1,430 research outputs found
Visualização de padrões temporais cíclicos em estudos de fenologia
Orientadores: Ricardo da Silva Torres, Leonor Patrícia Cerdeira MorellatoTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Em diversas aplicações, grandes volumes de dados multidimensionais têm sido gerados continuamente ao longo do tempo. Uma abordagem adequada para lidar com estas coleções consiste no uso de métodos de visualização de informação, a partir dos quais padrões de interesse podem ser identificados, possibilitando o entendimento de fenômenos temporais complexos. De fato, em diversos domínios, o desenvolvimento de ferramentas adequadas para apoiar análises complexas, por exemplo, aquelas baseadas na identificação de padrões de mudanças ou correlações existentes entre múltiplas variáveis ao longo do tempo é de suma importância. Em estudos de fenologia, por exemplo, especialistas observam as mudanças que ocorrem ao longo da vida de plantas e animais e investigam qual é a relação entre essas mudanças com variáveis ambientais. Neste cenário, especialistas em fenologia cada vez mais precisam de ferramentas para, adequadamente, visualizar séries temporais longas, com muitas variáveis e de diferentes tipos (por exemplo, texto e imagem), assim como identificar padrões temporais cíclicos. Embora diversas abordagens tenham sido propostas para visualizar dados que variam ao longo do tempo, muitas não são apropriadas ou aplicáveis para dados de fenologia, porque não são capazes de: (i) lidar com séries temporais longas, com muitas variáveis de diferentes tipos de dados e de uma ou mais dimensões; e (ii) permitir a identificação de padrões temporais cíclicos e drivers ambientais associados. Este trabalho aborda essas questões a partir da proposta de duas novas abordagens para apoiar a análise e visualização de dados temporais multidimensionais. Nossa primeira proposta combina estruturas visuais radiais com ritmos visuais. As estruturas radiais são usadas para fornecer informação contextual sobre fenômenos cíclicos, enquanto que o ritmo visual é usado para sumarizar séries temporais longas em representações compactas. Nós desenvolvemos, avaliamos e validamos nossa proposta com especialistas em fenologia em tarefas relacionadas à visualização de dados de observação direta da fenologia de plantas em nível tanto de indivíduos quanto de espécies. Nós também validamos a proposta usando dados temporais relacionados a imagens obtidas de sistemas de monitoramento de vegetação próxima à superfície. Nossa segunda abordagem é uma nova representação baseada em imagem, chamada Change Frequency Heatmap (CFH), usada para codificar mudanças temporais de dados numéricos multivariados. O método calcula histogramas de padrões de mudanças observados em sucessivos instantes de tempo. Nós validamos o uso do CFH a partir da criação de uma ferramenta de caracterização de mudanças no ciclo de vida de plantas de múltiplos indivíduos e espécies ao longo do tempo. Nós demonstramos o potencial do CFH para ajudar na identificação visual de padrões de mudanças temporais complexas, especialmente na identificação de variações entre indivíduos em estudos relacionados à fenologia de plantasAbstract: In several applications, large volumes of multidimensional data have been generated continuously over time. One suitable approach for handling those collections in a meaningful way consists in the use of information visualization methods, based on which patterns of interest can be identified, triggering the understanding of complex temporal phenomena. In fact, in several domains, the development of appropriate tools for supporting complex analysis based, for example, on the identification of change patterns in temporal data or existing correlations, over time, among multiple variables, is of paramount importance. In phenology studies, for instance, phenologists observe changes in the development of plants and animals throughout their lives and investigate what is the relationship between these changes with environmental changes. Therefore, phenologists increasingly need tools for visualizing appropriately long-term series with many variables of different data types, as well as for identifying cyclical temporal patterns. Although several approaches have been proposed to visualize data varying over time, most of them are not appropriate or applicable to phenology data, because they are not able: (i) to handle long-term series with many variables of different data types and one or more dimensions and (ii) to support the identification of cyclical temporal patterns and associated environmental drivers. This work addresses these shortcomings by presenting two new approaches to support the analysis and visualization of multidimensional temporal data. Our first proposal to visualize phenological data combines radial visual structures along with visual rhythms. Radial visual structures are used to provide contextual insights regarding cyclical phenomena, while the visual rhythm encoding is used to summarize long-term time series into compact representations. We developed, evaluated, and validated our proposal with phenology experts using plant phenology direct observational data both at individuals and species levels. Also we validated the proposal using image-related temporal data obtained from near-surface vegetation monitoring systems. Our second approach is a novel image-based representation, named Change Frequency Heatmap (CFH), used to encode temporal changes of multivariate numerical data. The method computes histograms of change patterns observed at successive timestamps. We validated the use of CFHs through the creation of a temporal change characterization tool to support complex plant phenology analysis, concerning the characterization of plant life cycle changes of multiple individuals and species over time. We demonstrated the potential of CFH to support visual identification of complex temporal change patterns, especially to decipher interindividual variations in plant phenologyDoutoradoCiência da ComputaçãoDoutora em Ciência da Computação162312/2015-62013/501550-0CNPQCAPESFAPES
