Sanctuary (CINMS) hosted a panel discussion at the October 1997 California Cooperative Oceanic and Fisheries Investigations (CalCOFI) Conference; it focused on ecosystem management implications for the burgeoning market squid fishery. Both panel and audience members addressed issues such as: the direct and indirect effects of commercial harvesting upon squid biomass; the effects of harvest and the role of squid in the broader marine community; the effects of environmental variation on squid population dynamics; the sustainability of the fishery from the point of view of both scientists and the fishers themselves; and the conservation management options for what is currently an open access and unregulated fishery. Herein are the key points of the ecosystem management panel discussion in the form of a preface, an executive summary, and transcript. (PDF contains 33 pages.)

The precautionary approach and the management of the European eel (Anguilla anguilla) – critical remarks

Recruitment and commercial catches of European eel have been in decline since the late 1970s. So far, the reasons are not well understood. A range of potential natural and anthropogenic reasons have been discussed, but the relative importance of the factors is unknown. As a consequence of the decline in recruitment an urgent need for protective management measures was concluded. The main approach is to restrict the fishery on eel, in particular with reference to the precautionary approach. However, in view of the lack of knowledge on the factors responsible for the recruitment decline and by considering that many yellow and silver eel stocks in freshwaters depend on restocking by the fishery, such simplified conclusions are critically discussed. A concept for the sustainable management of eel has to include 1) research on the factors determining the population dynamics, in particular during the oceanic stages, 2) a stronger consideration of socio-economic aspects, and 3) intensified research on artificial reproduction and rearing of eel.

Periodic solutions of integro-differential equations which arise in population dynamics

The problem of the existence and stability of periodic solutions of infinite-lag integra-differential equations is considered. Specifically, the integrals involved are of the convolution type with the dependent variable being integrated over the range (- ∞,t), as occur in models of population growth. It is shown that Hopf bifurcation of periodic solutions from a steady state can occur, when a pair of eigenvalues crosses the imaginary axis. Also considered is the existence of traveling wave solutions of a model population equation allowing spatial diffusion in addition to the usual temporal variation. Lastly, the stability of the periodic solutions resulting from Hopf bifurcation is determined with aid of a Floquet theory.

The first chapter is devoted to linear integro-differential equations with constant coefficients utilizing the method of semi-groups of operators. The second chapter analyzes the Hopf bifurcation providing an existence theorem. Also, the two-timing perturbation procedure is applied to construct the periodic solutions. The third chapter uses two-timing to obtain traveling wave solutions of the diffusive model, as well as providing an existence theorem. The fourth chapter develops a Floquet theory for linear integro-differential equations with periodic coefficients again using the semi-group approach. The fifth chapter gives sufficient conditions for the stability or instability of a periodic solution in terms of the linearization of the equations. These results are then applied to the Hopf bifurcation problem and to a certain population equation modeling periodically fluctuating environments to deduce the stability of the corresponding periodic solutions.

Exploitation of soil biota ecosystem services in agriculture: a bioeconomic approach

24 p.

A modelling approach to the development of an active management strategy for the Queen Elizabeth II reservoir

This article outlines the outcome of work that set out to provide one of the specified integral contributions to the overarching objectives of the EU- sponsored LIFE98 project described in this volume. Among others, these included a requirement to marry automatic monitoring and dynamic modelling approaches in the interests of securing better management of water quality in lakes and reservoirs. The particular task given to us was to devise the elements of an active management strategy for the Queen Elizabeth II Reservoir. This is one of the larger reservoirs supplying the population of the London area: after purification and disinfection, its water goes directly to the distribution network and to the consumers. The quality of the water in the reservoir is of primary concern, for the greater is the content of biogenic materials, including phytoplankton, then the more prolonged is the purification and the more expensive is the treatment. Whatever good that phytoplankton may do by way of oxygenation and oxidative purification, it is eventually relegated to an impurity that has to be removed from the final product. Indeed, it has been estimated that the cost of removing algae and microorganisms from water represents about one quarter of its price at the tap. In chemically fertile waters, such as those typifying the resources of the Thames Valley, there is thus a powerful and ongoing incentive to be able to minimise plankton growth in storage reservoirs. Indeed, the Thames Water company and its predecessor undertakings, have a long and impressive history of confronting and quantifying the fundamentals of phytoplankton growth in their reservoirs and of developing strategies for operation and design to combat them. The work to be described here follows in this tradition. However, the use of the model PROTECH-D to investigate present phytoplankton growth patterns in the Queen Elizabeth II Reservoir questioned the interpretation of some of the recent observations. On the other hand, it has reinforced the theories underpinning the original design of this and those Thames-Valley storage reservoirs constructed subsequently. The authors recount these experiences as an example of how simulation models can hone the theoretical base and its application to the practical problems of supplying water of good quality at economic cost, before the engineering is initiated.

