MARINE RESERVES FOR FISHERIES MANAGEMENT

Conventional methods of regulating commercial fisheries restrict catch by limiting either the quantity or efficiency of fishing effort, or by putting direct limits on catch. These regulatory practices are neither feasible nor desirable for many fisheries, and have failed to conserve fishery stocks in other fisheries. Marine reserves may be an effective alternative management strategy for some fisheries. Here we develop a dynamic model of marine reserves applicable to inshore fisheries. In contrast to previous models of reserves, the model is fully dynamic and provides information on both equilibrium conditions and the path to equilibrium. A simulation model based on red snapper data from the Gulf of Mexico is presented. The simulation results suggest that marine reserves can sustain or increase yields for moderate to heavily fished fisheries but will probably not improve yields for lightly fished fisheries.Resource /Energy Economics and Policy,

Sample Size Requirements for In Situ Vegetation and Substrate Classifications in Shallow, Natural Nebraska Lakes

We assessed the precision of visual estimates of vegetation and substrate along transects in 15 shallow, natural Nebraska lakes. Vegetation type (submergent or emergent), vegetation density (sparse, moderate, or dense), and substrate composition (percentage sand, muck, and clay; to the nearest 10%) were estimated at 25–70 sampling sites per lake by two independent observers. Observer agreement for vegetation type was 92%. Agreement ranged from 62.5% to 90.1% for substrate composition. Agreement was also high (72%) for vegetation density estimates. The relatively high agreement between estimates was likely attributable to the homogeneity of the lake habitats. Nearly 90% of the substrate sites were classified as 0% clay, and over 68% as either 0% or 100% sand. When habitats were homogeneous, less than 40 sampling sites per lake were required for 95% confidence that habitat composition was within 10% of the true mean, and over 100 sites were required when habitats were heterogeneous. Our results suggest that relatively high precision is attainable for vegetation and substrate mapping in shallow, natural lakes

Match–Mismatch Regulation for Bluegill and Yellow Perch Larvae and Their Prey in Sandhill Lakes

Food availability may regulate fish recruitment, both directly and indirectly. The availability of zooplankton, especially to newly hatched larvae, is thought to be crucial to their early growth and survival. We examined stomach contents of larval bluegill Lepomis macrochirus and yellow perch Perca flavescens in Pelican Lake and Cameron Lake, Nebraska, in 2004 and 2005. We also determined zooplankton availability and calculated prey selection using Chesson’s a. In addition, we investigated potential match–mismatch regulation of recruitment from 2004 to 2008. Bluegill positively selected copepod nauplii and Bosmina spp., and yellow perch often selected copepods. Abundant zooplankton populations were available for consumption. Matches of both larval bluegill and yellow perch abundance to zooplankton abundance were detected in all years; exact matches were common. Mismatches in predator and prey production were not observed. Predation by age-0 yellow perch on age-0 bluegill was not observed, even though yellow perch hatched 2 mo prior to bluegill. Given that zooplankton were abundant and well-timed to larval fish relative abundance over the time span of this study, the match–mismatch hypothesis alone may not fully account for observed recruitment variability in these populations. Environmental conditions may also affect recruitment and warrant further investigation

Match- mismatch Regulation for Bluegill and Yellow Perch Larvae and Their Prey in Sandhill Lakes

Food availability may regulate fish recruitment, both directly and indirectly. The availability of zooplankton, especially to newly hatched larvae, is thought to be crucial to their early growth and survival. We examined stomach contents of larval bluegill Lepomis macrochirus and yellow perch Perca flavescens in Pelican Lake and Cameron Lake, Nebraska, in 2004 and 2005. We also determined zooplankton availability and calculated prey selection using Chesson’s a. In addition, we investigated potential match–mismatch regulation of recruitment from 2004 to 2008. Bluegill positively selected copepod nauplii and Bosmina spp., and yellow perch often selected copepods. Abundant zooplankton populations were available for consumption. Matches of both larval bluegill and yellow perch abundance to zooplankton abundance were detected in all years; exact matches were common. Mismatches in predator and prey production were not observed. Predation by age-0 yellow perch on age-0 bluegill was not observed, even though yellow perch hatched 2 mo prior to bluegill. Given that zooplankton were abundant and well-timed to larval fish relative abundance over the time span of this study, the match–mismatch hypothesis alone may not fully account for observed recruitment variability in these populations. Environmental conditions may also affect recruitment and warrant further investigation

