A legacy of human-induced ecosystem changes: spatial processes drive the taxonomic and functional diversities of testate amoebae in Sphagnum peatlands of the Galápagos

Aim Our aims were to compare the composition of testate amoeba (TA) communities from Santa Cruz Island, Galápagos Archipelago, which are likely in existence only as a result of anthropogenic habitat transformation, with similar naturally occurring communities from northern and southern continental peatlands. Additionally, we aimed at assessing the importance of niche-based and dispersal-based processes in determining community composition and taxonomic and functional diversity. Location The humid highlands of the central island of Santa Cruz, Galápagos Archipelago. Methods We survey the alpha, beta and gamma taxonomic and functional diversities of TA, and the changes in functional traits along a gradient of wet to dry habitats. We compare the TA community composition, abundance and frequency recorded in the insular peatlands with that recorded in continental peatlands of Northern and Southern Hemispheres. We use generalized linear models to determine how environmental conditions influence taxonomic and functional diversity as well as the mean values of functional traits within communities. We finally apply variance partitioning to assess the relative importance of niche- and dispersal-based processes in determining community composition. Results TA communities in Santa Cruz Island were different from their Northern Hemisphere and South American counterparts with most genera considered as characteristic for Northern Hemisphere and South American Sphagnum peatlands missing or very rare in the Galápagos. Functional traits were most correlated with elevation and site topography and alpha functional diversity to the type of material sampled and site topography. Community composition was more strongly correlated with spatial variables than with environmental ones. Main conclusions TA communities of the Sphagnum peatlands of Santa Cruz Island and the mechanisms shaping these communities contrast with Northern Hemisphere and South American peatlands. Soil moisture was not a strong predictor of community composition most likely because rainfall and clouds provide sufficient moisture. Dispersal limitation was more important than environmental filtering because of the isolation of the insular peatlands from continental ones and the young ecological history of these ecosystems.

Diversidad funcional y diversidad filogenética en los bosques secos del sur del Ecuador

