Ecological applications of remote sensing data in neotropical rainforests

Understanding species' distributions is a central theme of biodiversity studies. A combination of data derived from moderate and high spectral resolution satellite imagery (vegetation indices and hyperspectral narrow bands, respectively) was used to address questions regarding tree species' distributions, vegetation phenology, and influences on bird seasonal movements in tropical rainforests. Vegetation indices were used in ecological niche modeling to predict movement patterns of a tropical canopy frugivorous bird in Central America: the predicted distributions generally recovered observed non-breeding ranges, but estimated lowland areas for the breeding range, which is restricted to middle elevations. Hyperspectral imagery provided sufficient spectral information to discriminate crowns of five different tree taxa that represent food resources for macaws and peccaries in southeastern Peru. Tree spectra showed significant temporal variation, suggesting that it is possible to study tree phenology remotely. Current and future developments of remote sensing techniques permit regional studies of ecosystem functions and structure

Imaging spectrometry-derived estimates of regional ecosystem composition for the Sierra Nevada, California

The composition of the plant canopy is a key attribute of terrestrial ecosystems, influencing the fluxes of carbon, water, and energy between the land surface and the atmosphere. Terrestrial ecosystem and biosphere models, which are used to predict how ecosystems are expected to respond to changes in climate, atmospheric CO2, and land-use change, require accurate representations of plant canopy composition at large spatial scales. The ability to accurately specify plant canopy composition is important because it determines the physiological and ecological properties of plants (such as leaf photosynthetic capacity, patterns of plant carbon allocation and tissue turnover, and the resulting dynamics of plant demography) that govern the biophysical and biogeochemical functioning of ecosystems. Traditionally, plant canopy composition has been represented in a coarse-grained manner within terrestrial biosphere models, with ecosystems being comprised of a single plant functional type (PFT). However, models are increasingly seeking to represent fine-scale spatial variation in plant functional diversity. In this study, we show how imaging spectrometry measurements can provide spatially-comprehensive estimates of within-biome heterogeneity in PFT composition across a functionally diverse and topographically heterogeneous ~710 km2 area in the Southern Sierra Mountains of California. AVIRIS (Airborne Visible Infrared Imaging Spectrometer) data at 18 m resolution from the recent HyspIRI Preparatory Mission (Hyperspectral InfraRed Imager) were used to estimate the sub-pixel fractions of seven PFTs represented in the ED2 terrestrial biosphere model: Shrub, Oak, Western Hardwood, Western Pine, Cedar/Fir, and High-elevation Pine, plus a Grass/NPV (Non-Photosynthetic Vegetation) fraction using Multiple Endmember Spectral Mixture Analysis (MESMA). ED2 is an individual-based terrestrial biosphere model capable of representing fine-scale sub-pixel ecosystem heterogeneity. Our results show that this methodology captures important elevation-related shifts in canopy composition that occur within the study area that are not resolved by existing multi-spectral land-cover products. These estimates modestly improved when the putative PFT endmembers considered in the mixture analysis were constrained using available geospatial data about the presence and absence of the PFTs in particular areas: the average RMSEs (root-mean-square errors) with the geospatially-constrained versus conventional method were 11.3% and 11.9% respectively, with larger reductions in the bias (i.e. mean error) in the abundances of Oak, Cedar/Fir, and Western Hardwood PFTs (ranging from 2.0% to 7.8%). At the hectare scale around four flux towers in the Southern Sierra Mountains, the overall composition improved from an RMSE of 18.2% (5.0-24.2% for individual PFTs) to RMSE 9.5% (3.3-13.2% for individual PFTs). Downgrading AVIRIS to 30 m resolution resulted in a reduction in accuracy of the constrained method to an RMSE of 12.7% (0-23.7%) with < 1% change in bias for all tree and shrub PFTs. Our results demonstrate that imaging spectrometry measurements from planned satellite missions such as HyspIRI, EnMAP (Environmental Mapping and Analysis Program), and HISUI (Hyper-spectral Imager SUIte) can provide important and much-needed information about fine-scale heterogeneity in the composition of plant canopies for constraining and improving terrestrial ecosystem and biosphere model simulations of regional- and global-scale vegetation dynamics and function

