Poor flight performance in deep-diving cormorants

Machine learning accurately predicts the multivariate performance phenotype from morphology in lizards

Completing the genotype-to-phenotype map requires rigorous measurement of the entire multivariate organismal phenotype. However, phenotyping on a large scale is not feasible for many kinds of traits, resulting in missing data that can also cause problems for comparative analyses and the assessment of evolutionary trends across species. Measuring the multivariate performance phenotype is especially logistically challenging, and our ability to predict several performance traits from a given morphology is consequently poor. We developed a machine learning model to accurately estimate multivariate performance data from morphology alone by training it on a dataset containing performance and morphology data from 68 lizard species. Our final, stacked model predicts missing performance data accurately at the level of the individual from simple morphological measures. This model performed exceptionally well, even for performance traits that were missing values for >90% of the sampled individuals. Furthermore, incorporating phylogeny did not improve model fit, indicating that the phenotypic data alone preserved sufficient information to predict the performance based on morphological information. This approach can both significantly increase our understanding of performance evolution and act as a bridge to incorporate performance into future work on phenomics.

How often should dead-reckoned animal movement paths be corrected for drift?

BACKGROUND

Understanding what animals do in time and space is important for a range of ecological questions, however accurate estimates of how animals use space is challenging. Within the use of animal-attached tags, radio telemetry (including the Global Positioning System, 'GPS') is typically used to verify an animal's location periodically. Straight lines are typically drawn between these 'Verified Positions' ('VPs') so the interpolation of space-use is limited by the temporal and spatial resolution of the system's measurement. As such, parameters such as route-taken and distance travelled can be poorly represented when using VP systems alone. Dead-reckoning has been suggested as a technique to improve the accuracy and resolution of reconstructed movement paths, whilst maximising battery life of VP systems. This typically involves deriving travel vectors from motion sensor systems and periodically correcting path dimensions for drift with simultaneously deployed VP systems. How often paths should be corrected for drift, however, has remained unclear.

METHODS AND RESULTS

Here, we review the utility of dead-reckoning across four contrasting model species using different forms of locomotion (the African lion Panthera leo, the red-tailed tropicbird Phaethon rubricauda, the Magellanic penguin Spheniscus magellanicus, and the imperial cormorant Leucocarbo atriceps). Simulations were performed to examine the extent of dead-reckoning error, relative to VPs, as a function of Verified Position correction (VP correction) rate and the effect of this on estimates of distance moved. Dead-reckoning error was greatest for animals travelling within air and water. We demonstrate how sources of measurement error can arise within VP-corrected dead-reckoned tracks and propose advancements to this procedure to maximise dead-reckoning accuracy.

CONCLUSIONS

We review the utility of VP-corrected dead-reckoning according to movement type and consider a range of ecological questions that would benefit from dead-reckoning, primarily concerning animal-barrier interactions and foraging strategies.

Seabird Biologging System with Compact Waterproof Airflow Sensor

This paper presents a seabird biologging system with a compact waterproof airflow sensor. Although biologging methods have attracted attention in the evaluation of seabird flight performance, a direct measurement method of airflow velocity has not yet been established. When an airflow sensor is added to a biologging system, a more accurate assessment of the flight performance can be obtained. We developed a compact Pitot tube-type airflow sensor that is specialized for seabird biologging systems. Here, we integrated micro electro mechanical system (MEMS) sensor chips and a sensing circuit into the Pitot tube housing. Then, we conducted a wind tunnel experiment using a stuffed seabird and the fabricated sensor. The results confirmed that the sensor responds to the wind speed even when attached to the dorsal surface of the seabird. Based on the above, we believe that the proposed sensor can be applied to practical seabird biologging systems.