El concepto tradicional de reglas de ensamblaje refleja la idea de que las especies no co-ocurren al azar sino que están restringidos en su co-ocurrencia por la competencia interespecífica o por un filtrado ambiental. En está tesis abordé la importancia de los procesos que determinan el ensamble de la comunidad en la estructuración de los Bosques Secos en el Sur del Ecuador. Este estudio se realizó en la región biogeográfica Tumbesina, donde se encuentra la mayor concentración de bosques secos tropicales bien conservados del sur de Ecuador, y que constituyen una de las áreas de endemismo más importantes del mundo. El clima se caracteriza por una estación seca que va desde mayo a diciembre y una estación lluviosa de enero a abril, su temperatura anual varía entre 20°C y 26°C y una precipitación promedio anual entre 300 y 700 mm. Mi primer tema fue orientado a evaluar si la distribución de los rasgos funcionales a nivel comunitario es compatible con la existencia de un filtro ambiental (filtrado del hábitat) o con la existencia de un proceso de limitación de la semejanza funcional impuesta por la competencia inter-específica entre 58 especies de plantas leñosas repartidas en 109 parcelas (10x50m). Para ello, se analizó la distribución de los valores de cinco rasgos funcionales (altura máxima, densidad de la madera, área foliar específica, tamaño de la hoja y de masa de la semilla), resumida mediante varios estadísticos (rango, varianza, kurtosis y la desviación estándar de la distribución de distancias funcionales a la especies más próxima) y se comparó con la distribución esperada bajo un modelo nulo con ausencia de competencia. Los resultados obtenidos apoyan que tanto el filtrado ambiental como la limitación a la semejanza afectan el ensamble de las comunidades vegetales de los bosques secos Tumbesinos. Un segundo tema fue identificar si la diversidad funcional está condicionada por los gradientes ambientales, y en concreto si disminuye en los ambientes más estresantes a causa del filtrado ambiental, y si por el contrario aumenta en los ambientes más benignos donde la competencia se vuelve más importante, teniendo en cuenta las posibles modificaciones a este patrón general a causa de las interacciones de facilitación. Para abordar este estudio analizamos tanto las variaciones en la diversidad funcional (respecto a los de los cinco rasgos funcionales empleados en el primer capítulo de la tesis) como las variaciones de diversidad filogenética a lo largo de un gradiente de estrés climático en los bosques tumbesinos, y se contrastaron frente a las diversidades esperadas bajo un modelo de ensamblaje completamente aleatorio de la comunidad. Los análisis mostraron que tan sólo la diversidad de tamaños foliares siguió el patrón de variación esperado, disminuyendo a medida que aumentó el estrés abiótico mientras que ni el resto de rasgos funcionales ni la diversidad funcional multivariada ni la diversidad filogenética mostraron una variación significativa a lo largo del gradiente ambiental. Un tercer tema fue evaluar si los procesos que organizan la estructura funcional de la comunidad operan a diferentes escalas espaciales. Para ello cartografié todos los árboles y arbustos de más de 5 cm de diámetro en una parcela de 9 Ha de bosque seco y caractericé funcionalmente todas las especies. Dicha parcela fue dividida en subparcelas de diferente tamaño, obteniéndose subparcelas a seis escalas espaciales distintas. Los resultados muestran agregación de estrategias funcionales semejantes a escalas pequeñas, lo que sugiere la existencia bien de filtros ambientales actuando a escala fina o bien de procesos competitivos que igualan la estrategia óptima a dichas escalas. Finalmente con la misma información de la parcela permanente de 9 Ha. Nos propusimos evaluar el efecto y comportamiento de las especies respecto a la organización de la diversidad taxonómica, funcional y filogenética. Para ello utilicé tres funciones sumario espaciales: ISAR- para el nivel taxonómico, IFDAR para el nivel funcional y IPSVAR para el nivel filogenética y las contrastamos frente a modelos nulos que describen la distribución espacial de las especies individuales. Los resultados mostraron que en todas las escalas espaciales consideradas para ISAR, IFDAR y IPSVAR, la mayoría de las especies se comportaron como neutras, es decir, que están rodeados por la riqueza de diversidad semejante a la esperada. Sin embargo, algunas especies aparecieron como acumuladoras de diversidad funcional y filogenética, lo que sugiere su implicación en procesos competitivos de limitación de la semejanza. Una pequeña proporción de las especies apareció como repelente de la diversidad funcional y filogenética, lo que sugiere su implicación en un proceso de filtrado de hábitat. En este estudio pone de relieve cómo el análisis de las dimensiones alternativas de la biodiversidad, como la diversidad funcional y filogenética, puede ayudarnos a entender la co-ocurrencia de especies en diversos ensambles de comunidad. Todos los resultados de este estudio aportan nuevas evidencias de los procesos de ensamblaje de la comunidad de