Sex is nearly ubiquitous among animals. Most animals have a stage in their life-cycle when genes from different individuals are shuffled to produce genetically mixed offspring. By doing so, natural selection acts more efficiently both to remove harmful mutations from populations and to allow beneficial combinations of genes to spread. Sex also has profound implications for speciation, namely how an ancestral species diverges into separate descendent species. Adaptation to different habitats and isolation in separate geographical areas can promote speciation, but a key step for sexual organisms is to acquire genetic or behavioural traits that prevent gene exchange. As a result, most speciation research has focused on reproductive isolating mechanisms that restrict gene exchange between diverging populations. Some organisms defy the general ubiquity of sexual reproduction. Bdelloid rotifers are microscopic animals that live in freshwater, such as ponds and the water film on mosses. No males or cellular signs of sex have ever been found, and recent genomic evidence indicates that their chromosome structure is incompatible with the normal pairing of chromosomes associated with sex. Despite the presumed costs of such a lifestyle, bdelloids comprise hundreds of morphologically distinct species. Our previous work confirmed that bdelloids have diversified into independently evolving groups akin to species and found evidence for morphological adaptation to different habitats. But what mechanisms led to divergence? Have bdelloids really evolved as asexuals or do they have hidden mechanisms for gene exchange? One recent discovery found another weird feature of bdelloids that might contribute to adaptation to different environments. Bdelloids harbour thousands of genes that appear to derive from bacteria, protists, plants and fungi and have been taken up into the bdelloid genome where they provide new functions. Some of those functions are previously unknown in the metabolic repertoire of animals. It is believed that uptake occurs (rarely) when bdelloids repair their DNA following damage caused by desiccation - another weird feature of bdelloids is their ability to survive desiccation, a stress that kills most other animals. The uptake of foreign DNA is well known in bacteria, where it contributes to specialisation to different niches (e.g. to cause disease in a new host), but the levels in bdelloids are unprecedented among animals. Might the uptake of foreign genes provide a way for bdelloids to acquire new functions and adapt to different environments, as in bacteria? Or perhaps there are other hidden mechanisms of gene exchange between bdelloids? We will use genome sequencing to test the importance of gene exchange and the uptake of foreign DNA in 4 closely related bdelloid species living in different habitats: 2 species in habitats that desiccate regularly and 2 that are fully aquatic and cannot recover from desiccation. Our prior work found that most foreign genes are shared, but a significant remainder appear to be unique to each species. We will sequence whole genomes to verify or refute the status of these genes. We will also sample genomic variation within each species to test whether shuffling of genes has occurred, and if so whether that conforms to hidden sexual exchange (unlikely) or other mechanisms. We will test whether gene exchange has shaped the pattern of natural selection across genes. The results will reveal the contribution of strictly asexual evolution versus gene exchange in bdelloid adaptation and speciation. Findings for these intriguing animals will contribute new knowledge of mechanisms that promote adaptation and speciation, in comparison to organisms with more conventional lifestyles.

Our planet is undergoing unprecedented environmental change and there is an urgent need to understand how species respond to altered abiotic conditions. Development of new technologies has recently seen a revolution in Biology with the advent of tools that enable us to quantify how organisms respond to environmental change at the level of molecules and genes in extremely fine detail. This technological approach to measuring how an organism responds to changes in their environment has become a central theme across Biology. However, technologies for measuring whole-organism level responses have not kept pace, leading to a disconnect between our understanding at these two levels of biological organization. This disconnect is due, in large part, to the challenge of quantifying, in a meaningful way, the complexity and diversity of form and function that is observed at the whole-organism level. The task of quantifying form and function at the whole-organism level is most challenging for organisms during their early development when both form and function are undergoing dynamic transitions. Yet it is at this time when organisms may be most sensitive to environmental stress. Furthermore, the experience of embryos to such stress can have impacts that persist into later life stages, including reproduction. It is therefore important that the effects of environmental stress on early life stages are incorporated into monitoring and prediction of how organisms will respond to forecasted global environmental change. A major objective in our laboratory is to gain a better understanding of how environmental stressors affect the physiology of early life stages of aquatic invertebrates. We have developed a unique bio-imaging capability that allows us to produce high-resolution (temporal and spatial) time lapse video of developing embryos, exposed to tightly controlled environmental conditions. We then extract data from these videos to quantify their physiological function using manual video analysis. Such manual data extraction is time consuming and can be an error-prone and subjective process. Consequently, the process of image analysis forms a major bottleneck in the efficacy and application of this approach to quantification of the responses of large numbers of organisms to environmental change. The main aim of this project is to develop an analytical platform encompassing image analysis pipelines that automate the measurement of a wide range of embryonic features from video. To achieve this we will build image analysis pipelines for measuring functionally relevant traits including growth, gross movement, muscle contraction, heart function, developmental stage and developmental rates. Image analysis pipelines will be embedded within an analytical platform creating a system for organism-wide measurement of different functional traits in individual embryos. Short- and long-term responses of two species (a marine shrimp and freshwater snail) to contrasting temperatures will be used to develop, optimize and validate the analytical framework. The resultant data will enable unrivalled measurement of the responses of developing organisms to factors including environmental stress. This analytical platform would be a powerful tool to any field with an interest in measuring phenotypes in organisms developing in transparent egg capsules e.g. environmental sensitivity measurement, ecotoxicology and drug discovery. Increasing mean global temperatures are threatening both freshwater and marine ecosystems and the use of contrasting temperature will enable assessment of the efficacy of the automated analytical platform in quantifying the sensitivity of early life stages to a current global threat. The analytical resource being developed in this project will facilitate the development of a fully automated capability for measuring the responses and sensitivities of embryonic stages to environmental stress across different aquatic species.

