Individuals of a group-living shorebird show smaller home range overlap when food availability is low

Background: Group living animals, such as shorebirds foraging on intertidal mudflats, may use social information about where to find hidden food items. However, flocking also increases intraspecific competition for resources, which may be exacerbated by food scarcity. Therefore, although aggregation may bring benefits, it may also increase the intensity of intraspecific competition. Methods: We examined this trade-off in adult great knots Calidris tenuirostris, a molluscivorous long-distance migrating shorebird species, using interannual variation based on 2 years with different levels of food availability during their northward migratory staging in the northern Yellow Sea, China. We estimated individual home ranges and the extent of spatial overlap of home ranges of individually tagged birds in 2012 and 2015, whilst discounting for possible differences in body size, body mass, sex and migration schedule between years. Results: We found that home range size was not associated with body mass, arrival date, body size, or sex of the individual. Despite a significant difference in food availability between the two study years, there was no significant change in the 50% and 95% home range size of great knots in the contrasting situations. However, there was a significantly smaller spatial overlap between individuals in the year when food was less available, suggesting that great knots operated more independently when food was scarce than when it was abundant. Conclusions: These results suggest that minimizing intraspecific competition became more important when food was scarce. Where it is impossible to monitor all habitats en route, monitoring the local movements of shorebirds may offer a way to detect changes in habitat quality in real time.</p

Individuals of a group-living shorebird show smaller home range overlap when food availability is low

Background: Group living animals, such as shorebirds foraging on intertidal mudflats, may use social information about where to find hidden food items. However, flocking also increases intraspecific competition for resources, which may be exacerbated by food scarcity. Therefore, although aggregation may bring benefits, it may also increase the intensity of intraspecific competition. Methods: We examined this trade-off in adult great knots Calidris tenuirostris, a molluscivorous long-distance migrating shorebird species, using interannual variation based on 2 years with different levels of food availability during their northward migratory staging in the northern Yellow Sea, China. We estimated individual home ranges and the extent of spatial overlap of home ranges of individually tagged birds in 2012 and 2015, whilst discounting for possible differences in body size, body mass, sex and migration schedule between years. Results: We found that home range size was not associated with body mass, arrival date, body size, or sex of the individual. Despite a significant difference in food availability between the two study years, there was no significant change in the 50% and 95% home range size of great knots in the contrasting situations. However, there was a significantly smaller spatial overlap between individuals in the year when food was less available, suggesting that great knots operated more independently when food was scarce than when it was abundant. Conclusions: These results suggest that minimizing intraspecific competition became more important when food was scarce. Where it is impossible to monitor all habitats en route, monitoring the local movements of shorebirds may offer a way to detect changes in habitat quality in real time.</p

Individuals of a group-living shorebird show smaller home range overlap when food availability is low

Background: Group living animals, such as shorebirds foraging on intertidal mudflats, may use social information about where to find hidden food items. However, flocking also increases intraspecific competition for resources, which may be exacerbated by food scarcity. Therefore, although aggregation may bring benefits, it may also increase the intensity of intraspecific competition. Methods: We examined this trade-off in adult great knots Calidris tenuirostris, a molluscivorous long-distance migrating shorebird species, using interannual variation based on 2 years with different levels of food availability during their northward migratory staging in the northern Yellow Sea, China. We estimated individual home ranges and the extent of spatial overlap of home ranges of individually tagged birds in 2012 and 2015, whilst discounting for possible differences in body size, body mass, sex and migration schedule between years. Results: We found that home range size was not associated with body mass, arrival date, body size, or sex of the individual. Despite a significant difference in food availability between the two study years, there was no significant change in the 50% and 95% home range size of great knots in the contrasting situations. However, there was a significantly smaller spatial overlap between individuals in the year when food was less available, suggesting that great knots operated more independently when food was scarce than when it was abundant. Conclusions: These results suggest that minimizing intraspecific competition became more important when food was scarce. Where it is impossible to monitor all habitats en route, monitoring the local movements of shorebirds may offer a way to detect changes in habitat quality in real time.</p

Individuals of a group-living shorebird show smaller home range overlap when food availability is low

Background: Group living animals, such as shorebirds foraging on intertidal mudflats, may use social information about where to find hidden food items. However, flocking also increases intraspecific competition for resources, which may be exacerbated by food scarcity. Therefore, although aggregation may bring benefits, it may also increase the intensity of intraspecific competition. Methods: We examined this trade-off in adult great knots Calidris tenuirostris, a molluscivorous long-distance migrating shorebird species, using interannual variation based on 2 years with different levels of food availability during their northward migratory staging in the northern Yellow Sea, China. We estimated individual home ranges and the extent of spatial overlap of home ranges of individually tagged birds in 2012 and 2015, whilst discounting for possible differences in body size, body mass, sex and migration schedule between years. Results: We found that home range size was not associated with body mass, arrival date, body size, or sex of the individual. Despite a significant difference in food availability between the two study years, there was no significant change in the 50% and 95% home range size of great knots in the contrasting situations. However, there was a significantly smaller spatial overlap between individuals in the year when food was less available, suggesting that great knots operated more independently when food was scarce than when it was abundant. Conclusions: These results suggest that minimizing intraspecific competition became more important when food was scarce. Where it is impossible to monitor all habitats en route, monitoring the local movements of shorebirds may offer a way to detect changes in habitat quality in real time.</p

