Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus) across Africa

Background: Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus) populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results: Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian) (R(ST) = 0.38 - 0.69). This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (R(ST) = 0.24 - 0.32). The lowest differentiations were observed among connected populations within a basin (R(ST) = 0.015 in the Volta basin). Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053). The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m similar to 0.094 - 0.097) in the Volta populations. Conclusions: This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were predominant at macro-geographic scale, and the significant effect of geographic connectivity was detected at micro-geographic scale. The estimated effective population size, the moderate level of dispersal and the rapid temporal change in genetic composition might reflect a potential effect of life history strategy on population dynamics. This hypothesis deserves further investigation. The dynamic pattern revealed at micro-geographic and temporal scales appears important from a genetic resource management as well as from a biodiversity conservation point of view.

Comparison of spatial and temporal pattern for fMRI obtained with BOLD and arterial spin labeling

Functional magnetic resonance imaging (fMRI) is presently either performed using blood oxygenation level-dependent (BOLD) contrast or using cerebral blood flow (CBF), measured with arterial spin labeling (ASL) technique. The present fMRI study aimed to provide practical hints to favour one method over the other. It involved three different acquisition methods during visual checkerboard stimulation on nine healthy subjects: 1) CBF contrast obtained from ASL, 2) BOLD contrast extracted from ASL and 3) BOLD contrast from Echo planar imaging. Previous findings were replicated; i) no differences between the three measurements were found in the location of the activated region; ii) differences were found in the temporal characteristics of the signals and iii) BOLD has significantly higher sensitivity than ASL perfusion. ASL fMRI was favoured when the investigation demands for perfusion and task related signal changes. BOLD fMRI is more suitable in conjunction with fast event related design.

An analysis of the spatial and temporal patterns of highly pathogenic avian influenza occurrence in Vietnam using national surveillance data

The objectives of this study were to describe the spatio-temporal pattern of an epidemic of highly pathogenic avian influenza (HPAI) in Vietnam and to identify potential risk factors for the introduction and maintenance of infection within the poultry population. The results indicate that during the time period 2004–early 2006 a sequence of three epidemic waves occurred in Vietnam as distinct spatial and temporal clusters. The risk of outbreak occurrence increased with a greater percentage of rice paddy fields, increasing domestic water bird and chicken density. It increased with reducing distance to higher population density aggregations, and in the third epidemic wave with increasing percentage of aquaculture. The findings indicate that agri-livestock farming systems involving domestic water birds and rice production in river delta areas are important for the maintenance and spread of infection. While the government’s control measures appear to have been effective in the South and Central parts of Vietnam, it is likely that in the North of Vietnam the vaccination campaign led to transmission of infection which was subsequently brought under control.

Spatial and temporal analysis of land cover and landscape structure change in Zagros Forests

The Zagros oak forests in Western Iran are critically important to the sustainability of the region. These forests have undergone dramatic declines in recent decades. We evaluated the utility of the non-parametric Random Forest classification algorithm for land cover classification of Zagros landscapes, and selected the best spatial and spectral predictive variables. The algorithm resulted in high overall classification accuracies (>85%) and also equivalent classification accuracies for the datasets from the three different sensors. We evaluated the associations between trends in forest area and structure with trends in socioeconomic and climatic conditions, to identify the most likely driving forces creating deforestation and landscape structure change. We used available socioeconomic (urban and rural population, and rural income), and climatic (mean annual rainfall and mean annual temperature) data for two provinces in northern Zagros. The most correlated driving force of forest area loss was urban population, and climatic variables to a lesser extent. Landscape structure changes were more closely associated with rural population. We examined the effects of scale changes on the results from spatial pattern analysis. We assessed the impacts of eight years of protection in a protected area in northern Zagros at two different scales (both grain and extent). The effects of protection on the amount and structure of forests was scale dependent. We evaluated the nature and magnitude of changes in forest area and structure over the entire Zagros region from 1972 to 2009. We divided the Zagros region in 167 Landscape Units and developed two measures— Deforestation Sensitivity (DS) and Connectivity Sensitivity (CS) — for each landscape unit as the percent of the time steps that forest area and ECA experienced a decrease of greater than 10% in either measure. A considerable loss in forest area and connectivity was detected, but no sudden (nonlinear) changes were detected at the spatial and temporal scale of the study. Connectivity loss occurred more rapidly than forest loss due to the loss of connecting patches. More connectivity was lost in southern Zagros due to climatic differences and different forms of traditional land use.