Near-surface remote sensing of spatial and temporal variation in canopy phenology
There is a need to document how plant phenology is responding to global change factors, particularly warming trends. “Near-surface” remote sensing, using radiometric instruments or imaging sensors, has great potential to improve phenological monitoring because automated observations can be made at high temporal frequency. Here we build on previous work and show how inexpensive, networked digital cameras (“webcams”) can be used to document spatial and temporal variation in the spring and autumn phenology of forest canopies. We use two years of imagery from a deciduous, northern hardwood site, and one year of imagery from a coniferous, boreal transition site. A quantitative signal is obtained by splitting images into separate red, green, and blue color channels and calculating the relative brightness of each channel for “regions of interest” within each image. We put the observed phenological signal in context by relating it to seasonal patterns of gross primary productivity, inferred from eddy covariance measurements of surface–atmosphere CO2 exchange. We show that spring increases, and autumn decreases, in canopy greenness can be detected in both deciduous and coniferous stands. In deciduous stands, an autumn red peak is also observed. The timing and rate of spring development and autumn senescence varies across the canopy, with greater variability in autumn than spring. Interannual variation in phenology can be detected both visually and quantitatively; delayed spring onset in 2007 compared to 2006 is related to a prolonged cold spell from day 85 to day 110. This work lays the foundation for regional- to continental-scale camera-based monitoring of phenology at network observatory sites, e.g., National Ecological Observatory Network (NEON) or AmeriFlux
Intercomparison of phenological transition dates derived from the PhenoCam Dataset V1.0 and MODIS satellite remote sensing
Phenology is a valuable diagnostic of ecosystem health, and has applications to environmental monitoring and management. Here, we conduct an intercomparison analysis using phenological transition dates derived from near-surface PhenoCam imagery and MODIS satellite remote sensing. We used approximately 600 site-years of data, from 128 camera sites covering a wide range of vegetation types and climate zones. During both “greenness rising” and “greenness falling” transition phases, we found generally good agreement between PhenoCam and MODIS transition dates for agricultural, deciduous forest, and grassland sites, provided that the vegetation in the camera field of view was representative of the broader landscape. The correlation between PhenoCam and MODIS transition dates was poor for evergreen forest sites. We discuss potential reasons (including sub-pixel spatial heterogeneity, flexibility of the transition date extraction method, vegetation index sensitivity in evergreen systems, and PhenoCam geolocation uncertainty) for varying agreement between time series of vegetation indices derived from PhenoCam and MODIS imagery. This analysis increases our confidence in the ability of satellite remote sensing to accurately characterize seasonal dynamics in a range of ecosystems, and provides a basis for interpreting those dynamics in the context of tangible phenological changes occurring on the ground
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Evaluating remote sensing of deciduous forest phenology at multiple spatial scales using PhenoCam imagery
Plant phenology regulates ecosystem services at local and global scales and is a sensitive indicator of global change. Estimates of phenophase transition dates, such as the start of spring or end of autumn, can be derived from sensor-based time series data at the near-surface and remote scales, but must be interpreted in terms of biologically relevant events. We use the PhenoCam archive of digital repeat photography to implement a consistent protocol for visual assessment of canopy phenology at 13 temperate deciduous forest sites throughout eastern North America, as well as to perform digital image analysis for time series-based estimates of phenology dates. We then compare these near-surface results to remote sensing metrics of phenology at the landscape scale, derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Advanced Very High Resolution Radiometer (AVHRR) sensors. We present a new type of curve fit, using a generalized sigmoid, to estimate phenology dates. We quantify the statistical uncertainty of phenophase transition dates estimated using this method and show that the generalized sigmoid results in less statistical uncertainty than other curve-fitting methods. Additionally, we find that dates derived from analysis of high-frequency PhenoCam imagery have smaller uncertainties than remote sensing metrics of phenology, and that dates derived from the remotely-sensed enhanced vegetation index (EVI) have smaller uncertainty than those derived from the normalized difference vegetation index (NDVI). Near-surface time series estimates for the start of spring are found to closely match visual assessment of leaf out, as well as remote sensing-derived estimates of the start of spring. However late spring and autumn phenology exhibit larger differences between near-surface and remote scales. Differences in late spring phenology between near-surface and remote scales are found to correlate with a landscape metric of deciduous forest cover. These results quantify the effect of landscape heterogeneity when aggregating to the coarser spatial scales of remote sensing, and demonstrate the importance of accurate curve fitting and vegetation index selection when analyzing and interpreting phenology time series.Organismic and Evolutionary Biolog
