A copula based method for fish species classification

The purpose of this thesis is to develop a method for classification of the species of a fish given in an image. This method uses the state of the art multi-dimensional image descriptor HOG (Histogram of Oriented Gradients), and colour histograms to create representative feature vectors. In this work copula theory have been used to summarize the multi-dimensional features. Copula theory has been used extensively for analysing the bivariate data however, not much exploration has been done to find its application for analysing multivariate data. This work is one of the few attempts where copulas have been used to analyse multivariate data. The classification accuracy of this method is comparable with other reported methods. --Leaf ii.The original print copy of this thesis may be available here: http://wizard.unbc.ca/record=b205591

Statolith morphometrics can discriminate among taxa of cubozoan jellyfishes

Identification of potentially harmful cubomedusae is difficult due to their gelatinous nature. The only hard structure of medusae, the statolith, has the potential to provide robust measurements for morphometric analysis. Traditional morphometric length to width ratios (L: W) and modern morphometric Elliptical Fourier Analysis (EFA) were applied to proximal, oral and lateral statolith faces of 12 cubozoan species. EFA outperformed L: W as L: W did not account for the curvature of the statolith. Best discrimination was achieved with Canonical Discriminant Analysis (CDA) when analysing proximal + oral + lateral statolith faces in combination. Normalised Elliptical Fourier (NEF) coefficients classified 98% of samples to their correct species and 94% to family group. Statolith shape agreed with currently accepted cubozoan taxonomy. This has potential to assist in identifying levels of risk and stock structure of populations in areas where box jellyfish envenomations are a concern as the severity of envenomation is family dependent. We have only studied 12 (27%) of the 45 currently accepted cubomedusae, but analyses demonstrated that statolith shape is an effective taxonomic discriminator within the Class

Ontogeny of the osteocranium in the African catfish, Clarias gariepinus burchell (1822) (Siluriformes: Clariidae): Ossification sequence as a response to functional demands

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Population structures and levels of connectivity for Scyphozoan and Cubozoan jellyfish

Understanding the hierarchy of populations from the scale of metapopulations to mesopopulations and member local populations is fundamental to understanding the population dynamics of any species. Jellyfish by definition are planktonic and it would be assumed that connectivity would be high among local populations, and that populations would minimally vary in both ecological and genetic clade-level differences over broad spatial scales (i.e., hundreds to thousands of km). Although data exists on the connectivity of scyphozoan jellyfish, there are few data on cubozoans. Cubozoans are capable swimmers and have more complex and sophisticated visual abilities than scyphozoans. We predict, therefore, that cubozoans have the potential to have finer spatial scale differences in population structure than their relatives, the scyphozoans. Here we review the data available on the population structures of scyphozoans and what is known about cubozoans. The evidence from realized connectivity and estimates of potential connectivity for scyphozoans indicates the following. Some jellyfish taxa have a large metapopulation and very large stocks (>1000 s of km), while others have clade-level differences on the scale of tens of km. Data on distributions, genetics of medusa and polyps, statolith shape, elemental chemistry of statoliths and biophysical modelling of connectivity suggest that some of the ~50 species of cubozoans have populations of surprisingly small spatial scales and low levels of connectivity. Despite their classification as plankton, therefore, some scyphozoans and cubozoans have stocks of small spatial scales. Causal factors that influence the population structure in many taxa include the distribution of polyps, behavior of medusa, local geomorphology and hydrodynamics. Finally, the resolution of patterns of connectivity and population structures will be greatest when multiple methods are used

The Copula Approach to Sample Selection Modelling: An Application to the Recreational Value of Forests

The sample selection model is based upon a bivariate or a multivariate structure, and distributional assumptions are in this context more severe than in univariate settings, due to the limited availability of tractable multivariate distributions. While the standard FIML estimation of the selectivity model assumes normality of the joint distribution, alternative approaches require less stringent distributional hypotheses. As shown by Smith (2003), copulas allow great flexibility also in FIML models. The copula model is very useful in situations where the applied researcher has a prior on the distributional form of the margins, since it allows separating their modelling from that of the dependence structure. In the present paper the copula approach to sample selection is first compared to the semiparametric approach and to the standard FIML, bivariate normal model, in an illustrative application on female work data. Then its performance is analysed more thoroughly in an application to Contingent Valuation data on recreational values of forests.Contingent valuation, Selectivity bias, Bivariate models, Copulas

Merizocotyle euzeti sp. N. (Monogenea: Monocotylidae) from the nasal tissue of three deep sea skates (Rajidae) in the Southwestern Atlantic Ocean