Spatial and Temporal Evolution of the Volcanics and Sediments of the Kenya Rift

New volumetric and mass flux estimates have been calculated for the Kenya Rift. Spatial and temporal histories for volcanic eruptions, lacustrine deposition, and hominin fossil sites are presented, aided by the compilation of a new digital geologic map. Distribution of volcanism over time indicates several periods of southward expansion followed by relative positional stasis. Volcanism occurs throughout the activated rift length, with no obvious abandonment as the rift system migrated. The main exception is a period of volcanic concentration around 10 Ma, when activity was constrained within 2° of the equator. Volumes derived from seismic data indicate a total volume of c. 310,000 km3 (2.47 x 1010 kg/yr ), which is significantly more than the map-derived volumes found here or published previously. Map-based estimates are likely affected by a bias against recognizing small volume events in the older record. Such events are, however, the main driver of erupted volume over the last 5 Ma. A technique developed here to counter this bias results in convergence of the two volume estimation techniques. Relative erupted composition over time is variable. Overall, the erupted material has a mafic to silicic ratio of 0.9:1. Basalts are distinctly more common in the Turkana region, which previously experienced Mesozoic rifting. Despite the near equal ratio of mafic to silicic products, the Kenya Rift otherwise fits the definition of a SLIP. It is proposed that the compositions would better fit the published definition if the Turkana region was not twice-rifted. Lacustrine sedimentation post-dates initial volcanism by about 5 million years, and follows the same volcanic trends, showing south and eastward migration over time. This sedimentation delay is likely related to timing of fault displacements. Evidence of hominin habitation is distinctly abundant in the northern and southern sections of the Kenya Rift, but there is an observed gap in the equatorial rift between 4 and 0.5 million years ago. After 0.5 Ma, sites appear to progress towards the equator. The pattern and timing of hominid site distributions suggests that the equatorial gap in habitation may be the result of active volcanic avoidance.

Spatial and temporal patterns in ungulate-ecosystem interactions

Ungulates are important components of a variety of ecosystems worldwide. This dissertation integrates aspects of ungulate and forest ecology to increase our understanding of how they work together in ways that are of interest to natural resource managers, educators, and those who are simply curious about nature. Although animal ecology and ecosystem ecology are often studied separately, one of the general goals of this dissertation is to examine how they interact across spatial and temporal scales. Forest ecosystems are heterogeneous across a range of scales. Spatial and temporal habitat use patterns of forest ungulates tend to be congregated in patches where food and/or cover are readily available. Ungulates interact with ecosystem processes by selectively foraging on plants and excreting waste products in concentrated patches. Positive feedbacks may develop where these activities increase the value of habitat through soil fertilization or the alteration of plant chemistry and architecture. Heterogeneity in ecosystem processes and plant community structure, observed at both stand and local scales, may be the integrated outcome of feedbacks between ungulate behavior and abiotic resource gradients. The first chapter of this dissertation briefly discusses pertinent background information on ungulate ecology, with a focus on white-tailed deer (Odocoileus virginianus) in the Upper Great Lakes region and moose (Alces acles) in Isle Royale National Park, Michigan, USA. The second chapter demonstrates why ecological context is important for studying ungulate ecology in forest ecosystems. Excluding deer from eastern hemlock (Tsuga canadensis) stands, which deer use primarily as winter cover, resulted in less spatial complexity in soil reactive nitrogen and greater complexity in diffuse light compared to unfenced stands. The spatial patterning of herbaceous-layer cover was more similar to nitrogen where deer were present, and was a combination of nitrogen and light within deer exclosures. This relationship depends on the seasonal timing of deer habitat use because deer fertilize the soil during winter, but leave during the growing season. The third chapter draws upon an eight-year, 39-stand data set of deer fecal pellet counts in hemlock stands to estimate the amount of nitrogen that deer are depositing in hemlock stands each winter. In stands of high winter deer use, deer-excreted nitrogen inputs consistently exceeded those of atmospheric deposition at the stand scale. At the neighborhood scale, deer-excreted nitrogen was often in excess of atmospheric deposition due to the patchy distribution of deer habitat use. Spatial patterns in habitat use were consistent over the eight-year study at both stand and neighborhood scales. The fourth chapter explores how foraging selectivity by moose interacts with an abiotic resource gradient to influence forest structure and composition. Soil depth on Isle Royale varies from east to west according to glacial history. Fir saplings growing in deeper soils on the west side are generally more palatable forage for moose (lower foliar C:N) than those growing in shallower soils on the east side. Therefore, saplings growing in better conditions are less likely to reach the canopy due to moose browsing, and fir is a smaller overstory component on the west side. Lastly, chapter five focuses on issues surrounding eastern hemlock regeneration failure, which is a habitat type that is important to many wildlife species. Increasing hemlock on the landscape is complicated by several factors including disturbance regime and climate change, in addition to the influence of deer.

