Quantitative population dynamics modeling is needed to evaluate the stock status and fisheries management plans to provide robust model and management strategies. Atlantic Weakfish (Cynoscion regalis), one important commercial and recreational fish species along the west coast of Atlantic Ocean that was found to be declining in recent years, was selected as an example species. My study aimed to explore the possible spatial heterogeneity of CPUE (catch per unit effort) year trend based on three fishery independent surveys and explore the influence of nonstationary natural mortality on the fisheries management through a MSE (Management Strategy Evaluation) algorithm based on the Weakfish stock assessment results. Five models for catch rate standardization were constructed based on the NEAMAP (NorthEast Area Monitoring and Assessment Program) survey data and the ‘best' two models were selected based on the ability to capture nonlinearity and spatial autocorrelation. The selected models were then used to fit the other two survey data to compare the CPUE year trend of Weakfish. Obvious differences in distribution pattern of Weakfish along latitude and longitude were detected from these three surveys as well as the CPUE year trend. To test the influence of the model selection on the MSE, five stock-recruitment models and two forms of statistical catch-at-age models were used to evaluate the fishery management strategies. The current biomass-based reference point tends to be high if the true population dynamics have nonstationary natural mortality. A flexible biomass based reference point to match the nonstationary process is recommended for future fisheries management. / Master of Science

Inherent uncertainties in the stock assessment for weakfish have precluded accurate and consistent advice concerning the management of commercial and recreational fisheries. Error within ageing techniques, used to assess relative age frequencies within commercial and recreational harvest, has been cited as a potential source for uncertainty during assessments of the weakfish fishery. The implications for age-reading error on weakfish stock assessment were explored using measurement-error growth models (i.e. Chapter 1), ageing error matrices within a statistical catch-at-age framework (i.e. Chapter 2), and Monte Carlo simulations to gauge robustness of ignoring this type of uncertainty during fisheries stock assessment (i.e. Chapter 3). Measurement-error growth models typically resulted in weakfish that grew to reach larger sizes, but at slower rates, with median length-at-age being overestimated by traditional von Bertalanffy growth curves, at least for the observed age range. Measurement-error growth models allow for incorporation of ageing uncertainty during nonlinear growth curve estimation, as well as the ability to estimate the ageing error variance. Age-reading error was further considered during statistical catch-at-age analysis of the weakfish fishery, mainly through permutations of true catch-at-age via ageing error matrices constructed from estimates of the ageing error variance, thus reflecting changes in relative age compositions as a consequence of ageing uncertainty. As a result, absolute levels of key population parameters were influenced, but general trends in those parameters tended to be similar, with strong congruency across models as to weakfish stock dynamics in most recent years. Finally, Monte Carlo simulations showed that implications for age-reading error on weakfish stock assessment are varied, depending upon the direction and magnitude of the ageing uncertainty. However, relative trends of parameter estimates over time tended to be similar, resulting in proper allocation of weakfish stock status, regardless of the type of ageing error considered. Furthermore, assuming negligible ageing uncertainty within fishery-independent surveys appears reasonable, as simulations incorporating ageing error within indices of relative abundance showed similar patterns to situations that only considered observation noise. / Master of Science

A importância do pescado no Brasil tem crescido, principalmente nos últimos 50 anos, com a criação do Ministério da Pesca e Aquicultura, o aumento da produção pesqueira e do consumo de pescado per capita. A pescada-foguete Macrodon ancylodon pertence à família Sciaenidae é um peixe de alto consumo no Brasil. A qualidade do frescor do pescado é avaliada perante diferentes parâmetros: avaliações sensoriais, físico-químicas, microbiológicas, parasitológica e determinação de metais pesados, ou contaminantes inorgânicos. Para as avaliações foram coletados na CEAGESP 60 elementos amostrais para as avaliações sensoriais, microbiológicas, parasitológicas e de contaminantes inorgânicos (30 inverno / 30 verão). Para as avaliações físico-químicas foram coletados 33 elementos amostrais (15 inverno / 18 verão). Pela a avaliação sensorial as amostras do inverno e do verão tiveram resultados entre bom e moderado perante diferentes atributos avaliados. Pela avaliação físico-química