Flocking, the collective motion displayed by large groups of birds in the absence of an obvious leader, is one of the most spectacular examples of emergent collective behavior in nature and has fascinated inquiring minds for a long time. Flocking, is not only restricted to birds, but can be observed in an extremely wide range of active matter systems - systems composed by "active particles" able to extract and dissipate energy from their surroundings to produce systematic and coherent motion -- as diverse as fish schools, vertebrate herds, bacteria colonies, insect swarms, active macromolecules in living cells and even driven granular matter. While our knowledge of collective motion has greatly advanced in recent years thanks to the study of minimal models of self propelled particles (SPP) and hydrodynamic continuum theories, as well as the development of the first quantitative experiments, little is known concerning the response of moving groups to perturbations, a question of both theoretical interest (fluctuation-response in out-of-equilibrium physics) and of great ethological importance (biological significance of group response, spatio-temporal mechanisms of information propagation in cases of alert). Protection from external threats is thought to be one of the most important factors in the evolution towards collective behavior, and there is indeed evidence that certain collective properties observed in animal groups cannot be understood in the context of unperturbed theories. Experimental observations in starlings, for instance, have revealed that flocks are much more internally correlated, and thus have a more efficient collective response mechanism than expected from standard unperturbed flocking theories. Our working hypothesis, supported by preliminary results in simple spin systems, is that certain properties of collectively moving animal groups can only be understood in terms of the system response to localized, dynamical perturbations. We will characterize the response of flocks to such perturbations, devoting particular attention to the role of information transmission from the boundaries to the bulk of a finite system. We will also address the origin of such perturbations. They may be exogenous, due to environmental stimuli such as attacking predators or the perception of non-homogeneous landscapes. But perturbations may also be endogenous: even in the absence of external stimuli, individuals may suddenly switch their behavioral patterns so that the group sets itself constantly into a state of dynamical excitation, possibly because this behavior enhances collective response when true perturbations strike. We will consider finite perturbations, which induce a nonlinear response in flocks, but also the limit of infinitesimal perturbations, which may allow for a deeper theoretical analysis of linear response by extension of the fluctuation-dissipation relation (FDR) to flocking systems (out-of-equilibrium generalization of the FDR are already known, but flocking systems remain largely unexplored). This is an issue of great interest for the study of animal group behavior, since it could provide relevant information (at least at the linear level) concerning the response to perturbations starting only from the knowledge of unperturbed fluctuations. It is our goal to extend and test a generalized FDR to flocking systems. This project aims at a well-defined advance in the scientific knowledge and will have direct impact on the academic communities of out-of-equilibrium statistical mechanics and group animal behavior. On a longer time scale, however, a better understanding of emergent collective phenomena in living matter could beneficially impact a number of important fields ranging from biotechnologies (subcellular dynamics of protein filaments, swarming nanorobots) to environmental resources conservation and management (animal group behavior, animal populations response to environmental changes).

