A probabilistic procedure for estimating an optimal echo-integration threshold using the Expectation-Maximisation algorithm★

To obtain reliable fish biomass estimates by acoustic methods, it is essential to filter out the signals from unwanted scatterers (e.g. zooplankton). When acoustic data are collected at more than one frequency, methods that exploit the differences in reflectivity of scatterers can be used to achieve the separation of targets. These methods cannot be applied with historical data nor recent data collected on board fishing vessels employed as scientific platforms, where only one transducer is available. Instead, a volume backscattering strength (Sv) threshold is set to separate fish from plankton, both for echogram visualisation or, more importantly, during echo-integration. While empirical methods exist for selecting a threshold, it often depends on the subjective decision of the user. A−47 dB threshold was empirically established in 2008 at the beginning of a series of surveys conducted by Mexico's National Fisheries Institute to assess the biomass of Pacific sardine in the Gulf of California. Until 2012, when a 120 kHz transducer was installed, only data collected at 38 kHz are available. Here, we propose a probabilistic procedure to estimate an optimal Sv threshold using the Expectation-Maximisation algorithm for fitting a mixture of Gaussian distributions to Sv data sampled from schools associated with small pelagic fish and their surrounding echoes. The optimal threshold is given by the Bayes decision function for classifying an Sv value in one of the two groups. The procedure was implemented in the R language environment. The optimal threshold found for 38 kHz data was −59.4 dB, more than 12 dB lower than the currently used value. This difference prompts the need to revise the acoustic biomass estimates of small pelagics in the Gulf of California

Population dynamics and spatial distribution of flatfish species in shrimp trawl bycatch in the Gulf of California

By determining the specific composition, spatial distribution and population dynamics of flatfish species captured in shrimp trawls bycatch in the Gulf of California, this study aims to contribute to the knowledge of bycatch fish population which has thus far been of little interest. Samplings were taken from shrimp trawls in two fishing seasons (2002 and 2003) onboard shrimp fleets and also from two research cruises during closed shrimp season. The results showed 15 species of flatfish belonging to 5 families: Achiridae, Bothidae, Cynoglossidae, Pleuronectidae and Paralichthyidae. Paralichthyidae was the most abundant with 9 species. The range in sizes of these flatfish species varied in total length from 20 to 380 mm, with the most frequent sizes ranging from 60 to 180 mm and only a few species of the Paralichthysgenera surpassing 250 mm in total length. The growth estimate parameter for the most abundant flatfish species varied according to the longevity of these species. More than 50 % of the organisms sampled were of small size, and the majority of these were captured before the sexual maturity which may have caused a potential effect on the population; however the consequences of this action on the population are unknown

Interaction Between Marine Fauna and the Small Pelagic Fishery in the Coastal Environment of the Gulf of California, Mexico

The first steps have been taken to analyze the effects of small pelagic harvests on the Gulf of California ecosystem. The primary goal of this study was to estimate the latitudinal differences in regionalized baselines of endangered and threatened marine species attracted to a purse seine in a Mexican fishery of small pelagic fish. We also analyzed the spatial patterns in fishing effort in the Gulf of California. Seven zones were analyzed in the Gulf of California, including the east and west coasts, and a total of 3,051 fishing sets were analyzed during January 2013 and July 2014; the data provided a comprehensive picture of the distribution of the fishing effort, small pelagic fishes harvested, and the presence of species attracted to the fishing sets. The region in the upper Gulf of California showed a low presence of individuals, and the east coast recorded more sightings than the west coast; consequently the fishing effort was mainly distributed in the east coast. The number of individuals for several species sighted and counted by fishing set was used for each zone in the Gulf of California, and a conservative baseline based on the Pennington estimator was computed. It provided an average value of endangered and threatened marine species attracted to a purse seine for each zone. The Pennington estimator is recommended due to the precision of the confidence intervals and the nature of the uncertainty in the data collection based on sightings

A probabilistic procedure for estimating an optimal echo-integration threshold using the Expectation-Maximisation algorithm

