Optimal transportation theory for species interaction networks

Observed biotic interactions between species, such as in pollination, predation, and competition, are determined by combinations of population densities, matching in functional traits and phenology among the organisms, and stochastic events (neutral effects). We propose optimal transportation theory as a unified view for modeling species interaction networks with different intensities of interactions. We pose the coupling of two distributions as a constrained optimization problem, maximizing both the system's average utility and its global entropy, that is, randomness. Our model follows naturally from applying the MaxEnt principle to this problem setting. This approach allows for simulating changes in species relative densities as well as to disentangle the impact of trait matching and neutral forces. We provide a framework for estimating the pairwise species utilities from data. Experimentally, we show how to use this framework to perform trait matching and predict the coupling in pollination and host-parasite networks

Spiking neural models & machine learning for systems neuroscience: Learning, Cognition and Behavior.

Learning, cognition and the ability to navigate, interact and manipulate the world around us by performing appropriate behavior are hallmarks of artificial as well as biological intelligence. In order to understand how intelligent behavior can emerge from computations of neural systems, this thesis suggests to consider and study learning, cognition and behavior simultaneously to obtain an integrative understanding. This involves building detailed functional computational models of nervous systems that can cope with sensory processing, learning, memory and motor control to drive appropriate behavior. The work further considers how the biological computational substrate of neurons, dendrites and action potentials can be successfully used as an alternative to current artificial systems to solve machine learning problems. It challenges the simplification of currently used rate-based artificial neurons, where computational power is sacrificed by mathematical convenience and statistical learning. To this end, the thesis explores single spiking neuron computations for cognition and machine learning problems as well as detailed functional networks thereof that can solve the biologically relevant foraging behavior in flying insects. The obtained results and insights are new and relevant for machine learning, neuroscience and computational systems neuroscience. The thesis concludes by providing an outlook how application of current machine learning methods can be used to obtain a statistical understanding of larger scale brain systems. In particular, by investigating the functional role of the cerebellar-thalamo-cortical system for motor control in primates

UBI MEL, IBI APES: On the evolutionary ecology of infectious diseases and intersections with apiculture.

Infectious diseases shape almost every aspect of nature and society; understanding the multitude of factors influencing infectious diseases is a critical goal of modern evolutionary ecology. This thesis explores this broad topic using theoretical and empirical approaches to understand the forces at work in infectious disease ecology and evolution, with application to the specific system of managed honeybees (Apis mellifera L.). I demonstrate that a well-documented evolutionary trade-off governing pathogen resistance is both constitutive and genetic – critical for supporting assumptions made by mathematical theory. I go further to demonstrate that this trade-off breaks down when the action of selection is reversed, in that when the ‘cost of resistance’ phenotype is selective for, we do not incidentally select for higher resistance too. This is important for understanding genetic linkage of traits and downstream evolutionary modelling. I undertake theoretical modelling on the topic of spatial structure and how it affects pathogen evolution. In doing so I interrogate a critical assumption made in much of the prior theoretical body, showing that the effect of spatial structure on virulence is quantitatively changed when a core assumption concerning reproduction is relaxed, but is otherwise qualitatively robust. I continue on the theme of spatial structuring and pathogens by developing novel theoretical models on how changing apicultural management alters honeybee population spatial structure, surprisingly leading to only marginal changes in pathogen burden. I stay on this topic to examine empirical data on honeybee colony viriomes in an observation experiment showing that colonies from very intensively managed, migratory backgrounds show elevated viral titres – critical for management and wild bee conservation. I synthesise that the honeybee system is our most informative natural experiment in showing that vectored pathogens are more virulent than directly transmitted counterparts. I also show that outbreaking human epidemics (Zika virus) can threaten apiculture – and by extension livelihoods and agriculture.Natural Environment Research Council (NERC

Analysis and network simulations of honeybee interneurons responsive to waggle dance vibration signals