The effects of charge transfer inefficiency (CTI) on galaxy shape measurements

(Abridged) We examine the effects of charge transfer inefficiency (CTI) during CCD readout on galaxy shape measurements required by studies of weak gravitational lensing. We simulate a CCD readout with CTI such as that caused by charged particle radiation damage. We verify our simulations on data from laboratory-irradiated CCDs. Only charge traps with time constants of the same order as the time between row transfers during readout affect galaxy shape measurements. We characterize the effects of CTI on various galaxy populations. We baseline our study around p-channel CCDs that have been shown to have charge transfer efficiency up to an order of magnitude better than several models of n-channel CCDs designed for space applications. We predict that for galaxies furthest from the readout registers, bias in the measurement of galaxy shapes, Delta(e), will increase at a rate of 2.65 +/- 0.02 x 10^(-4) per year at L2 for accumulated radiation exposure averaged over the solar cycle. If uncorrected, this will consume the entire shape measurement error budget of a dark energy mission within about 4 years. Software mitigation techniques demonstrated elsewhere can reduce this by a factor of ~10, bringing the effect well below mission requirements. CCDs with higher CTI than the ones we studeied may not meet the requirements of future dark energy missions. We discuss ways in which hardware could be designed to further minimize the impact of CTI.Comment: 11 pages, 6 figures, and 2 tables. Accepted for publication in PAS

Overwinter Mortality of Sympatric Juvenile Bluegill and Yellow Perch in Mid-Temperate Sandhill lakes, Nebraska, U.S.A

Substantial mortality can occur in age-0 fish populations during their first year of life, especially in winter; this can potentially influence overall recruitment into the adult population. As such, we compared relative abundances between fall and spring catches of sympatric juvenile bluegill Lepomis macrochirus Rafinesque and yellow perch Perca flavescens (Mitchill) to evaluate the magnitude of overwinter mortality across locations (five lakes for two years) and through time (one lake for six years). In addition, we compared both quantile-quantile and increment plots, based on length-frequency histograms from fall- and spring-caught cohorts from 2004 to 2010, to determine if mortality was sizeselective while accounting for over winter growth. Bluegill relative abundances (as indexed by catch-per-unit-effort) significantly decreased from fall to spring, although size-selective mortality was not detected in 10 instances. Yellow perch relative abundances were similar from fall to spring in five Nebraska Sandhill lakes; however, size-selective mortality was detected, with size-selective over winter mortality of smaller individuals occurring in one of eight instances, whereas greater mortality in larger individuals occurred in two instances. Positive growth occurred in both species but was variable among lakes and appeared to be system-specific. In Nebraska Sandhill lakes, over winter mortality likely differs between these two species in its severity, size-selective effect, and scale (i.e., lake-specific vs. large-scale processes), and is likely influenced by combinations of these (and potentially other) factors

Overwinter Mortality of Sympatric Juvenile Bluegill and Yellow Perch in Mid-temperate Prairie Lakes

Substantial mortality can occur in age-0 fish populations during their first year of life, especially in winter; this can potentially influence overall recruitment into the adult population. As such, we compared relative abundances between fall and spring catches of sympatric juvenile bluegill Lepomis macrochirus Rafinesque and yellow perch Perca flavescens (Mitchill) to evaluate the magnitude of overwinter mortality across locations (five lakes for two years) and through time (one lake for six years). In addition, we compared both quantile-quantile and increment plots, based on length-frequency histograms from fall- and spring-caught cohorts from 2004 to 2010, to determine if mortality was sizeselective while accounting for over winter growth. Bluegill relative abundances (as indexed by catch-per-unit-effort) significantly decreased from fall to spring, although size-selective mortality was not detected in 10 instances. Yellow perch relative abundances were similar from fall to spring in five Nebraska Sandhill lakes; however, size-selective mortality was detected, with size-selective over winter mortality of smaller individuals occurring in one of eight instances, whereas greater mortality in larger individuals occurred in two instances. Positive growth occurred in both species but was variable among lakes and appeared to be system-specific. In Nebraska Sandhill lakes, over winter mortality likely differs between these two species in its severity, size-selective effect, and scale (i.e., lake-specific vs. large-scale processes), and is likely influenced by combinations of these (and potentially other) factors