Locating Amazonian Dark Earths (ADE) in the Brazilian Amazon using Satellite Imagery

Amazonian Dark Earths (ADE) are patches of archaeological soils scattered throughout the Amazon Basin. These soils are anthropogenic and most evidence suggests that they are the result of unintentional cultural deposits as well as intentional efforts of Amerindian populations to improve the quality of their farmlands. ADE are a mixture of charcoal, organic matter and the underlying Oxisol soil. ADE are extremely fertile soils in comparison to the surrounding Oxisols and they are sought after by local residents for agricultural purposes. In the first chapter I discuss the value and physical properties of ADE in detail. Research is being conducted to learn how ADE were created and to explore the possibility of replicating them to sequester carbon and to reclaim depleted soils in the Amazon Basin. This dissertation seeks to assist in that effort by attempting to map currently unknown ADE sites hidden beneath the dense tropical forest canopy

Paleogene monsoons across India and South China: Drivers of biotic change

Monsoonal climates at low latitudes (2. Fossil leaf form reveals that under such 'hothouse' conditions megathermal early Eocene to earliest Miocene forests were exposed to strong monsoonal climates typical of those experienced today arising from annual migrations of the ITCZ, possibly enhanced by a lower equator-to-pole temperature gradient. Throughout the Paleogene an elevated Tibetan highland produced no discernable modification of this ITCZ monsoon, although rainfall seasonality similar to that of the modern South Asia Monsoon (SAM) is observed in northern India as early as the beginning of the Eocene, despite its near-equatorial palaeoposition. In South China rainfall seasonality increased progressively achieving modern monsoon-like wet season/dry season precipitation ratios by the early Oligocene. Despite evidencing weak rainfall seasonality overall, fossil leaves from South China have exhibited monsoon-adapted morphologies, comparable to those seen in today's Indonesia-Australia Monsoon, for at least 45 million years. Together, the Indian and South China fossil leaf assemblages show that the evolution of megathermal ecosystems across southern Asia has been influenced profoundly by monsoonal climates for at least the last 56 million years. The Paleogene ITCZ-driven monsoon system strongly impacted India as it transited the Equator likely eliminating Gondwanan taxa not able to adapt to seasonal precipitation extremes. Furthermore, powerful seasonally-reversing winds, and associated surface ocean currents, are likely to have facilitated two-way biotic transfer between India and Eurasia long before closure of the Tethys Ocean

The value of using landsat 8 indices to describe large herbivore distribution

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg in fulfillment of the requirements for the degree of Masters in Science.Satellite imagery and remote sensing techniques provide a way to collect data over large temporal and spatial scales, and build indices that gauge ecological variables. These indices can explain the distribution of animals in their environment. In this study I compare the ability of various indices derived from Landsat 8, to reliably predict locations of different large herbivore species across diverse habitats. The study was undertaken in the Kgaswane Mountain Reserve, North West Province, South Africa. Daily locations of two herds of sable antelope (Hippotragus niger) and one herd of eland (Tragelaphus oryx) were used. One sable antelope herd (vlei herd) occupied a grassland plateau with a wetland and the other sable antelope herd (woodland herd), shared the wooded area at the base of the mountains with the eland herd. I described vegetation communities, burnt areas, geology and soil templates at animal locations during foraging bouts in the dry season; coinciding with the times of the Landsat images. The overall aim of this study was to see whether an index or a combination of indices could better describe animal locations than the normally used NDVI. I calculated a number of indices, and compared their predictive ability to define areas used by the study animals. Specifically, I compared the Normalised Difference Vegetation Index (NDVI) to Soil Adjusted Vegetation Index (SAVI), Visible Atmospherically Resistant Index (VARIgreen), Green Atmospherically Resistant Index (GARI), Normalised Difference Water Index (NDWI), a proxy for soil moisture; and mineral composite indices assessing clay minerals, ferrous minerals and iron oxide. I chose these indices as they describe the basic characteristics of an ecologically functioning unit. The locations of one of the sable antelope herds, located in grassland areas underlined by quartzite, were best described by NDVI, SAVI and VARIgreen. The locations of the other sable antelope herd, occurring in an open wooded area with shallow sandy soils on norite and quartzite, were best described by clay minerals and GARI. Eland locations, found in woodland areas characterised by deep norite soils, were best described by a combination of iron oxide, NDVI and SAVI. Therefore, NDVI proved to be an adequate indicator in open grassland areas, where it could be interchanged with SAVI, and improved by VARIgreen. In closed woodlands NDVI, SAVI and NDWI could all be used to describe browser locations. NDVI was not a suitable index when it came to describe locations of a grazer in a woodland/grassland matrix. However, it is important to keep in mind that my results pertain only to one dry season and two herbivore species, and therefore further studies would be needed to be able to generalise the results further.MT201