Galapagos Islands Endemic Vertebrates: A Population Genetics Perspective

The organisms of the Galapagos Islands played a central role in the development of the theory of evolution by Charles Darwin. Examination of the population genetics factors of many of these organisms with modern molecular methods has expanded our understanding of their evolution. Here, I provide a perspective on how selection, gene flow, genetic drift, mutation, and inbreeding have contributed to the evolution of 6 iconic Galapagos species: flightless cormorant, pink iguana, marine iguana, Galapagos hawk, giant tortoises, and Darwin's finches. Because of the inherent biological differences among these species that have colonized the Galapagos, different population genetic factors appear to be more or less important in these different species. For example, the Galapagos provided novel environments in which strong selection took place and the Darwin's finches diversified to produce new species and the cormorant adapted to the nutrient-rich western shores of the Galapagos by losing its ability to fly and genomic data have now identified candidate genes. In both the pink iguana, which exists in one small population, and the Galapagos hawk, which has small population sizes, genetic drift has been potentially quite important. There appears to be very limited interisland gene flow in the flightless cormorant and the Galapagos hawk. On the other hand, both the marine iguana and some of the Darwin's finches appear to have significant interisland gene flow. Hybridization between species and subspecies has also introduced new adaptive variation, and in some cases, hybridization might have resulted in despeciation. Overall, new population genetics and genomics research has provided additional insight into the evolution of vertebrate species in the Galapagos.

The energetic cost of parasitism in a wild population

Parasites have profound fitness effects on their hosts, yet these are often sub-lethal, making them difficult to understand and quantify. A principal sub-lethal mechanism that reduces fitness is parasite-induced increase in energetic costs of specific behaviours, potentially resulting in changes to time and energy budgets. However, quantifying the influence of parasites on these costs has not been undertaken in free-living animals. We used accelerometers to estimate energy expenditure on flying, diving and resting, in relation to a natural gradient of endo-parasite loads in a wild population of European shags Phalacrocorax aristotelis. We found that flight costs were 10% higher in adult females with higher parasite loads and these individuals spent 44% less time flying than females with lower parasite loads. There was no evidence for an effect of parasite load on daily energy expenditure, suggesting the existence of an energy ceiling, with the increase in cost of flight compensated for by a reduction in flight duration. These behaviour specific costs of parasitism will have knock-on effects on reproductive success, if constraints on foraging behaviour detrimentally affect provisioning of young. The findings emphasize the importance of natural parasite loads in shaping the ecology and life-history of their hosts, which can have significant population level consequences.

A genetic signature of the evolution of loss of flight in the Galapagos cormorant

We have a limited understanding of the genetic and molecular basis of evolutionary changes in the size and proportion of limbs. We studied wing and pectoral skeleton reduction leading to flightlessness in the Galapagos cormorant (Phalacrocorax harrisi). We sequenced and de novo assembled the genomes of four cormorant species and applied a predictive and comparative genomics approach to find candidate variants that may have contributed to the evolution of flightlessness. These analyses and cross-species experiments in Caenorhabditis elegans and in chondrogenic cell lines implicated variants in genes necessary for transcriptional regulation and function of the primary cilium. Cilia are essential for Hedgehog signaling, and humans affected by skeletal ciliopathies suffer from premature bone growth arrest, mirroring skeletal features associated with loss of flight.

Great cormorants (Phalacrocorax carbo) can detect auditory cues while diving

In-air hearing in birds has been thoroughly investigated. Sound provides birds with auditory information for species and individual recognition from their complex vocalizations, as well as cues while foraging and for avoiding predators. Some 10% of existing species of birds obtain their food under the water surface. Whether some of these birds make use of acoustic cues while underwater is unknown. An interesting species in this respect is the great cormorant (Phalacrocorax carbo), being one of the most effective marine predators and relying on the aquatic environment for food year round. Here, its underwater hearing abilities were investigated using psychophysics, where the bird learned to detect the presence or absence of a tone while submerged. The greatest sensitivity was found at 2 kHz, with an underwater hearing threshold of 71 dB re 1 μPa rms. The great cormorant is better at hearing underwater than expected, and the hearing thresholds are comparable to seals and toothed whales in the frequency band 1-4 kHz. This opens up the possibility of cormorants and other aquatic birds having special adaptations for underwater hearing and making use of underwater acoustic cues from, e.g., conspecifics, their surroundings, as well as prey and predators.