los Bosques Estacionalmente secos y como las variables ambientales y la competencia juegan un papel importante en la estructuración de la comunidad. ABSTRACT The traditional concept of the rules assembly for species communities reflects the idea that species do not co-occur at random but are restricted in their co-occurrence by interspecific competition or an environmental filter. In this thesis, I addressed the importance of the se processes in the assembly of plant communities in the dry forests of southern Ecuador. This study was conducted in the biogeographic region of Tumbesina has the largest concentration of well-conserved tropical dry forests of southern Ecuador, and is recognized as one of the most important areas of endemism in the world. The climate is characterized by a dry season from May to December and a rainy season from January to April. The annual temperature varies between 20 ° C and 26 ° C and an average annual rainfall between 300 and 700 mm. I first assessed whether the distribution of functional traits at the level of the community is compatible with the existence of an environmental filter (imposed by habitat) or the existence of a limitation on functional similarity imposed by interspecific competition. This analysis was conducted for 58 species of woody plants spread over 109 plots of 10 x 50 m. Specifically, I compared the distribution of values of five functional traits (maximum height, wood density, specific leaf area, leaf size and mass of the seed), via selected statistical properties (range, variance, kurtosis and analyzed the standard deviation of the distribution of the closest functional species) distances and compared with a expected distribution under a null model of no competition. The results support that both environmental filtering and a limitation on trait similarity affect the assembly of plant communities in dry forests Tumbesina. My second chapter evaluated whether variation in functional diversity is conditioned by environmental gradients. In particular, I tested whether it decreases in the most stressful environments because of environmental filters, or if, on the contrary, functional diversity is greater in more benign environments where competition becomes more important (notwithstanding possible changes to this general pattern due to facilitation). To address this theme I analyzed changes in both the functional diversity (maximum height, wood density, specific leaf area, leaf size and mass of the seed) and the phylogenetic diversity, along a gradient of climatic stress in Tumbes forests. The observed patterns of variation were contrasted against the diversity expected under a completely random null model of community assembly. Only the diversity of leaf sizes followed the hypothesis decreasing in as trait variation abiotic stress increased, while the other functional traits multivariate functional diversity and phylogenetic diversity no showed significant variation along the environmental gradient. The third theme assess whether the processes that organize the functional structure of the community operate at different spatial scales. To do this I mapped all the trees and shrubs of more than 5 cm in diameter within a plot of 9 hectares of dry forest and functionally classified each species. The plot was divided into subplots of different sizes, obtaining subplots of six different spatial scales. I found aggregation of similar functional strategies at small scales, which may indicate the existence of environmental filters or competitive processes that correspond to the optimal strategy for these fine scales. Finally, with the same information from the permanent plot of 9 ha, I evaluated the effect and behavior of individual species on the organization of the taxonomic, functional and phylogenetic diversity. The analysis comprised three spatial summary functions: ISAR- for taxonomic level analysis, IFDAR for functional level analysis, and IPSVAR for phylogenetic level analysis, in each case the pattern of diversity was contrasted against null models that randomly reallocate describe the spatial distribution of individual species and their traits. For all spatial scales considering ISAR, IFDAR and IPSVAR, most species behaved as neutral, i.e. they are surrounded by the diversity of other traits similar to that expected under a null model. However, some species appeared as accumulator of functional and phylogenetic diversity, suggesting that they may play a role in competitive processes that limiting similarity. A small proportion of the species appeared as repellent of functional and phylogenetic diversity, suggesting their involvement in a process of habitat filtering. These analysis highlights that the analysis of alternative dimensions of biodiversity, such as functional and phylogenetic diversity, can help us understand the co-occurrence of species in the assembly of biotic communities. All results of this study provide further evidence of the processes of assembly of the community of the seasonally dry forests as environmental variables and competition play an important role in structuring the community.

