Flexible and practical modeling of animal telemetry data: hidden Markov models and extensions

We discuss hidden Markov-type models for fitting a variety of multistate random walks to wildlife movement data. Discrete-time hidden Markov models (HMMs) achieve considerable computational gains by focusing on observations that are regularly spaced in time, and for which the measurement error is negligible. These conditions are often met, in particular for data related to terrestrial animals, so that a likelihood-based HMM approach is feasible. We describe a number of extensions of HMMs for animal movement modeling, including more flexible state transition models and individual random effects (fitted in a non-Bayesian framework). In particular we consider so-called hidden semi-Markov models, which may substantially improve the goodness of fit and provide important insights into the behavioral state switching dynamics. To showcase the expediency of these methods, we consider an application of a hierarchical hidden semi-Markov model to multiple bison movement paths

Ultrabroadband Nonlinear Optics in Nanophotonic Periodically Poled Lithium Niobate Waveguides

Quasi-phasematched interactions in waveguides with quadratic nonlinearities enable highly efficient nonlinear frequency conversion. In this article, we demonstrate the first generation of devices that combine the dispersion-engineering available in nanophotonic waveguides with quasi-phasematched nonlinear interactions available in periodically poled lithium niobate (PPLN). This combination enables quasi-static interactions of femtosecond pulses, reducing the pulse energy requirements by several orders of magnitude, from picojoules to femtojoules. We experimentally demonstrate two effects associated with second harmonic generation. First, we observe efficient quasi-phasematched second harmonic generation with <100 fJ of pulse energy. Second, in the limit of strong phase-mismatch, we observe spectral broadening of both harmonics with as little as 2-pJ of pulse energy. These results lay a foundation for a new class of nonlinear devices, in which co-engineering of dispersion with quasi-phasematching enables efficient nonlinear optics at the femtojoule level

Nonlinear interaction between two heralded single photons

Harnessing nonlinearities strong enough to allow two single photons to interact with one another is not only a fascinating challenge but is central to numerous advanced applications in quantum information science. Currently, all known approaches are extremely challenging although a few have led to experimental realisations with attenuated classical laser light. This has included cross-phase modulation with weak classical light in atomic ensembles and optical fibres, converting incident laser light into a non-classical stream of photon or Rydberg blockades as well as all-optical switches with attenuated classical light in various atomic systems. Here we report the observation of a nonlinear parametric interaction between two true single photons. Single photons are initially generated by heralding one photon from each of two independent spontaneous parametric downconversion sources. The two heralded single photons are subsequently combined in a nonlinear waveguide where they are converted into a single photon with a higher energy. Our approach highlights the potential for quantum nonlinear optics with integrated devices, and as the photons are at telecom wavelengths, it is well adapted to applications in quantum communication.Comment: 4 pages, 4 figure

Incorporating Animal Movement Into Distance Sampling

Distance sampling is a popular statistical method to estimate the density of wild animal populations. Conventional distance sampling represents animals as fixed points in space that are detected with an unknown probability that depends on the distance between the observer and the animal. Animal movement can cause substantial bias in density estimation. Methods to correct for responsive animal movement exist, but none account for nonresponsive movement independent of the observer. Here, an explicit animal movement model is incorporated into distance sampling, combining distance sampling survey data with animal telemetry data. Detection probability depends on the entire unobserved path the animal travels. The intractable integration over all possible animal paths is approximated by a hidden Markov model. A simulation study shows themethod to be negligibly biased (\u3c5%) in scenarioswhere conventional distance sampling overestimates abundance by up to 100%. The method is applied to line transect surveys (1999– 2006) of spotted dolphins (Stenella attenuata) in the eastern tropical Pacific where abundance is shown to be positively biased by 21% on average, which can have substantial impact on the population dynamics estimated from these abundance estimates and on the choice of statistical methodology applied to future surveys. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement

A bird’s eye view on turbulence: Seabird foraging associations with evolving surface flow features