Combined bio-logging and stable isotopes reveal individual specialisations in a benthic coastal seabird, the Kerguelen shag

Individual specialisations, which involve the repetition of specific behaviours or dietary choices over time, have been suggested to benefit animals by avoiding competition with conspecifics and increasing individual foraging efficiency. Among seabirds, resident and benthic species are thought to be good models to study inter-individual variation as they repetitively exploit the same environment. We investigated foraging behaviour, isotopic niche and diet in the Kerguelen shag Phalacrocorax verrucosus during both the incubation and chick-rearing periods for the same individuals to determine the effect of sex, breeding stage, body mass and morphometrics on mean foraging metrics and their consistency. There were large differences between individuals in foraging behaviour and consistency, with strong individual specialisations in dive depths and heading from the colony. Stable isotopes revealed specialisations in feeding strategies, across multiple temporal scales. Specifically, individuals showed medium term specialisations in feeding strategies during the breeding season, as well as long-term consistency. A clustering analysis revealed 4 different foraging strategies displaying significantly different δ¹⁵N values and body masses. There were no sex or stage biases to clusters and individuals in different clusters did not differ in their morphology. Importantly, the results suggest that the different strategies emphasized were related to individual prey preferences rather than intrinsic characteristics.

European shags optimize their flight behavior according to wind conditions

Aerodynamics results in two characteristic speeds of flying birds: the minimum power speed and the maximum range speed. The minimum power speed requires the lowest rate of energy expenditure per unit time to stay airborne and the maximum range speed maximizes air distance traveled per unit of energy consumed. Therefore, if birds aim to minimize the cost of transport under a range of wind conditions, they are predicted to fly at the maximum range speed. Furthermore, take-off is predicted to be strongly affected by wind speed and direction. To investigate the effect of wind conditions on take-off and cruising flight behavior, we equipped 14 European shags Phalacrocorax aristotelis with a back-mounted GPS logger to measure position and hence ground speed, and a neck-mounted accelerometer to record wing beat frequency and strength. Local wind conditions were recorded during the deployment period. Shags always took off into the wind regardless of their intended destination and take-off duration was correlated negatively with wind speed. We combined ground speed and direction during the cruising phase with wind speed and direction to estimate air speed and direction. Whilst ground speed was highly variable, air speed was comparatively stable, although it increased significantly during strong head winds, because of stronger wing beats. The increased air speeds in head winds suggest that birds fly at the maximum range speed, not at the minimum power speed. Our study demonstrates that European shags actively adjust their flight behavior to utilize wind power to minimize the costs of take-off and cruising flight.

Counting calories in cormorants: dynamic body acceleration predicts daily energy expenditure measured in pelagic cormorants

The integral of the dynamic component of acceleration over time has been proposed as a measure of energy expenditure in wild animals. We tested that idea by attaching accelerometers to the tails of free-ranging pelagic cormorants (Phalacrocorax pelagicus) and simultaneously estimating energy expenditure using doubly labelled water. Two different formulations of dynamic body acceleration, [vectorial and overall DBA (VeDBA and ODBA)], correlated with mass-specific energy expenditure (both R(2)=0.91). VeDBA models combining and separately parameterizing flying, diving, activity on land and surface swimming were consistently considered more parsimonious than time budget models and showed less variability in model fit. Additionally, we observed evidence for the presence of hypometabolic processes (i.e. reduced heart rate and body temperature; shunting of blood away from non-essential organs) that suppressed metabolism in cormorants while diving, which was the most metabolically important activity. We concluded that a combination of VeDBA and physiological processes accurately measured energy expenditure for cormorants.