Estructura espacial y dinámica del bosque montano del sur del Ecuador. Interacciones bióticas y limitaciones abióticas

Muchos estudios han descrito la composición y diversidad de los bosques montanos tropicales, pero los patrones espaciales y las diferentes tipos de relaciones de estos, entre especies o entre grupos funcionales ha sido poco documentada. El presente trabajo se realizó en tres parcelas completamente censadas del bosque de la Estación Biológica “Chamusquin” (Zamora Chinchipe, Ecuador), y se plantea como objetivo principal conocer la estructura espacial y dinámica del bosque montano tropical del sur del Ecuador, así como las interacciones bióticas y limitaciones abióticas que influyen en esta dinámica, para ello se planteó cuatro objetivos de estudio que son: conocer los patrones espaciales de los gremios ecológicos dentro de la zona de estudio; conocer la influencia de la dependencia negativa de la densidad sobre dos especies de helechos arborescentes (Cyatheaceae); conocer si existen especies o grupos ecológicos acumuladoras o repulsoras de diversidad en el área de estudio; y conocer cómo influyen la diversidad filogenética y la densidad del vecindario en la incidencia de herbivoría y parasitismo sobre las fases iniciales del establecimiento forestal (brinzales) así como en la supervivencia de los mismos Como paso previo para el análisis del resto de objetivos, dentro de cada parcela se marcaron todos los individuos con DAP ≥5 cm y se tomaron sus coordenadas (X, Y). Además se tomaron datos de variables superficiales y muestras del suelo. Las especies encontradas se clasificaron de acuerdo a sus características biológicas, asignándolas a cada uno de los cuatro gremios forestales usualmente distinguidos en los bosques tropicales: tolerantes a la sombra (TS), tolerantes parciales a la sombra (TPS), pioneras de vida larga (PVL) y pioneras de vida corta (PVC). Para el estudio del primer objetivo tas se emplearon funciones K de Ripley inhomogéneas, ajustando la heterogeneidad en base a la variación espacial de las variables ambientales registradas . Los resultados demostraron que tanto la frecuencia relativa como el patrón espacial de las diferentes estrategias funcionales varían a lo largo de la sucesión y que éste además está influido por la variación ambiental. En adición, tanto el patrón espacial como la respuesta a la variación ambiental de los diferentes gremios es distinta entre adultos y juveniles. Todo ello sugiere que el ensamblaje de la diversidad en los bosque montanos andinos está controlado por procesos deterministas más que por procesos neutrales. Para responder el segundo objetivo se estudiaron los efectos de la dependencia negativa de la densidad (DND) y la heterogeneidad ambiental en las poblaciones de dos especies de helechos arborescentes abundantes, Cyathea caracasana y Alsophila engelii, y cómo estos efectos cambian a través de un gradiente sucesional. Los patrones de especies albergan información sobre procesos tales como la competencia que puede ser revelado fácilmente utilizando técnicas de análisis de patrones punto. Sin embargo, su detección puede ser difícil debido a los efectos de factores de confusión heterogeneidad del hábitat. Aquí, empleamos funciones K y funciones de correlación de par homogéneas y no homogéneas para cuantificar el cambio en el patrón espacial de diferentes clases de tamaño con un diseño de casos-controles para estudiar las asociaciones entre helechos arborescentes jóvenes y adultos. Usando estimaciones espaciales de la biomasa de los cuatro tipos de gremios ecológicos (PVC, PVL, TPS, TS) como covariables, hemos ajustado modelos de Poisson heterogéneos a los patrones de puntos de de los helechos juveniles y los adultos y hemos explorado además la existencia de dependencia del hábitat en estos patrones. Nuestro estudio reveló efectos de la DND para C. caracasana y un fuerte filtrado ambiental que subyace al patrón de A. engelii. Encontramos también que las poblaciones de adultos y juveniles de ambas especies respondieron de manera diferente a la heterogeneidad del hábitat y en la mayoría de los casos esta heterogeneidad se asoció con la distribución espacial de la biomasa de los cuatro tipos de gremios. Estos resultados muestran la eficacia de controlar los efectos de la heterogeneidad ambiental para evitar su confusión con los patrones derivados de interacciones biológicas cuando se estudia la DND y demuestran la utilidad de los mapas de covariables derivados de comunidades biológicas como resumen de la heterogeneidad ambiental. Para nuestro tercer objetivo nos centramos en explorar cómo influyen las especies más abundantes en la organización espacial de la diversidad a lo largo de un gradiente sucesional en el bosque montano del sur del Ecuador. Para ello utilizamos la función ISAR (Individual Species Area Relationship). Encontramos que la frecuencia de especies neutras, repulsoras y acumuladoras de diversidad taxonómica varía dependiendo del grado de sucesión. Además se comprobó que la mayoría de los gremios forestales se comportó de forma neutral, pero la proporción de acumuladores, aumentó al avanzar la sucesión hacia estados más maduros, lo que indica el establecimiento de fuertes procesos competitivos a medida que avanza la sucesión y la mayor importancia del papel de las especies individuales en dichos estados. Finalmente, examinamos el efecto de la vecindad taxonómica y filogenética, así como la estrategia de vida, sobre la incidencia de la herbivoría y el parasitismo en las poblaciones de brinzales de tres fragmentos forestales en una secuencia sucesional del bosque montano húmedo. Evaluamos además los efectos de herbivoría, parasitismo, estrategia de vida y diferentes indicadores de la vecindad sobre la supervivencia de los brinzales. Por último contrastamos la posible existencia de una tendencia compensatoria de la comunidad (CCT) a nivel de fragmento forestal. Nuestros análisis no consiguieron detectar una CCT pero si pusieron de manifiesto la existencia de efectos locales de dependencia negativa de la densidad. Por ejemplo, la presencia de herbivoría y parasitismo sobre los brinzales se relacionó significativamente con una menor supervivencia de estos. Por otro lado, indicadores del