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Find video protocols related to scientific articles indexed in Pubmed.
Information visualisation for science and policy: engaging users and avoiding bias.
Trends Ecol. Evol. (Amst.)
PUBLISHED: 01-11-2014
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Visualisations and graphics are fundamental to studying complex subject matter. However, beyond acknowledging this value, scientists and science-policy programmes rarely consider how visualisations can enable discovery, create engaging and robust reporting, or support online resources. Producing accessible and unbiased visualisations from complicated, uncertain data requires expertise and knowledge from science, policy, computing, and design. However, visualisation is rarely found in our scientific training, organisations, or collaborations. As new policy programmes develop [e.g., the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES)], we need information visualisation to permeate increasingly both the work of scientists and science policy. The alternative is increased potential for missed discoveries, miscommunications, and, at worst, creating a bias towards the research that is easiest to display.
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Landscape complexity influences route-memory formation in navigating pigeons.
Biol. Lett.
PUBLISHED: 01-01-2014
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Observations of the flight paths of pigeons navigating from familiar locations have shown that these birds are able to learn and subsequently follow habitual routes home. It has been suggested that navigation along these routes is based on the recognition of memorized visual landmarks. Previous research has identified the effect of landmarks on flight path structure, and thus the locations of potentially salient sites. Pigeons have also been observed to be particularly attracted to strong linear features in the landscape, such as roads and rivers. However, a more general understanding of the specific characteristics of the landscape that facilitate route learning has remained out of reach. In this study, we identify landscape complexity as a key predictor of the fidelity to the habitual route, and thus conclude that pigeons form route memories most strongly in regions where the landscape complexity is neither too great nor too low. Our results imply that pigeons process their visual environment on a characteristic spatial scale while navigating and can explain the different degrees of success in reproducing route learning in different geographical locations.
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Pairs of pigeons act as behavioural units during route learning and co-navigational leadership conflicts.
J. Exp. Biol.
PUBLISHED: 03-29-2013
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In many species, group members obtain benefits from moving collectively, such as enhanced foraging efficiency or increased predator detection. In situations where the groups decision involves integrating individual preferences, group cohesion can lead to more accurate outcomes than solitary decisions. In homing pigeons, a classic model in avian orientation studies, individuals learn habitual routes home, but whether and how co-navigating birds acquire and share route-based information is unknown. Using miniature GPS loggers, we examined these questions by first training pairs (the smallest possible flocks) of pigeons together, and then releasing them with other pairs that had received separate pair-training. Our results show that, much like solitary individuals, pairs of birds are able to establish idiosyncratic routes that they recapitulate together faithfully. Also, when homing with other pairs they exhibit a transition from a compromise- to a leadership-like mechanism of conflict resolution as a function of the degree of disagreement (distance separating the two preferred routes) between the two pairs, although pairs tolerate a greater range of disagreements prior to the transition than do single birds. We conclude that through shared experiences during past decision-making, pairs of individuals can become units so closely coordinated that their behaviour resembles that of single birds. This has implications for the behaviour of larger groups, within which certain individuals have closer social affiliations or share a history of previous associations.
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Homing pigeons respond to time-compensated solar cues even in sight of the loft.
PLoS ONE
PUBLISHED: 01-01-2013
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The sun has long been thought to guide bird navigation as the second step in a two-stage process, in which determining position using a map is followed by course setting using a compass, both over unfamiliar and familiar terrain. The animals endogenous clock time-compensates the solar compass for the suns apparent movement throughout the day, and this allows predictable deflections in orientation to test for the compass influence using clock-shift manipulations. To examine the influence of the solar compass during a highly familiar navigational task, 24 clock-shifted homing pigeons were precision-tracked from a release site close to and in sight of their final goal, the colony loft. The resulting trajectories displayed significant partial deflection from the loft direction as predicted by either fast or slow clock-shift treatments. The partial deflection was also found to be stable along the entire trajectory indicating regular updating of orientation via input from the solar compass throughout the final approach flight to the loft. Our results demonstrate that time-compensated solar cues are deeply embedded in the way birds orient during homing flight, are accessed throughout the journey and on a remarkably fine-grained scale, and may be combined effectively simultaneously with direct guidance from familiar landmarks, even when birds are flying towards a directly visible goal.
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Predictive ethoinformatics reveals the complex migratory behaviour of a pelagic seabird, the Manx Shearwater.
J R Soc Interface
PUBLISHED: 01-01-2013
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Understanding the behaviour of animals in the wild is fundamental to conservation efforts. Advances in bio-logging technologies have offered insights into the behaviour of animals during foraging, migration and social interaction. However, broader application of these systems has been limited by device mass, cost and longevity. Here, we use information from multiple logger types to predict individual behaviour in a highly pelagic, migratory seabird, the Manx Shearwater (Puffinus puffinus). Using behavioural states resolved from GPS tracking of foraging during the breeding season, we demonstrate that individual behaviours can be accurately predicted during multi-year migrations from low cost, lightweight, salt-water immersion devices. This reveals a complex pattern of migratory stopovers: some involving high proportions of foraging, and others of rest behaviour. We use this technique to examine three consecutive years of global migrations, revealing the prominence of foraging behaviour during migration and the importance of highly productive waters during migratory stopover.
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A dispersive migration in the Atlantic Puffin and its implications for migratory navigation.