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The effect of environmental variables on amphibian breeding phenology
Amphibian breeding phenology has generally been associated with temperature and rainfall, but these variables are not able to explain all of the variation in the timing of amphibian migrations, mating and spawning. This thesis examines some additional, previously under-acknowledged geophysical variables that may affect amphibian breeding phenology: lunar phase and the K-index of geomagnetic activity. A serendipitous observation of a large earthquake during the amphibian breeding season enabled a rare record of animal behaviour prior to an earthquake and led to an investigation into the effect of seismicity on amphibians. Data were collected on breeding migrations at three sites in the UK and Italy for frogs (Rana temporaria) and toads (Bufo bufo). Additional data were collated from published literature. Data on the arrivals of two newt species (Triturus cristatus and Lissotriton helveticus) were also analysed. Lunar phase was found to be important in Rana temporaria and Bufo bufo, with more individuals migrating, in amplexus and spawning around the full moon. Newts' response to the full moon was less clear. A meta-analysis of published data revealed that the effect of the lunar cycle on amphibians may be more prevalent than previously supposed and is species-specific, depending on the unique ecology of each species. The effects of the K- index on amphibian reproduction are unclear because of the low number of days when geomagnetism was high. Five days before a large earthquake in L'Aquila, Italy the majority of toads left the breeding site, only re- appearing when the earthquake was over. Numbers of toads were significantly correlated with days since the earthquake but not with weather variables. Finally I attempted to use the variables of interest (two measures of moon phase, plus the K-index of magnetic activity), along with weather variables to construct statistical models of amphibian breeding phenology and to predict arrivals and spawning / amplexus in single years based on the models. This met with variable success; there was a high variability between years in the ability of the models to predict breeding phenology, which could be due to site-specific factors, unmeasured environmental variables, or an endogenous component to breeding phenology
Cambial growth periodicity studies of South American woody species: A review
This paper reviews histological studies of cambium activity in South American woody species and provides future research prospects. The majority of the studies almost exclusively describe radial increment and/or its periodicity. There are 15 papers concerning the cambial activity of 17 woody species from the South American flora and 3 exotic species in 4 countries that were published to date. Despite endogenous factors affecting the radial meristem, the seasonality of rains has been identified as the main factor influencing cambial activity in the tropics and subtropics. There is a lack of standardization and a need for improvement and discussion concerning the methods used. Moreover, radial growth studies conducted by monitoring cambium cell production are still scarce in South America, especially when considering the high diversity of the continents flora and ecosystems.Fil: Callado, Cátia Henriques. Universidade do Estado do Rio de
Janeiro. Departamento de Biologia Vegetal. Laboratório de Anatomia Vegetal; BrasilFil: Roig Junent, Fidel Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Científico Tecnológico Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Tomazello Filho, Mário. Universidade de São Paulo. Escola Superior de Agricultura Luis de Queiroz. Departamento de Ciências Florestais; BrasilFil: Barros, Claudia Franca. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; Brasi
In the darkness of the polar night, scallops keep on a steady rhythm
Published version. Source at http://doi.org/10.1038/srep32435.
License CC BY 4.0.Although the prevailing paradigm has held that the polar night is a period of biological quiescence, recent studies have detected noticeable activity levels in marine organisms. In this study, we investigated the circadian rhythm of the scallop Chlamys islandica by continuously recording the animal’s behaviour over 3 years in the Arctic (Svalbard). Our results showed that a circadian rhythm persists throughout the polar night and lasts for at least 4 months. Based on observations across three polar nights, we showed that the robustness and synchronicity of the rhythm depends on the angle of the sun below the horizon. The weakest rhythm occurred at the onset of the polar night during the nautical twilight. Surprisingly, the circadian behaviour began to recover during the darkest part of the polar night. Because active rhythms optimize the fitness of an organism, our study brings out that the scallops C. islandica remain active even during the polar night
Camouflage mismatch in seasonal coat color due to decreased snow duration: Will snowshoe hares keep up with climate change?
