Costs and benefits of social relationships in the collective motion of bird flocks

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this record.Supplementary Figs. 1–12 and Supplementary Tables 1–3 are available in the Supplementary Information. Raw images captured by one of the four cameras and the reconstructed birds’ 3D movement trajectories are provided in Supplementary Videos 1–6. Plain text files, each including bird ID number, position, time, velocity, acceleration and wingbeat frequency at every time step, are provided in Supplementary Data 1–7. A plain text file that includes mean wingbeat frequency, flight speed and local density (approximated by the number of neighbours within a distance of 5 m from the focal bird) for paired and unpaired birds in six flocks, as well as for birds flying alone, is provided in Supplementary Data 8. All data required to reproduce the results in this study are included in Supplementary Data 1–8. Supplementary Data and Supplementary Videos are available at https://figshare.com/s/c55eb82bab800571d25d.Current understanding of collective behaviour in nature is based largely on models that assume that identical agents obey the same interaction rules, but in reality interactions may be influenced by social relationships among group members. Here, we show that social relationships transform local interactions and collective dynamics. We tracked individuals’ three-dimensional trajectories within flocks of jackdaws, a species that forms lifelong pair-bonds. Reflecting this social system, we find that flocks contain internal sub-structure, with discrete pairs of individuals tied together by spring-like effective forces. Within flocks, paired birds interacted with fewer neighbours than unpaired birds and flapped their wings more slowly, which may result in energy savings. However, flocks with more paired birds had shorter correlation lengths, which is likely to inhibit efficient information transfer through the flock. Similar changes to group properties emerge naturally from a generic self-propelled particle model. These results reveal a critical tension between individual- and group-level benefits during collective behaviour in species with differentiated social relationships, and have major evolutionary and cognitive implications.Human Frontiers in Science Programm

Simultaneous measurements of three-dimensional trajectories and wingbeat frequencies of birds in the field

This is the author accepted manuscript. The final version is available from the Royal Society via the DOI in this recordData accessibility: We provide data including images recorded by four cameras, camera parameters, videos showing the time variation of the bird 3D positions, and plain text files that include bird id number, positions, times, velocities, accelerations, and wingbeat frequencies at every time step. We also provide the Matlab codes that were used to: (i) detect birds on images; (ii) reconstruct birds' 3D locations using the new stereo-matching algorithm; (iii) track individual's 3D motions; and (iv) calculate wing motion and wingbeat frequency from tracking results. The code and data are available at: https://github.com/linghj/3DTracking.git and https://figshare.com/s/3c572f91b07b06ed30aa.Tracking the movements of birds in three dimensions is integral to a wide range of problems in animal ecology, behaviour and cognition. Multi-camera stereo-imaging has been used to track the three-dimensional (3D) motion of birds in dense flocks, but precise localization of birds remains a challenge due to imaging resolution in the depth direction and optical occlusion. This paper introduces a portable stereo-imaging system with improved accuracy and a simple stereo-matching algorithm that can resolve optical occlusion. This system allows us to decouple body and wing motion, and thus measure not only velocities and accelerations but also wingbeat frequencies along the 3D trajectories of birds. We demonstrate these new methods by analysing six flocking events consisting of 50 to 360 jackdaws (Corvus monedula) and rooks (Corvus frugilegus) as well as 32 jackdaws and 6 rooks flying in isolated pairs or alone. Our method allows us to (i) measure flight speed and wingbeat frequency in different flying modes; (ii) characterize the U-shaped flight performance curve of birds in the wild, showing that wingbeat frequency reaches its minimum at moderate flight speeds; (iii) examine group effects on individual flight performance, showing that birds have a higher wingbeat frequency when flying in a group than when flying alone and when flying in dense regions than when flying in sparse regions; and (iv) provide a potential avenue for automated discrimination of bird species. We argue that the experimental method developed in this paper opens new opportunities for understanding flight kinematics and collective behaviour in natural environments.Human Frontier Science Progra

