From Leaf to Litter : Nutrient resorption in a changing environment

Aerts, M.A.P.A. [Promotor]Toet, S. [Copromotor

Relative Humidity as an Indicator for Cloud Formation over Heterogeneous land surfaces

The influence of land surface heterogeneity on potential cloud formation is investigated using relative humidity as an indicator. This is done by performing numerical experiments using a large-eddy simulation model (LES). The land surface in the model was divided into two patches that had the same sum of latent and sensible heat flux but different Bowen ratios to simulate heterogeneous land surfaces. For heterogeneity in the meso-¿ scale (2¿20 km), sensitivity analyses were carried out on the heterogeneity amplitude (Bowen ratio difference between contrasting areas) and the inversion strength of potential temperature and specific humidity. The competition between absolute temperature decrease by ABL growth and dry air entrainment in heterogeneous conditions is analyzed using the LES results. First, it is shown that entrainment is located and enhanced over patches with higher Bowen ratios (warm patches) than their surroundings (cold patches). The heterogeneity-induced strong thermals can further penetrate the inversion at the ABL top, thereby reaching lower absolute temperatures than in homogeneous conditions. Second, because of the heterogeneity-induced circulations the moisture is located over the warm patch, and higher time-averaged RH values at the ABL top (RHzi) than over the cold patches are found here, even for dry atmospheres. These RHzi exceed values found over homogeneous land surfaces and are an indication that surface heterogeneity may facilitate cloud formation. In vertical profiles of RH, few differences are found between the homogeneous and heterogeneous cases, but the essential heterogeneity-induced modifications are within the domain variability

Surface evaporation and water vapor transport in the convective boundary layer

cum laude graduation (with distinction

Population genetics of traditionally managed maize : farming practice as a determinant of genetic structure and identity of maize landraces in Mexico