Aquatic burst locomotion by hydroplaning and paddling in common eiders (Somateria mollissima)

Common eiders (Somateria mollissima) are heavy sea-ducks that spend a large portion of their time swimming at the water surface. Surface swimming generates a bow and hull wave that can constructively interfere and produce wave drag. The speed at which the wavelengths of these waves equal the waterline length of the swimming animal is the hull speed. To increase surface swimming speed beyond the hull speed, an animal must overtake the bow wave. This study found two distinct behaviors that eider ducks used to exceed the hull speed: (1) “steaming,” which involved rapid oaring with the wings to propel the duck along the surface of the water, and (2) “paddle-assisted flying,” during which the ducks lifted their bodies out of the water and used their hind feet to paddle against the surface while flapping their wings in the air. An average hull speed (0.732±0.046 ms−1) was calculated for Somateria mollissima by measuring maximum waterline length from museum specimens. On average, steaming ducks swam 5.5 times faster and paddle-assisted flying ducks moved 6.8 times faster than the hull speed. During steaming, ducks exceeded the hull speed by increasing their body angle and generating dynamic lift to overcome wave drag and hydroplane along the water surface. During paddle-assisted flying, ducks kept their bodies out of the water, thereby avoiding the limitations of wave drag altogether. Both behaviors provided alternatives to flight for these ducks by allowing them to exceed the hull speed while staying at or near the water surface.

Launching the AquaMAV: bioinspired design for aerial-aquatic robotic platforms

Current Micro Aerial Vehicles (MAVs) are greatly limited by being able to operate in air only. Designing multimodal MAVs that can fly effectively, dive into the water and retake flight would enable applications of distributed water quality monitoring, search and rescue operations and underwater exploration. While some can land on water, no technologies are available that allow them to both dive and fly, due to dramatic design trade-offs that have to be solved for movement in both air and water and due to the absence of high-power propulsion systems that would allow a transition from underwater to air. In nature, several animals have evolved design solutions that enable them to successfully transition between water and air, and move in both media. Examples include flying fish, flying squid, diving birds and diving insects. In this paper, we review the biological literature on these multimodal animals and abstract their underlying design principles in the perspective of building a robotic equivalent, the Aquatic Micro Air Vehicle (AquaMAV). Building on the inspire-abstract-implement bioinspired design paradigm, we identify key adaptations from nature and designs from robotics. Based on this evaluation we propose key design principles for the design of successful aerial-aquatic robots, i.e. using a plunge diving strategy for water entry, folding wings for diving efficiency, water jet propulsion for water takeoff and hydrophobic surfaces for water shedding and dry flight. Further, we demonstrate the feasibility of the water jet propulsion by building a proof-of-concept water jet propulsion mechanism with a mass of 2.6 g that can propel itself up to 4.8 m high, corresponding to 72 times its size. This propulsion mechanism can be used for AquaMAV but also for other robotic applications where high-power density is of use, such as for jumping and swimming robots.

Factors affecting the foraging behaviour of the European shag: implications for seabird tracking studies

Seabird tracking has become an ever more popular tool to aid environmental procedures such as the designation of marine protected areas and environmental impact assessments. However, samples used are usually small and little consideration is given to experimental design and sampling protocol. European shags Phalacrocorax aristotelis were tracked using GPS technology over three breeding seasons and the following foraging trip characteristics: trip duration, trip distance, maximum distance travelled from the colony, size of area used and direction travelled from colony were determined for each foraging trip. The effect of sex, year of study, breeding site, number and age of chicks and the timing of tracking on foraging behaviour were investigated using a General Estimation Equation model. A range of sampling scenarios reflecting likely field sampling were also tested to compare how foraging behaviour differed depending on composition of the sample of birds tracked. Trip distance, trip duration, maximum distance travelled and size of area used were all significantly affected by the breeding site, and the number of chicks a tracked adult was raising. The effect of sex was also seen when examining trip distance, trip duration and the maximum distance travelled. The direction travelled on a foraging trip was also significantly affected by breeding site. This study highlights the importance of sampling regime and the influence that year, sex, age, number of chicks and breeding site can have on the foraging trip characteristics for this coastal feeding seabird. Given the logistical and financial constraints in tracking large numbers of individuals, this study identifies the need for researchers to consider the composition of their study sample to ensure any identified foraging areas are as representative as possible of the whole colony's foraging area.