Local interactions and their group-level consequences in flocking jackdaws

This is the author accepted manuscript. The final version is available from the Royal Society via the DOI in this recordData accessibility: Data and code are available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.kb8js06As one of nature's most striking examples of collective behaviour, bird flocks have attracted extensive research. However, we still lack an understanding of the attractive and repulsive forces that govern interactions between individuals within flocks and how these forces influence neighbours' relative positions and ultimately determine the shape of flocks. We address these issues by analysing the three-dimensional movements of wild jackdaws (Corvus monedula) in flocks containing 2–338 individuals. We quantify the social interaction forces in large, airborne flocks and find that these forces are highly anisotropic. The long-range attraction in the direction perpendicular to the movement direction is stronger than that along it, and the short-range repulsion is generated mainly by turning rather than changing speed. We explain this phenomenon by considering wingbeat frequency and the change in kinetic and gravitational potential energy during flight, and find that changing the direction of movement is less energetically costly than adjusting speed for birds. Furthermore, our data show that collision avoidance by turning can alter local neighbour distributions and ultimately change the group shape. Our results illustrate the macroscopic consequences of anisotropic interaction forces in bird flocks, and help to draw links between group structure, local interactions and the biophysics of animal locomotion.Human Frontiers in Science Programm

Behavioural plasticity and the transition to order in jackdaw flocks

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: Raw images captured by one of the four cameras and the reconstructed 3D movement trajectories of the jackdaws are provided in Supplementary Movies 1 to 3. The group density and group order for 154 groups are provided in Supplementary Data 1. Plain text files, each including bird ID number, position, time, and velocity at every time step are provided in Supplementary Data 2 to 4. All data required to reproduce the results in this study are included in Supplementary Data 1 to 4. The data analysis codes (including the self-propelled particle model) to generate all figures in the paper are also provided. Supplementary Data, Supplementary Movies, and data analysis codes are available at: https://figshare.com/s/472d354cc9e823a8f48fCollective behaviour is typically thought to arise from individuals following fixed interaction rules. The possibility that interaction rules may change under different circumstances has thus only rarely been investigated. Here we show that local interactions in flocks of wild jackdaws (Corvus monedula) vary drastically in different contexts, leading to distinct group-level properties. Jackdaws interact with a fixed number of neighbours (topological interactions) when traveling to roosts, but coordinate with neighbours based on spatial distance (metric interactions) during collective anti-predator mobbing events. Consequently, mobbing flocks exhibit a dramatic transition from disordered aggregations to ordered motion as group density increases, unlike transit flocks where order is independent of density. The relationship between group density and group order during this transition agrees well with a generic self-propelled particle model. Our results demonstrate plasticity in local interaction rules and have implications for both natural and artificial collective systems.Human Frontier Science Progra

Collective turns in jackdaw flocks: kinematics and information transfer

This is the author accepted manuscript. The final version is available from The Royal Society via the DOI in this record.The rapid, cohesive turns of bird flocks are one of the most vivid examples of collective behaviour in nature, and have attracted much research. Three-dimensional imaging techniques now allow us to characterize the kinematics of turning and their group-level consequences in precise detail. We measured the kinematics of flocks of wild jackdaws executing collective turns in two contexts: during transit to roosts and anti-predator mobbing. All flocks reduced their speed during turns, probably because of constraints on individual flight capability. Turn rates increased with the angle of the turn so that the time to complete turns remained constant. We also find that context may alter where turns are initiated in the flocks: for transit flocks in the absence of predators, initiators were located throughout the flocks, but for mobbing flocks with a fixed ground-based predator, they were always located at the front. Moreover, in some transit flocks, initiators were far apart from each other, potentially because of the existence of subgroups and variation in individual interaction ranges. Finally, we find that as the group size increased the information transfer speed initially increased, but rapidly saturated to a constant value. Our results highlight previously unrecognized complexity in turning kinematics and information transfer in social animals.Human Frontier Science Progra

Turbulence drives microscale patches of motile phytoplankton

Patchiness plays a fundamental role in phytoplankton ecology by dictating the rate at which individual cells encounter each other and their predators. The distribution of motile phytoplankton species is often considerably more patchy than that of non-motile species at submetre length scales, yet the mechanism generating this patchiness has remained unknown. Here we show that strong patchiness at small scales occurs when motile phytoplankton are exposed to turbulent flow. We demonstrate experimentally that Heterosigma akashiwo forms striking patches within individual vortices and prove with a mathematical model that this patchiness results from the coupling between motility and shear. When implemented within a direct numerical simulation of turbulence, the model reveals that cell motility can prevail over turbulent dispersion to create strong fractal patchiness, where local phytoplankton concentrations are increased more than 10-fold. This "unmixing" mechanism likely enhances ecological interactions in the plankton and offers mechanistic insights into how turbulence intensity impacts ecosystem productivity

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe