Tropical ecosystems are some of the most diverse and productive ecosystems on the planet. These ecosystems are also some of the most threatened worldwide and this is largely driven by agricultural expansion. Predicting biotic responses to such forms of environmental change is a challenge that requires an increased understanding of the factors structuring these communities in both pristine environments as well as environments that are undergoing environmental change. Studying patterns in the spatial structure of communities can provide important insights into ecological and evolutionary processes structuring communities. Combining such approaches with analyses of the distribution of activity and the genomic content of communities can help us better understand relationships between community structure and function. I explore the topics of microbial spatial scaling, activity, and gene content in both pristine tropical rainforest environments as well as tropical regions undergoing agricultural conversion. I first pose a fundamental question in microbial spatial ecology, i.e. why do microorganisms tend to show weaker spatial patterns than macro-organisms? I show that trees and soil microorganisms differ in the rates at which their communities change over space. I test the hypothesis that low rates of spatial turnover in microbial communities are an artifact of how we assess the community structure of microbial communities and show that sampling extent is likely the main driver of these differences. Next, I examine a Central Africa ecosystem that is undergoing conversion to agriculture. I show that there are numerous indications of biotic homogenization in these soil microbial communities and that the active fraction of the community shows a more pronounced response to environmental change. Finally, I examine two microbial processes in the Amazon Basin that have been reported to change following conversion to agriculture: methane production and methane consumption. I investigate changes to the genes and taxa involved in these processes and propose a new conceptual framework for how these processes might be changing. Work in this thesis contributes to a broader understanding of the spatial and functional ecology of tropical microorganisms and offers perspectives useful for those interested in predicting and mitigating the impacts of environmental change on these communities. / 2019-02-17

<p>Amazonia contains the largest remaining tracts of undisturbed tropical forest on earth, and is thus critical to international nature conservation and carbon sequestration efforts. Amazonian forests are notoriously difficult to study, however, due to their species richness and inaccessibility. This has limited efforts to produce the accurate, high-resolution biodiversity maps needed for conservation and development. The aims of the research described here were to identify efficient solutions to the problems of tropical forest inventory; to use these methods to identify floristic patterns and their causes in western Amazonia; and propose new means to map floristic patterns in these forests.</p><p> Using tree inventories in the vicinity of Iquitos, Peru, I and a colleague systematically evaluated methods for rapid tropical forest inventory. Of these, inventory of particular taxonomic groups, or taxonomic scope inventory, was the most efficient, and was able to capture a majority of the pattern observed by traditional inventory techniques with one-fifth to one-twentieth the number of stems and species. Based on the success of this approach, I and colleagues specifically evaluated two plant groups, the Pteridophytes (ferns and fern allies) and the Melastomataceae (a family of shrubs and small trees), for use in rapid inventory. Floristic patterns based on inventories from either group were significantly associated with those based on the tree flora, and inventories of Pteridophytes in particular were in most cases able to capture the majority of floristic patterns identified by tree inventories. These findings indicate that Pteridophyte and Melastomataceae inventories are useful tools for rapid tropical forest inventory.</p><p> Using Pteridophyte and Melastomataceae inventories from 138 sites in northwestern Amazonia, combined with satellite data and soil sampling, I and colleagues studied the causes of vegetation patterns in western Amazonian forests. On the basis of these data, we identified a floristic discontinuity of at least 300km in northern Peru, corresponding to a 15-fold difference in soil cation concentrations and an erosion-generated geological boundary. On the basis of this finding, we assembled continent-scale satellite image mosaics, and used these to search for additional discontinuities in western Amazonia. These mosaics indicate a floristic and geological discontinuity of at least 1500km western Brasil, driven by similar erosional processes identified in our study area. We suggest that this represents a chemical and ecological boundary between western and central Amazonia.</p><p> Using a second network of 52 pteridophyte and soil inventories in northwestern Amazonia, we further studied the role of geology in generating floristic pattern. Consistent with earlier findings, we found that two widespread geological formations in western Amazonia differ eight-fold difference in soil cation concentrations and in a majority of their species. Difference in elevation, used as a surrogate for geological formation, furthermore explained up to one-third of the variation in plant species composition between these formations. Significant correlations between elevation, and cation concentrations and soil texture, confirmed that differences in species composition between these formations are driven by differences in soil properties. On the basis of these findings, we were able to use SRTM elevation data to accurately model species composition throughout our study area.</p><p> I argue that Amazonian forests are partitioned into large-area units on the basis of geological formations and their edaphic properties. This finding has implications for both the ecology and evolution of these forests, and suggests that conservation strategies be implemented on a region-by-region basis. Fortunately, the methods described here provide a means for generating accurate and detailed maps of floristic patterns in these vast and remote forests.</p> / Dissertation