To obtain reliable fish biomass estimates by acoustic methods, it is essential to filter out the signals from unwanted scatterers (e.g. zooplankton). When acoustic data are collected at more than one frequency, methods that exploit the differences in reflectivity of scatterers can be used to achieve the separation of targets. These methods cannot be applied with historical data nor recent data collected on board fishing vessels employed as scientific platforms, where only one transducer is available. Instead, a volume backscattering strength (Sv) threshold is set to separate fish from plankton, both for echogram visualisation or, more importantly, during echo-integration. While empirical methods exist for selecting a threshold, it often depends on the subjective decision of the user. A−47 dB threshold was empirically established in 2008 at the beginning of a series of surveys conducted by Mexico's National Fisheries Institute to assess the biomass of Pacific sardine in the Gulf of California. Until 2012, when a 120 kHz transducer was installed, only data collected at 38 kHz are available. Here, we propose a probabilistic procedure to estimate an optimal Sv threshold using the Expectation-Maximisation algorithm for fitting a mixture of Gaussian distributions to Sv data sampled from schools associated with small pelagic fish and their surrounding echoes. The optimal threshold is given by the Bayes decision function for classifying an Sv value in one of the two groups. The procedure was implemented in the R language environment. The optimal threshold found for 38 kHz data was −59.4 dB, more than 12 dB lower than the currently used value. This difference prompts the need to revise the acoustic biomass estimates of small pelagics in the Gulf of California

Spatial distribution and species composition of small pelagic fishes in the Gulf of California

Traditional regionalization methods in fisheries based on provinces or major fishing areas, includes large and arbitrary grids in which basic statistics or inferences on distribution or abundance are made. We describe a method for regionalization and analysis of fishing activities for small pelagic fisheries in the Gulf of California, based on spatial patterns of landing and catch data in a Geographic Information System (GIS) environment. A fisheries database from logbooks with spatial attributes from October 2002 to June 2007 was analyzed. Landings and catching data were transformed to a Weighted Region Index (WRI) by using fuzzy logic operators. The WRI revealed fishing action centers characterized by areas with the highest WRI values, and a hierarchy for the relative importance of the regions was established. Guaymas, Desemboque de Caborca, Isla Patos, and Bahía San Rafael were the most prominent ones. An analysis of the relative frequency of species composition showed that the Pacific sardine had over 80% abundance in the midriff islands, and remained as the most important in the upper gulf regions, while in the central part of the gulf, relative abundances of Pacific sardine and Northern anchovy were more balanced. Relative abundance of mackerel was significantly larger around Isla Patos than in any other place. Guaymas had the largest relative composition of Northern anchovy and the lowest values for Pacific sardine. Desemboque de Caborca showed the largest homogeneity in species relative composition. It is important to highlight that this results come from in situ data, while the results previously reported come from landing statistics by port. Therefore, the present method acknowledges the spatial differences of species by regions, additional to the traditional time series analysis

Distribución latitudinal y batimétrica de las especies más abundantes y frecuentes en la fauna acompañante del camarón del Golfo de California, México

Latitudinal and bathymetric distribution of the most abundant and frequent species in the shrimp bycatch from the Gulf of California, Mexico. The Gulf of California is one of the most mega-diverse regions in the world, for which few fishery information is available. We present here latitudinal and bathymetric distribution of the most abundant and frequent bycatch species from the Gulf of California. The samples were obtained from a total of 111 hauls taken during seven research cruises of the closed shrimp season (2002-2005-2007), and also, from research cruises made at depths up to 90m. Due to the high variety species in this experimental shrimp bycatch, only those with highest biological value index (BVI) were selected. A total of fifteen species had the highest BVI and represented about 60% of the total abundance. A total of 16 508 organisms were analyzed, representing 243 fish, crustacean, mollusk and echinoderm species. Fish were the most abundant, being the most frequent species: Urobatis halleri, Synodus scituliceps, Diplectrum pacificum, Haemulopsis nitidus and Eucinostomus argenteus. A wide latitudinal distribution of these species along the study area, as well as a bathymetric distribution from 9 to 67m depth, was observed. Two of these species were found at 325m depth. Due to the wide bathymetric distribution obtained, total abundances and sizes for each species by depth strata should be determined, and one can assume that deeper than 25m, the capture of these species decreases, and these areas can be used as natural repopulation areas, for depths where they are mainly captured by the commercial shrimp fishery. Rev. Biol. Trop. 59 (1): 255- 267. Epub 2011 March 01

Population size of the jumbo squid Dosidicus gigas in the central Gulf of California, Mexico, based on mark-recapture data