A guide to pre-processing high-throughput animal tracking data

1. Modern, high-throughput animal tracking studies collect increasingly large volumes of data at very fine temporal scales. At these scales, location error can exceed the animal’s step size, leading to mis-estimation of key movement metrics such as speed. ‘Cleaning’ the data to reduce location errors prior to analyses is one of the main ways movement ecologists deal with noisy data, and has the advantage of being more scalable to massive datasets than more complex methods. Though data cleaning is widely recommended, and ecologists routinely consider cleaned data to be the ground-truth, inclusive uniform guidance on this crucial step, and on how to organise the cleaning of massive datasets, is still rather scarce. 2. A pipeline for cleaning massive high-throughput datasets must balance ease of use and computationally efficient signal vs. noise screening, in which location errors are rejected without discarding valid animal movements. Another useful feature of a pre-processing pipeline is efficiently segmenting and clustering location data for statistical methods, while also being scalable to large datasets and robust to imperfect sampling. Manual methods being prohibitively time consuming, and to boost reproducibility, a robust pre-processing pipeline must be automated. 3. In this article we provide guidance on building pipelines for pre-processing high-throughput animal tracking data in order to prepare it for subsequent analysis. Our recommended pipeline, consisting of removing outliers, smoothing the filtered result, and thinning it to a uniform sampling interval, is applicable to many massive tracking datasets. We apply this pipeline to simulated movement data with location errors, and also show a case study of how large volumes of cleaned data can be transformed into biologically meaningful ‘residence patches’, for quick biological inference on animal space use. We use calibration data to illustrate how pre-processing improves its quality, and to verify that the residence patch synthesis accurately captures animal space use. Finally, turning to tracking data from Egyptian fruit bats (Rousettus aegyptiacus), we demonstrate the pre-processing pipeline and residence patch method in a fully worked out example. 4. To help with fast implementation of standardised methods, we developed the R package atlastools, which we also introduce here. Our pre-processing pipeline and atlastools can be used with any high-throughput animal movement data in which the high data-volume combined with knowledge of the tracked individuals’ movement capacity can be used to reduce location errors. The atlastools function is easy to use for beginners, while providing a template for further development. The use of common pre-processing steps that are simple yet robust promotes standardised methods in the field of movement ecology and leads to better inferences from data

Exploration speed in captivity predicts foraging tactics and diet in free-living red knots

1. Variation in foraging tactics and diet is usually attributed to differences in morphology, experience and prey availability. Recently, consistent individual differences in behaviour (personality) have been shown to be associated with foraging strategies. Bolder or more exploratory individuals are predicted to have a faster pace‐of‐life and offset the costs of moving more or in risky areas, with higher energetic gains by encountering profitable foraging opportunities and prey. However, the relationship between personality, foraging and diet is poorly understood. 2. We investigated how exploratory behaviour in red knots Calidris canutus is associated with foraging tactics and diet by combining laboratory experiments, field observations and stable isotope analysis. First, we developed a mobile experimental arena to measure exploration speed in controlled settings. We validated the method by repeated testing of individuals over time and contexts. This setup allowed us to measure exploratory personality at the field site, eliminating the need to bring birds into captivity for long periods of time. After releasing birds within days of their capture, we asked whether exploration speed was associated with differences in foraging tactics and diet in the wild. 3. We found that tactile foraging red knots mainly caught hard‐shelled prey that are buried in the sediment, whereas visual foraging knots only captured soft preys located close to or on the surface. We also found that faster explorers showed a higher percentage of visual foraging than slower explorers. By contrast, morphology (bill length and gizzard size) had no significant effect on foraging tactics. Diet analysis based on δ(15)N and δ(13)C stable isotope values of plasma and red blood cells confirmed our field observations with slower explorers mainly consumed hard‐shelled prey while faster explorers consumed more soft than hard‐shelled prey. 4. Our results show that foraging tactics and diet are associated with a personality trait, independent of morphological differences. We discuss how consistent behaviour might develop early in life through positive feedbacks between foraging tactics, prey type and foraging efficiency

