cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g4f4qrfsw
title: Estimation of skeletal kinematics in freely-moving rodents

description: Forming a complete picture of the relationship between neural activity and
 skeletal kinematics requires quantification of skeletal joint biomechanics
 during free behavior. However, without detailed knowledge of the
 underlying skeletal motion, inferring limb kinematics during free motion
 using surface tracking approaches is difficult, especially for animals
 where the relationship between the surface and underlying skeleton changes
 during motion. Here we developed a videography-based method enabling
 detailed three-dimensional kinematic quantification of an anatomically
 defined skeleton in untethered freely-behaving rats and mice. This
 skeleton-based model was constrained using anatomical principles and joint
 motion limits and provided skeletal pose estimates for two rodent species
 and a range of body sizes, even when limbs were occluded. Model-inferred
 limb positions and joint kinematics during gait and gap-crossing behaviors
 were verified by direct measurement of either limb placement or limb
 kinematics using inertial measurement units (IMU). Together we show that
 complex decision-making behaviors can be accurately reconstructed at the
 level of skeletal kinematics using our anatomically constrained model.
description: Data is processed by the Python 3 scripts published on Github and also included here. Data is provided in the structure required by the scripts. A base path may have to be adjusted in ACM/data.py or the head of the respective script. Linked scripts generate the figures published in related manuscript. A description of the data is included in the respective folders.
DOI: 10.5061/dryad.r2280gbg5
title: Metabarcoding to decipher the fish diet of Eurasian otters and seals

description: Long-lived top predators shape biodiversity structure in their ecosystems
 and predator-prey interactions are critical in decoding how communities
 function. Studies on the foraging ecology of seals and Eurasian
 otters in Western Europe are outdated and most studies solely performed
 traditional hard part analysis. Molecular metabarcoding can be
 used as an innovative non-invasive diet analysis tool, which has proven
 efficient and complementary to hard part analysis, however lacking
 application in the wider North Sea area. In this study, DNA from
 digesta, collected between 2014-2020, were used to identify fish species
 in the diet of 47 Eurasian otters, 54 harbour seals and 21 grey seals by
 applying a next-generation metabarcoding approach. A newly designed 16S
 rRNA primer, providing the best coverage of &gt;130 local marine and
 freshwater fish species, was used to amplify prey DNA from seal scats and
 otter gut content sampled from the North Sea and regional freshwater
 bodies. Frequent fish species included tench, ninespine
 stickleback and white bream in otters; hooknose
 and common roach in grey seals and Pleuronectidae and sand
 gobies in harbour seals. Bipartite network analysis showed a
 strong overlap of harbour and grey seal diets. Otter diet intersected with
 both seal species in terms of freshwater species. This study
 provides new knowledge about dietary composition and community assemblage
 of fish prey in otters and seals in the North Sea and regional
 freshwaters, and a new molecular tool to elucidate predator-prey
 interactions and interspecies competition in complex and changing
 ecosystems under pressure from anthropogenic activities.
DOI: 10.5061/dryad.4tmpg4fcx
title: Artificial selection in human-wildlife feeding interactions

description: The artificial selection of traits in wildlife populations through hunting
 and fishing has been well documented. However, despite their rising
 popularity, the role that artificial selection may play in non-extractive
 wildlife activities, e.g., recreational feeding activities, remains
 unknown. If only a subset of a population takes advantage of
 human-wildlife feeding interactions, and if this results in different
 fitness advantages for these individuals, then artificial selection may be
 at work. We have tested this hypothesis using a wild fallow deer
 population living at the edge of a capital city as our model population.
 In contrast to previous assumptions on the randomness of human-wildlife
 feeding interactions, we found that a limited non-random portion of an
 entire population is continuously engaging with people. We found that the
 willingness to beg for food from humans exists on a continuum of
 inter-individual repeatable behaviour; which ranges from risk-taking
 individuals repeatedly seeking and obtaining food, to shyer individuals
 avoiding human contact and not receiving food at all, despite all
 individuals having received equal exposure to human presence from birth
 and coexisting in the same herds together. Bolder individuals obtain
 significantly more food directly from humans, resulting in early
 interception of food offerings and preventing other individuals from
 obtaining supplemental feeding. Those females that beg consistently also
 produce significantly heavier fawns (300-500g heavier), which may provide
 their offspring with a survival advantage. This indicates that these
 interactions result in disparity in diet and nutrition across the
 population, impacting associated physiology and reproduction, and may
 result in artificial selection of the begging behavioural trait. This is
 the first time that this consistent variation in behaviour and its
 potential link to artificial selection has been identified in a wildlife
 population and reveals new potential effects of human-wildlife feeding
 interactions in other species across both terrestrial and aquatic
 habitats. 22-Jun-2022 --
DOI: 10.5061/dryad.w0vt4b8v7
title: Dataset for contaminant risk assesment in groundwater

