Body shrinkage due to Arctic warming reduces red knot fitness in tropical wintering range

Reductions in body size are increasingly being identified as a response to climatewarming. Here we present evidence for a case of such body shrinkage, potentially dueto malnutrition in early life. We show that an avian long-distance migrant (red knot,Calidris canutus canutus), which is experiencing globally unrivaled warming rates at itshigh-Arctic breeding grounds, produces smaller offspring with shorter bills duringsummers with early snowmelt. This has consequences half a world away at their tropicalwintering grounds, where shorter-billed individuals have reduced survival rates. This isassociated with these molluscivores eating fewer deeply buried bivalve prey and moreshallowly buried seagrass rhizomes. We suggest that seasonal migrants can experiencereduced fitness at one end of their range as a result of a changing climate at theother end

Data from: Life history trade-offs: are they linked to personality in a precocial mammal (Cavia aperea)?

Life-history trade-offs are predicted to contribute to the maintenance of personality variation. Individuals with ‘fast’ lifestyles should develop faster, reproduce earlier and exhibit more risky behaviours. Evidence for such predicted links, however, remains equivocal. Here, I test how growth rate, timing of maturation, litter size and maternal effort correlate with exploration, boldness, fearlessness, docility and escape latency. I found several links that were predicted by recent theory while others were against theoretical predictions, e.g. fast growing individuals were more fearful. Thus, while I found personality to be integrated with life-history, I cannot fully support recent hypotheses aiming to explain such behaviour-life-history associations.,raw data supporting manuscript "Life history trade-offs: are they linked to personality in a precocial mammal"These are raw data for life history traits (growth, maturation, litter size, reproductive effort) and behaviours (exploration, boldness, escape latency and docility) repeatedly measured in 100 female Cavia aperea. The animals were held in captivity, either under indoor or combined indoor-outdoor housing. All animals experienced natural photoperiods, animals in combined indoor-outdoor housing experienced natural temperatures in addition. For description of variables, see "read.me".data_LH trade-off personality.xlsx

Density-dependent individual variation in male attractiveness in a wild field cricket

Social environments modify a male’s ability to attract females and thus affect its fitness. Theory implies that an individual’s fitness should trade-off with its ability to cope with competition. Individuals are expected to solve this trade-off differently: some males should be more attractive at low but others instead at high density. This prediction has rarely been tested in the wild. We used an automated RFID-surveillance system to quantify for each hour of the day, over 30 days (i.e. almost the entire adult lifespan of our model organism), whether a male had attracted a female in its burrow. The data were collected across a range of naturally varying local densities in wild field crickets, G.campestris. We also estimated whether the shape of the relationship between attractiveness and density was under selection. At the population level, attractiveness increased from low to intermediate density, suggesting an Allee effect. Attractiveness subsequently declined at higher densities, for example, because of detrimental effects of increased competition. Opposite to expectations, males that were more attractive under low densities were also more attractive under higher densities. However, the increase in attractiveness with density varied among males, suggesting that Allee effects were individual-specific. Finally, selection was not acting on density-dependent attractiveness but males that lived longer acquired more mating partners. Our study reveals that social environments shape attractiveness in wild male insects, and imply the occurrence of individual-specific Allee effect that may be evolvable.,The data is collected by using automated RIFD-surveillance system. Data is processed so that for all individuals, one location data point was extracted for each hour.,Explanation for the variables in the provided data sets: Main data Fitness = binary trait for whether a male was with a female in its focal burrow during the focal hour (1 = yes, 0 = no). Thus, this variable represents attractiveness. Age = age for each focal male as days after molting to maturation. Age_2 = squared age. Max_ages = number of days each focal male was alive as adult. Max_ages_2 = squared Max_age. Distance_wall = distance of each burrow (in centimeters) from the edge of the study area. Tag = identity of each male. Datez = date since 201505-08, i.e. since the first maturation in a population was confirmed. Burrow = identity of each burrow. Hours = identity of each hour (i.e. 24 hours). Max_100NEW max_700NEW = maximum experienced density of other males for each focal male within 100 – 700 centimeter distance from the focal burrow. max_100NEW_2 max_700NEW_2 = squared Max_100NEW - max_700NEW. d100NEW d700NEW = hourly density of other males for each male for each focal hour within 100 – 700 centimeter distance from the focal burrow the focal male was occupying. d100NEW_2 – d700NEW_2 = squared d100NEW_2 – d700NEW_2. Selection gradient data: relative_unique_females = relative amount of unique females confronted in the same focal burrow throughout the data collection period for each focal male. Intercept_stand = standardized BLUP for the intercept of the reaction norm. Linear_stand = standardized BLUP for the linear slope of the reaction norm. Quadratic_stand = standardized BLUP for the nonlinear slope of the reaction norm. Survival_stand = standardized number of days alive after molting to maturation. Tag = identity of each focal male.