First trial of spatial and temporal fractionations of the delivered dose using synchrotron microbeam radiation therapy

The technical feasibility of temporal and spatial fractionations of the radiation dose has been evaluated using synchrotron microbeam radiation therapy for brain tumors in rats. A significant increase in lifespan (216%, p < 0.0001) resulted when three fractions of microbeam irradiation were applied to the tumor through three different ports, orthogonal to each other, at 24 h intervals. However, there were no long-term survivors, and immunohistological studies revealed that 9 L tumors were not entirely ablated.

The annexins: spatial and temporal coordination of signaling events during cellular stress

Annexins are a family of structurally related, Ca2+-sensitive proteins that bind to negatively charged phospholipids and establish specific interactions with other lipids and lipid microdomains. They are present in all eukaryotic cells and share a common folding motif, the "annexin core", which incorporates Ca2+- and membrane-binding sites. Annexins participate in a variety of intracellular processes, ranging from the regulation of membrane dynamics to cell migration, proliferation, and apoptosis. Here we focus on the role of annexins in cellular signaling during stress. A chronic stress response triggers the activation of different intracellular pathways, resulting in profound changes in Ca2+ and pH homeostasis and the production of lipid second messengers. We review the latest data on how these changes are sensed by the annexins, which have the ability to simultaneously interact with specific lipid and protein moieties at the plasma membrane, contributing to stress adaptation via regulation of various signaling pathways.

Spatial and temporal patterns of greenness on the Yamal Peninsula, Russia: interactions of ecological and social factors affecting the Arctic normalized difference vegetation index

The causes of a greening trend detected in the Arctic using the normalized difference vegetation index (NDVI) are still poorly understood. Changes in NDVI are a result of multiple ecological and social factors that affect tundra net primary productivity. Here we use a 25 year time series of AVHRR-derived NDVI data (AVHRR: advanced very high resolution radiometer), climate analysis, a global geographic information database and ground-based studies to examine the spatial and temporal patterns of vegetation greenness on the Yamal Peninsula, Russia. We assess the effects of climate change, gas-field development, reindeer grazing and permafrost degradation. In contrast to the case for Arctic North America, there has not been a significant trend in summer temperature or NDVI, and much of the pattern of NDVI in this region is due to disturbances. There has been a 37% change in early-summer coastal sea-ice concentration, a 4% increase in summer land temperatures and a 7% change in the average time-integrated NDVI over the length of the satellite observations. Gas-field infrastructure is not currently extensive enough to affect regional NDVI patterns. The effect of reindeer is difficult to quantitatively assess because of the lack of control areas where reindeer are excluded. Many of the greenest landscapes on the Yamal are associated with landslides and drainage networks that have resulted from ongoing rapid permafrost degradation. A warming climate and enhanced winter snow are likely to exacerbate positive feedbacks between climate and permafrost thawing. We present a diagram that summarizes the social and ecological factors that influence Arctic NDVI. The NDVI should be viewed as a powerful monitoring tool that integrates the cumulative effect of a multitude of factors affecting Arctic land-cover change.