efecto de la vecindad como la densidad de brinzales del mismo género y el área basal de árboles vecinos del mismo género incrementaron la prevalencia de la herbivoría o el parasitismo en los brinzales. El incremento de la incidencia de la herbivoría o el parasitismo no está exclusivamente ligado a tener una vecindad taxonómicamente idéntica (vecinos de la misma especie) sino que categorías taxonómicas más laxas como el "género" o simplemente relaciones de semejanza filogenética son capaces de predecir los efectos negativos de la vecindad. Los efectos detectados variaron en los diferentes grupos funcionales distinguidos. Los resultados que hemos obtenido en este trabajo parecen indicar que el funcionamiento de las comunidades de brinzales del bosque montano tropical no difiere mucho del reportado para comunidades de plántulas en otros bosques tropicales y cumple las predicciones de la hipótesis de Janzen y Connell, aunque matizadas por la mayor resistencia de los brinzales al efecto de herbivoría y parasitismo. ABSTRACT Many studies have described the composition and diversity of tropical montane forests, but the different spatial patterns and types of relationships between species or between functional groups has been poorly documented. This work was made in three completely surveyed forest plots at Biological Station "Chamusquin" (Zamora Chinchipe, Ecuador). Our main objective was to know the spatial structure and dynamics of the tropical montane forest in southern Ecuador, as well as the biotic interactions and abiotic constraints affecting this dynamic. More specifically, we aimed to understand the spatial patterns of ecological guilds; to explore the influence of negative density dependence on two species of tree ferns (Cyatheaceae); to determine whether some species or ecological groups structure spatially plant diversity in these forests; and to test the effects of biological neighborhood on the incidence of herbivory and parasitism and on the survival of saplings. We mapped within each plot all trees with DBH ≥5 cm. Besides, surface data variables and soil samples they were taken. The species found were classified according to their biological characteristics in four forest guilds: shade-tolerant (ST), partial shade tolerant (PST), long-lived pioneer (LLP) and short-lived pioneer (SLP). To analyze the spatial patterns of the ecological guilds, we employed the inhomogeneous version of Ripley's K-function and adjusted heterogeneity surfaces based on the spatial variation of the measured environmental variables. The results showed that both the relative frequency of each functional guild as well as their spatial pattern varied throughout succession and that the spatial pattern is explained by environmental variation. In addition, both spatial pattern and the response to spatial variation of each guild varied throughout ontogeny. All in all suggest that diversity assembly in the studied forests is ruled by deterministic instead of neutral processes. We also addressed the negative effects of density dependence (NDD) and environmental heterogeneity in populations of two species of abundant tree ferns, Cyathea caracasana and Alsophila engelii, and how these effects change across a successional gradient.. Here, we used homogeneous and inhomogeneous K and pair-correlation functions to quantify the change in the spatial pattern of different size classes with a case-control design to study associations between young and adult tree ferns. Using spatial estimates of the biomass of the four types of ecological guilds (SLP, LLP, PST, ST) as co-variables, we fitted heterogeneous Poisson models to juvenile and adult tree fern point patterns and explored the existence of habitat dependence. Our study revealed NDD effects for C. caracasana and strong environmental filtering underlying the pattern of A. engelii. We found that adult and juvenile populations of both species responded differently to habitat heterogeneity and in most cases this heterogeneity was associated with the spatial distribution of biomass of the four functional tree types. These findings show the effectiveness of factoring out environmental heterogeneity to avoid confounding factors when studying NDD and demonstrate the usefulness of covariate maps derived from mapped communities. For our third objective we focused on exploring how the most abundant species influence the spatial organization of tree diversity in these forests. For this, we used the individual species-area relationship function (ISAR). We found that the proportion of accumulator, repeller and neutral species, varied depending on the degree of succession. We found also that most guilds behaved neutrally but the proportion of accumulator guilds increased as succession advanced to more mature stages. This point, to the existence of strong competitive effects mediated by individual species in these mature forests. Finally, we examined the effects of life strategies and taxonomic and phylogenetic neighborhood on the incidence of herbivory and parasitism in the communities of saplings in the same forest fragments. We evaluated also the effects of life strategies, herbivory, parasitism and some indicators of neighborhood on sapling survival. Finally we tested for the existences of a compensatory community trend at plot scale. We did not found a CCT but we found proof of local NND effects. For instance, the prevalence of herbivory and parasitism were related to lower sapling survival. On the other hand the density of con-generic saplings and the basal area of neighbor con-generic trees were related to a higher prevalence of herbivory or parasitism in the saplings. We demonstrated that the increase in the prevalence of herbivory or parasitism it s not exclusive of a conspecific neighborhood but instead larger taxonomic categories such as "genus" or simple phylogenetic relationships are also able to predict NND effects. The NND effects varied among functional guilds. Our results show that the dynamic of sapling communities in Ecuadorian montane forests is similar to seedling dynamics in other tropical forest and follows the predictions of Janzen-Connell hypothesis, although softened by the strong resilience of saplings in comparison to seedlings.

