Reproductive biology of the bullseye puffer Sphoeroides annulatus: Gonadosomatic index and its suitability for estimating length at maturity.

This study aimed to describe updated information on the basic reproductive biology of Sphoeroides annulatus females and potential use of the gonadosomatic index I G as input data to assess length at 50% maturity ( L 50 ) and identify the breeding season. From April 2014 to December 2015, 767 females were analysed along the north-west coast of the Mexican Pacific Ocean. Both immature and mature females were represented in the total length ( L T ), which ranged from 81 to 440 mm, and the smallest mature female was 92 mm (new record for the species). Gonadal maturity phases were assigned through histological analysis. A I G threshold value I cut was established using the lower whisker value for maturity phase spawning capable (2.06%). The monthly variation of I G supported the annual spawning seasonality, and the presence of reproductively active mature females I G ≥ I cut coincided with the observed periods with histological data and the peaks for both seasons 2014 and 2015. Also the presence of reproductively inactive I G < I cut mature females confirmed the nonreproductive season observed from January to April 2015. Estimates of L 50 were based on the cumulative proportion of reproductively active mature females: both datasets showed a 'bumpy trajectory'. Considering the functional form of data and models, a second objective was to verify if each dataset presented a simple or double sigmoid trajectory and select the most suitable model through the Akaike information criterion. For both datasets, the best fitted model was the double sigmoidal M DS , while the single sigmoidal M SS had low performance and did not have statistical support. The M DS provided a L 50 value ca. 254 mm L T for both data sets. A trade-off between the model's correct fit and a reliable L 50 value was found, but this fact is not always considered when calculating the maturity, resulting in biased parameters. Correct data fitting may seem trivial, but the consequences for the conservation of immature individuals could be dramatic, affecting the population recruitment. In conclusion, the histologically calibrated I cut was suitable for classifying females of S. annulatus into reproductively inactive or active types, with an agreement percentage of 99%. The I cut  = 2.06% can be useful for subsequent studies for this species.

Molecular analysis of bacterial microbiota associated with oysters (Crassostrea gigas and Crassostrea corteziensis) in different growth phases at two cultivation sites.

Microbiota presumably plays an essential role in inhibiting pathogen colonization and in the maintenance of health in oysters, but limited data exist concerning their different growth phases and conditions. We analyzed the bacterial microbiota composition of two commercial oysters: Crassostrea gigas and Crassostrea corteziensis. Differences in microbiota were assayed in three growth phases: post-larvae at the hatchery, juvenile, and adult at two grow-out cultivation sites. Variations in the microbiota were assessed by PCR analysis of the 16S rRNA gene in DNA extracted from depurated oysters. Restriction fragment length polymorphism (RFLP) profiles were studied using Dice's similarity coefficient (Cs) and statistical principal component analysis (PCA). The microbiota composition was determined by sequencing temperature gradient gel electrophoresis (TGGE) bands. The RFLP analysis of post-larvae revealed homology in the microbiota of both oyster species (Cs > 88 %). Dice and PCA analyses of C. corteziensis but not C. gigas showed differences in the microbiota according to the cultivation sites. The sequencing analysis revealed low bacterial diversity (primarily ß-Proteobacteria, Firmicutes, and Spirochaetes), with Burkholderia cepacia being the most abundant bacteria in both oyster species. This study provides the first description of the microbiota in C. corteziensis, which was shown to be influenced by cultivation site conditions. During early growth, we observed that B. cepacia colonized and remained strongly associated with the two oysters, probably in a symbiotic host-bacteria relationship. This association was maintained in the three growth phases and was not altered by environmental conditions or the management of the oysters at the grow-out site.

Length at Maturity, Sex Ratio, and Proportions of Maturity of the Giant Electric Ray, Narcine entemedor, in Its Septentrional Distribution.