MEASURING, UNDERSTANDING AND MODELING ECOHYDROLOGICAL SEPARATION

My dissertation sought to answer some of the fundamental questions on how subsurface water may be partitioned between root water uptake and streamflow. I explored a phenomenon called ecohydrological separation – plants using water of a character different from the mobile water found in soils, groundwater and streams. The generality of ecohydrological separation, however, remained wanting; and, possible controls in both space and time was elusive. I began with testing the generality of ecohydrological separation, first at two sites in the tropics with contrasting moisture conditions, and then at the global scale. Using a global database of water stable isotopes, I then quantified the degree of groundwater use by vegetation. Finally, I unscrambled the possible process controls behind the partitioning of subsurface water between root water uptake, groundwater recharge, and streamflow generation by conducting controlled drought-rewetting experiments in a tropical mesocosm. Key results of these research efforts were: (1) ecohydrological separation was widespread across biomes of the world, providing clues to fundamental controls; (2) groundwater use by vegetation globally was not as widespread as increasingly assumed in the literature; and, (3) transpiration flux was older than groundwater recharge flux, supporting a perceptual model whereby transpiration and groundwater recharge fluxes were sourced from separate storage volumes and sampled at markedly different average sampling flux. Because determining the ages and sources of water that supply transpiration and groundwater recharge was a major challenge in ecohydrology, these findings are ground-breaking. Indeed, I was the first to measure and quantify what was referred heretofore as the “missing exit age” of transpiration. The mechanisms underlying the phenomenological manifestations of ecohydrological separation, as explored and uncovered in my dissertation, have direct implications for how we measure and model the transport of water, nutrients, and pollutants at various scales in space and time

Acoustic And Olfactory Communication In Eastern Sifakas (Propithecus Sp.) And Rhesus Macaques (Macaca Mullata)

This dissertation contains three studies of acoustic and olfactory communication in several species of nonhuman primates. The first is a longitudinal study of "gecker" distress vocalizations in infant rhesus monkeys (Macaca mullata) during the first 24 months of life. Acoustic and behavioral analyses revealed age, sex, and maternal response differences across several temporal, spectral, and amplitude measures, but little context-specific acoustic differentiation. Female geckers showed higher spectral peaks and bout durations, while male geckers were higher in amplitude and less noisy. Developmentally, gecker usage peaked at four months of age for both sexes, with male geckers nonetheless tending to occur at younger ages than those of females. In sum, gecker acoustics appear to be well designed to draw the attention of mothers and other listeners, while also potentially becoming aversive. The second study examines the acoustic structure and function of "zzuss" vocalizations in wild silky sifakas (Propithecus candidus) in northeastern Madagascar. Acoustically, the calls combined separate turbulent noise and tonal components, often including frequency jumps and rapid, highly frequency-modulated components. Although silky sifakas are sexually monomorphic, male and female zzuss calls were acoustically different, most importantly in fundamental frequency and amplituderelated features. All acoustic measures differed between individuals, with fundamental frequency related variables again playing the largest role. Overall, zzuss calls are multi-function vocalizations used both for terrestrial disturbance and group coordination. They are shaped for salience, localizability, and caller identification, rather than to have word-like meaning. The final study examines non-nutritive tree gouging by wild silky sifakas (P. candidus) and Milne-Edwards' sifakas (P. edwardsi). Species differences were found in gouge mark morphology. Dominant males had longer gouge marks and gouged most frequently, with seasonal peaks just before and during the mating season. The resource gouging hypothesis was tested and supported in silky sifakas. A multiple regression analysis revealed that the number of gouges per tree species was predicted by the percentile rank of those species as food tree species and sleep tree species. Gouging appears to be an honest species specific signal of male status which may promote scent longevity and attract the visual attention of conspecifics

