Automated movement tracking is essential for high‐throughput quantitative analyses of the behaviour and kinematics of organisms. Automated tracking also improves replicability by avoiding observer ...bias and allowing reproducible workflows. However, few automated tracking programs exist that are open access, open source and capable of tracking unmarked organisms in noisy environments.
Tracktor is an image‐based tracking freeware designed to perform single‐object tracking in noisy environments, or multi‐object tracking in uniform environments while maintaining individual identities. Tracktor is code‐based but requires no coding skills other than the user being able to specify tracking parameters in a designated location, much like in a graphical user interface. The installation and use of the software is fully detailed in a user manual.
Through four examples of common tracking problems, we show that Tracktor is able to track a variety of animals in diverse conditions. The main strengths of Tracktor lie in its ability to track single individuals under noisy conditions (e.g. when the object shape is distorted), its robustness to perturbations (e.g. changes in lighting conditions during the experiment), and its capacity to track multiple unmarked individuals while maintaining their identities. Additionally, summary statistics and plots allow measuring and visualising common metrics used in the analysis of animal movement (e.g. cumulative distance, speed, acceleration, activity, time spent in specific areas and distance to conspecific, etc.).
Tracktor is a versatile, reliable and easy‐to‐use automated tracking software that is compatible with all operating systems and provides many features not available in other existing freeware. Access Tracktor and the complete user manual here: https://github.com/vivekhsridhar/tracktor
Authorship should acknowledge and reward those deserving of such credit. Moreover, being an author on a paper also means that one assumes ownership of the content.
Journals are increasingly requiring ...author roles to be specified at time of submission using schemes such as the contributor roles taxonomy (CRediT) system, which relies on 14 different roles. Yet, there are many other aspects of research that are not adequately captured by the list of roles, particularly in applied environmental disciplines such as conservation science, environmental science and applied ecology.
The growing recognition that authorship should reflect contributions that extend beyond the usual data collection, analysis and writing provides the ideal backdrop for rethinking contributions in conservation science. Here we propose a more inclusive approach to authorship that recognizes and values diverse contributions and contributors using an expanded list of CRediT roles.
Determining who is deserving of authorship is challenging. That is particularly salient in conservation science where contributions are diverse and may extend beyond data collection, analysis or writing. This image illustrates the interconnectedness of contributors and the challenges with determining who has earned authorship.
The partial pressure of CO
in the oceans has increased rapidly over the past century, driving ocean acidification and raising concern for the stability of marine ecosystems
. Coral reef fishes are ...predicted to be especially susceptible to end-of-century ocean acidification on the basis of several high-profile papers
that have reported profound behavioural and sensory impairments-for example, complete attraction to the chemical cues of predators under conditions of ocean acidification. Here, we comprehensively and transparently show that-in contrast to previous studies-end-of-century ocean acidification levels have negligible effects on important behaviours of coral reef fishes, such as the avoidance of chemical cues from predators, fish activity levels and behavioural lateralization (left-right turning preference). Using data simulations, we additionally show that the large effect sizes and small within-group variances that have been reported in several previous studies are highly improbable. Together, our findings indicate that the reported effects of ocean acidification on the behaviour of coral reef fishes are not reproducible, suggesting that behavioural perturbations will not be a major consequence for coral reef fishes in high CO
oceans.
Fast-start escape responses are critical behaviours used by fishes during predator-prey encounters and some interactions with hetero- and conspecifics. In experimental studies, escape responses are ...often measured once per individual and considered representative of maximum performance. However, few studies have compared variability and repeatability in escape performances within and among individuals. Using the tropical damselfish Amblyglyphidodon curacao, we quantified inter- and intra-individual variation in behavioural and kinematic components of escape performance during repeated presentations of a stimulus at 15 min intervals. Individual maximum escape performance was repeatable through time, but there was considerable variation in the magnitude of responses both among and within fish. We found no evidence of habituation or fatigue due to repeated stimulations, suggesting that fish can be stimulated multiple times to ensure that an accurate estimate of maximum escape performance is obtained.
Work carried out since the late 1970s has provided key insights into the comparative biomechanics, kinematics, behaviour and neurobiology of fish escape responses. An escape response is an ...ecologically important behaviour used by fishes to evade predation and aggression via rapid swimming movements. With environmental change expected to affect the physiology and biomechanics of aquatic ectotherms, there is a growing interest in understanding how environmental stressors affect the swimming performance and behaviour of fishes during escape responses, particularly in the context of predator-prey interactions. As the study of fish swimming continues to expand, there have been repeated calls to standardise experiments and reporting practices to facilitate integrative and comparative studies. Here, we provide a set of practical guidelines for conducting, analysing and reporting experiments on escape responses in fish, including a reporting checklist to assist authors undertaking these experiments. These resources will facilitate executing and reporting escape response experiments in a rigorous and transparent fashion, helping to advance the study of fish swimming in an era of rapid environmental change.