The size at which a certain fraction of a fish population reaches sexual maturity is an important parameter of life history. The estimation of this parameter based on logistic or sigmoid models could provide different ogives and values of length at maturity, which must be analyzed and considered as a basic feature of biological reproduction for the species. A total of 305 individuals of Narcine entemedor (N. entemedor) were obtained from artisanal fisheries in the Bahía de La Paz, Mexico. For the organisms sampled, sexes were determined and total length (TL) in cm was measured from October 2013 to December 2015. The results indicated that the females were larger, ranging from 48.5 cm to 84 cm TL, while males varied from 41.5 cm to 58.5 cm TL. The sex ratio was dominated by males ranging from 45-55 cm TL, while females were more abundant from 60 to 85 cm TL. Mature females were present all year long, exhibiting a continuous annual reproductive cycle. The length at maturity data were described by the Gompertz model with value of 55.87 cm TL. The comparison between models, and the model selection between them, showed that the Gompertz model had maximum likelihood and smaller Akaike information criterion, indicating that this model was a better fit to the maturity proportion data of N. entemedor.

Improving the gnomonic approach with the gnomonicM R-package to estimate natural mortality throughout different life stages.

Natural mortality (M) is defined as the rate of loss that occurs in a fish stock due to natural (non-fishing) causes and can be influenced by density-dependent or density-independent factors. Different methods have been used to estimate M, one of these is the gnomonic approach. This method estimates M rates by dividing the life cycle of a species into subunits of time that increase as a constant proportion of the time elapsed from birth up to the initiation of each subdivision. In this study, an improved gnomonic approach is proposed to estimate natural mortality throughout different life stages in marine stocks using the gnomonicM package written in R software. This package was built to require data about (i) the number of gnomonic intervals, (ii) egg stage duration, (iii) longevity, and (iv) fecundity. With this information, it is possible to estimate the duration and natural mortality (Mi) of each gnomonic interval. The gnomonicM package uses a deterministic or stochastic approach, the latter of which assesses variability in M by assuming that the mean lifetime fecundity (MLF) is the main source of uncertainty. Additionally, the gnomonicM package allows the incorporation of auxiliary information related to the observed temporal durations of specific gnomonic intervals, which is useful for calibrating estimates of M vectors. The gnomonicM package, tested via deterministic and stochastic functions, was supported by the reproducibility and verification of the results obtained from different reports, thus guaranteeing its functionality, applicability, and performance in estimating M for different ontogenetic developmental stages. Based on the biological information of Pacific chub mackerel (Scomber japonicus), we presented a new case study to provide a comprehensive guide to data collection to obtain results and explain the details of the application of the gnomonicM package and avoid its misuse. This package could provide an alternative approach for estimating M and provide basic input data for ecological models, allowing the option of using estimates of variable natural mortality across different ages, mainly for life stages affected by fishing. The inputs for the gnomonicM packages are composed of numbers, vectors, or characters depending on whether the deterministic or stochastic approach is used, making the package quick, flexible, and easy to use; this allows users to focus on obtaining and interpreting results rather than the calculation process.

Growth Modeling of the Giant Electric Ray Narcine entemedor in the Southern Gulf of California: Analyzing the Uncertainty of Three Data Sets.

The age and growth rate of the giant electric ray, Narcine entemedor, was estimated using growth bands deposited in the vertebral centra of 245 specimens. Differences in size and age distribution were found between the sexes, a pattern that suggests the annual deposition of band pairs, possibly occurring in April. Multimodel inference and back-calculation were performed to three age data sets of females considering their reproductive cycle and time of capture, among which the von Bertalanffy growth function was found to be the most appropriate (L∞ = 81.87 cm TL, k = 0.17 year-1). Our research supports the idea that age can be determined via biological features such as birth date and growth band periodicity. We concluded that N. entemedor is of a moderate body size, moderate longevity and is a fast-growing elasmobranch species.

Evidence of overfishing of geoduck clam Panopea globosa from a length-based stock assessment approach.

Stock assessment of the geoduck clam Panopea globosa in Mexico has been based on data-poor without consideration of the biological traits of the species, promoting a passive management strategy without biological reference points for its harvest and conservation, which results in limited advice regarding the sustainability of the fishery. The stock assessment was supported on an integrated catch-at-size assessment model. The model described the population changes, including recruitment, selectivity, fishing mortality, individual growth patterns and survival over time, providing management quantities for the geoduck clam fishery, such as biomass-at-length (total and vulnerable) and harvest rate-at-length. The results indicated overfishing of the geoduck clam population; the harvest rate exceeded the management tactics established for this fishery, even the individuals smaller than the minimum legal size (130 mm) were harvested. Thus, declines in the total biomass (from 3,262 to 1,130 t) and recruitment (representing an 86% decrease) were observed from 2010 to 2012. Although the results showed a recovery trend in recruitment and total biomass from 2014 to 2016, this trend may have been due to the spatial relocation of fishing mortality.