Genetic variation and resilience to climate change in Mediterranean-type trees

Climate models predict that temperature means will continuously increase globally, and that heatwaves and drought periods will become more frequent and intense, particularly in Mediterranean-type climates. The Southwest Western Australia (SWWA) Biodiversity Hotspot has extensive forest environments that have been subject to heatwaves and drought-induced forest mortality in recent years, impacting forest carbon sequestration and local ecological structure. Although, species may persist through enhanced physiological tolerance, phenotypic plasticity and/or genetic adaptation. Genetic variation is critical for ecological adaptive capacity - the potential and ability to adjust to, and persist through, external factors - and consequently, the evolutionary potential of the species. Evolution to a specific environment through natural selection results in patterns of local adaptation (when a local population experiences higher fitness compared to non-local counterparts). Local adaptation can be identified by either genome wide surveys that link genetic variants to climate variables or measuring plant traits indicative of plant performance and survival through reciprocal transplants in common environments. Exploring genetic adaptation patterns associated with physiological tolerance to climate can guide forest management approaches to enhance forests’ resilience to climate change, such as assisted gene migration. The genetic survey (Chapter 2) sampled natural jarrah populations and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. Three genotype-association analyses were used to identify putatively adapted SNPs associated with independent climate variables. While overall levels of population differentiation were low (FST=0.04), environmental association analyses found a total of 2,336 unique SNPs associated with temperature and precipitation variables, with 1,440 SNPs annotated to genic regions. Considerable allelic turnover was identified for SNPs associated with temperature seasonality and mean precipitation of the warmest quarter, suggesting that both temperature and precipitation are important factors in adaptation. SNPs with similar gene functions, had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had uncorrelated patterns of adaptation. These contrasting patterns provide evidence that there may be standing genomic variation adapted to current climate gradients, providing the basis for adaptive management strategies to bolster forest resilience in the future. The second experimental chapter (Chapter 3) explored seed germination response to temperature in jarrah and marri populations from wide-ranging climate origins, to estimate the thermal optima and constraints. Seeds from across the entire geographic distribution were collected from independent populations of each species. Patterns of germination observed differences between species on a thermal gradient plate (5-40°C) and provided a temperature range for explicit germination tests. Germination tests were carried out at five constant temperatures between 9 and 33°C. We discuss how the germination niche (1) differs between species, (2) varies among populations, and (3) relates to climatic origin. Temperature response of germination differed among species, specifically the optimum temperature for germination (jarrah – 23.4°C; marri - 31°C). Temperature response of germination also differed among populations within species and was related to the climate-origin only for marri. Lastly, for the third experimental chapter (Chapter 4), a reciprocal transplant common garden experiment was used to investigate variation in marri`s functional traits using hyperspectral data. Hyperspectral remote sensing has the potential to assess plant functional status rapidly and non-destructively across climatic gradients to support conservation and management strategies, such as assisted migration, for forests under climate change. This study explored the variability of functional traits in marri to estimate patterns of local adaptation. Trees from natural populations spanning marri’s geographic distribution were grown in two common garden plantation sites with different climate settings. High-resolution field-based spectral measurements were collected from leaves of adult plants at both sites in two seasons (summer and autumn). Partial least squares regression analyses of full reflectance spectra highlighted differences among populations, sites, and seasons in spectral regions associated with photosynthetic pigments and water content, among other spectral traits, related to leaf condition and stress responses. Variation in these traits was further explored with analyses of spectral indices tailored to pigment and water absorptions. Analyses of spectral indices variation identified significant differences between populations, suggesting there is heritable variation in climatic tolerances, but stronger effects of season and site