Future fish distributions constrained by depth in warming seas

European continental shelf seas have experienced intense warming over the past 30 years1. In the North Sea, fish have been comprehensively monitored throughout this period and resulting data provide a unique record of changes in distribution and abundance in response to climate change2, 3. We use these data to demonstrate the remarkable power of generalized additive models (GAMs), trained on data earlier in the time series, to reliably predict trends in distribution and abundance in later years. Then, challenging process-based models that predict substantial and ongoing poleward shifts of cold-water species4, 5, we find that GAMs coupled with climate projections predict future distributions of demersal (bottom-dwelling) fish species over the next 50 years will be strongly constrained by availability of habitat of suitable depth. This will lead to pronounced changes in community structure, species interactions and commercial fisheries, unless individual acclimation or population-level evolutionary adaptations enable fish to tolerate warmer conditions or move to previously uninhabitable locations.

Future fish distributions constrained by depth in warming seas

European continental shelf seas have experienced intense warming over the past 30 years1. In the North Sea, fish have been comprehensively monitored throughout this period and resulting data provide a unique record of changes in distribution and abundance in response to climate change2, 3. We use these data to demonstrate the remarkable power of generalized additive models (GAMs), trained on data earlier in the time series, to reliably predict trends in distribution and abundance in later years. Then, challenging process-based models that predict substantial and ongoing poleward shifts of cold-water species4, 5, we find that GAMs coupled with climate projections predict future distributions of demersal (bottom-dwelling) fish species over the next 50 years will be strongly constrained by availability of habitat of suitable depth. This will lead to pronounced changes in community structure, species interactions and commercial fisheries, unless individual acclimation or population-level evolutionary adaptations enable fish to tolerate warmer conditions or move to previously uninhabitable locations.

Statistical forecasting of the Australian macadamia crop

Three types of forecasts of the total Australian production of macadamia nuts (t nut-in-shell) have been produced early each year since 2001. The first is a long-term forecast, based on the expected production from the tree census data held by the Australian Macadamia Society, suitably scaled up for missing data and assumed new plantings each year. These long-term forecasts range out to 10 years in the future, and form a basis for industry and market planning. Secondly, a statistical adjustment (termed the climate-adjusted forecast) is made annually for the coming crop. As the name suggests, climatic influences are the dominant factors in this adjustment process, however, other terms such as bienniality of bearing, prices and orchard aging are also incorporated. Thirdly, industry personnel are surveyed early each year, with their estimates integrated into a growers and pest-scouts forecast. Initially conducted on a 'whole-country' basis, these models are now constructed separately for the six main production regions of Australia, with these being combined for national totals. Ensembles or suites of step-forward regression models using biologically-relevant variables have been the major statistical method adopted, however, developing methodologies such as nearest-neighbour techniques, general additive models and random forests are continually being evaluated in parallel. The overall error rates average 14% for the climate forecasts, and 12% for the growers' forecasts. These compare with 7.8% for USDA almond forecasts (based on extensive early-crop sampling) and 6.8% for coconut forecasts in Sri Lanka. However, our somewhatdisappointing results were mainly due to a series of poor crops attributed to human reasons, which have now been factored into the models. Notably, the 2012 and 2013 forecasts averaged 7.8 and 4.9% errors, respectively. Future models should also show continuing improvement, as more data-years become available.

Tendências das aves noturnas em Portugal: metodologias e análise de um programa de monitorização baseado em colaboradores voluntários

Uma avaliação das metodologias de análise e recolha de dados aplicadas pelo Programa NOCTUAPortugal é de extrema importância para se apurar se estas são as mais indicadas em estudos de citizen science. Comparou-se os resultados de diferentes metodologias analíticas de estimação das tendências populacionais das espécies de aves noturnas durante o período de realização do Programa NOCTUA-Portugal (análise gráfica simples, modelos lineares generalizados (GLM-Poisson e GLMM), modelos aditivos generalizados (GAM-LOESS e GAM-mgcv) e software TRIM). Analisou-se a metodologia de censo de modo a avaliar o número de registos face à duração dos pontos de escuta, comparar a eficiência do ponto de deteção com outros estudos, variação das respostas ao longo da noite e efeito da época do ano, vento, nebulosidade e luminosidade da lua. Os resultados mostraram que a metodologia analítica mais indicada era o GLMM e que não era necessário realizar nenhum ajuste em particular na metodologia de censo; Trends in nocturnal birds in Portugal Methods and analysis of a volunteer-based monitoring program ABSTRACT: An evaluation of the methodologies of analysis and data collection applied by NOCTUA-Portugal Program is extremely important to determine whether these are the most suitable in citizen science studies. We compared the results of different analytical methodologies to estimate population trends of the species of nocturnal birds during the period of the NOCTUA-Portugal Program (simple graphical analysis, generalized linear models (GLM-Poisson and GLMM), generalized additive models (GAM-LOESS and GAMmgcv) and software TRIM). We analyzed the field methodology to assess the effect of point duration on the number of records, compared the point count efficiency with other sources, the variation of responses throughout the night, the effect of time of year, wind, cloud cover and moon luminosity. The results showed that the most suitable analytical methodology was the GLMM and it was not necessary to make any particular adjustment in the field methodology.