Seagrass Halodule wrightii as a new habitat for the amphioxus Branchiostoma californiense (Cephalochordata, Branchiostomidae) in the southern Gulf of California, Mexico.

The first record of the amphioxus Branchiostoma californiense on seagrass patches of Halodule wrightii in the Gulf of California is reported. Sixty individuals (19 males, 18 females, and 23 undifferentiated) were collected in May 2017 at Bahía Balandra, Gulf of California, from subtidal seagrass patches at a depth of 0.5 m at low tide. The length and weight ranged from 15.88-28.44 mm and from 0.01-0.11 g for females and 11.7-27.9 mm and 0.01-0.09 g for males, respectively. The minimum size of sexually mature individuals was 11.70 mm for males and 15.88 mm for females; 62% of the specimens were sexually mature. Analysis of the total length-weight relationship suggested an allometric growth pattern among females, males and undifferentiated individuals, whereas an analysis of the entire sample suggested an isometric growth pattern. Typical and additional morphological characters were used to identify the amphioxi. High morphological variability between individuals was found, suggesting the presence of several morphotypes. Branchiostoma californiense had been previously reported as exclusively associated with bare sandy areas, but our study shows that this species can also be found in seagrass patches, using them as breeding and feeding grounds. Thus, seagrass patches are evidenced as suitable habitats for amphioxus.

Modeling the temporal periodicity of growth increments based on harmonic functions.

Age estimation methods based on hard structures require a process of validation to confirm the periodical pattern of growth marks. Among such processes, one of the most used is the marginal increment ratio (MIR), which was stated to follow a sinusoidal cycle in a population. Despite its utility, in most cases, its implementation has lacked robust statistical analysis. Accordingly, we propose a modeling approach for the temporal periodicity of growth increments based on single and second order harmonic functions. For illustrative purposes, the MIR periodicities for two geoduck species (Panopea generosa and Panopea globosa) were modeled to identify the periodical pattern of growth increments in the shell. This model identified an annual periodicity for both species but described different temporal patterns. The proposed procedure can be broadly used to objectively define the timing of the peak, the degree of symmetry, and therefore, the synchrony of band deposition of different species on the basis of MIR data.

Seasonal variations of biochemical, pigment, fatty acid, and sterol compositions in female Crassostrea corteziensis oysters in relation to the reproductive cycle.

Wild female Crassostrea corteziensis oyster (n=245) were analyzed over one year to understand the main ecophysiological events associated to gonad development. Different indicators (mainly biochemical) were analyzed to infer: i) utilization and accumulation of energy reserves (e.g. neutral lipids, carbohydrates, proteins; vitellogenin), ii) membrane components provided by the diet as essential nutrients and indicative of cell proliferation (e.g. highly unsaturated fatty acids linked to phospholipids, sterols), iii) indicators of food availability (chlorophyll a in water, pigments in tissues, specific fatty acids and sterols), iv) gonad development (e.g. gonad coverage area, vitellin). A PCA analysis was applied to 269 measured variables. The first PC (PC1) was composed of total carbohydrate and lipid concentration, percentage of esterified sterols, fatty acids specific of diatoms; 16:1n-7/16:0, 20:5n-3 in neutral lipids with positive loadings and non methylene-interrupted fatty acids (NMI) in neutral lipids with negative loadings. The second PC (PC2) was composed of 18:4n-3 in lipid reserves and the concentration of zeaxanthin, a pigment typical of cyanobacteria with positive loadings and the proportion of 20:4n-6 in polar lipids with negative loading. The third PC (PC3) was composed of gonad coverage area (GCA) and the concentration of vitellin. Variation in GCA confirms that gonad development began in April with an extended period of spawning and rematuration from April to November. The PCA further shows that a second period of minimal maturation from November to March corresponds to the accumulation of reserves (PC1) together with an initial high availability of food (PC2) at the beginning of this period. These two periods are in accordance with the classical periods of allocation of energy to reserves followed by gonad development reported for several mollusks.