os valores de BVT variaram de 7,410 a 39,240mg/100g; os valores de TMA variaram de 0,00 a 11,30mg/100g; os valores de TBA variaram de 0,250 a 1,070mgAM/100g; os valores de pH variaram de 6,890 a 7,200. Pela avaliação microbiológica a contagem de microrganismos mesófilos aeróbios estritos e facultativos viáveis variou de 9,0x103 a 8,5x105UFC/g; a contagem de microrganismos psicrotróficos aeróbios estritos e facultativos viáveis variou de 1,9x104 a >2,5x107UFC/g; a contagem de coliformes totais variou de 8,0x10 a 1,8x105UFC/g; a contagem de coliformes termotolerantes variou de <10 a 7,5x102 UFC/g; não houveram testes positivos na pesquisa de Salmonella spp. Pela avaliação parasitológica 30% dos elementos amostrais foram positivos para anisaquíase, sendo encontrados 17 elementos com Contracaecum spp. e um com Pseudoterranova spp. Pela determinação de contaminantes inorgânicos, os valores de As variaram de 0,011 a 1,700mg/Kg; os valores de Cd variaram de 0,003 a 0,031mg/Kg; os valores de Cr variaram de 0,00 a 0,124mg/Kg; os valores de Pb variaram de 0,007 a 0,458mg/Kg; os valores de Hg total variaram de 0,001 a 0,099mg/Kg. Houve diferença estatisticamente significativa a 5% entre os grupos do inverno e do verão para os seguintes parâmetros: aceitabilidade da aparência e do frescor e intenção de compra na avaliação sensorial; BVT na avaliação físico-química; microrganismos mesófilos, microrganismos psicrotróficos e coliformes totais na avaliação microbiológica; As, Cr e Hg total na determinação de contaminantes inorgânicos. Foi verificado que a análise sensorial e a microbiológica são bons avaliadores do estado de frescor. A análise de BVT e a contagem de coliformes termotolerantes são bons indicadores do frescor da pescada. Os valores de pH obtidos sugerem que para a pescada Macrodon ancylodon ocorra variação em uma escala superior a de outras espécies de pescado. A região de origem parece influenciar nos resultados parasitológicos e de metais pesados. O presente trabalho deve contribuir com o setor da inspeção e sistemas de autocontrole da qualidade comercial e frescor do pescado marinho de origem extrativista nacional. / The importance of seafood in Brazil has grown, especially in the last 50 years, with the creation of the Ministério da Pesca e Aquicultura and the increase in seafood production and consumption of fish per capita. The king weakfish Macrodon ancylodon belongs to the family Sciaenidae and is highly consumed fish in Brazil. The quality of fresh fish is evaluated against different parameters: sensory, physical-chemical and microbiological evaluations, parasitological assessment and determination of heavy metals or inorganic contaminants. For the assessments were collected 60 sample elements at CEAGESP for sensory evaluation, microbiology, parasitology and inorganic contaminants (30 winter / 30 summer). For the physical-chemical evaluations were collected 33 sample elements (15 winter / summer 18). For the sensory evaluation samples of winter and summer were between good and moderate results with regard to different attributes. For physical and chemical evaluation BVT values ranged 7.410 to 39.240 mg/100g; TMA values ranged from 0.00 to 11.30 mg/100g; TBA values ranged from 0.250 to 1.070 mgAM/100g; values pH ranged from 6.890 to 7.200. For the microbiological count of mesophilic and facultative aerobe viable ranged from 9.0x103 to 8.5x105UFC/g; the count of psychrotrophic and facultative aerobe viable ranged from 1.9x104 to >2.5x107UFC/g; count total coliforms ranged from 8.0x10 to 1.8x105UFC/g; fecal coliform counts ranged from <10 to 7.5X102 UFC/g; there were no positive tests for Salmonella spp. Parasitological assessment by 30% of sample elements were positive for anisakiasis, and were found 17 elements with Contracaecum spp. and one with Pseudoterranova spp. For the determination of inorganic contaminants, the As values ranged from 0.011 to 1.700mg/kg; the Cd values ranged from 0.003 to 0.031mg/kg; the Cr values ranged from 0.00 to 0.124mg/kg; the Pb values ranged from 0.007 to 0.458 mg/kg; the total Hg values ranged from 0.001 to 0.099 mg/kg. A statistically significant at 5% between groups of winter and summer for the following parameters: appearance and freshness acceptability and purchase intent in the sensory evaluation; BVT in physical chemistry assessment; mesophilic, psychrotrophic and total coliforms in microbiological evaluation; As, Cr and total Hg in the determination of inorganic contaminants. It was found that the microbiological and sensory analysis are good evaluators of the state of freshness. The analysis of BVT and fecal coliform counts are good indicators of freshness of king weakfish. The pH values obtained suggest that for king weakfish Macrodon ancylodon variation occurs on a scale greater than other species of fish. The region of origin seems to influence the results of parasitological and heavy metals. This work should contribute to the sector of self-control and inspection systems of commercial quality and freshness of marine fisherie in Brazil.