Phosphoglucose isomerase variability of Cerastoderma glaucum as a model for testing the influence of environmental conditions and dispersal patterns through quantitative ecology approaches

Extreme conditions of coastal lagoons could directly modify the genetic patterns of species. The aim of this work was to investigate the influence of environmental conditions and small scale dispersal patterns on the phosphoglucose isomerase (PGI*) genetic variability of Cerastoderma glaucum from the Mar Menor coastal lagoon. For this purpose, 284 cockles were collected around the perimeter of the lagoon. Vertical polyacrylamide gel electrophoresis was used to scan for PGI* polymorphisms, giving a total of seven alleles. The spatial genetic distribution of the PGI* variability, which seems to be marked by the main circulation in the lagoon, discriminates four hydrological basins. In the central basin, a gradient of allelic composition reflects the circulation forced by the dominant winds and the main channel communicated to the open sea. This result is well supported by the salinity GAM model that defines this gradient. The other three basins are defined by the distribution of fine sand in a more complex model that tries to explain the isolation of the three sites localized inside these basins. The southern, western and northern basins show the lowest degree of interconnection and are considered the most confined areas of the Mar Menor lagoon. This situation agrees with the confinement theory for benthic assemblages in the lagoon. The greater degree of differentiation seen in the Isla del Ciervo population is probably due to recent human intervention on the nearby Marchamalo channel, which has been drained in recent years thus altering the influence of the Mediterranean Sea on the southern basin.

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species.

Genetic diversity and connectivity remain high in Holothuria polii (Delle Chiaje 1823) across a coastal lagoon-open sea environmental gradient

Coastal lagoons represent habitats with widely heterogeneous environmental conditions, particularly as regards salinity and temperature,which fluctuate in both space and time. These characteristics suggest that physical and ecological factors could contribute to the genetic divergence among populations occurring in coastal lagoon and opencoast environments. This study investigates the genetic structure of Holothuria polii at a micro-geographic scale across theMar Menor coastal lagoon and nearbymarine areas, estimating the mitochondrial DNA variation in two gene fragments, cytochrome oxidase I (COI) and 16S rRNA (16S). Dataset of mitochondrial sequences was also used to test the influence of environmental differences between coastal lagoon andmarine waters on population genetic structure. All sampled locations exhibited high levels of haplotype diversity and low values of nucleotide diversity. Both genes showed contrasting signals of genetic differentiation (non-significant differences using COI and slight differences using 16S, which could due to different mutation rates or to differential number of exclusive haplotypes. We detected an excess of recent mutations and exclusive haplotypes, which can be generated as a result of population growth. However, selective processes can be also acting on the gene markers used; highly significant generalized additive models have been obtained considering genetic data from16S gene and independent variables such as temperature and salinity.

Prevalencia e incidencia de cáncer en habitantes de Sibaté, y georeferenciación de casos 2010-2014

Introducción: El Cáncer es prevenible en algunos casos, si se evita la exposición a sustancias cancerígenas en el medio ambiente. En Colombia, Cundinamarca es uno de los departamentos con mayores incrementos en la tasa de mortalidad y en el municipio de Sibaté, habitantes han manifestado preocupación por el incremento de la enfermedad. En el campo de la salud ambiental mundial, la georreferenciación aplicada al estudio de fenómenos en salud, ha tenido éxito con resultados válidos. El estudio propuso usar herramientas de información geográfica, para generar análisis de tiempo y espacio que hicieran visible el comportamiento del cáncer en Sibaté y sustentaran hipótesis de influencias ambientales sobre concentraciones de casos. Objetivo: Obtener incidencia y prevalencia de casos de cáncer en habitantes de Sibaté y georreferenciar los casos en un periodo de 5 años, con base en indagación de registros. Metodología: Estudio exploratorio descriptivo de corte transversal,sobre todos los diagnósticos de cáncer entre los años 2010 a 2014, encontrados en los archivos de la Secretaria de Salud municipal. Se incluyeron unicamente quienes tuvieron residencia permanente en el municipio y fueron diagnosticados con cáncer entre los años de 2010 a 2104. Sobre cada caso se obtuvo género, edad, estrato socioeconómico, nivel académico, ocupación y estado civil. Para el análisis de tiempo se usó la fecha de diagnóstico y para el análisis de espacio, la dirección de residencia, tipo de cáncer y coordenada geográfica. Se generaron coordenadas geográficas con un equipo GPS Garmin y se crearon mapas con los puntos de la ubicación de las viviendas de los pacientes. Se proceso la información, con Epi Info 7 Resultados: Se encontraron 107 casos de cáncer registrados en la Secretaria de Salud de Sibaté, 66 mujeres, 41 hombres. Sin división de género, el 30.93% de la población presento cáncer del sistema reproductor, el 18,56% digestivo y el 17,53% tegumentario. Se presentaron 2 grandes casos de agrupaciones espaciales en el territorio estudiado, una en el Barrio Pablo Neruda con 12 (21,05%) casos y en el casco Urbano de Sibaté con 38 (66,67%) casos. Conclusión: Se corroboro que el análisis geográfico con variables espacio temporales y de exposición, puede ser la herramienta para generar hipótesis sobre asociaciones de casos de cáncer con factores ambientales.