Data from: Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability. In this paper we evaluate the performance of the recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as to unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (800–130 000 species) and variation in the completeness of the reference data bases (representing 15–100% of known species). Our results demonstrate that PROTAX yields essentially unbiased probabilities of taxonomic placement, which means its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence data bases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels. We conclude that reliable species-level identification from environmental samples is still challenging and that neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion of taxonomic and reference sequence data bases and making these two types of data compatible

Data from: Micro- and macroparasite species richness in birds: the role of host life history and ecology

1.Identifying the factors shaping variation in parasite diversity among host species is crucial to understand wildlife diseases. Although micro‐ and macroparasites may exert different selective pressures on their hosts, studies investigating the determinants of parasite species richness in animals have rarely considered this divide. 2.Here, we investigated the role of host life history and ecology in explaining the species richness of helminths (macroparasites) and haemosporidians (microparasites) in birds worldwide. We collated data from multiple global datasets on diverse bird traits (longevity, body mass, coloniality, migration distance/tendency, geographic range size and dietary and habitat breadths) and the species richness of their helminth and haemosporidian parasites. We tested predictors of helminth and haemosporidian parasite richness using phylogenetic generalised linear mixed models in a Bayesian framework. 3.We found that, after controlling for research effort and host phylogeny, the richness of helminths, but not of haemosporidians, increased with host longevity, range size, migration distance and dietary breadth. Overall, these correlates were also important across different helminth groups (acanthocephalans, cestodes, nematodes and trematodes), and two additional ones (body mass, coloniality) emerged as important for cestodes and acanthocephalans. 4.We propose that long lifespans may promote the diversity of helminth parasite assemblages over evolutionary time, thus resulting in richer helminth faunas. Similarly, longer‐distance migrations, larger ranges and broader dietary breadths are likely to lead to greater encounter rates and the accumulation of trophically‐transmitted helminths. In contrast, vector‐borne haemosporidians may be influenced more by factors related to vector ecology than by the host traits included in the analyses. The lack of strong associations between haemosporidian species richness and host characteristics emphasizes the need to find appropriate traits to model the distribution and diversity of parasites with different environmental preferences in order to anticipate disease emergence risks associated with global change.,Dataset on bird host species and parasite richnessThis dataset contains all bird species with either helminth or haemosporidian data used in this study. This data file also matches the dataset used in the corresponding Supporting Information (markdown file) to this paper.parasites_birdsv3.txt

Data underlying the publication: Sex differentiation in seasonal distribution of the starry smooth hound Mustelus asterias

The data underlies the publication (Brevé et al. 2020). This data set has data on reported recaptures. Between 2011 and 2019, almost 4000 starry smooth-hound sharks (Mustelus asterias) were tagged in the Netherlands. The total number of reported recaptures was 220 (4.9%: Table 1): 114 females (50-124 cm LT), 102 males (47-105 cm LT), and 4 non-sexed (56-100 cm LT)