BACKGROUND: Honeybees have long fascinated neuroscientists with their highly evolved social structure and rich behavioral repertoire. They sense air vibrations with their antennae, which is vital for several activities during foraging, like waggle dance communication and flight. GOALS: This thesis presents the investigation of the function of an identified vibration-sensitive interneuron, DL-Int-1. Primary goals were the investigation of (i) adaptations during maturation and (ii) the role of DL-Int-1 in networks encoding distance information of waggle dance vibration signals. RESULTS: Visual inspection indicated that DL-Int-1 morphologies had similar gross structure, but were translated, rotated and scaled relative to each other. To enable detailed spatial comparison, an algorithm for the spatial co-registration of neuron morphologies, Reg-MaxS-N was developed and validated. Experimental data from DL-Int-1 was provided by our Japanese collaborators. Comparison of morphologies from newly emerged adult and forager DL-Int-1 revealed minor changes in gross dendritic features and consistent, region-dependent and spatially localized changes in dendritic density. Comparison of electrophysiological response properties showed an increase in firing rate differences between stimulus and non-stimulus periods during maturation. A putative disinhibitory network in the honeybee primary auditory center was proposed based on experimental evidence. Simulations showed that the network was consistent with experimental observations and clarified the central inhibitory role of DL-Int-1 in shaping the network output. RELEVANCE: Reg-MaxS-N presents a novel approach for the spatial co-registration of morphologies. Adaptations in DL-Int-1 morphology during maturation indicate improved connectivity and signal propagation. The central role of DL-Int-1 in a disinhibitory network in the honeybee primary auditory center combined with adaptions in its response properties during maturation could indicate better encoding of distance information from waggle dance vibration sig- nals

Analysis and network simulations of honeybee interneurons responsive to waggle dance vibration signals

BACKGROUND: Honeybees have long fascinated neuroscientists with their highly evolved social structure and rich behavioral repertoire. They sense air vibrations with their antennae, which is vital for several activities during foraging, like waggle dance communication and flight. GOALS: This thesis presents the investigation of the function of an identified vibration-sensitive interneuron, DL-Int-1. Primary goals were the investigation of (i) adaptations during maturation and (ii) the role of DL-Int-1 in networks encoding distance information of waggle dance vibration signals. RESULTS: Visual inspection indicated that DL-Int-1 morphologies had similar gross structure, but were translated, rotated and scaled relative to each other. To enable detailed spatial comparison, an algorithm for the spatial co-registration of neuron morphologies, Reg-MaxS-N was developed and validated. Experimental data from DL-Int-1 was provided by our Japanese collaborators. Comparison of morphologies from newly emerged adult and forager DL-Int-1 revealed minor changes in gross dendritic features and consistent, region-dependent and spatially localized changes in dendritic density. Comparison of electrophysiological response properties showed an increase in firing rate differences between stimulus and non-stimulus periods during maturation. A putative disinhibitory network in the honeybee primary auditory center was proposed based on experimental evidence. Simulations showed that the network was consistent with experimental observations and clarified the central inhibitory role of DL-Int-1 in shaping the network output. RELEVANCE: Reg-MaxS-N presents a novel approach for the spatial co-registration of morphologies. Adaptations in DL-Int-1 morphology during maturation indicate improved connectivity and signal propagation. The central role of DL-Int-1 in a disinhibitory network in the honeybee primary auditory center combined with adaptions in its response properties during maturation could indicate better encoding of distance information from waggle dance vibration sig- nals

Collective behavior and morphological complexity in Pseudomonas aeruginosa

In nature, many animals are capable of performing complex behaviors without centralized coordination. A well-studied focus is collective motion in flocks of birds and shoals of fish, both of which are capable of changing collective behavior as a function of individuals responding to their local environment. Similarly, despite their microscopic individual size, groups of bacteria are capable of collectively responding to and restructuring their environment. In this thesis I focus on the gamma proteobacterium Pseudomonas aeruginosa (PA), a well-studied opportunistic pathogen that is known to engage in complex collective behaviors, often controlled by a form of cell-cell communication mediated by diffusible signal molecules called quorum sensing (QS). First, I query the sensing capacity of QS, quantifying the ability to sense cell density by tracking QS-regulated secreted protease (lasB) expression on the population and single-cell scale. We find that PA can deliver a graded behavioral response (or ‘reaction norm’) to fine-scale variation in population density and show that populations generate graded responses to environmental variation through shifts in the proportion of cells responding and the intensity of responses. Given this ability of PA to quantitatively respond to discrete density environments, I then ask how the molecular machinery of QS shapes the reaction norms to changing density, via signal synthase knockout and complementation experiments. We find that the wildtype reaction norm is robust to the addition of density-independent signal supplements and more broadly, that a positive reaction norm to density is robust to multiple combinations of gene deletion and density-independent signal supplementation. Switching from QS control of a single gene (lasB), I turn to a complex multigenic and multicellular trait of colony growth. Using a collection of diverse environmental and clinical PA isolates, we develop a colony image library of 69 strains in four-fold replication. We then use a combination of image processing techniques to quantify colony morphology and complexity and find that, under common laboratory conditions, morphology and complexity form a robust, repeatable phenotype on the level of individual strains. Based on this replicable visual “fingerprint” per strain, we reasoned that colony image data could be used to classify previously unseen colony images to the strain level. Using a combination of transfer learning and data augmentation we trained a neural network to classify strains, resulting in high-level accuracy (94%). These results indicate that not only do PA strains have characteristic, replicable ‘fingerprints’, but also that these ‘fingerprints’ are learnable and classifiable. These results could provide a basis for predicting other strain-dependent behaviors including virulence or antibiotic resistance. Overall, these results highlight that complex and heterogeneous single-cell behaviors can produce robust and consistent patterns on the collective scale of environmental sensing and colony growth.Ph.D