Amazonian evergreen forests are of broad interest, attributable to their ecological, economic, aesthetic, and cultural importance. However, their fate under climate change remains uncertain, largely due to unclear mechanisms in regulating tropical photosynthetic metabolism. Understanding mechanistic controls on these dynamics across time scales (e.g. hours to years) is essential and a prerequisite for realistically predicting tropical forest responses to inter-annual and longer-term climate variation and change. Tropical forest photosynthesis can be conceptualized as being driven by two interacting causes: variation due to changes in environmental drivers (e.g. solar radiation, diffuse light fraction, and vapor pressure deficit) interacting with model parameters that govern photosynthetic behavior, and variation in photosynthetic capacity (PC) due to changes in the parameters themselves. In this thesis, I aim to reveal photosynthetic controls by addressing three fundamental but complementary questions: (1) What are the mechanisms by which the subtle tropical phenology exert controls on tropical photosynthetic seasonality? (2) How do the extrinsic and intrinsic controls regulate the photosynthesis processes at hourly to interannual time scales in an Amazonian evergreen forest? (3) Are there sufficiently consistent relations among leaf traits, ages, and spectra that allow a single model predict the leaf aging process of Amazonian evergreen trees? To address question 1, I firstly show that seasonal change in ecosystem-scale photosynthetic capacity (PC), rather than environmental drivers, is the primary driver of seasonality of gross primary productivity (GPP) at four Amazonian evergreen forests spanning gradients in rainfall seasonality, forest composition, and flux seasonality. Using novel near-surface camera-detected leaf phenology to drive a simple leaf-cohort canopy model at two of these sites, I further show that leaf ontogeny and demography explain the changes in ecosystem photosynthetic capacity. The coordination of new leaf growth and old leaf divestment (litterfall) during the dry season shifts canopy composition towards younger leaves with higher photosynthetic capacity, driving large seasonal increases (~27%) in ecosystem photosynthetic capacity. To address question 2, I used the 7-year eddy covariance (EC) measurements in an Amazonian tropical evergreen forest. I used a statistical model to partition the variability of 7-year EC-derived GPP into two main causes: variation due to changes in extrinsic environmental drivers and variation in intrinsic PC. The fitted model well predicts variability in EC-derived GPP at hourly (R²=0.71) to interannaul (R²=0.81) timescales. Attributing model predictions to causal factors at different timescales, I find that ~92% of the variability in modeled hourly GPP could be attributed to environmental driver variability, and ~5% to variability in PC. When aggregating the modeled GPP into the annual time-step, the attribution is reversed (only ~4% to environment and ~91% to PC). These results challenge conventional approaches for modeling evergreen forests, which neglect intrinsic controls on PC and assume that the primary photosynthetic control at both long and short timescales is due to changes in the hourly-to-diurnal environment on the physiological phenotype. This work thus highlights the importance of accounting for differential regulation of different components of GPP at different timescales, and of identifying the underlying feedbacks and adaptive mechanisms which regulate them. To address question 3, I explored the potential for a general spectrally based leaf age model across tropical sites and within the vertical canopy profiles using a phenological dataset of 1831 leaves collected at two lowland Amazonian forests in Peru (12 species) and Brazil (11 species). This work shows that a simple model (parameterized using only Peruvian canopy leaves) successfully predicts ages of canopy leaves from both Peru (R²=0.83) and Brazil (R²=0.77), but ages for Brazilian understory leaves with significantly different growth environment and leaf trait values have lower prediction accuracy (R²=0.48). Prediction accuracy for all Brazilian samples is improved when information on growth environment and leaf traits were added into the model (5% R² increase; R²=0.69), or when leaves from the full range of trait values are used to parameterize the model (15% R² increase; R²=0.79). This work shows that fundamental ecophysiological rules constrain leaf traits and spectra to develop consistently across species and growth environment, providing a basis for a general model associating leaf age with spectra in tropical forests. In sum, in this thesis, I (1) conceptualize photosynthesis as being driven by two interacting dynamics, extrinsic and intrinsic, (2) propose and validate a model for biological mechanisms that mediate seasonal dynamics of tropical forest photosynthesis, (3) assess and quantify the factors controlling tropical forest photosynthesis on timescales from hourly to interannual, and (4) develop a general model for monitoring leaf aging processes of tropical trees across sites and growth environments. The revealed mechanisms (and proposed models) in this thesis greatly improve our mechanistic understanding of the photosynthetic and phenological processes in tropical evergreen forests. Strategic incorporation of these mechanisms will improve ecological, evolutionary and earth system theories describing tropical forests structure and function, allowing more accurate representation of forest dynamics and feedbacks to climate in earth system models.