A importância do pescado no Brasil tem crescido, principalmente nos últimos 50 anos, com a criação do Ministério da Pesca e Aquicultura, o aumento da produção pesqueira e do consumo de pescado per capita. A pescada-foguete Macrodon ancylodon pertence à família Sciaenidae é um peixe de alto consumo no Brasil. A qualidade do frescor do pescado é avaliada perante diferentes parâmetros: avaliações sensoriais, físico-químicas, microbiológicas, parasitológica e determinação de metais pesados, ou contaminantes inorgânicos. Para as avaliações foram coletados na CEAGESP 60 elementos amostrais para as avaliações sensoriais, microbiológicas, parasitológicas e de contaminantes inorgânicos (30 inverno / 30 verão). Para as avaliações físico-químicas foram coletados 33 elementos amostrais (15 inverno / 18 verão). Pela a avaliação sensorial as amostras do inverno e do verão tiveram resultados entre bom e moderado perante diferentes atributos avaliados. Pela avaliação físico-química os valores de BVT variaram de 7,410 a 39,240mg/100g; os valores de TMA variaram de 0,00 a 11,30mg/100g; os valores de TBA variaram de 0,250 a 1,070mgAM/100g; os valores de pH variaram de 6,890 a 7,200. Pela avaliação microbiológica a contagem de microrganismos mesófilos aeróbios estritos e facultativos viáveis variou de 9,0x103 a 8,5x105UFC/g; a contagem de microrganismos psicrotróficos aeróbios estritos e facultativos viáveis variou de 1,9x104 a >2,5x107UFC/g; a contagem de coliformes totais variou de 8,0x10 a 1,8x105UFC/g; a contagem de coliformes termotolerantes variou de <10 a 7,5x102 UFC/g; não houveram testes positivos na pesquisa de Salmonella spp. Pela avaliação parasitológica 30% dos elementos amostrais foram positivos para anisaquíase, sendo encontrados 17 elementos com Contracaecum spp. e um com Pseudoterranova spp. Pela determinação de contaminantes inorgânicos, os valores de As variaram de 0,011 a 1,700mg/Kg; os valores de Cd variaram de 0,003 a 0,031mg/Kg; os valores de Cr variaram de 0,00 a 0,124mg/Kg; os valores de Pb variaram de 0,007 a 0,458mg/Kg; os valores de Hg total variaram de 0,001 a 0,099mg/Kg. Houve diferença estatisticamente significativa a 5% entre os grupos do inverno e do verão para os seguintes parâmetros: aceitabilidade da aparência e do frescor e intenção de compra na avaliação sensorial; BVT na avaliação físico-química; microrganismos mesófilos, microrganismos psicrotróficos e coliformes totais na avaliação microbiológica; As, Cr e Hg total na determinação de contaminantes inorgânicos. Foi verificado que a análise sensorial e a microbiológica são bons avaliadores do estado de frescor. A análise de BVT e a contagem de coliformes termotolerantes são bons indicadores do frescor da pescada. Os valores de pH obtidos sugerem que para a pescada Macrodon ancylodon ocorra variação em uma escala superior a de outras espécies de pescado. A região de origem parece influenciar nos resultados parasitológicos e de metais pesados. O presente trabalho deve contribuir com o setor da inspeção e sistemas de autocontrole da qualidade comercial e frescor do pescado marinho de origem extrativista nacional. / The importance of seafood in Brazil has grown, especially in the last 50 years, with the creation of the Ministério da Pesca e Aquicultura and the increase in seafood production and consumption of fish per capita. The king weakfish Macrodon ancylodon belongs to the family Sciaenidae and is highly consumed fish in Brazil. The quality of fresh fish is evaluated against different parameters: sensory, physical-chemical and microbiological evaluations, parasitological assessment and determination of heavy metals or inorganic contaminants. For the assessments were collected 60 sample elements at CEAGESP for sensory evaluation, microbiology, parasitology and inorganic contaminants (30 winter / 30 summer). For the physical-chemical evaluations were collected 33 sample elements (15 winter / summer 18). For the sensory evaluation samples of winter and summer were between good and moderate results with regard to different attributes. For physical and chemical evaluation BVT values ranged 7.410 to 39.240 mg/100g; TMA values ranged from 0.00 to 11.30 mg/100g; TBA values ranged from 0.250 to 1.070 mgAM/100g; values pH ranged from 6.890 to 7.200. For the microbiological count of mesophilic and facultative aerobe viable ranged from 9.0x103 to 8.5x105UFC/g; the count of psychrotrophic and