A new species of Merizocotyle Cerfontaine, 1894 (Monogenea: Monocotylidae) is described from the nasal tissues of three deep sea rajid skates: the southern thorny skate, Amblyraja doellojuradoi (Pozzi), broadnose skate, Bathyraja brachyurops (Fowler), and yellownose skate, Zearaja chilensis (Guichenot), collected off Buenos Aires Province, Argentina, southwest Atlantic Ocean. Two additional species of sympatric rajid, the white-dotted skate, Bathyraja albomaculata (Norman), and the Patagonian skate, Bathyraja macloviana (Norman), were also examined but no merizocotylines were found. The taxonomy of the Merizocotylinae is not widely accepted and, as a result, the status of Thaumatocotyle and Mycteronastes, and their proposed synonymy with Merizocotyle are currently under discussion. The new species differs from its congeners by having a unique haptoral structure, 6 peripheral loculi that are asymmetrically arranged (one much smaller, indistinctly located in the left or right side of the haptor). The presence of the new species in three sympatric species of Rajidae belonging to distinct genera and subfamilies, as well as its absence in sympatric congenerics indicates the lack of phylogenetic host specificity. Host ecology and geographical distribution appear to be more important than host phylogeny in determining the distribution of this parasite across potential hosts in the region. This constitutes the first record of Merizocotyle in the southwestern Atlantic Ocean.Fil: Irigoitia, Manuel Marcial. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Cantatore, Delfina María Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Delpiani, Gabriela Elina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Departamento de Ciencias Marinas. Laboratorio de Ictiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Incorvaia, Inés Silvia. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Lanfranchi, Ana Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Timi, Juan Tomas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentin

The Economic Valuation of Marine Ecosystems

In a democratic system, policy makers have to take the preferences of the citizens into account. Since we live in a world with scarce resources, one is asked to make choices regarding the use and management of these resources. In this context, if policy makers decide to invest in the protection of marine ecosystems, less financial resources will be available for other policy areas, for example national health. Moreover, the investment in the protection of marine ecosystems brings along with it the provision of a wide range of benefits to humans though most are not priced in the existing markets – for example climate regulation and provision of habitat for biodiversity. Given that most human activities are priced in one way or other, in some decision contexts, the temptation exists to downplay or ignore these important marine ecosystem benefits on the basis of the non-existence of prices. The simple and simplistic idea in the minds of many policymakers is that a lack of prices is equivalent to a lack of values. Clearly, this is a biased perspective. Against this background, this paper explores the motivation for an economic valuation of this complex resource. The state-of-the-art economic valuation methodologies follow the guidelines proposed by the Millennium Ecosystem Assessment, taking into account the existing scientific knowledge on the functioning of marine ecosystems, marine ecosystem goods and services and its impacts on human welfare. Finally, we critically review some economic valuation studies, arguing that the economic valuation of marine ecosystem services and biodiversity can make sense if and only if important guidelines are observed.Economic Valuation, Marine Ecosystem, Millennium Ecosystem Assessment Approach, Europe

An Applied Framework for Incorporating Multiple Sources of Uncertainty in Fisheries Stock Assessments

Estimating fish stock status is very challenging given the many sources and high levels of uncertainty surrounding the biological processes (e.g. natural variability in the demographic rates), model selection (e.g. choosing growth or stock assessment models) and parameter estimation. Incorporating multiple sources of uncertainty in a stock assessment allows advice to better account for the risks associated with proposed management options, pro- moting decisions that are more robust to such uncertainty. However, a typical assessment only reports the model fit and variance of estimated parameters, thereby underreporting the overall uncertainty. Additionally, although multiple candidate models may be considered, only one is selected as the ‘best’ result, effectively rejecting the plausible assumptions behind the other models. We present an applied framework to integrate multiple sources of uncertainty in the stock assessment process. The first step is the generation and condition- ing of a suite of stock assessment models that contain different assumptions about the stock and the fishery. The second step is the estimation of parameters, including fitting of the stock assessment models. The final step integrates across all of the results to reconcile the multi-model outcome. The framework is flexible enough to be tailored to particular stocks and fisheries and can draw on information from multiple sources to implement a broad variety of assumptions, making it applicable to stocks with varying levels of data avail- ability The Iberian hake stock in International Council for the Exploration of the Sea (ICES) Divisions VIIIc and IXa is used to demonstrate the framework, starting from length-based stock and indices data. Process and model uncertainty are considered through the growth, natural mortality, fishing mortality, survey catchability and stock-recruitment relationship. Estimation uncertainty is included as part of the fitting process. Simple model averaging is used to integrate across the results and produce a single assessment that considers the multiple sources of uncertainty.Versión del edito

The most prevalent respiratory and gastrointestinal parasites in Herring Gulls -Larus argentatus- admitted in a wildlife rehabilitation centre in South-East England