Quantification of marine benthic communities with metabarcoding

DNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the abundance is required. However, this relationship is complicated by many factors, and it is often unknown. In this study, we validate estimates of biomass and abundance from molecular approaches with those from the traditional morphological approach. Abundance and biomass were quantified from 126 samples of benthic intertidal mudflat using traditional morphological approaches and compared with frequency of occurrence and relative read abundance estimates from a molecular approach. A relationship between biomass and relative read abundance was found for two widely dispersed annelid taxa (Pygospio and Scoloplos). None of the other taxons, however, showed such a relationship. We discuss how quantification of abundance and biomass using molecular approaches are hampered by the ecology of DNA i.e. all the processes that determine the amount of DNA in the environment, including the ecology of the benthic species as well as the compositional nature of sequencing data

Landscape-scale experiment demonstrates that Wadden Sea intertidal flats are used to capacity by molluscivore migrant shorebirds

P>1. Whether intertidal areas are used to capacity by shorebirds can best be answered by large-scale manipulation of foraging areas. The recent overexploitation of benthic resources in the western Dutch Wadden Sea offers such an 'experimental' setting. 2. We review the effects of declining food abundances on red knot Calidris canutus islandica numbers, based on a yearly large-scale benthic mapping effort, long-term colour-ringing and regular bird-counts from 1996 to 2005. We focus on the three-way relationships between suitable foraging area, the spatial predictability of food and red knot survival. 3. For each benthic sampling position, red knot intake rate (mg AFDM s-1) was predicted by a multiple prey species functional response model, based on digestive rate maximization (this model explained diet and intake rate in earlier studies on red knots). This enabled us to derive the spatial distribution of the suitable foraging area, which in each of the 10 years was analysed with a measure of autocorrelation, i.e. Moran's I. 4. Over the 10 years, when accounting for a threshold value to meet energetic demands, red knots lost 55% of their suitable foraging area. This ran parallel to a decrease in red knot numbers by 42%. Although there was also a decrease in patchiness (i.e. less information about the location of the suitable feeding sites), this did not yet lead to additional loss of birds. 5. To cope with these landscape-scale declines in food stocks, an increase in the capacity for instantaneous food processing would be required. Although we show that red knots indeed enlarged their muscular gizzards, the increase in gizzard size was not enough to compensate for the decreased feeding area. 6. Survival of islandica knots in the western Dutch Wadden Sea, based on colour-ring resightings, declined from 89% in the first half of our study period to 82% in the second half of our study period and could account for almost half of the decline in red knot numbers; the rest must have moved elsewhere in winter. 7. Densities of red knots per unit suitable foraging area remained constant at 10 knots ha-1 between 1996 and 2005, which suggests that red knots have been using the Dutch Wadden Sea to full capacity

Predictive performance of deep-learning-enhanced remote-sensing data for ecological variables of tidal flats over time

Tidal flat systems with a diverse benthic community (e.g., bivalves, polychaetes and crustaceans) is important in the food chain for migratory birds and fish. The geographical distribution of macrozoobenthos depends on physical factors, among which sediment characteristics are key aspects. Although high-resolution and high-frequency mapping of benthic indices (i.e., sediment composition and benthic fauna) of these coastal systems are essential to coastal management plans, it is challenging to gather such information on tidal flats through in-situ measurements. The Synoptic Intertidal Benthic Survey (SIBES) database provides this field information for a 500m grid annual for the Dutch Wadden Sea, but continuous coverage and seasonal dynamics are still lacking. Remote sensing may be the only feasible monitoring method to fill in this gap, but it is hampered by the lack of spectral contrast and variation in this environment. In this study, we used a deep-learning model to enhance the information extraction from remote-sensing images for the prediction of environmental and ecological variables of the tidal flats of the Dutch Wadden Sea. A Variational Auto Encoder (VAE) deep-learning model was trained with Sentinel-2 satellite images with four bands (blue, green, red and near-infrared) over three years (2018, 2019 and 2020) of the tidal flats of the Dutch Wadden Sea. The model was trained to derive important characteristics of the tidal flats as image features by reproducing the input image. These features contain representative information from the four input bands, like spatial texture and band ratios, to complement the low-contrast spectral signatures. The VAE features, the spectral bands and the field-collected samples together were used to train a random forest model to predict the sediment characteristics: median grain size and silt content, and macrozoobenthic biomass and species richness. The prediction was done on the tidal flats of Pinkegat and Zoutkamperlaag of the Dutch Wadden sea. The encoded features consistently increased the accuracy of the predictive model. Compared to a model trained with just the spectral bands, the use of encoded features improved the prediction (coefficient of determination, R2) by 10-15% points for 2018, 2019 and 2020. Our approach improves the available techniques for mapping and monitoring of sediment and macrozoobenthic properties of tidal flat systems and thereby contribute towards their sustainable management