Between and within-year effects of haying on grassland bird

In recent years, haying has extended to Iberian Mediterranean dry grasslands potentially threatening grassland birds. We evaluate the between and within-year effects of haying on grassland birds in Alentejo region, Portugal. Our main goals were: (1) to investigate variations on bird abundance and species richness in the fields hayed, with respect to past haying events occurred in a field and its surroundings and (2) to investigate the shifts in bird abundance, species richness and spatial dynamics resulting from haying a field and its surrounding area in a given year. We conducted grassland bird censuses during the breeding season through point counts from 2012 to 2015. The relationship between bird abundance/richness and past haying events was investigated using Generalized Linear Models whereas within-year effects of haying were analysed using Generalized Additive Models. Bird abundance in a field was positively related with the surface hayed in the vicinity of that field in the previous year. However, contrasting yearly effects were found for non passerines. Also, some species prefer fields with less haying events or surface hayed, whereas others occur mostly in fields frequently managed for haying. Haying a field leads, in the short term, to its abandonment by birds, and thus to a decrease in bird abundance and, for some species, to spatial concentration in surrounding fields offering suitable habitat. We conclude that within-year effects of haying have higher impact on grassland birds than between-year effects. Maintaining haying at low levels by rotating haying yearly through the different fields in each farm and using partial haying may be an adequate way to ensure an effective management of grassland bird populations.

Additive genetic relationship of longevity with fertility and production traits in Nellore cattle based on bivariate models

Survival or longevity is an economically important trait in beef cattle. The main inconvenience for its inclusion in selection criteria is delayed recording of phenotypic data and the high computational demand for including survival in proportional hazard models. Thus, identification of a longevity-correlated trait that could be recorded early in life would be very useful for selection purposes. We estimated the genetic relationship of survival with productive and reproductive traits in Nellore cattle, including weaning weight (WW), post-weaning growth (PWG), muscularity (MUSC), scrotal circumference at 18 months (SC18), and heifer pregnancy (HP). Survival was measured in discrete time intervals and modeled through a sequential threshold model. Five independent bivariate Bayesian analyses were performed, accounting for cow survival and the five productive and reproductive traits. Posterior mean estimates for heritability (standard deviation in parentheses) were 0.55 (0.01) for WW, 0.25 (0.01) for PWG, 0.23 (0.01) for MUSC, and 0.48 (0.01) for SC18. The posterior mean estimates (95% confidence interval in parentheses) for the genetic correlation with survival were 0.16 (0.13-0.19), 0.30 (0.25-0.34), 0.31 (0.25-0.36), 0.07 (0.02-0.12), and 0.82 (0.78-0.86) for WW, PWG, MUSC, SC18, and HP, respectively. Based on the high genetic correlation and heritability (0.54) posterior mean estimates for HP, the expected progeny difference for HP can be used to select bulls for longevity, as well as for post-weaning gain and muscle score.

Additive functions in boolean models of gene regulatory network modules.

Gene-on-gene regulations are key components of every living organism. Dynamical abstract models of genetic regulatory networks help explain the genome's evolvability and robustness. These properties can be attributed to the structural topology of the graph formed by genes, as vertices, and regulatory interactions, as edges. Moreover, the actual gene interaction of each gene is believed to play a key role in the stability of the structure. With advances in biology, some effort was deployed to develop update functions in Boolean models that include recent knowledge. We combine real-life gene interaction networks with novel update functions in a Boolean model. We use two sub-networks of biological organisms, the yeast cell-cycle and the mouse embryonic stem cell, as topological support for our system. On these structures, we substitute the original random update functions by a novel threshold-based dynamic function in which the promoting and repressing effect of each interaction is considered. We use a third real-life regulatory network, along with its inferred Boolean update functions to validate the proposed update function. Results of this validation hint to increased biological plausibility of the threshold-based function. To investigate the dynamical behavior of this new model, we visualized the phase transition between order and chaos into the critical regime using Derrida plots. We complement the qualitative nature of Derrida plots with an alternative measure, the criticality distance, that also allows to discriminate between regimes in a quantitative way. Simulation on both real-life genetic regulatory networks show that there exists a set of parameters that allows the systems to operate in the critical region. This new model includes experimentally derived biological information and recent discoveries, which makes it potentially useful to guide experimental research. The update function confers additional realism to the model, while reducing the complexity and solution space, thus making it easier to investigate.