From organism to population: the role of life-history theory

The role of life-history theory in population and evolutionary analyses is outlined. In both cases general life histories can be analysed, but simpler life histories need fewer parameters for their description. The simplest case, of semelparous (breed-once-then-die) organisms, needs only three parameters: somatic growth rate, mortality rate and fecundity. This case is analysed in detail. If fecundity is fixed, population growth rate can be calculated direct from mortality rate and somatic growth rate, and isoclines on which population growth rate is constant can be drawn in a ”state space” with axes for mortality rate and somatic growth rate. In this space density-dependence is likely to result in a population trajectory from low density, when mortality rate is low and somatic growth rate is high and the population increases (positive population growth rate) to high density, after which the process reverses to return to low density. Possible effects of pollution on this system are discussed. The state-space approach allows direct population analysis of the twin effects of pollution and density on population growth rate. Evolutionary analysis uses related methods to identify likely evolutionary outcomes when an organism's genetic options are subject to trade-offs. The trade-off considered here is between somatic growth rate and mortality rate. Such a trade-off could arise because of an energy allocation trade-off if resources spent on personal defence (reducing mortality rate) are not available for somatic growth rate. The evolutionary implications of pollution acting on such a trade-off are outlined.

The Status of the United States Population of Night Shark, Carcharhinus signatus

Night sharks, Carcharhinus signatus, are an oceanic species generally occurring in outer continental shelf waters in the western North Atlantic Ocean including the Caribbean Sea and Gulf of Mexico. Although not targeted, night sharks make up a segment of the shark bycatch in the pelagic longline fishery. Historically, night sharks comprised a significant proportion of the artisanal Cuban shark fishery but today they are rarely caught. Although information from some fisheries has shown a decline in catches of night sharks, it is unclear whether this decline is due to changes in fishing tactics, market, or species identification. Despite the uncertainty in the decline, the night shark is currently listed as a species of concern due to alleged declines in abundance resulting from fishing effort, i.e. overutilization. To assess their relevance to the species of concern list, we collated available information on the night shark to provide an analysis of its status. Night shark landings were likely both over- and under-reported and thus probably did not reflect all commercial and recreational catches, and overall they have limited relevance to the current status of the species. Average size information has not changed considerably since the 1980’s based on information from the pelagic longline fishery when corrected for gear bias. Analysis of biological information indicates night sharks have intrinsic rates of increase (r) about 10% yr–1 and have moderate rebound potential and an intermediate generation time compared to other sharks. An analysis of trends in relative abundance from four data sources gave conflicting results, with one series in decline, two series increasing, and one series relatively flat. Based on the analysis of all currently available information, we believe the night shark does not qualify as a species of concern but should be retained on the prohibited species list as a precautionary approach to management until a more comprehensive stock assessment can be conducted.

Modeling the Potential Spread of the Recently Identified Non-Native Panther Grouper (Chromileptes altivelis)in the Atlantic Using a Cellular Automaton Approach

The Indo-pacific panther grouper (Chromileptes altiveli) is a predatory fish species and popular imported aquarium fish in the United States which has been recently documented residing in western Atlantic waters. To date, the most successful marine invasive species in the Atlantic is the lionfish (Pterois volitans/miles), which, as for the panther grouper, is assumed to have been introduced to the wild through aquarium releases. However, unlike lionfish, the panther grouper is not yet thought to have an established breeding population in the Atlantic. Using a proven modeling technique developed to track the lionfish invasion, presented is the first known estimation of the potential spread of panther grouper in the Atlantic. The employed cellular automaton-based computer model examines the life history of the subject species including fecundity, mortality, and reproductive potential and combines this with habitat preferences and physical oceanic parameters to forecast the distribution and periodicity of spread of this potential new invasive species. Simulations were examined for origination points within one degree of capture locations of panther grouper from the United States Geological Survey Nonindigenous Aquatic Species Database to eliminate introduction location bias, and two detailed case studies were scrutinized. The model indicates three primary locations where settlement is likely given the inputs and limits of the model; Jupiter Florida/Vero Beach, the Cape Hatteras Tropical Limit/Myrtle Beach South Carolina, and Florida Keys/Ten Thousand Islands locations. Of these locations, Jupiter Florida/Vero Beach has the highest settlement rate in the model and is indicated as the area in which the panther grouper is most likely to become established. This insight is valuable if attempts are to be made to halt this potential marine invasive species