facultative aerobe viable ranged from 1.9x104 to >2.5x107UFC/g; count total coliforms ranged from 8.0x10 to 1.8x105UFC/g; fecal coliform counts ranged from <10 to 7.5X102 UFC/g; there were no positive tests for Salmonella spp. Parasitological assessment by 30% of sample elements were positive for anisakiasis, and were found 17 elements with Contracaecum spp. and one with Pseudoterranova spp. For the determination of inorganic contaminants, the As values ranged from 0.011 to 1.700mg/kg; the Cd values ranged from 0.003 to 0.031mg/kg; the Cr values ranged from 0.00 to 0.124mg/kg; the Pb values ranged from 0.007 to 0.458 mg/kg; the total Hg values ranged from 0.001 to 0.099 mg/kg. A statistically significant at 5% between groups of winter and summer for the following parameters: appearance and freshness acceptability and purchase intent in the sensory evaluation; BVT in physical chemistry assessment; mesophilic, psychrotrophic and total coliforms in microbiological evaluation; As, Cr and total Hg in the determination of inorganic contaminants. It was found that the microbiological and sensory analysis are good evaluators of the state of freshness. The analysis of BVT and fecal coliform counts are good indicators of freshness of king weakfish. The pH values obtained suggest that for king weakfish Macrodon ancylodon variation occurs on a scale greater than other species of fish. The region of origin seems to influence the results of parasitological and heavy metals. This work should contribute to the sector of self-control and inspection systems of commercial quality and freshness of marine fisherie in Brazil.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-07-22T13:02:35Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação Flávia Thuane Duarte do Monte (PDF).pdf: 1029138 bytes, checksum: ded4d1bd5809aa8f26493c20c0169546 (MD5) / Made available in DSpace on 2016-07-22T13:02:35Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação Flávia Thuane Duarte do Monte (PDF).pdf: 1029138 bytes, checksum: ded4d1bd5809aa8f26493c20c0169546 (MD5) Previous issue date: 2016-02-22 / FACEPE / O colágeno é a proteína fibrosa de origem animal mais abundante, que representa 30% de proteína total e 6% em peso no corpo humano. A pele e os ossos de bovinos e suínos geralmente são as principais fontes de colágeno e gelatina. No entanto, devido ao risco de transferência de zoonoses, existe uma necessidade de obtenção desta proteína por meio de outras fontes. A pescada amarela (Cynoscion acoupa) é um importante representante da pesca nacional e possui grande valor comercial. O objetivo deste estudo foi utilizar resíduos do processamento de pescada amarela para obter colágeno e sugerir sua utilização como fonte alternativa para o colágeno mamífero. Colágeno pepsino solúvel (PSC) foi isolado a partir de escamas de pescada amarela e caracterizado com sucesso. O rendimento da extração de PSC foi de 8,3% (baseado no peso seco). A SDS-PAGE (7,5%) mostrou que o padrão de bandas do PSC consistiu de uma cadeia α1 e α2 na proporção de 2:1, bem como cadeias β e γ, sendo caracterizado como colágeno do tipo I. O espectro de absorção ultravioleta (UV) mostrou uma máxima absorção em 222 nm. PSC foi solúvel na faixa de pH de 1 à 4, com a máxima solubilidade em pH 1. O colágeno também demonstrou maior solubilidade na faixa de concentração de 0 à 2% (w/v) de NaCl. A temperatura máxima de transição (Tmax) para PSC foi de 30,4°C, tal como determinado por calorimetria exploratória diferencial (DSC). Os resultados obtidos neste estudo indicam a possibilidade do uso de escamas de pescada amarela como uma fonte de colágeno do tipo I, com grande potencial para aplicações biotecnológicas. / Collagen is the most abundant fibrous protein of animal origin, representing 30% of the total protein and 6% in weight of the human body. The skin and bones of bovines and pigs usually are the main sources of collagen. However, due to the risk of transfer of diseases, there is a need for obtaining this protein form other sources. The acoupa weakfish (Cynoscion acoupa) is an important representative of the national fishing and has great commercial value. The aim of this study was to use acoupa weakfish waste processing for obtain collagen and suggest its use as an alternative source mammal collagen. Pepsin soluble collagen (PSC) from scales of acoupa weakfish was isolated and characterized. The yield of PSC was 