Validation of age determination from Otoliths for Bay of Biscay anchovy

Comprehension of the annual pattern of annulus formation throughout the anchovy life span was first achieved from the observations of the strong 1982 year class which showed a neat annual progression of modal lengths passing through the fishery until the exceptional age of 5. Validation of the proposed method was subsequently obtained through monitoring of the progression of the strong 1987, 1989 and 1991 year-classes, both by spring annual surveys and by continuous sampling of the commercial catches, coupled to the monitoring of the seasonal marginal edge formation of the otoliths. Since then Age validation has been confirmed by the correlation between the pulses of recruitments (at age 1), as reflected in their relative occurrence in the population in Spring, and the abundance of those recruitments according to surveys. Typically, annual growth of anchovy otoliths of the one and two years old diminish to about 2/3-1/2 and 1/3 of that occurring in their previous ages respectively. Growth of older ages (three and four) are rather similar as, or slightly lesser than, at age 2. Maximum growth (white band formation) occurs in summer and growth detentions (with translucent annulus formation) in winter time. However the opaque edge formation begins sooner at the age of 1 (around February-March) than at older ages (May or June). During the first winter several translucent rings are occasionally formed resulting in a composite annulus formation. In addition during June/July, at peak spawning, a check is formed in many of the one year old anchovies. However, not all year classes, neither all anchovies lay down the same amount of checks and many of them may not show any. As such age determination requires the knowledge of the typical annual growth pattern of otoliths, of their seasonal edge formation by ages and of the most typical checks

Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images

We describe a protocol for fully automated detection and segmentation of asymmetric, presumed excitatory, synapses in serial electron microscopy images of the adult mammalian cerebral cortex, taken with the focused ion beam, scanning electron microscope (FIB/SEM). The procedure is based on interactive machine learning and only requires a few labeled synapses for training. The statistical learning is performed on geometrical features of 3D neighborhoods of each voxel and can fully exploit the high z-resolution of the data. On a quantitative validation dataset of 111 synapses in 409 images of 1948×1342 pixels with manual annotations by three independent experts the error rate of the algorithm was found to be comparable to that of the experts (0.92 recall at 0.89 precision). Our software offers a convenient interface for labeling the training data and the possibility to visualize and proofread the results in 3D. The source code, the test dataset and the ground truth annotation are freely available on the website http://www.ilastik.org/synapse-detection

Testing spatial heterogeneity with stock assessment models

This paper describes a methodology that combines meta-population theory and stock assessment models to gain insights about spatial heterogeneity of the meta-population in an operational time frame. The methodology was tested with stochastic simulations for different degrees of connectivity between sub-populations and applied to two case studies, North Sea cod (Gadus morua) and Northeast Atlantic sardine (Sardina pilchardus). Considering that the biological components of a population can be partitioned into discrete spatial units, we extended this idea into a property of additivity of sub-population abundances. If the additivity results hold true for putative sub-populations, then assessment results based on sub-populations will provide information to develop and monitor the implementation of finer scale/local management. The simulation study confirmed that when sub-populations are independent and not too heterogeneous with regards to productivity, the sum of stock assessment model estimates of sub-populations’ SSB is similar to the SSB estimates of the meta-population. It also showed that a strong diffusion process can be detected and that the stronger the connection between SSB and recruitment, the better the diffusion process will be detected. On the other hand it showed that weak to moderate diffusion processes are not easy to identify and large differences between sub-populations productivities may be confounded with weak diffusion processes. The application to North Sea cod and Atlantic sardine exemplified how much insight can be gained. In both cases the results obtained were sufficiently robust to support the regional analysi

Testing spatial heterogeneity with stock assessment models

This paper describes a methodology that combines meta-population theory and stock assessment models to gain insights about spatial heterogeneity of the meta-population in an operational time frame. The methodology was tested with stochastic simulations for different degrees of connectivity between sub-populations and applied to two case studies, North Sea cod (\emph{Gadus morua}) and Northeast Atlantic sardine (\emph{Sardina pilchardus}). Considering that the biological components of a population can be partitioned into discrete spatial units, we extended this idea into a property of additivity of sub-population abundances. If the additivity results hold true for putative sub-populations, then the sub-populations are isolated spatial components of the meta-population and assessment results based on sub-populations will provide information to develop and monitor the implementation of finer scale/local management. The simulation study confirmed that when sub-populations are independent and not too heterogeneous with regards to productivity, the sum of stock assessment model estimates of sub-populations' SSB is similar to the SSB estimates of the meta-population. It also showed that a strong diffusion process can be detected and that the stronger the connection between SSB and recruitment, the better the diffusion process will be detected. On the other hand it showed that weak to moderate diffusion processes are not easy to identify and large differences between sub-populations productivities may be confounded with weak diffusion processes. The application to North Sea cod and Atlantic sardine exemplified how much insight can be gained. For the North Sea cod there is a large amount of information that advocates the existence of sub-populations and our results support such claim. In relation to sardine not so much information exists, nevertheless the results obtained were sufficiently robust to support the regional analysis.JRC.D.2-Water and Marine Resource

Surplus production, variability, and climate change in the great sardine and anchovy fisheries

We used fishery and survey data to calculate annual surplus production (ASP) and instantaneous surplus production rates (ISPR) for eight anchovy and nine sardine stocks. In addition, we calculated ASP per unit spawning area for six anchovy and six sardine stocks. Median ASP was highest for stocks with highest median biomass (mostly anchovies), and ASP was typically about 16% of stock biomass. ASP was often negative, more frequently for anchovies (36% of years) than for sardines (17% of years). ISPR was less variable for sardines and autocorrelated for longer-lived stocks (mostly sardines). Strong biomass increases tended to be preceded by short, abrupt increases in ISPR, and declines were pronounced when catches exceeded ASP for 5 years or more. The longest "runs" of positive and negative production were 21 and 4 years for sardine off Japan, 10 and 3 years for sardine off California, 8 and 2 years for anchovy off Peru, and 4 and 3 years for anchovy off California. ISPR is more sensitive to environmental changes than catch, biomass, or ASP and appear to be better for identifying environmentally induced regime shifts. Long time series show evidence of density-dependent effects on ASP in anchovies and sardines, but environmentally induced variation appears to dominate

Estimates of spawning stock biomass (<i>SSB</i>) for the Northeast Atlantic sardine.

<p>The left top figure refers to spawning stock biomass and the left bottom to recruitment. In both cases points show the median values and vertical lines represent 95% confidence intervals. The right panel shows the stock recruitment plot and model fits, to the meta-population and each sub-population.</p