Degree of multicollinearity and variables involved in linear dependence in additive-dominant models

The objective of this work was to assess the degree of multicollinearity and to identify the variables involved in linear dependence relations in additive-dominant models. Data of birth weight (n=141,567), yearling weight (n=58,124), and scrotal circumference (n=20,371) of Montana Tropical composite cattle were used. Diagnosis of multicollinearity was based on the variance inflation factor (VIF) and on the evaluation of the condition indexes and eigenvalues from the correlation matrix among explanatory variables. The first model studied (RM) included the fixed effect of dam age class at calving and the covariates associated to the direct and maternal additive and non-additive effects. The second model (R) included all the effects of the RM model except the maternal additive effects. Multicollinearity was detected in both models for all traits considered, with VIF values of 1.03 - 70.20 for RM and 1.03 - 60.70 for R. Collinearity increased with the increase of variables in the model and the decrease in the number of observations, and it was classified as weak, with condition index values between 10.00 and 26.77. In general, the variables associated with additive and non-additive effects were involved in multicollinearity, partially due to the natural connection between these covariables as fractions of the biological types in breed composition.

Some Applications of Markov Additive Processes as Models in Insurance and Financial Mathematics

Cette thèse est principalement constituée de trois articles traitant des processus markoviens additifs, des processus de Lévy et d'applications en finance et en assurance. Le premier chapitre est une introduction aux processus markoviens additifs (PMA), et une présentation du problème de ruine et de notions fondamentales des mathématiques financières. Le deuxième chapitre est essentiellement l'article "Lévy Systems and the Time Value of Ruin for Markov Additive Processes" écrit en collaboration avec Manuel Morales et publié dans la revue European Actuarial Journal. Cet article étudie le problème de ruine pour un processus de risque markovien additif. Une identification de systèmes de Lévy est obtenue et utilisée pour donner une expression de l'espérance de la fonction de pénalité actualisée lorsque le PMA est un processus de Lévy avec changement de régimes. Celle-ci est une généralisation des résultats existant dans la littérature pour les processus de risque de Lévy et les processus de risque markoviens additifs avec sauts "phase-type". Le troisième chapitre contient l'article "On a Generalization of the Expected Discounted Penalty Function to Include Deficits at and Beyond Ruin" qui est soumis pour publication. Cet article présente une extension de l'espérance de la fonction de pénalité actualisée pour un processus subordinateur de risque perturbé par un mouvement brownien. Cette extension contient une série de fonctions escomptée éspérée des minima successives dus aux sauts du processus de risque après la ruine. Celle-ci a des applications importantes en gestion de risque et est utilisée pour déterminer la valeur espérée du capital d'injection actualisé. Finallement, le quatrième chapitre contient l'article "The Minimal entropy martingale measure (MEMM) for a Markov-modulated exponential Lévy model" écrit en collaboration avec Romuald Hervé Momeya et publié dans la revue Asia-Pacific Financial Market. Cet article présente de nouveaux résultats en lien avec le problème de l'incomplétude dans un marché financier où le processus de prix de l'actif risqué est décrit par un modèle exponentiel markovien additif. Ces résultats consistent à charactériser la mesure martingale satisfaisant le critère de l'entropie. Cette mesure est utilisée pour calculer le prix d'une option, ainsi que des portefeuilles de couverture dans un modèle exponentiel de Lévy avec changement de régimes.

Comparative analysis between a CAD model design and physical models obtained by manufacturing additive technologies using optical scan

This article presents a detailed study of the application of different additive manufacturing technologies (sintering process, three-dimensional printing, extrusion and stereolithographic process), in the design process of a complex geometry model and its moving parts. The fabrication sequence was evaluated in terms of pre-processing conditions (model generation and model STL SLI), generation strategy and physical model post-processing operations. Dimensional verification of the obtained models was undertook by projecting structured light (optical scan), a relatively new technology of main importance for metrology and reverse engineering. Studies were done in certain manufacturing time and production costs, which allowed the definition of an more comprehensive evaluation matrix of additive technologies.

Additive genetic relationship of longevity with fertility and production traits in Nellore cattle based on bivariate models

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)