Quantum information science is the field of research that studies the information present in a quantum system. It opens the way to the knowledge of unexplored fundamental physical mechanisms and to the development of novel technologies that will profoundly transform the way we communicate and process our data. Indeed, a number of new technological applications can be envisaged thanks to exquisitely quantum phenomena. While classical information encoding relies on bits, which can be either 0s or 1s, the quantum bits (or qubits) are associated to the state of quantum objects, e.g., single atoms, single spins, or single photons. Because of the quantum superposition principle, the qubits can then be 0s, 1s, or coherent superposition of both, thus giving access to an exceptionally richer alphabet. Quantum information science also exploits quantum entanglement, i.e., strong correlation between quantum objects, as a resource for fast and secure quantum communication protocols. In view of realizing networks for quantum communication, quantum memories are fundamental devices as they act as interfaces between the photons, used as information carriers (or flying qubits), and stationary qubits, exploited for information storage and processing. While atomic gases enabled the first remarkable quantum storage experiments, solid-state systems, and specifically rare earth ion doped crystals, also offer interesting perspectives thanks to the absence of atomic motion and the high density, and the fact that they unleash prospects of integration, which facilitates scalability and employability in real-life quantum technology demonstrations. As a matter of fact, the implementation of quantum information protocols on a small chip has the potential to replicate the revolution of modern electronic miniaturization and intense research efforts are indeed devoted to developing miniaturized photonic integrated circuits for quantum information processing. Yet, on chip memories for single photons, key components of future quantum communication technology, are currently missing. This Fellowship addresses this pressing challenge by developing waveguide quantum memories based on ultrafast laser micromachining of rare earth ion doped crystals. We will engineer the necessary tool kit for the integrated quantum memories to fulfil simultaneously all the requirements for their employability in real-life quantum networks, as on-demand read-out, high efficiency, long storage time, and multimodality. Moreover, we will demonstrate how the integrated design gives access to functionalities that are not possible with bulk devices, like the non-destructive detection of single photons. This vision represents a technological breakthrough toward the realization of complex memory-enhanced quantum photonics circuitry on chip.

Quantum information science is the field of research that studies the information present in a quantum system. A number of new technological applications can be envisaged thanks to exquisitely quantum phenomena. While classical information encoding relies on bits, which can be either 0s and 1s, the quantum bits (or qubits) are associated to the state of quantum objects, e.g. single atoms, single spins, or single photons. Because of the quantum superposition principle, the qubits can then be 0s, 1s, or coherent superposition of both, thus giving access to an exceptionally richer alphabet. Quantum information science also exploits quantum entanglement, i.e. strong correlation between quantum objects, as a resource for fast and secure quantum communication protocols. In view of realising networks for quantum communication, quantum memories are fundamental devices as they act as interfaces between the photons, used as information carriers, and atoms, exploited for information storage and processing. To be useful in quantum networks, the quantum memories must fulfil specific requirements, as on-demand read-out, high efficiency and fidelity, long storage time, and multimodality. While atomic gases enabled the first remarkable quantum storage experiments, solid-state systems also offer interesting perspectives. Among these, the rare-earth doped crystals recently emerged as attractive candidates because they are ensembles of optically active ions naturally trapped in inert media, which do not require external trapping fields and ultra-high vacuum chambers. They have already featured performances equalising or overcoming those of trapped atoms or cold atomic ensembles in terms of efficiency and storage times. These crystals exhibit transitions both in the optical and in the radio- and micro-wave range, thus they could serve as photonic or microwave memories, but also as interfaces between optical and microwave frequencies, thus opening the way to hybrid systems employing superconducting devices. Despite their very promising performances and the milestone experiments realised in the last decade, a unique rare-earth doped crystal that fulfils all the requirements of an ideal photonic quantum memory does not yet exist. This project exactly tackles this problem and aims at developing a novel platform for telecom-compatible integrated quantum devices, containing solid-state quantum memories with unprecedented functionalities. The central idea is to employ not rare-earth doped crystals but stoichiometric crystals, i.e. where the rare-earth ions fully substitute one element of the crystal matrix, with the two-fold aim of increasing the absorption of light and narrowing the inhomogeneous linewidth of the electronic transitions, thanks to a lower local mechanical stress. The challenges addressed are: - the optimisation of the coherence properties of bulk crystals that will enable the implementation of quantum storage protocols, never demonstrated in these kind of materials; - the exploration of confined environment, i.e. laser written waveguides, for the realisation of integrated quantum memories. We expect the waveguide fabrication to facilitate the realisation of fibre-coupled devices and the efficient manipulation of the atomic transitions by means of electric fields, and to boost the interaction strength between the light and the rare-earth ions. This might give access to the storage of telecom light exploiting optical transitions that in diluted bulk samples would be too weak. Therefore, the proposed platform might permit the simultaneous demonstration of efficient, long-lived and multiplexed storage devices, which are also compatible with existing telecom fibre network. Such quantum memories would outperform the existing quantum storage devices, and their demonstration would open new avenues for the use of solid-state technologies for real quantum information applications.