An approach to estimating rockfish biomass based on larval production, with application to Sebastes jordani

An assessment of the total biomass of shortbelly rockfish (Sebastes jordani) off the central California coast is presented that is based on a spatially extensive but temporally restricted ichthyoplankton survey conducted during the 1991 spawning season. Contemporaneous samples of adults were obtained by trawl sampling in the study region. Daily larval production (7.56 × 1010 larvae/d) and the larval mortality rate (Z=0.11/d) during the cruise were estimated from a larval “catch curve,” wherein the logarithm of total age-specific larval abundance was regressed against larval age. For this analysis, larval age compositions at each of the 150 sample sites were determined by examination of otolith microstructure from subsampled larvae (n=2203), which were weighted by the polygonal Sette-Ahlstrom area surrounding each station. Female population weight-specific fecundity was estimated through a life table analysis that incorporated sex-specific differences in adult growth rate, female maturity, fecundity, and natural mortality (M). The resulting statistic (102.17 larvae/g) was insensitive to errors in estimating M and to the pattern of recruitment. Together, the two analyses indicated that a total biomass equal to 1366 metric tons (t)/d of age-1+ shortbelly rockfish (sexes combined) was needed to account for the observed level of spawning output during the cruise. Given the long-term seasonal distribution of spawning activity in the study area, as elucidated from a retrospective examination of California Cooperative Oceanic Fisheries Investigation (CalCOFI) ichthyoplankton samples from 1952 to 1984, the “daily” total biomass was expanded to an annual total of 67,392 t. An attempt to account for all sources of error in the derivation of this estimate was made by application of the delta-method, which yielded a coefficient of variation of 19%. The relatively high precision of this larval production method, and the rapidity with which an absolute biomass estimate can be obtained, establishes that, for some species of rockfish (Sebastes spp.), it is an attractive alternative to traditional age-structured stock assessments.

Feasibility of damage detection using vibration data in a population of cylinders

The feasibility of vibration data to identify damage in a population of cylindrical shells is assessed. Vibration data from a population of cylinders were measured and modal analysis was employed to obtain natural frequencies and mode shapes. The mode shapes were transformed into the Coordinate Modal Assurance Criterion (COMAC). The natural frequencies and the COMAC before and after damage for a population of structures show that modal analysis is a viable route to damage identification in a population of nominally identical cylinders. Modal energies, which are defined as the integrals of the real and imaginary components of the frequency response functions over various frequency ranges, were extracted and transformed into the Coordinate Modal Energy Assurance Criterion (COMEAC). The COMEAC before and after damage show that using modal energies is a viable approach to damage identification in a population of cylinders.

A markov chain Monte Carlo method for estimating population mixing using Y-chromosome markers: Mixing of the Han people in China

We present a new approach for estimating mixing between populations based on non-recombining markers, specifically Y-chromosome microsatellites. A Markov chain Monte Carlo (MCMC) Bayesian statistical approach is used to calculate the posterior probability

Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana)

Golden monkey (Rhinopithecus roxellana), namely the snub-nosed monkey, is a well-known endangered primate, which distributes only in the central part of mainland China. As an effort to understand the current genetic status as well as population history of this species, we collected a sample of 32 individuals from four different regions, which cover the major habitat of this species. Forty-four allozyme loci were surveyed in our study by allozyme electrophoresis, none of which was found to be polymorphic. The void of polymorphism compared with that of other nonhuman primates is surprising particularly considering that the current population size is many times larger than that of some other endangered species. Since many independent loci are surveyed in this Study, the most plausible explanation for our observation is that the population has experienced a recent bottleneck. We used a coalescent approach to explore various scenarios of population bottleneck and concluded that the most recent bottleneck could have happened within the last 15,000 years. Moreover, the proposed simulation approach could be useful to researchers who need to analyze the non- or low-polymorphism data.

Lack of mtDNA control region variation in Hainan Eld's deer: Consequence of a recent population bottleneck?

We find no genetic variation at 550bp of mtDNA control region among 55 Hainan Eld's deer in an island population that has suffered recent population contractions. Congeneric species show high levels of variation at this locus. We use a simulation approach to test the likelihood of various bottleneck scenarios, and show, in the context of what is known about the recent demographic history of this population, that there are credible scenarios for a bottleneck driven by hunting pressure in the 1960s that could account for the lack of variation at this locus.