Data from: Diet preferences as the cause of individual differences rather than the consequence

Behavioural variation within a species is usually explained as the consequence of individual variation in physiology. However, new evidence suggests that the arrow of causality may well be in the reverse direction: behaviours such as diet preferences cause the differences in physiological and morphological traits. Recently, diet preferences were proposed to underlie consistent differences in digestive organ mass and movement patterns (patch residence times) in red knots (Calidris canutus islandica). Red knots are molluscivorous and migrant shorebirds for which the size of the muscular stomach (gizzard) is critical for the food processing rate. In this study, red knots (C. c. canutus, n = 46) were caught at Banc d'Arguin, an intertidal flat ecosystem in Mauritania, and released with radio-tags after the measurement of gizzard mass. Using a novel tracking system (time-of-arrival), patch residence times were measured over a period of three weeks. Whether or not gizzard mass determined patch residence times was tested experimentally by offering 12 of the 46 tagged red knots soft diets prior to release; this reduced an individual's gizzard mass by 20-60%. To validate whether the observed range of patch residence times would be expected from individual diet preferences, we simulated patch residence times as a function of diet preferences via a simple departure rule. Consistent with previous empirical studies, patch residence times in the field were positively correlated with gizzard mass. The slope of this correlation, as well as the observed range of patch residence times, was in accordance with the simulated values. The 12 birds with reduced gizzard masses did not decrease patch residence times in response to the reduction in gizzard mass. These findings suggest that diet preferences can indeed cause the observed among-individual variation in gizzard mass and patch residence times. We discuss how early diet experiences can have cascading effects on the individual expression of both behavioural and physiomorphic traits. This emphasizes that to understand the ecological consequences of individual differences, knowledge of the environment during development is required. The datapackage contains two sets: - patches Table of residence time patches: foraging locations visited by red knots, deployed with radiotransmitters, during the low tide. A description of each column can be found in a separate sheet. Further information is found in the methods section of the publication. - benthos Table containing sampled prey items for the red knot, consisting of molluscs of ingestable sizes in the top 4 cm of the sediment. The file contains a separate sheet with column discriptions. More information can be found in the methods section of the publication

Figures resulting from the research into Preventing bird strikes: testing an artificial predator, the RobotFalcon, to deter flocks of birds

This dataset contains the data for the article: "Improved deterrence of birds using an artificial predator, the RobotFalcon". Figures 3 and s2: The responses of bird flocks to deterrence by a RobotFalcon, a DJI Mavic Pro drone and control (no action). The data concerns the amount of brief  landings the birds performed when flown at with the RobotFalcon and drone and the time it took for the flocks  to fly away.  Figures 4 and 5: Data on the distance at which flocks initiated flight to a RobotFalcon and the frequency of collective escape exhibited by flocks hunted by a RobotFalcon and a drone.   Figure 6: The time it takes for birds to return after deterrence by a RobotFalcon at Workum and by regular deterrence methods (pyrotechnics and distress calls) used at airbase Leeuwarden.</p

Figures resulting from the research into Preventing bird strikes: testing an artificial predator, the RobotFalcon, to deter flocks of birds

This dataset contains the data for the article: "Improved deterrence of birds using an artificial predator, the RobotFalcon". Figures 3 and s2: The responses of bird flocks to deterrence by a RobotFalcon, a DJI Mavic Pro drone and control (no action). The data concerns the amount of brief  landings the birds performed when flown at with the RobotFalcon and drone and the time it took for the flocks  to fly away.  Figures 4 and 5: Data on the distance at which flocks initiated flight to a RobotFalcon and the frequency of collective escape exhibited by flocks hunted by a RobotFalcon and a drone.   Figure 6: The time it takes for birds to return after deterrence by a RobotFalcon at Workum and by regular deterrence methods (pyrotechnics and distress calls) used at airbase Leeuwarden.</p