The use of mark-recapture data can be an alternative to other methods for estimating abundance of the jumbo squid Dosidicus gigas and can be used when catch-per-unit-effort data applied to depletion models or estimates from survey research are not available. Two mark-recapture events were analyzed in the central Gulf of California, Mexico, during October 2001 and April 2002 to assess the status of jumbo squid. Results from October 2001 yielded a population size of 20.2 million squid with a 95% CI of 16 to 26.5 million squid (p < 0.05). In April the population size was estimated at 132.6 million squid with a 95% CI of 85.5 to 222 million squid (p < 0.05). The results for October and April show 2 different periods of abundance. Estimates of tag return rates were higher in April (5.5%) than in October (1.7%), and recruitment is the most plausible explanation. In the Gulf of California, recruitment of jumbo squid commonly occurs during April and May

Population size and exploitation of giant squid (Dosidicus gigas D'Orbigny, 1835) in the Gulf of California, Mexico

The most important landing sites of the giant squid (Dosidicus gigas D´Orbigny, 1835) fishery in the Gulf of California, Mexico are Guaymas, in Sonora and Santa Rosalía, in Baja California Sur. An increase in the species biomass resulted in increased landings, ranging from 6, 200 tons in 1994 to 140,000 tons in 1996. The development of a management strategy for this fishery based on the proportional escapement has been suggested. This necessitates the estimation of the population size when the fishing season begins in order to determine the amount of fishing effort. Weekly catch and effort data were reported from October 1995 to March 1996 for three fleets operating in the Gulf of California. The population size estimated using a maximum likelihood model was 82,000 tons with a proportional escapement of 66%.No disponibl

Estructura de tallas, selectividad y composición específica de las capturas en trampas para peces marinos en el Golfo de California

Se realizó un estudio orientado a evaluar tres tipos de trampas (eficiencia de captura, estructura de tallas, selectividad y composición de especies) para la captura de peces marinos en el Golfo de California. La recolecta de muestras se efectuó con trampas de 90 cm de ancho, 120 cm de largo y 50 cm de alto, con malla galvanizada cuadrangular en tres tamaños: una trampa completamente construida con abertura de malla de 5 x 5 cm (trampa 1); otra con malla de 5 x 5 cm, pero con el panel trasero de 5 x 10 cm (trampa 2) y la tercera con malla de 5 x 10 cm (trampa 3). Los experimentos se llevaron a cabo entre octubre del 2005 y agosto del 2006. Las especies que presentaron mayor incidencia de captura en cuanto a proporción del volumen total fueron el extranjero (Paralabrax auroguttatus), pierna (Caulolatilus princeps), cabrilla arenera (P. maculatofaciatus) y conejo (C. affinis) y prácticamente todas las capturas tuvieron valor comercial. El número de organismos por trampa por lance decreció al aumentar el tamaño de malla, mientras que la talla media se incrementó con el tamaño de malla de las trampas. Además las tallas son más grandes en cualquiera de las trampas que las obtenidas con piola de mano con anzuelos (el arte de pesca autorizado). Los resultados de la selectividad de tallas indicaron que las trampas de malla grande fueron más selectivas que las de malla más pequeña. En consecuencia, la captura con tram-pas es mejor que con los anzuelos y línea de mano, por lo que las trampas serían una muy útil adición al conjunto de artes de pesca usados en la pesca artesanal de la costa de Sonora, México.<br>Size structure, selectivity and specific composition of the catch in traps for marine fish in the Gulf of California. We analyzed the performance of three traps for marine fish between October 2005 and August 2006 in the Gulf of California, Mexico. The performance was measured as difference in selectivity, fish diversity, size structure and yield. The samples were collected with quadrangular traps 90 cm wide, 120 cm long and 50 cm high. Trap type 1 had a 5 x 5 cm mesh (type 2: 5 x 5 cm including a rear panel of 5 x 10 cm; trap 3: 5 x 10 cm). Most abundant in our traps were: Goldspotted sand bass (Paralabrax auroguttatus), Ocean whitefish (Caulolatilus princeps), Spotted sand bass (P. maculatofaciatus) and Bighead tilefish (C. affinis); there was no bycatch. The number of fish per trap per haul decreased when mesh size was increased. We also observed a direct relationship between mesh size and average fish length. By comparing our traps with the authorized fishing gear (hooks-and-line) we found that the size structure is larger in traps. Traps with larger mesh size were more selective. Consequently, we recommend adding traps to hooks-and-line as authorized fishing gear in the small scale fisheries of the Sonora coast, Mexico. Rev. Biol. Trop. 56 (3): 1403-1417. Epub 2008 September 30