La communication par émission sonore est un trait comportemental répandu chez les animaux terrestres. Les riches textures sonores de la forêt neotropicale nous suggèrent que la faune est non seulement abondante, mais aussi diverse et dynamique. Cette facette de la biodiversité peut révéler des informations précieuses sur les communautés animales qui habitent les milieux tropicaux, mais reste largement méconnue. Comment mesurer la diversité acoustique tropicale pour aborder des questions écologiques ? Dans le cadre de l'écoacoustique, nous avons cherché à révéler des structures dissimulées dans le paysage sonore de la forêt neotropicale, et tenter d’expliquer leurs présences à travers les processus écologiques sous-jacents. Tout d’abord, nous avons suivi la dynamique spatio-temporelle d’une empreinte sonore amazonienne, le chant de l’oiseau tropical Lipaugus vociferans, montrant une activité liée à des caractéristiques spécifiques d’habitat. Puis, nous nous sommes intéressés aux communautés d’amphibiens. L’analyse de variables acoustiques et météorologiques nous a permis de mieux comprendre les causes, patrons et conséquences du comportement reproductif explosif. Enfin, nous avons adapté de nouveaux outils de calcul, issus des disciplines de l'apprentissage automatique et de la reconnaissance de formes, pour proposer une analyse efficace, objective et facilement reproductible de grands jeux de données acoustiques. L’écoacoustique, renforcée par des algorithmes informatiques, émerge comme une approche clé pour les programmes de suivis de biodiversité à large échelle, permettant de mieux comprendre et valoriser la diversité de formes de vies unique abritée par la forêt tropicale. / Acoustic signalling is a common behavioural trait among terrestrial animals. The rich sound textures of neotropical forest echo that wildlife is not only abundant, but also diverse and dynamic. This facet of biodiversity can reveal valuable insights of animal communities inhabiting tropical environments, yet remains poorly understood. How to best measure tropical acoustic diversity to address ecological questions? Based on the ecoacoustic framework, we explored the soundscape of neotropical forest, revealing patterns and investigating the ecological underlying processes. First, we tracked the spatiotemporal dynamics of an amazonian soundmark, the song of the bird Lipaugus vociferans, showing activity patterns related to specific habitat features. Then, we investigated amphibian communities with very brief reproduction periods. Coupling acoustic and environmental variables, we shed light on the causes, patterns and consequences of explosive breeding events. Finally, we adapted novel computational tools from the machine learning and pattern recognition disciplines to provide an efficient, objective and replicable analysis of large acoustic datasets. Ecoacoustics, powered with computer algorithms, emerge as a suitable approach to scale-up biodiversity monitoring programs, allowing to better understand and cherish the unique diversity of life sustained by tropical forest.

No description available.

Expanding anthropogenic development within the tropical forest biome is driving the loss of an irreplaceable global resource. Mega-diverse tropical forests are vital for regulating the global carbon cycle, and are essential for climate change mitigation. Today, over half of the world’s remaining tropical forest is degraded or regenerating secondary forest. Tropical forests are becoming increasingly fragmented through the expansion of agriculture and roads. Landscape-scale flooding of terrestrial habitats caused by dam construction is an emerging driver of habitat loss and fragmentation. Much attention has been paid to the long-term impacts of tropical forest fragmentation for biodiversity, ecosystem functioning, and carbon emissions. Most of our understanding of the impacts associated with habitat fragmentation originates from systems in which the habitat matrix surrounding remnant forest patches is another, albeit low quality, terrestrial habitat. However, dam-induced habitat fragmentation results in remnant terrestrial biological communities becoming isolated on islands within a water matrix. A water matrix presents the worst-case scenario for remnant habitat fragments. In Chapter 2 I synthesise the results of numerous studies reporting the responses of taxonomic groups to isolation on reservoir land-bridge islands, and uncover a globally-applicable pattern of extinction debt acting upon remnant biological communities on reservoir islands. All islands, regardless of taxonomic group, habitat type, or island area lose species as island isolation time increases. Moreover, I show that contrary to existing ecological theory, once terrestrial habitat becomes isolated within a water matrix, it is effectively too isolated for species losses to be buffered by metapopulation dynamics. Dam development is rapidly expanding in the largest remaining tract of intact tropical forest, the Amazon Basin. In Chapters 3 and 4 I study the Balbina mega-dam system in the central Brazilian Amazon. Here, I use detailed field inventories of trees and lianas on islands and in continuous mainland habitat to determine the impact of landscape-scale habitat fragmentation caused by reservoir creation on these taxonomic groups. I find that islands maintain tree communities at significantly lower densities, richness and diversity compared to continuous forest. Furthermore, tree communities on islands exhibit compositional divergence from those found in mainland continuous forest. Island tree assemblages are dominated by low-wood