A large amount of crop genetic diversity is being maintained in farmers' fields worldwide. The population genetics of traditionally managed landraces is therefore of interest to the conservation of genetic resources. The growing trend towards agricultural modernization and the prospect of introducing genetically modified varieties into centers of origin have increased the need to understand the determinants of genetic structure in landraces of our basic food crops. Patterns of genetic diversity are known to be affected by environmental and geographic factors, but there has been an increasing interest in the role of farmers. Recent years have seen work on both genetic differentiation between seedlots, as well as on the agricultural practices that are expected to influence this differentiation. Unfortunately, few studies have been able to link observed patterns of differentiation to farming practice. The lack of a proper analytical framework has probably contributed to this omission. The population genetics of landraces is complex, with many human and environmental factors affecting the distribution of genetic variation. In this thesis, we aim at achieving a better understanding of the processes that underlie the genetic structure maize landraces in their centre of origin, Mexico. We combine a wide range of theoretical and empirical methods in order to provide explanations for observed patterns of genetic structure. In addition, we use these tools to predict some present and future consequences of seed management by farmers on the genetic identity of landrace populations. In chapter II, we present a metapopulation model that accounts for several features that are unique to managed maize populations. We developed a coalescence-based model of a metapopulation undergoing pollen and seed flow as well as extinction in the form of seed replacement. Unlike previous models, our model treats seed migration as episodic-, partial replacement from a single source rather than as constant immigration from the entire metapopulation. We showed that this particular form of migration leads to novel results. Contrary to classical predictions, within-deme coalescence time was not invariant to the amount of migrating seed. Genetic structure had a parabolic relationship to the amount of migrating seed instead of showing the expected exponential decrease. In contrast, the effects of seed migration frequency on diversity and structure were in line with classical predictions. We concluded that is impossible to describe seed migration by a single parameter. Genetic structure was shown to depend on deme size when the amount of migrant seed is large. Extinction decreased or increased genetic structure depending on the level of migration and number of demes. Finally, we demonstrated that higher levels of pollen migration can mask the effects of seed management. This model provides an important first step in our ability to understand the effects of farming practice on the population genetics of maize landraces. In chapter III, we study the joint role of the environment and humans as determinants of genetic differentiation. We present results on the hierarchical genetic structure in a sample of seedlots in highland and lowland environments in central Mexico. Within-and between village Fsl and Qsl values were used as measures of neutral and agronomic genetic differentiation respectively. We developed and used a new computer model to predict Fst in the two environments on the basis of data on local seed management practice and planting patterns. Strong genetic differences were found between highland and lowland maize, for both markers and traits. Three highland villages planted maize of admixed origin, as evidenced by both molecular markers and phenological traits. This suggested that human mediated gene flow from lowland to highland environments has taken place. Molecular differentiation was low for molecular markers but was notably higher in the lowlands. Our model correctly predicted this difference based on lower pollen flow and smaller seedlot sizes in the lowlands. Agronomical traits showed higher differentiation between villages and were probably subject to diversifying selection. Phenological traits showed the strongest differentiation. Field data suggested that different planting dates may explain the observed differences. Phenological differentiation was highest in the transect containing the admixed seedlots, proving that genetic structure may result from the introgression of traits that diverged in a foreign environment. In chapter IV, we address the issue of genetic erosion in modernized subsistence agriculture. Genetic erosion is thought to occur when modern varieties replace traditional landraces. Actual proof of genetic erosion for any particular area or crop has been rarely found however. A complicating factor in the study of diversity loss in traditional agriculture is the often-noted coexistence between traditional and improved varieties. Moreover, adoption of modern varieties into the traditional seed supply system may blur the distinction between modern and traditional varieties. The inability to classify germplasm into discrete types makes it hard to measure diversity. We addressed these problems by means of a case study on modernized smallholder maize agriculture in southern Mexico. We characterized seedlots obtained from both farmers and commercial seed vendors, for agronomical traits and molecular markers. Farmer interviews were used to distinguish between traditional landraces and recycled modern varieties. We calculated genetic diversity, defined as the mean differentiation between individual seedlots, for different types of germplasm. Modem germplasm was clearly distinct from traditional landraces. Close resemblance between modem- and recycled modem varieties proved that despite years of independent evolution, recycled varieties have not diverged much from their ancestral stocks. We showed that different traits reveal different levels of relative diversity, demonstrating the inherent difficulty of assessing diversity loss. The group of recycled modem varieties presented the lowest diversity for all measured traits. We could therefore predict that complete replacement of landraces by these varieties will reduce diversity in the traditional seed system. Under current patterns of coexistence however, the distinctness of modem and traditional varieties caused only a limited reduction of genetic diversity. Chapter V. deals with the effects of reproductive and population genetic processes on the probability of detecting inadvertently introduced transgenes in maize landraces. This subject has become relevant since initial findings suggesting contamination of Mexican landraces with transgenes were followed by contradictory results in subsequent years. Theoretical and simulation results showed that certain aspects of maize reproductive biology negatively affect the detection probability. We demonstrated that the strongest potential limitation on detection was caused by the aggregated frequency distribution that is a consequence of farmer-mediated introduction of transgenes. Analysis of recent sampling efforts reveals that detection probabilities may be much lower than previously assumed, partly explaining the recent inconsistent results 12

Mean and Flux Horizontal Variability of Virtual Potential Temperature, Moisture, and Carbon Dioxide: Aircraft Observations and LES Study

The effects of the horizontal variability of surface properties on the turbulent fluxes of virtual potential temperature, moisture, and carbon dioxide are investigated by combining aircraft observations with large-eddy simulations (LESs). Daytime fair-weather aircraft measurements from the 2002 International H2O Project¿s 45-km Eastern Track over mixed grassland and winter wheat in southeast Kansas reveal that the western part of the atmospheric boundary layer was warmer and drier than the eastern part, with higher values of carbon dioxide to the east. The temperature and specific humidity patterns are consistent with the pattern of surface fluxes produced by the High-Resolution Land Data Assimilation System. However, the observed turbulent fluxes of virtual potential temperature, moisture, and carbon dioxide, computed as a function of longitude along the flight track, do not show a clear east¿west trend. Rather, the fluxes at 70 m above ground level related better to the surface variability quantified in terms of the normalized differential vegetation index (NDVI), with strong correlation between carbon dioxide fluxes and NDVI

Understanding the daily cycle of evapotranspiration: a method to quantify the influence of forcings and feedbacks