As wild species face anthropogenic stressors, they will either adapt, shift their geographic range, or decline, perhaps towards extinction. The relative scope of these responses has not been well studied, especially for climate change where geographic range shifts and population declines have been widely discussed but the potential for adaptation mostly ignored. Adaptation to anthropogenic stressors can occur through phenotypic plasticity and/or evolution. My thesis first establishes, based on field studies of wild snowshoe hares, a novel and high-profile stressor directly linked to climate change. The stressor arises from a decrease in snow duration due to climate change, which causes seasonal coat color molt of individual hares to become mismatched with their background. The immediate adaptive solution to this form of camouflage mismatch is phenotypic plasticity, either in phenology of seasonal color molts or in behaviors that reduce mismatch or its consequences. Based on nearly 200 snowshoe hares across a wide range of snow conditions and two study sites in Montana, USA that differed in elevation and climate, I found minimal plasticity in response to mismatch between coat color and background. I found that molt phenology varied between study sites, likely due to differences in photoperiod and climate, but was largely fixed within study sites where seasonal changes in phenology were limited across years of very different snow duration. Hares exhibited some plasticity in the rate of the spring molt in response to immediate snow conditions but temperature or snow cover were not strong modifiers of the white-to-brown molt phenology. I also found no evidence that individual hares modify their behavior in response to color mismatch. Hiding and fleeing behaviors and immediate microsite preference of hares were more affected by variables related to season, site, and concealment, than by color mismatch. Although hares do not appear to be responding to camouflage mismatch with behavioral plasticity, adaptation could also occur through evolutionary changes facilitated by natural selection. We found that the raw material for natural selection to act on does exist in our populations in the form of individual variation in coat color phenology and consequently in color mismatch. We also found high fitness costs of coat color mismatch, with hares suffering 3 to 7% lower weekly survival rates when mismatched against their background. Coupling these fitness costs to local estimates of increased seasonal color mismatch as snow duration decreases in the future, we predict that annual hare survival will decline up to 12% by mid- and 24% by late century. Such changes in survival are sufficient to cause increasing hare populations to decline strongly towards extinction, with annual population geometric growth rate decreasing by 11% (24%) by mid (late) century. We conclude that plasticity in molt phenology and behaviors in snowshoe hares is insufficient for adaptation to camouflage mismatch, and that potential adaptive responses to future climate change will have to be facilitated by natural selection. These results form the basis for future work to evaluate whether evolution by natural selection can operate fast enough to prevent decline of this species
Larval dispersal in a changing ocean with an emphasis on upwelling regions
Dispersal of benthic species in the sea is mediated primarily through small, vulnerable larvae that must survive minutes to months as members of the plankton community while being transported by strong, dynamic currents. As climate change alters ocean conditions, the dispersal of these larvae will be affected, with pervasive ecological and evolutionary consequences. We review the impacts of oceanic changes on larval transport, physiology, and behavior. We then discuss the implications for population connectivity and recruitment and evaluate life history strategies that will affect susceptibility to the effects of climate change on their dispersal patterns, with implications for understanding selective regimes in a future ocean. We find that physical oceanographic changes will impact dispersal by transporting larvae in different directions or inhibiting their movements while changing environmental factors, such as temperature, pH, salinity, oxygen, ultraviolet radiation, and turbidity, will affect the survival of larvae and alter their behavior. Reduced dispersal distance may make local adaptation more likely in well-connected populations with high genetic variation while reduced dispersal success will lower recruitment with implications for fishery stocks. Increased dispersal may spur adaptation by increasing genetic diversity among previously disconnected populations as well as increasing the likelihood of range expansions. We hypothesize that species with planktotrophic (feeding), calcifying, or weakly swimming larvae with specialized adult habitats will be most affected by climate change. We also propose that the adaptive value of retentive larval behaviors may decrease where transport trajectories follow changing climate envelopes and increase where transport trajectories drive larvae toward increasingly unsuitable conditions. Our holistic framework, combined with knowledge of regional ocean conditions and larval traits, can be used to produce powerful predictions of expected impacts on larval dispersal as well as the consequences for connectivity, range expansion, or recruitment. Based on our findings, we recommend that future studies take a holistic view of dispersal incorporating biological and oceanographic impacts of climate change rather than solely focusing on oceanography or physiology. Genetic and paleontological techniques can be used to examine evolutionary impacts of altered dispersal in a future ocean, while museum collections and expedition records can inform modern-day range shifts
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