density species, and may be on a trajectory towards communities characteristic of early successional forests with reduced carbon storage capacity. In contrast, liana assemblages remain compositionally intact and are becoming increasingly dominant relative to trees. Thus, lianas appear robust to many of the negative impacts associated with landscape-scale habitat fragmentation. As insular tree communities continue to degrade through area- and edge-effects, lianas may become a key feature of this archipelagic landscape due to their competitive advantage over trees in disturbed forest habitats. Lianas significantly inhibit tree recruitment and carbon storage. Thus, findings from Chapters 3 and 4 provide strong evidence for additional, and currently unaccounted-for biodiversity and carbon impacts associated with tropical dams. As development of tropical forest regions increases, there is an urgent need to reconcile the need for resources with the need for ecosystem service provision, such as carbon storage, particularly as we attempt to mitigate the impacts of rising atmospheric carbon. Recent studies have shown that secondary tropical forests have the potential to rapidly uptake atmospheric carbon, and act as a powerful tool in climate change mitigation policy. Broad-scale estimates of secondary forest carbon uptake are currently based on above-ground biomass alone. In Chapter 5 I present carbon stock estimates of additional tropical forest carbon pools - soil and dead woody biomass - in secondary forests ranging from 40-120 years. I find that soil fertility (nitrogen concentration) is key in determining carbon storage in secondary forests, and that the stability of carbon stocks held in dead woody biomass increases with secondary forest stand age. I highlight the need to integrate detailed site-specific information into broad-scale predictive models of secondary tropical forest carbon sequestration. This thesis links ecological theory and landscape-scale field inventories, to provide new understanding of the long-term costs of tropical forest fragmentation for biodiversity conservation and carbon storage, and provides further evidence of the important role secondary tropical forests may play in carbon sequestration and climate change mitigation.

El sur de los Andes Ecuatorianos alberga una extraordinaria riqueza de especies. Muchos factores ambientales diferentes influyen entre sí en un espacio muy limitado y crean ecosistemas únicos y complejos. Sin embargo, esta área está altamente en peligro debido al creciente impacto humano a través de la intensificación del uso de la tierra y cambio global. Sólo poco se sabe acerca de la historia paleoecológica y dinámica del paisaje de esta zona. Sin embargo, la información acerca del por qué y cómo los ecosistemas han cambiado en el pasado es crucial para el desarrollo de estrategias innovadoras para la conservación y futuras predicciones del clima. En este estudio, presentamos los análisis palinológicos realizados en la región sur de los Andes Ecuatorianos, que ayudan aclarar los patrones y procesos de los ecosistemas presentes y pasados. El estudio paleoecológico de la cuenca volcánica Quimsacocha en la cresta oriental de la Cordillera Occidental revela cambios del clima, la vegetación y del régimen del fuego desde el período del Holoceno temprano. El Holoceno medio fue un período de severos cambios ambientales debido a un clima más seco y supuestamente más cálido en esta área. Durante el Holoceno tardío, varias fases cálidas y frías se indican en el registro. El fuego estuvo presente en la zona desde el Holoceno temprano y puede ser el primer signo del impacto humano. El análisis multivariado combinado con otros núcleos de sedimentos en el sur de los Andes Ecuatorianos reveló acontecimientos, en parte, contrastantes, los cuales supuestamente son debido a la heterogeneidad ambiental de los diferentes sitios. Por otra parte, un estudio de tres años entre la relación lluvia de polen actual – vegetación se llevó a cabo en la región del Parque Nacional Podocarpus, con el fin de comprender los patrones de dispersión de polen de los diferentes tipos de vegetación del bosque premontano, bosque montano bajo, bosque montano alto y páramo para crear una base más sólida para la interpretación de los datos de polen fósil. Una comparación entre la abundancia y los datos de presencia-ausencia a nivel de familia para el polen y la vegetación mostró que los patrones de diversidad, distribución y abundancia tienen una buena correspondencia el uno con el otro en ambos conjuntos de datos. Sin embargo, cantidades variables del polen transportado de larga distancia, la productividad desigual de polen de los diferentes taxones y los sistemas heterogéneos del viento impactan los patrones. Los análisis de las tasas de acumulación de polen indican poca variación interanual pero una alta variación espacial en los datos de polen. La evaluación de los dos diferentes tipos de trampa de polen utilizados con frecuencia en estudios palinológicos tropicales, la trampa Oldfield modificada y la trampa Behling, en comparación con muestras de suelo superficial y una trampa de referencia, mostró que en las muestras de suelo, los taxones con una exina frágil se representan en menor medida que en las trampas. Además, señaló que mientras que en el bosque, todos los tipos de trampas proporcionan resultados similares, la trampa Behling se debe preferir en el páramo, ya que resiste mejor a la alta radiación y periodos de sequía. Todos los análisis amplían el conocimiento preciso y completo de la dinámica de la vegetación de los Andes Tropicales en el espacio y el tiempo.