A method to analyze the daily cycle of evapotranspiration over land is presented. It quantifies the influence of external forcings, such as radiation and advection, and of internal feedbacks induced by boundary layer, surface layer, and land surface processes on evapotranspiration. It consists of a budget equation for evapotranspiration that is derived by combining a time derivative of the Penman–Monteith equation with a mixed-layer model for the convective boundary layer. Measurements and model results for days at two contrasting locations are analyzed using the method: midlatitudes (Cabauw, Netherlands) and semiarid (Niamey, Niger). The analysis shows that the time evolution of evapotranspiration is a complex interplay of forcings and feedbacks. Although evapotranspiration is initiated by radiation, it is significantly regulated by the atmospheric boundary layer and the land surface throughout the day. In both cases boundary layer feedbacks enhance the evapotranspiration up to 20 W m-2 h-1. However, in the case of Niamey this is offset by the land surface feedbacks since the soil drying reaches -30 W m-2 h-1. Remarkably, surface layer feedbacks are of negligible importance in a fully coupled system. Analysis of the boundary layer feedbacks hints at the existence of two regimes in this feedback depending on atmospheric temperature, with a gradual transition region in between the two. In the low-temperature regime specific humidity variations induced by evapotranspiration and dry-air entrainment have a strong impact on the evapotranspiration. In the high-temperature regime the impact of humidity variations is less pronounced and the effects of boundary layer feedbacks are mostly determined by temperature variation

Interactions between dry-air entrainment, surface evaporation and convective boundary-layer development

The influence of dry-air entrainment on surface heat fluxes and the convective boundary-layer (CBL) properties is studied for vegetated land surfaces, using a mixed-layer CBL model coupled to the Penman¿Monteith equation under a wide range of conditions. In order to address the complex behaviour of the system, the feedback mechanisms involved were put into a mathematical framework. Simple expressions for the evaporative fraction and the Priestley¿Taylor parameter were derived, based on the concept of equilibrium evaporation. Dry-air entrainment enhances the surface evaporation under all conditions, but the sensitivity of the evaporation rate to the moisture content of the free troposphere falls as temperature rises. Due to the evaporation enhancement, shallower CBLs develop beneath dry atmospheres. In all cases, dry-air entrainment reduces the relative humidity at the land surface and at the top of the CBL. However, because of dry-air entrainment-induced land¿atmosphere feedback mechanisms, relative humidity at the top of the CBL responds nonlinearly to temperature rise; it decreases as temperature rises beneath a moist free troposphere, whereas it increases beneath a dry free troposphere. Finally, it was found that in certain conditions the evolution of the surface fluxes, relative humidity and CBL height can be as sensitive to the free tropospheric moisture conditions as to the land-surface properties. Therefore, studies of the land surface and of convective clouds have to take into account the influence of dry-air entrainment through land¿atmosphere feedback mechanism

A Spatial Autoregressive Graphical Model with Applications in Intercropping

Within the statistical literature, there is a lack of methods that allow for asymmetric multivariate spatial effects to model relations underlying complex spatial phenomena. Intercropping is one such phenomenon. In this ancient agricultural practice multiple crop species or varieties are cultivated together in close proximity and are subject to mutual competition. To properly analyse such a system, it is necessary to account for both within- and between-plot effects, where between-plot effects are asymmetric. Building on the multivariate spatial autoregressive model and the Gaussian graphical model, the proposed method takes asymmetric spatial relations into account, thereby removing some of the limiting factors of spatial analyses and giving researchers a better indication of the existence and extend of spatial relationships. Using a Bayesian-estimation framework, the model shows promising results in the simulation study. The model is applied on intercropping data consisting of Belgian endive and beetroot, illustrating the usage of the proposed methodology. An R package containing the proposed methodology can be found on https:// CRAN.R-project.org/package=SAGM

The influence of land surface heterogeneities on cloud size development

This study analyzes the effects of land surface heterogeneities at various horizontal scales on the transition from shallow to deep convection and on the cloud size distribution. An idealized case of mid-latitude summertime convection is simulated by means of large-eddy simulations coupled to an interactive land surface. The transition is accelerated over heterogeneous surfaces. The simulation with an intermediate patch size of 12.8 km exhibits the fastest transition with a transition time two thirds that over a homogeneous surface. A similar timing is observed for the precipitation onset whereas the total accumulated rainfall tends to increase with patch size. The cloud size distribution can be approximated by a power law with a scale break. The exponent of the power law is independent of the heterogeneity scale, implying a similar cloud cover between the simulations. In contrast, the scale break varies with patch size. The size of the largest clouds does not scale with the boundary layer height, although their maximum size scales with the patch size. Finally, the idea that larger clouds grow faster, known from homogeneous surface conditions, is not fully valid over heterogeneous surfaces. These various aspects can be understood from the complex interplay between the characteristics of the triggered mesoscale circulations and a cloud development acting in response to the diurnal cycle in surface heating. The results also call for adequate representation of such effects in convective parameterizations