EnvironmentalWaveletTool: Continuous and discrete wavelet analysis and filtering for environmental time series

A MATLAB-based computer code has been developed for the simultaneous wavelet analysis and filtering of several environmental time series, particularly focused on the analyses of cave monitoring data. The continuous wavelet transform, the discrete wavelet transform and the discrete wavelet packet transform have been implemented to provide a fast and precise time–period examination of the time series at different period bands. Moreover, statistic methods to examine the relation between two signals have been included. Finally, the entropy of curves and splines based methods have also been developed for segmenting and modeling the analyzed time series. All these methods together provide a user-friendly and fast program for the environmental signal analysis, with useful, practical and understandable results.

Content-based birdcall retrieval from environmental audio

This research investigates techniques to analyse long duration acoustic recordings to help ecologists monitor birdcall activities. It designs a generalized algorithm to identify a broad range of bird species. It allows ecologists to search for arbitrary birdcalls of interest, rather than restricting them to just a very limited number of species on which the recogniser is trained. The algorithm can help ecologists find sounds of interest more efficiently by filtering out large volumes of unwanted sounds and only focusing on birdcalls.

Influence of filtering and biodeposition by the cultured scallop Chlamys farreri on benthic-pelagic coupling in a eutrophic bay in China

In coastal ecosystems, suspension-cultured bivalve filter feeders may exert a strong impact on phytoplankton and other suspended particulate matter and induce strong pelagic-benthic coupling via intense filtering and biodeposition. We designed an in situ method to determine spatial variations in the filtering-biodeposition process by intensively suspension-cultured scallops Chlamys farreri in summer in a eutrophic bay (Sishili Bay, China), using cylindrical biodeposition traps directly suspended from longlines under ambient environmental conditions. Results showed that bivalve filtering-biodeposition could substantially enhance the deposition of total suspended material and the flux of C, N and P to the benthos, indicating that the suspended filter feeders could strongly enhance pelagic-benthic coupling and exert basin-scale impacts in the Sishili Bay ecosystem. The biodeposition rates of 1-yr-old scallops varied markedly among culture sites (33.8 to 133.0 mg dry material ind.(-1) d(-1)), and were positively correlated with seston concentrations. Mean C, N and P biodeposition rates were 4.00, 0.51, 0.11 mg ind.-1 d-1, respectively. The biodeposition rates of 2-yr-old scallops were almost double these values. Sedimentation rates at scallop culture sites averaged 2.46 times that at the reference site. Theoretically, the total water column of the bay could be filtered by the cultured scallops in 12 d, with daily seston removal amounting to 64%. This study indicated that filtering-biodeposition by suspension-cultured scallops could exert long-lasting top-down control on phytoplankton biomass and other suspended material in the Sishili Bay ecosystem. In coastal waters subject to anthropogenic N and P inputs, suspended bivalve aquaculture could be advantageous, not only economically, but also ecologically, by functioning as a biofilter and potentially mitigating eutrophication pressures. Compared with distribution-restricted wild bivalves, suspension-cultured bivalves in deeper coastal bays may be more efficient in processing seston on a basin scale.

Combining multi-band and frequency-filtering techniques for speech recognition in noisy environments

While current speech recognisers give acceptable performance in carefully controlled environments, their performance degrades rapidly when they are applied in more realistic situations. Generally, the environmental noise may be classified into two classes: the wide-band noise and narrow band noise. While the multi-band model has been shown to be capable of dealing with speech corrupted by narrow-band noise, it is ineffective for wide-band noise. In this paper, we suggest a combination of the frequency-filtering technique with the probabilistic union model in the multi-band approach. The new system has been tested on the TIDIGITS database, corrupted by white noise, noise collected from a railway station, and narrow-band noise, respectively. The results have shown that this approach is capable of dealing with noise of narrow-band or wide-band characteristics, assuming no knowledge about the noisy environment.

Environmental control for layers

Light patterns have less effect on numbers of eggs laid by current stocks than on those of forty years ago, but the principles have not changed. Ovarian activity is stimulated by increasing photoperiods and suppressed by decreasing photoperiods. The light pattern used during rearing can still have large effects on age at 50% lay, even for modern stocks. Early sexual maturity maximises egg numbers but gives smaller eggs. Late maturity maximises egg size at the expense of numbers. The relationship between egg output (g/hen d) and age at first egg is curvilinear, with maximum yield occurring in flocks maturing in about the centre of their potential range. Fancy patterns of increasing daylength after maturity are probably not justified. A flock held on a constant 14h day will lay as many eggs as one given step up lighting. Intermittent lighting saves about 5% of feed consumption with no loss of output, provided that the feed has adequate amino acid content to allow for the reduced feed intake. Producers with light-proof laying houses should be taking advantage of intermittent lighting. The recommended light intensity for laying houses is still 10 lx, although the physiological threshold for response to changes in photoperiod is closer to 2 lx. Very dim (0.05 lx) light filtering into blacked out houses will not stimulate the hypothalamic receptors responsible for photo-sexual responses, but may affect the bird's biological clock, which can alter its response to a constant short photoperiod. Feed intake shows a curvilinear dependence on environmental temperature. At temperatures below the panting threshold, performance can be maintained by adjusting the feed so as to maintain an adequate intake of critical amino acids. Above the panting threshold, the hen is unable to take in enough energy to maintain normal output. There is no dietary modification which can effectively offset this problem. Diurnally cycling temperatures result in feed intake and egg production equivalent to that observed under a constant temperature equal to the mean of the cycle. When the poultry house is cooler at night than by day, it helps to provide light so that the birds can feed during the cooler part of the cycle.

Aspects of particle filtering in high-dimensional spaces

Nonlinear data assimilation is high on the agenda in all fields of the geosciences as with ever increasing model resolution and inclusion of more physical (biological etc.) processes, and more complex observation operators the data-assimilation problem becomes more and more nonlinear. The suitability of particle filters to solve the nonlinear data assimilation problem in high-dimensional geophysical problems will be discussed. Several existing and new schemes will be presented and it is shown that at least one of them, the Equivalent-Weights Particle Filter, does indeed beat the curse of dimensionality and provides a way forward to solve the problem of nonlinear data assimilation in high-dimensional systems.