8.3% (based on dry weight). SDS-PAGE (7.5%) pattern showed that both PSC consisted of one α1 and one α2 chains in proportion 2:1, as well as β and  chains, and were characterized to be type I collagen. The PSC ultraviolet (UV) absorption spectrum showed a maximum absorption at 222 nm. The PSC was soluble at pH between 1 and 4, with maximum solubility at pH 1. He have also shown solubility majority at NaCl concentration from 0 to 2% (w/v). The maximum transition temperature (Tmax) for PSC was 30.4°C, as determined by differential scanning calorimetry (DSC). The results obtained in this study indicate the possibility of using acoupa weakfish scales as a source of type I collagen with great potential for biotechnological application.

The biological characteristics of fisheries stocks that are assessed for management considerations are rarely homogeneous over time or space. However, stock assessment scientists largely ignore this heterogeneity in their models. This thesis addresses the effects of spatial and temporal heterogeneity on stock assessment models using Atlantic Weakfish (Cynoscion regalis) as a case study. First, spatial and temporal variation was incorporated into length-, weight-, and maturity-at-age estimates using mixed-effects models (Chapter Two). The resulting heterogeneous weight and maturity parameters then were applied to per-recruit analyses to examine the sensitivity of biological reference points to spatial and temporal variation in life history attributes (Chapter Three). Mixed-effects life history models incorporating spatial and temporal variation revealed distinct regional and annual trends that were not visible from standard homogeneous models. In several instances, the homogeneous modelling approach produced life history estimates that varied significantly from the spatial and temporal means produced by the heterogeneous models. In some cases, this difference was so great that the homogeneous means were much higher or lower than the heterogeneous means for all regions or years. Minimized AIC statistics revealed that spatially and temporally integrated mixed-effects models were more robust and descriptive of Atlantic Weakfish life history than the standard homogeneous models. Per-recruit and biological reference points derived from these life history estimates in Chapter Three were found to be highly sensitive to spatial and temporal variations in weight parameters. In several cases, reference points used as management targets were so significantly different that ignoring spatial and temporal heterogeneity in Atlantic Weakfish life history would likely cause overfishing and decline of Weakfish in certain regions and years. / Master of Science / Many stocks of commercially and recreationally harvested marine fish have displayed a declining trend in recent years. Marine fisheries are a vital component of the global economy, and, as such, sophisticated management measures have been developed to reduce and reverse this trend. These management strategies are based on regular reports from fisheries stock assessment scientists, who evaluate the status of fish stocks by modelling life history and productivity trends. One of the greatest challenges to stock assessments is the identification and incorporation of variability in fish populations. There is an inherent variation in fish growth, maturity, and productivity among geographical locations and over time. To produce the most effective management strategies, stock assessments must incorporate this spatial (regional) and temporal (annual) variation. In this thesis, I used mixed effects models to integrate spatial and temporal variation in life history and productivity using Atlantic Weakfish (Cynoscion regalis) as a case study. Distinct trends were observed in fishery-independent data for this species that were reflected in spatially and temporally incorporated models. However, these trends were masked in the standard models which incorporated neither spatial nor temporal variation. This oversight could cause weakfish to be overfished in certain regions and years and underfished in others. To maximize the effectiveness of management and the sustainable fisheries yield in all regions and years for Atlantic Weakfish and other harvested species, I highly recommend using spatially and temporally incorporated life history and productivity models such as the ones developed in this thesis.