Evidence for Bluegill Spawning Plasticity Obtained by Disentangling Complex Factors Related to Recruitment

Fishes can exhibit many forms of plasticity to maximize fitness. However, limited information exists on the ability of freshwater fish to adjust spawning behavior and characteristics (e.g., timing, duration, magnitude of spawning events) to minimize mortality of recruits and ultimately maximize fitness.Wewanted to test the life history hypothesis for bluegill (Lepomis macrochirus) (i.e., opportunistic strategy) utilizing existing literature and results from our study to further evaluate the potential for spawning plasticity in this species. Our objective was to identify bluegill recruitment bottlenecks (i.e., periods of high mortality) and factors associated with these events in a single lake during 7 consecutive years. Bluegills exhibited shorter spawning durations and fewer spawning pulses (i.e., peaks in larval production) compared with bluegill in previous studies. Late-hatched (compared with early-hatched) bluegills consistently contributed the most to the fall juvenile population; these recruitment patterns were primarily attributed to biotic drivers. Our study suggests that bluegill could exhibit spawning plasticity and extends our current understanding of adaptations that are potentially capable of increasing fitness for a freshwater fish species under a wide range of environmental conditions and uncertainty. Les poissons peuvent présenter différentes formes de plasticité leur permettant de maximiser leur aptitude. Peu de renseignements sont toutefois disponibles sur la capacité des poissons d\u27eau douce d\u27ajuster leur comportement de frai et les caractéristiques de ce dernier (p. ex. moment, durée, magnitude des évènements de frai) afin de minimiser la mortalité des recrues et, au final, maximiser leur aptitude. Nous voulions tester l\u27hypothèse du cycle biologique (c.-a` -d. stratégie opportuniste) pour le crapet arlequin (Lepomis macrochirus) a` la lumière d\u27études existantes et des résultats de notre étude pour évaluer plus en détail le potentiel de plasticité du frai chez cette espèce. L\u27objectif consistait a` cerner les goulots d\u27étranglement en ce qui concerne le recrutement de crapets arlequins (c.-a` -d. périodes de mortalité élevée) et les facteurs associés a` ces évènements dans un seul lac pendant 7 années consécutives. Comparativement aux études antérieures, les crapets arlequins présentaient des durées de frai plus courtes et moins de pointes de frai (ou de production de larves). La contribution a` la population juvénile automnale des crapets arlequins a` éclosion tardive était uniformément plus importante que celle des individus a` éclosion précoce, ces motifs de recrutement étant principalement attribuables a` des facteurs biotiques. L\u27étude donne a` penser que les crapets arlequins pourraient présenter une plasticité de frai et elle élargit la compréhension actuelle des adaptations pouvant potentiellement accroître l\u27aptitude d\u27une espèce de poissons dulcicoles pour un vaste éventail de conditions ambiantes et de niveaux d\u27incertitude

Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses

Human immunodeficiency virus (HIV-1 or simply HIV) induces a persistent infection, which in the absence of treatment leads to AIDS and death in almost all infected individuals. HIV infection elicits a vigorous immune response starting about 2-3 weeks post infection that can lower the amount of virus in the body, but which cannot eradicate the virus. How HIV establishes a chronic infection in the face of a strong immune response remains poorly understood. It has been shown that HIV is able to rapidly change its proteins via mutation to evade recognition by virus-specific cytotoxic T lymphocytes (CTLs). Typically, an HIV-infected patient will generate 4-12 CTL responses specific for parts of viral proteins called epitopes. Such CTL responses lead to strong selective pressure to change the viral sequences encoding these epitopes so as to avoid CTL recognition. Here we review experimental data on HIV evolution in response to CTL pressure, mathematical models developed to explain this evolution, and highlight problems associated with the data and previous modeling efforts. We show that estimates of the strength of the epitope-specific CTL response depend on the method used to fit models to experimental data and on the assumptions made regarding how mutants are generated during infection. We illustrate that allowing CTL responses to decay over time may improve the fit to experimental data and provides higher estimates of the killing efficacy of HIV-specific CTLs. We also propose a novel method for simultaneously estimating the killing efficacy of multiple CTL populations specific for different epitopes of HIV using stochastic simulations. Lastly, we show that current estimates of the efficacy at which HIV-specific CTLs clear virus-infected cells can be improved by more frequent sampling of viral sequences and by combining data on sequence evolution with experimentally measured CTL dynamics