PLoS ONE
PUBLISHED: 04-04-2011
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Navigational control of avian migration is understood, largely from the study of terrestrial birds, to depend on either genetically or culturally inherited information. By tracking the individual migrations of Atlantic Puffins, Fratercula arctica, in successive years using geolocators, we describe migratory behaviour in a pelagic seabird that is apparently incompatible with this view. Puffins do not migrate to a single overwintering area, but follow a dispersive pattern of movements changing through the non-breeding period, showing great variability in travel distances and directions. Despite this within-population variability, individuals show remarkable consistency in their own migratory routes among years. This combination of complex population dispersion and individual route fidelity cannot easily be accounted for in terms of genetic inheritance of compass instructions, or cultural inheritance of traditional routes. We suggest that a mechanism of individual exploration and acquired navigational memory may provide the dominant control over Puffin migration, and potentially some other pelagic seabirds, despite the apparently featureless nature of the ocean.
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Group decisions and individual differences: route fidelity predicts flight leadership in homing pigeons (Columba livia).
Biol. Lett.
PUBLISHED: 09-01-2010
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How social-living animals make collective decisions is currently the subject of intense scientific interest, with increasing focus on the role of individual variation within the group. Previously, we demonstrated that during paired flight in homing pigeons, a fully transitive leadership hierarchy emerges as birds are forced to choose between their own and their partners habitual routes. This stable hierarchy suggests a role for individual differences mediating leadership decisions within homing pigeon pairs. What these differences are, however, has remained elusive. Using novel quantitative techniques to analyse habitual route structure, we show here that leadership can be predicted from prior route-following fidelity. Birds that are more faithful to their own route when homing alone are more likely to emerge as leaders when homing socially. We discuss how this fidelity may relate to the leadership phenomenon, and propose that leadership may emerge from the interplay between individual route confidence and the dynamics of paired flight.
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Objectively identifying landmark use and predicting flight trajectories of the homing pigeon using Gaussian processes.
J R Soc Interface
PUBLISHED: 07-23-2010
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Pigeons home along idiosyncratic habitual routes from familiar locations. It has been suggested that memorized visual landmarks underpin this route learning. However, the inability to experimentally alter the landscape on large scales has hindered the discovery of the particular features to which birds attend. Here, we present a method for objectively classifying the most informative regions of animal paths. We apply this method to flight trajectories from homing pigeons to identify probable locations of salient visual landmarks. We construct and apply a Gaussian process model of flight trajectory generation for pigeons trained to home from specific release sites. The model shows increasing predictive power as the birds become familiar with the sites, mirroring the animals learning process. We subsequently find that the most informative elements of the flight trajectories coincide with landscape features that have previously been suggested as important components of the homing task.
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Black Petrels (Procellaria parkinsoni) patrol the ocean shelf-break: GPS tracking of a vulnerable procellariiform seabird.
PLoS ONE
PUBLISHED: 01-15-2010
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Determining the foraging movements of pelagic seabirds is fundamental for their conservation. However, the vulnerability and elusive lifestyles of these animals have made them notoriously difficult to study. Recent developments in satellite telemetry have enabled tracking of smaller seabirds during foraging excursions.
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Not just passengers: pigeons, Columba livia, can learn homing routes while flying with a more experienced conspecific.
Proc. Biol. Sci.
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For animals that travel in groups, the directional choices of conspecifics are potentially a rich source of information for spatial learning. In this study, we investigate how the opportunity to follow a locally experienced demonstrator affects route learning by pigeons over repeated homing flights. This test of social influences on navigation takes advantage of the individually distinctive routes that pigeons establish when trained alone. We found that pigeons learn routes just as effectively while flying with a partner as control pigeons do while flying alone. However, rather than learning the exact route of the demonstrator, the paired routes shifted over repeated flights, which suggests that the birds with less local experience also took an active role in the navigational task. The efficiency of the original routes was a key factor in how far they shifted, with less efficient routes undergoing the greatest changes. In this context, inefficient routes are unlikely to be maintained through repeated rounds of social transmission, and instead more efficient routes are achieved because of the interaction between social learning and information pooling.
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Behavioural mapping of a pelagic seabird: combining multiple sensors and a hidden Markov model reveals the distribution of at-sea behaviour.
J R Soc Interface
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The use of miniature data loggers is rapidly increasing our understanding of the movements and habitat preferences of pelagic seabirds. However, objectively interpreting behavioural information from the large volumes of highly detailed data collected by such devices can be challenging. We combined three biologging technologies-global positioning system (GPS), saltwater immersion and time-depth recorders-to build a detailed picture of the at-sea behaviour of the Manx shearwater (Puffinus puffinus) during the breeding season. We used a hidden Markov model to explore discrete states within the combined GPS and immersion data, and found that behaviour could be organized into three principal activities representing (i) sustained direct flight, (ii) sitting on the sea surface, and (iii) foraging, comprising tortuous flight interspersed with periods of immersion. The additional logger data verified that the foraging activity corresponded well to the occurrence of diving. Applying this approach to a large tracking dataset revealed that birds from two different colonies foraged in local waters that were exclusive, but overlapped in one key area: the Irish Sea Front (ISF). We show that the allocation of time to each activity differed between colonies, with birds breeding furthest from the ISF spending the greatest proportion of time engaged in direct flight and the smallest proportion of time engaged in foraging activity. This type of analysis has considerable potential for application in future biologging studies and in other taxa.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.