The thesis describes diversity of birds along a complete altitudinal gradient and in forest fragments in lowlands of Papua New Guinea. It focuses separately on the diversity of different feeding guilds, and discusses their links to habitat and food resources. More specifically, it focuses on forest insectivorous birds, their predation pressure on arthropods, feeding specializations and preferences, and some of the ways how insectivores search for food.

It has been more than two centuries since the latitudinal pattern of increase in taxonomic richness from poles to equator was first documented. After two centuries of research, and with more than two dozen hypotheses proposed, an understanding of the mechanisms underlying this pattern and their relative importance remains incomplete. Factors such as evolutionary history, area and latitude associated variables such as temperature, solar energy, climatic stability and seasonality are known to influence species richness by affecting geographic range size and location over ecological and evolutionary time. Understanding the forces that affect geographic range size is, therefore, integral to our understanding of latitudinal patterns in species richness. Using woody plants as a study system, my dissertation deciphers the latitudinal pattern, if any, in species richness within the evergreen forests of the Western Ghats. These wet evergreen forests form an evolutionarily distinct biogeographic zone, which has remained isolated from its counterparts. This has resulted in a high percentage of endemism among the evergreen woody plants and, therefore, the global geographic ranges of most of these plants are restricted within the boundaries of the Western Ghats. The first main objective of this dissertation is to understand the determinants of geographic range size in the evergreen woody plants of the Western Ghats. Further, the Western Ghats are characterized by a sharp climatic gradient in temperature and rainfall seasonality that is not correlated with mean annual temperature or annual rainfall. This allows a direct test of the hypotheses and predictions that are based on climatic seasonality, without the confounding effect of other climatic correlates of latitude. Therefore, the second main objective of this dissertation is to understand the mechanisms underlying latitudinal patterns in species richness of evergreen woody plants in the Western Ghats. Regional species richness is an outcome of two factors- local species richness of each location within the region and turnover in species composition among the locations, which in turn are a result of patterns in range size, range location and range overlap. To address these two objectives, I first test the effect of climatic niche of a species in determining geographic range size and then examine the effect of latitude associated climatic seasonality on range location and range overlap. Next, I link the observed pattern in range geometry to latitudinal patterns in species turnover and finally to latitudinal patterns in species richness. While the first part of my dissertation study deals with factors that generate spatial variation in species richness, the second part deals with the factors underlying spatial variation in species composition. Environmental heterogeneity and dispersal are considered the most important determinants of species turnover i.e. change in species composition. However, their relative importance in structuring in diverse plant communities within tropical regions across different scales is poorly understood. Hence, the third objective of this dissertation is to understand the processes that influence change in species composition of woody plants within the Western Ghats. Geographic range size and population size are important attributes of species rarity, which are directly linked to their extinction risk. Hence, data on distribution and population status of species can help us focus our efforts on those species that require conservation attention. This is achieved through carrying out species threat assessments based on attributes such as range and population size and then assigning then to a threat category. A majority of species endemic to the Western Ghats have not yet been assessed, largely due to lack of data on their population and distribution status. Therefore, the fourth and the final part of my dissertation explores the application of information on species range size and abundance in prioritizing species for conservation. To address these objectives, I sampled the wet evergreen forests of the Western Ghats along a series of locations distributed across its entire latitudinal gradient. Based on 156 plots, covering a latitudinal gradient of more than 1200 km and comprising of more than 20,000 occurrence locations belonging to more than 450 species of woody plants, I derived quantitative estimates of latitudinal gradients in range size, local and regional richness as well as species turnover. I used a combination of statistical and simulation approaches to discern the mechanisms underlying large-scale pattern in species ranges, richness and turnover. My dissertation is structured as follows.