Challenges and opportunities of using ecological and remote sensing variables for crop pest and disease mapping

Crop pest and diseases are responsible for major economic losses in the agricultural systems in Africa resulting in food insecurity. Potential yield losses for major crops across Africa are mainly caused by pests and diseases. Total losses have been estimated at 70% with approximately 30% caused by inefficient crop protection practices. With newly emerging crop pests and disease, monitoring plant health and detecting pathogens early is essential to reduce disease spread and to facilitate effective management practices. While many pest and diseases can be acquired from another host or via the environment, the majority are transmitted by biological vectors. Thus, vector ecology can serve an indirect explanation of disease cycles, outbreaks, and prevalence. Hence, better understanding of the vector niche and the dependence of pest and disease processes on their specific spatial and ecological contexts is therefore required for better management and control. While research in disease ecology has revealed important life history of hosts with the surrounding environment, other aspects need to be explored to better understand vector transmission and control strategies. For instance, choosing appropriate farming practices have proved to be an alternative to the use of synthetic pesticides. For instance, intercropping can serve as a buffer against the spread of plant pests and pathogens by attracting pests away from their host plant and also increasing the distance between plants of the same species, making it more exigent for the pest to target the main crop. Many studies have explored the potential applications of geospatial technology in disease ecology. However, pest and disease mapping in crops is rather crudely done thus far, using Spatial Distribution Models (SDM) on a regional scale. Previous research has explored climatic data to model habitat suitability and the distribution of different crop pests and diseases. However, there are limitation to using climate data since it ignores the dispersal and competition from other factors which determines the distribution of vectors transmitting the disease, thus resulting in model over prediction. For instance, vegetation patterns and heterogeneity at the landscape level has been identified to play a key role in influencing the vector-host-pathogen transmission, including vector distribution, abundance and diversity at large. Such variables can be extracted from remote sensing dataset with high accuracy over a large extent. The use of remotely sensed variables in modeling crop pest and disease has proved to increase the accuracy and precision of the models by reducing over fitting as compared to when only climatic data which are interpolated over large areas thus disregarding landscape heterogeneity.When used, remotely sensed predictors may capture subtle variances in the vegetation characteristic or in the phenology linked with the niche of the vector transmitting the disease which cannot be explained by climatic variables. Subsequently, the full potential of remote sensing applications to detect changes in habitat condition of species remains uncharted. This study aims at exploring the potential behind developing a framework which integrates both ecological and remotely sensed dataset with a robust mapping/modelling approach with aim of developing an integrated pest management approach for pest and disease affecting both annual and perrennial crops and whom currently there is no cure or existing germplasm to control further spread across sub Saharan Africa.Herausforderungen und Möglichkeiten der Verwendung von ökologischen und Fernerkundungsvariablen für die Schädlings- und Krankheitskartierung Pflanzenschädlinge und Krankheiten in der Landwirtschaft sind für große wirtschaftliche Verluste in Afrika verantwortlich, die zu Ernährungsunsicherheit führen. Die Verluste werden auf 70% geschätzt, wobei etwa 30% auf ineffiziente Pflanzenschutzpraktiken zurückzuführen sind. Bei neu auftretenden Pflanzenschädlingen und Krankheiten ist die Überwachung des Pflanzenzustands und die frühzeitige Erkennung von Krankheitserregern unerlässlich, um die Ausbreitung von Krankheiten zu reduzieren und effektive Managementpraktiken zu erleichtern. Während viele Schädlinge und Krankheiten von einem