Dissertação de Mestrado Integrado em Medicina VeterináriaHerring gull (Larus argentatus) is one of the most widespread species throughout the British coastal areas. In the last 40 years, there has been a decline of 30% in the global population followed by a decrease in the natural breeding sites and sharp increase in the urban nesting populations. RSPCA Mallydams Woods, is a wildlife rehabilitation centre situated in the South-East of England that has been receiving increasing numbers of Herring gulls that end up being euthanized due to respiratory signs with the suspicion of the persistence of a parasitological agent (Cyathostoma sp.), previously identified in 2004. In the meantime, no further parasitological studies in this species were performed by the centre. Therefore, a total 65 necropsies and coprological analysis were performed in order to assess the main respiratory and gastrointestinal parasites as well as the main pathological alterations suggestive of other infectious agents. The general results showed that 32% (21/65) were positive for the presence of parasites. These results included gulls that had not received worming treatment, who showed 60% of positives (12/20) and dewormed gulls, who still showed 20% positives (9/45). Around 24.6% (16/65) presented Syngamidae eggs including two mixed infection cases, one with Porrocaecum eggs (1.54%) and the other with Contracaecum (1.54%). Among those 16 cases, 44.8% also presented visible worms in the infraorbital area of the nasal cavity. Nematodes of the species Cyathostoma lari were detected in 16.9% (11/65) of the cases and genus Syngamus in 1.54% (1/65). As to the McMaster method, it was shown that 23.1% (15/65) gulls had ˃50 EPG counts, including 9.2% (6/65) within the dewormed gulls. During necropsy procedures, signs of acute inflammation on the lungs were the most prevalent findings (30%). The longer rehabilitation periods and higher number of doses of wormer were the only factors to show significant association with the lower prevalence of parasites. This study demonstrated that the inefficacy of the worming protocol, the high animal density and presence of other infectious agents are the most probable causes of the persistence of respiratory signs within the admitted gulls. However, to the best of the author’s knowledge, this is the first parasitological study on Herring gulls performed in a British rehabilitation centre and there is a difference of 40 years between this study and the previous ones performed in wild populations, which shows that there is a serious need for more projects in this field.RESUMO - Parasitas respiratórios e gastrointestinais mais prevalentes em Gaivotas Cinzentas (Larus argentatus) admitidas num centro de reabilitação de animais selvagens no Sudeste de Inglaterra - A gaivota-cinzenta (Larus argentatus) é uma das espécies mais amplamente distribuídas na orla costeira britânica. Nos últimos 40 anos, houve um declínio de 30% na população mundial, seguido de uma diminuição nas zonas naturais de reprodução e um aumento acentuado nas populações de nidificação urbana. RSPCA Mallydams Woods, é um centro de reabilitação de animais selvagens situado no sudeste Inglês, que tem recebido um número crescente de gaivotas cinzentas que acabam por ser submetidas a eutanásia devido à presença de sinais respiratórios com a suspeita de persistência de um agente parasitário (Cyathostoma sp.), previamente identificado em 2004. Até à data, nenhum outro estudo parasitológico na espécie foi realizado pelo centro. Deste modo, um total de 65 necrópsias e análises coprológicas foram efetuadas para avaliar os principais parasitas respiratórios e gastrointestinais envolvidos, bem como as principais alterações patológicas sugestivas de outros agentes infeciosos. Os resultados gerais mostraram que 32% (21/65) eram positivas à presença de parasitas. Estes resultados incluíam gaivotas que não receberam desparasitante, apresentando 60% de positivos (12/20) e gaivotas desparasitadas, que ainda assim apresentavam 20% de positivos (9/45). Cerca de 24,6% (16/65) apresentavam ovos do tipo dos observados na família Syngamidae, incluindo 2 casos de infeção mista, um com ovos de Porrocaecum sp. (1,54%) e outro com ovos de Contracaecum sp. (1,54%). Entre estes 16 casos, 44,8% também apresentaram parasitas visíveis na zona infraorbitária da cavidade nasal. Os nemátodes da espécie Cyathostoma lari foram detetados em 16,9% (11/65) dos casos e Syngamus sp. em 1,54% (1/65). Relativamente ao método de McMaster, demonstrou-se que 23,1% (15/65) das gaivotas tinham ˃50 EPG, incluindo 9,2% (6/65) das gaivotas desparasitadas. Durante as necrópsias, os sinais de inflamação aguda nos pulmões foram o achado mais prevalente (30%). Períodos de reabilitação mais longos e maior número de doses de desparasitante foram os únicos fatores que mostraram uma associação significativa com a menor prevalência de parasitas. Este estudo demonstrou que a ineficácia do protocolo de desparasitação, a elevada densidade de animais no espaço existente e a presença de outros agentes infeciosos no centro de reabilitação, são as causas mais prováveis da persistência de sinais respiratórios nas gaivotas admitidas. No entanto, este parece ser o primeiro estudo parasitológico sobre gaivotas cinzentas realizado num centro de reabilitação britânico e há uma diferença de 40 anos entre este estudo e os previamente realizados em populações selvagens, o que demostra a elevada necessidade de mais projetos nesta área.N/