Lieber L, Langrock R, Nimmo-Smith WAM. A bird's-eye view on turbulence: seabird foraging associations with evolving surface flow features. Proceedings of the Royal Society B: Biological Sciences. 2021;288(1949): 20210592.Understanding physical mechanisms underlying seabird foraging is fundamental to predict responses to coastal change. For instance, turbulence in the water arising from natural or anthropogenic structures can affect foraging opportunities in tidal seas. Yet, identifying ecologically important localized turbulence features (e.g. upwellings approximately 10–100 m) is limited by observational scale, and this knowledge gap is magnified in volatile predators. Here, using a drone-based approach, we present the tracking of surface-foraging terns (143 trajectories belonging to three tern species) and dynamic turbulent surface flow features in synchrony. We thereby provide the earliest evidence that localized turbulence features can present physical foraging cues. Incorporating evolving vorticity and upwelling features within a hidden Markov model, we show that terns were more likely to actively forage as the strength of the underlying vorticity feature increased, while conspicuous upwellings ahead of the flight path presented a strong physical cue to stay in transit behaviour. This clearly encapsulates the importance of prevalent turbulence features as localized foraging cues. Our quantitative approach therefore offers the opportunity to unlock knowledge gaps in seabird sensory and foraging ecology on hitherto unobtainable scales. Finally, it lays the foundation to predict responses to coastal change to inform sustainable ocean development

Joint modelling of multi-scale animal movement data using hierarchical hidden Markov models

1.Hidden Markov models are prevalent in animal movement modelling, where they are widely used to infer behavioural modes and their drivers from various types of telemetry data. To allow for meaningful inference, observations need to be equally spaced in time, or otherwise regularly sampled, where the corresponding temporal resolution strongly affects what kind of behaviours can be inferred from the data. 2.Recent advances in biologging technology have led to a variety of novel telemetry sensors which often collect data from the same individual simultaneously at different time scales, e.g. step lengths obtained from GPS tags every hour, dive depths obtained from time‐depth recorders once per dive, or accelerations obtained from accelerometers several times per second. However, to date, statistical machinery to address the corresponding complex multi‐stream and multi‐scale data is lacking. 3.We propose hierarchical hidden Markov models as a versatile statistical framework that naturally accounts for differing temporal resolutions across multiple variables. In these models, the observations are regarded as stemming from multiple, connected behavioural processes, each of which operates at the time scale at which the corresponding variables were observed. 4.By jointly modelling multiple data streams, collected at different temporal resolutions, corresponding models can be used to infer behavioural modes at multiple time scales, and in particular help to draw a much more comprehensive picture of an animal's movement patterns, e.g. with regard to long‐term vs. short‐term movement strategies. 5.The suggested approach is illustrated in two real‐data applications, where we jointly model i) coarse‐scale horizontal and fine‐scale vertical Atlantic cod (Gadus morhua) movements throughout the English Channel, and ii) coarse‐scale horizontal movements and corresponding fine‐scale accelerations of a horn shark (Heterodontus francisci) tagged off the Californian coast

Ultrabroadband Nonlinear Optics in Dispersion Engineered Periodically Poled Lithium Niobate Waveguides

We experimentally demonstrate the first generation of dispersion-engineered periodically poled lithium niobate (PPLN) waveguides. These waveguides achieve ultra-broadband second-harmonic generation (SHG) and multi-octave supercontinuum generation (SCG) with record-low pulse energies

Ultrabroadband Nonlinear Optics in Nanophotonic Periodically Poled Lithium Niobate Waveguides

Quasi-phasematched interactions in waveguides with quadratic nonlinearities enable highly efficient nonlinear frequency conversion. In this article, we demonstrate the first generation of devices that combine the dispersion-engineering available in nanophotonic waveguides with quasi-phasematched nonlinear interactions available in periodically poled lithium niobate (PPLN). This combination enables quasi-static interactions of femtosecond pulses, reducing the pulse energy requirements by several orders of magnitude, from picojoules to femtojoules. We experimentally demonstrate two effects associated with second harmonic generation. First, we observe efficient quasi-phasematched second harmonic generation with <100 fJ of pulse energy. Second, in the limit of strong phase-mismatch, we observe spectral broadening of both harmonics with as little as 2-pJ of pulse energy. These results lay a foundation for a new class of nonlinear devices, in which co-engineering of dispersion with quasi-phasematching enables efficient nonlinear optics at the femtojoule level

Long-distance entanglement-based quantum key distribution over optical fiber

We report the first entanglement-based quantum key distribution (QKD) experiment over a 100-km optical fiber. We used superconducting single photon detectors based on NbN nanowires that provide high-speed single photon detection for the 1.5-µm telecom band, an efficient entangled photon pair source that consists of a fiber coupled periodically poled lithium niobate waveguide and ultra low loss filters, and planar lightwave circuit Mach-Zehnder interferometers (MZIs) with ultra stable operation. These characteristics enabled us to perform an entanglement-based QKD experiment over a 100-km optical fiber. In the experiment, which lasted approximately 8 hours, we successfully generated a 16 kbit sifted key with a quantum bit error rate of 6.9 % at a rate of 0.59 bits per second, from which we were able to distill a 3.9 kbit secure key