anderen Wirt oder über die Umwelt erworben werden können, wird die Mehrheit durch biologische Vektoren übertragen. Daraus folgt, dass die Vektorökologie als indirekte Erklärung von Krankheitszyklen, Ausbrüchen und Prävalenz untersucht werden sollte. Um effektive Vektorkontrollmaßnahmen zu entwickeln ist ein besseres Verständnis der ökologischen Vektor-Nischen und der Abhängigkeit von Schädlings- und Krankheits-Prozessen von ihrem spezifischen räumlichen und ökologischen Kontext wichtig. Während die Forschung in der Krankheitsökologie wichtige Lebenszyklen von Wirten mit der Umgebung schon gut aufgezeigt hat, müssen weitere Aspekte noch besser untersucht werden, um Vektorübertragungs- und Kontroll-Strategien zu entwickeln. So hat sich beispielsweise die Wahl geeigneter Anbaumethoden als Alternative zum Einsatz synthetischer Pestizide erwiesen. In einigen Fällen wurde der Zwischenfruchtanbau als ‚Puffer' gegen die Ausbreitung von Pflanzenschädlingen und Krankheitserregern vorgeschlagen. Bei diesem Anbausystem werden Schädlinge von ihrer Wirtspflanze abgezogen und auch der Abstand zwischen Pflanzen derselben Art vergrößert (was eine Übertragung erschwert). Viele Studien haben bereits die Einsatzmöglichkeiten von Geodaten in der Krankheitsökologie untersucht. Die Kartierung von Schädlingen und Krankheiten in Nutzpflanzen ist jedoch bisher eher großskalig erfolgt, unter der Zunahme von sogenannten ‚Spatial Distribution Models (SDM)' auf regionaler Ebene. Etliche Studien haben diesbezüglich klimatische Daten verwendet, um die Eignung und Verteilung verschiedener Pflanzenschädlinge und Krankheiten zu modellieren. Es gibt jedoch Einschränkungen bei der Verwendung von Klimadaten, da dabei andere landschaftsbezogene Verbreitungs-Faktoren ignoriert werden, die die Verteilung der Vektoren und Krankheitserreger bestimmen, was zu einer Modell-Überprognose führt. Vegetationsmuster und Heterogenität auf Landschaftsebene beeinflussen maßgeblich die Diversität und Verteilung eines Vektors und spielen somit eine wichtige Rolle bei der Vektor-Wirt-Pathogen-Übertragung. Bei der Verwendung von Fernerkundungsdaten können subtile Abweichungen in der Vegetationscharakteristik oder in der Phänologie, die mit der Nische des Vektors verbunden sind, besser erfasst werden. Es besteht noch Forschungs-Bedarf hinsichtlich der Rolle von Fernerkundungsdaten bei der Verbesserung von Artenmodellen, die zum Ziel haben den Lebensraum von Krankheitsvektoren besser zu erfassen. Ziel dieser Studie ist es, das Potenzial für die Entwicklung eines Rahmens zu untersuchen, der sowohl ökologische als auch aus der Ferne erfasste Daten mit einem robusten Mapping- / Modellierungsansatz kombiniert, um einen integrierten Ansatz zur Schädlingsbekämpfung für Schädlinge und Krankheiten zu entwickeln, der sowohl einjährige als auch mehrjährige Kulturpflanzen betrifft Keine Heilung oder vorhandenes Keimplasma zur weiteren Verbreitung in Afrika südlich der Sahara

Honey Bee Health

Over the past decade, the worldwide decline in honey bee populations has been an important issue due to its implications for beekeeping and honey production. Honey bee pathologies are continuously studied by researchers, in order to investigate the host–parasite relationship and its effect on honey bee colonies. For these reasons, the interest of the veterinary community towards this issue has increased recently, and honey bee health has also become a subject of public interest. Bacteria, such as Melissococcus plutonius and Paenibacillus larvae, microsporidia, such as Nosema apis and Nosema ceranae, fungi, such as Ascosphaera apis, mites, such as Varroa destructor, predatory wasps, including Vespa velutina, and invasive beetles, such as Aethina tumida, are “old” and “new” subjects of important veterinary interest. Recently, the role of host–pathogen interactions in bee health has been included in a multifactorial approach to the study of these insects’ health, which involves a dynamic balance among a range of threats and resources interacting at multiple levels. The aim of this Special Issue is to explore honey bee health through a series of research articles that are focused on different aspects of honey bee health at different levels, including molecular health, microbial health, population genetic health, and the interaction between invasive species that live in strict contact with honey bee populations