Wide range of mercury contamination in chicks of southern ocean seabirds

Using top predators as sentinels of the marine environment, Hg contamination was investigated within the large subantarctic seabird community of Kerguelen Islands, a remote area from the poorly known Southern Indian Ocean. Chicks of 21 sympatric seabirds presented a wide range of Hg concentrations, with the highest contaminated species containing ∼102 times more feather Hg than the less contaminated species. Hence, Kerguelen seabirds encompass the whole range of chick feather Hg values that were previously collected worldwide in poorly industrialized localities. Using stable isotopes, the effects of foraging habitats (reflected by δ¹³C) and trophic positions (reflected by δ¹⁵N) on Hg concentrations were investigated. Species-related Hg variations were highly and positively linked to feather δ¹⁵N values, thus highlighting the occurrence of efficient Hg biomagnification processes within subantarctic marine trophic webs. By contrast, Hg contamination overall correlated poorly with feeding habitats, because of the pooling of species foraging within different isotopic gradients corresponding to distinct seabird habitats (benthic, pelagic, neritic and oceanic). However, when focusing on oceanic seabirds, Hg concentration was related to feather δ¹³C values, with species feeding in colder waters (lower δ¹³C values) south of Kerguelen Islands being less prone to be contaminated than species feeding in northern warmer waters (higher δ¹³C values). Within the context of continuous increase in global Hg emissions, Kerguelen Islands that are located far away from anthropogenic sources can be considered as an ideal study site to monitor the temporal trend of global Hg contamination. The present work helps selecting some seabird species as sentinels of environmental pollution according to their high Hg concentrations and their contrasted foraging ecology.

Swimming away or clamming up: the use of phasic and tonic adductor muscles during escape responses varies with shell morphology in scallops

The simple locomotor system of scallops facilitates the study of muscle use during locomotion. We compared five species of scallops with different shell morphologies to see whether shell morphology and muscle use change in parallel or whether muscle use can compensate for morphological constraints. Force recordings during escape responses revealed that the use of tonic and phasic contractions varied markedly among species. The active species, Amusium balloti, Placopecten magellanicus and Pecten fumatus, made more phasic contractions than the more sedentary species, Mimachlamys asperrima and Crassadoma gigantea. Tonic contractions varied considerably among these species, with the two more sedentary species often starting their response to the predator with a tonic contraction and the more active species using shorter tonic contractions between series of phasic contractions. Placopecten magellanicus made extensive use of short tonic contractions. Pecten fumatus mounted an intense series of phasic contractions at the start of its response, perhaps to overcome the constraints of its unfavourable shell morphology. Valve closure by the more sedentary species suggests that their shell morphology protects them against predation, whereas swimming by the more active species relies upon intense phasic contractions together with favourable shell characteristics.

Using tri-axial acceleration data to identify behavioral modes of free-ranging animals: general concepts and tools illustrated for griffon vultures

Integrating biomechanics, behavior and ecology requires a mechanistic understanding of the processes producing the movement of animals. This calls for contemporaneous biomechanical, behavioral and environmental data along movement pathways. A recently formulated unifying movement ecology paradigm facilitates the integration of existing biomechanics, optimality, cognitive and random paradigms for studying movement. We focus on the use of tri-axial acceleration (ACC) data to identify behavioral modes of GPS-tracked free-ranging wild animals and demonstrate its application to study the movements of griffon vultures (Gyps fulvus, Hablizl 1783). In particular, we explore a selection of nonlinear and decision tree methods that include support vector machines, classification and regression trees, random forest methods and artificial neural networks and compare them with linear discriminant analysis (LDA) as a baseline for classifying behavioral modes. Using a dataset of 1035 ground-truthed ACC segments, we found that all methods can accurately classify behavior (80-90%) and, as expected, all nonlinear methods outperformed LDA. We also illustrate how ACC-identified behavioral modes provide the means to examine how vulture flight is affected by environmental factors, hence facilitating the integration of behavioral, biomechanical and ecological data. Our analysis of just over three-quarters of a million GPS and ACC measurements obtained from 43 free-ranging vultures across 9783 vulture-days suggests that their annual breeding schedule might be selected primarily in response to seasonal conditions favoring rising-air columns (thermals) and that rare long-range forays of up to 1750 km from the home range are performed despite potentially heavy energetic costs and a low rate of food intake, presumably to explore new breeding, social and long-term resource location opportunities.