Effects of environmental factors on community structure of Leptophlebiidae (Insecta, Ephemeroptera) in Cerrado streams, Brazil

O efeito de fatores ambientais sobre a abundância, riqueza de espécies e grupos funcionais alimentares de Leptophlebiidae foi analisado em 16 locais pertencentes a quatro córregos de Cerrado, a partir de coletas de substrato em três períodos de 2005. Foram amostradas 5.492 larvas distribuídas em 14 espécies, classificadas em três grupos funcionais alimentares: raspadores, coletores-filtradores e fragmentadores. A abundância e riqueza de espécies não foram afetadas por nenhum dos fatores ambientais investigados, mas a integridade dos hábitats exerceu efeito positivo sobre a abundância dos fragmentadores, consequência da intrínseca interação desses organismos com a mata ciliar. Dessa forma, acreditamos que este trabalho agrega informações bioecológicas sobre as espécies e grupos funcionais de insetos aquáticos e poderá contribuir no monitoramento e conservação de riachos do Cerrado.

Micropollutants affect the ability of phytoplankton communities to track environmental changes

Human activities strongly influence environmental processes, and while human domination increases, biodiversity progressively declines in ecosystems worldwide. High genetic and phenotypic variability ensures functionality and stability of ecosystem processes through time and increases the resilience and the adaptive capacity of populations and communities, while a reduction in functional diversity leads to a decrease in the ability to respond in a changing environment. Pollution is becoming one of the major threats in aquatic ecosystem, and pharmaceutical and personal care products (PPCPs) in particular are a relatively new group of environmental contaminants suspected to have adverse effects on aquatic organisms. There is still a lake of knowledge on the responses of communities to complex chemical mixtures in the environment. We used an individual-trait-based approach to assess the response of a phytoplankton community in a scenario of combined pollution and environmental change (steady increasing in temperature). We manipulated individual-level trait diversity directly (by filtering out size classes) and indirectly (through exposure to PPCPs mixture), and studied how reduction in trait-diversity affected community structure, production of biomass and the ability of the community to track a changing environment. We found that exposure to PPCPs slows down the ability of the community to respond to an increasing temperature. Our study also highlights how physiological responses (induced by PPCPs exposure) are important for ecosystem processes: although from an ecological point of view experimental communities converged to a similar structure, they were functionally different.

Perceptual learning reflects external noise filtering and internal noise reduction through channel reweighting

To investigate the nature of plasticity in the adult visual system, perceptual learning was measured in a peripheral orientation discrimination task with systematically varying amounts of external (environmental) noise. The signal contrasts required to achieve threshold were reduced by a factor or two or more after training at all levels of external noise. The strong quantitative regularities revealed by this novel paradigm ruled out changes in multiplicative internal noise, changes in transducer nonlinearites, and simple attentional tradeoffs. Instead, the regularities specify the mechanisms of perceptual learning at the behavioral level as a combination of external noise exclusion and stimulus enhancement via additive internal noise reduction. The findings also constrain the neural architecture of perceptual learning. Plasticity in the weights between basic visual channels and decision is sufficient to account for perceptual learning without requiring the retuning of visual mechanisms.

Mitigating inconsistencies by coupling data cleaning, filtering, and contextual data validation in wireless sensor networks

With the advent of peer to peer networks, and more importantly sensor networks, the desire to extract useful information from continuous and unbounded streams of data has become more prominent. For example, in tele-health applications, sensor based data streaming systems are used to continuously and accurately monitor Alzheimer's patients and their surrounding environment. Typically, the requirements of such applications necessitate the cleaning and filtering of continuous, corrupted and incomplete data streams gathered wirelessly in dynamically varying conditions. Yet, existing data stream cleaning and filtering schemes are incapable of capturing the dynamics of the environment while simultaneously suppressing the losses and corruption introduced by uncertain environmental, hardware, and network conditions. Consequently, existing data cleaning and filtering paradigms are being challenged. This dissertation develops novel schemes for cleaning data streams received from a wireless sensor network operating under non-linear and dynamically varying conditions. The study establishes a paradigm for validating spatio-temporal associations among data sources to enhance data cleaning. To simplify the complexity of the validation process, the developed solution maps the requirements of the application on a geometrical space and identifies the potential sensor nodes of interest. Additionally, this dissertation models a wireless sensor network data reduction system by ascertaining that segregating data adaptation and prediction processes will augment the data reduction rates. The schemes presented in this study are evaluated using simulation and information theory concepts. The results demonstrate that dynamic conditions of the environment are better managed when validation is used for data cleaning. They also show that when a fast convergent adaptation process is deployed, data reduction rates are significantly improved. Targeted applications of the developed methodology include machine health monitoring, tele-health, environment and habitat monitoring, intermodal transportation and homeland security.