Parasites and Host Performance Binning, Sandra A.; Shaw, Allison K.; Roche, Dominique G.
Integrative and comparative biology,
08/2017, Letnik:
57, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Studies of animal locomotion and movement largely assume that individuals are healthy and performing to the best of their abilities in ways which are adapted to their survival. However, wild animals ...face numerous ecological challenges that can compromise their health, reduce their performance capacity, impair their movement abilities and, ultimately, lower their fitness. By diverting resources and increasing host energetic demands, parasites, bacteria, and viruses (hereafter parasites) can dramatically influence the ways in which their hosts allocate energy to movement. Yet, the role of parasites in influencing animal locomotor performance and movement remains relatively unexplored, perhaps because animals often hide outward signs of sickness, and parasites tend to be small and inconspicuous to researchers. Here, we review how parasite infection can alter host locomotor performance via impacts on host morphology and physiology. We also give examples of behavioral strategies that some hosts employ to help overcome the disadvantages imposed by infection. Finally, we discuss how parasites can lead to both increased and decreased host movement patterns, either as an adaptive strategy for the host or due to manipulation by the parasite. The dynamic interplay between host movement (such as migration and dispersal) and infection has profound consequences for population and ecosystem-level processes that are influenced by movement. Acknowledging the important functional role played by parasites in driving the evolution of host locomotor performance and behavior is a critical step toward developing a comprehensive understanding of the causes and consequences of animal movement.
Evidence has highlighted the importance of immune cells in various gut disorders. Both the quantification and localization of these cells are essential to the understanding of the complex mechanisms ...implicated in these pathologies. Even if quantification can be assessed (e.g., by flow cytometry), simultaneous cell localization and quantification of whole tissues remains technically challenging. Here, we describe the use of a computer learning-based algorithm created in the Tissue Studio interface that allows for a semi-automated, robust and rapid quantitative analysis of immunofluorescence staining on whole colon sections according to their distribution in different tissue areas. Indeed, this algorithm was validated to characterize gut immune microenvironment. Its application to the preclinical colon cancer APC
mouse model is illustrated by the simultaneous counting of total leucocytes and T cell subpopulations, in the colonic mucosa, lymphoid follicles and tumors. Moreover, we quantify T cells in lymphoid follicles for which quantification is not possible with classical methods. Thus, this algorithm is a new and robust preclinical research tool, for investigating immune contexture exemplified by T cells but it is also applicable to other immune cells such as other myeloid and lymphoid populations or other cellular phenomenon along mouse gut.
The multiresolution frequency domain parflow (MR-FDPF) approach is applied to radio wave propagation in indoor environments. This method allows for a better understanding of indoor propagation and ...hence greatly assists the development of WiFi-like network planning tools. The efficiency of such wireless design tools is strongly impacted by the quality of the coverage predictions which have to be estimated with a limited computational load. The usual approaches are based either on an empirical modeling relying on measurement campaigns or on geometrical optics leading to ray-tracing. While the former approach suffers from a lack of accuracy, the later one needs to balance accuracy with computational load requirements. The new approach proposed herein is based on a finite difference formalism, i.e., the transmission line matrix (TLM). Once the problem is developed in the frequency domain, the linear system thus obtained is solved in two steps: a pre-processing step which consists of an adaptive MR (multigrid) pre-conditioning and a propagation step. The first step computes a MR data structure represented as a binary tree. In the second step the coverage of a point source is obtained by up-and-down propagating through the binary tree. This approach provides an exact solution for the linear system whilst significantly reducing the computational complexity when compared with the time domain approach
Many leading journals in ecology and evolution now mandate open data upon publication. Yet, there is very little oversight to ensure the completeness and reusability of archived datasets, and we ...currently have a poor understanding of the factors associated with high-quality data sharing. We assessed 362 open datasets linked to first- or senior-authored papers published by 100 principal investigators (PIs) in the fields of ecology and evolution over a period of 7 years to identify predictors of data completeness and reusability (data archiving quality). Datasets scored low on these metrics: 56.4% were complete and 45.9% were reusable. Data reusability, but not completeness, was slightly higher for more recently archived datasets and PIs with less seniority. Journal open data policy, PI gender and PI corresponding author status were unrelated to data archiving quality. However, PI identity explained a large proportion of the variance in data completeness (27.8%) and reusability (22.0%), indicating consistent inter-individual differences in data sharing practices by PIs across time and contexts. Several PIs consistently shared data of either high or low archiving quality, but most PIs were inconsistent in how well they shared. One explanation for the high intra-individual variation we observed is that PIs often conduct research through students and postdoctoral researchers, who may be responsible for the data collection, curation and archiving. Levels of data literacy vary among trainees and PIs may not regularly perform quality control over archived files. Our findings suggest that research data management training and culture within a PI's group are likely to be more important determinants of data archiving quality than other factors such as a journal's open data policy. Greater incentives and training for individual researchers at all career stages could improve data sharing practices and enhance data transparency and reusability.
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