Mitigating Inconsistencies by Coupling Data Cleaning, Filtering, and Contextual Data Validation in Wireless Sensor Networks

With the advent of peer to peer networks, and more importantly sensor networks, the desire to extract useful information from continuous and unbounded streams of data has become more prominent. For example, in tele-health applications, sensor based data streaming systems are used to continuously and accurately monitor Alzheimer's patients and their surrounding environment. Typically, the requirements of such applications necessitate the cleaning and filtering of continuous, corrupted and incomplete data streams gathered wirelessly in dynamically varying conditions. Yet, existing data stream cleaning and filtering schemes are incapable of capturing the dynamics of the environment while simultaneously suppressing the losses and corruption introduced by uncertain environmental, hardware, and network conditions. Consequently, existing data cleaning and filtering paradigms are being challenged. This dissertation develops novel schemes for cleaning data streams received from a wireless sensor network operating under non-linear and dynamically varying conditions. The study establishes a paradigm for validating spatio-temporal associations among data sources to enhance data cleaning. To simplify the complexity of the validation process, the developed solution maps the requirements of the application on a geometrical space and identifies the potential sensor nodes of interest. Additionally, this dissertation models a wireless sensor network data reduction system by ascertaining that segregating data adaptation and prediction processes will augment the data reduction rates. The schemes presented in this study are evaluated using simulation and information theory concepts. The results demonstrate that dynamic conditions of the environment are better managed when validation is used for data cleaning. They also show that when a fast convergent adaptation process is deployed, data reduction rates are significantly improved. Targeted applications of the developed methodology include machine health monitoring, tele-health, environment and habitat monitoring, intermodal transportation and homeland security.

Variational ensemble Kalman filtering applied to data assimilation problems in computational fluid dynamics

One challenge on data assimilation (DA) methods is how the error covariance for the model state is computed. Ensemble methods have been proposed for producing error covariance estimates, as error is propagated in time using the non-linear model. Variational methods, on the other hand, use the concepts of control theory, whereby the state estimate is optimized from both the background and the measurements. Numerical optimization schemes are applied which solve the problem of memory storage and huge matrix inversion needed by classical Kalman filter methods. Variational Ensemble Kalman filter (VEnKF), as a method inspired the Variational Kalman Filter (VKF), enjoys the benefits from both ensemble methods and variational methods. It avoids filter inbreeding problems which emerge when the ensemble spread underestimates the true error covariance. In VEnKF this is tackled by resampling the ensemble every time measurements are available. One advantage of VEnKF over VKF is that it needs neither tangent linear code nor adjoint code. In this thesis, VEnKF has been applied to a two-dimensional shallow water model simulating a dam-break experiment. The model is a public code with water height measurements recorded in seven stations along the 21:2 m long 1:4 m wide flume’s mid-line. Because the data were too sparse to assimilate the 30 171 model state vector, we chose to interpolate the data both in time and in space. The results of the assimilation were compared with that of a pure simulation. We have found that the results revealed by the VEnKF were more realistic, without numerical artifacts present in the pure simulation. Creating a wrapper code for a model and DA scheme might be challenging, especially when the two were designed independently or are poorly documented. In this thesis we have presented a non-intrusive approach of coupling the model and a DA scheme. An external program is used to send and receive information between the model and DA procedure using files. The advantage of this method is that the model code changes needed are minimal, only a few lines which facilitate input and output. Apart from being simple to coupling, the approach can be employed even if the two were written in different programming languages, because the communication is not through code. The non-intrusive approach is made to accommodate parallel computing by just telling the control program to wait until all the processes have ended before the DA procedure is invoked. It is worth mentioning the overhead increase caused by the approach, as at every assimilation cycle both the model and the DA procedure have to be initialized. Nonetheless, the method can be an ideal approach for a benchmark platform in testing DA methods. The non-intrusive VEnKF has been applied to a multi-purpose hydrodynamic model COHERENS to assimilate Total Suspended Matter (TSM) in lake Säkylän Pyhäjärvi. The lake has an area of 154 km2 with an average depth of 5:4 m. Turbidity and chlorophyll-a concentrations from MERIS satellite images for 7 days between May 16 and July 6 2009 were available. The effect of the organic matter has been computationally eliminated to obtain TSM data. Because of computational demands from both COHERENS and VEnKF, we have chosen to use 1 km grid resolution. The results of the VEnKF have been compared with the measurements recorded at an automatic station located at the North-Western part of the lake. However, due to TSM data sparsity in both time and space, it could not be well matched. The use of multiple automatic stations with real time data is important to elude the time sparsity problem. With DA, this will help in better understanding the environmental hazard variables for instance. We have found that using a very high ensemble size does not necessarily improve the results, because there is a limit whereby additional ensemble members add very little to the performance. Successful implementation of the non-intrusive VEnKF and the ensemble size limit for performance leads to an emerging area of Reduced Order Modeling (ROM). To save computational resources, running full-blown model in ROM is avoided. When the ROM is applied with the non-intrusive DA approach, it might result in a cheaper algorithm that will relax computation challenges existing in the field of modelling and DA.