description: This data that helps in mapping groundwater contaminant risk (nitrate and
 phosphate) using the DRASTIC model for a case study in Ethiopia. The data
 contains a total of 9 parameters, each having data points ranging from 10
 to 33 (196 records in total).
DOI: 10.5061/dryad.xksn02vjk
title: Timing and synchrony of birth in Eurasian lynx across Europe

description: The ecology and evolution of reproductive timing and synchrony has been a
 topic of great interest in evolutionary ecology for decades. Originally
 motivated by questions related to behavioural and reproductive adaptation
 to environmental conditions, the topic has acquired new relevance in the
 face of climate change. However, there has been relatively little research
 on reproductive phenology in mammalian carnivores. The Eurasian lynx (Lynx
 lynx) occurs across the Eurasian continent, covering three of the four
 main climate regions of the world. Thus their distribution includes a
 large variation in climatic conditions, making it an ideal species to
 explore reproductive phenology. Here, we used data on multiple
 reproductive events from 169 lynx females across Europe. Mean birth date
 was May 28 (April 23 to July 1), but was ~10 days later in northern Europe
 than in central and southern Europe. Birth dates were relatively
 synchronised across Europe, but more so in the north than in the south.
 Timing of birth were delayed by colder May temperatures. Severe and cold
 weather may affect neonatal survival via hypothermia and avoiding
 inclement weather early in the season may select against early births,
 especially at northern latitudes. Overall, only about half of the kittens
 born survived until onset of winter but whether kittens were born
 relatively late or early did not affect kitten survival. Lynx are strict
 seasonal breeders but still show a degree of flexibility to adapt the
 timing of birth to surrounding environmental conditions. We argue that
 lynx give birth later when exposed to colder spring temperatures and have
 more synchronized births when the window of favourable conditions for
 raising kittens is shorter. This suggest that lynx are well adapted to
 different environmental conditions, from dry and warm climates to alpine,
 boreal and arctic climates. This variation in reproductive timing is
 favourable in times of climate change, as organisms with high plasticity
 are more likely to adjust to new environmental conditions.
description: Includes date of birth for Eurasian lynx,  litter sizes and
 environmental covariables. For details see README and the main
 paper.
description: Excel or R
DOI: 10.5061/dryad.n8pk0p2zb
title: Collective ferromagnetism of artificial square spin ice

description: We have studied the temperature and magnetic field dependence of the total
 magnetic moment of large-area permalloy artificial square spin ice arrays.
 The temperature dependence and hysteresis behavior are consistent with the
 coherent magnetization reversal expected in the Stoner-Wohlfarth model,
 with clear deviations due to inter-island interactions at small lattice
 spacing. Through micromagnetic simulations, we explore this behavior and
 demonstrate that the deviations result from increasingly complex
 magnetization reversal at small lattice spacing, induced by inter-island
 interactions, and depending critically on details of the island shapes.
 These results establish new means to tune the physical properties of
 artificial spin ice structures and other interacting nanomagnet systems,
 such as patterned magnetic media.
DOI: 10.5061/dryad.02v6wwq61
title: Eastern monarch larval performance may not be affected by shifts in phenological synchrony with milkweed

description: 1. Interacting species are experiencing disruptions in the relative timing
 of their key life history events due to climate change. These shifts can
 sometimes be detrimental to the fitness of the consumer in trophic
 interactions but not always. 2. The potential consequences of phenological
 asynchrony for the monarch butterfly (Danaus plexippus) and its host plant
 (Asclepias spp.) have not been well studied. Given that plants generally
 undergo seasonal declines in quality, if climate change delays the timing
 of the larval stage relative to the availability of younger milkweed
 plants, monarch performance could be negatively affected. 3. Here we
 explore the potential consequences for the eastern monarch population due
 to probable asynchrony with milkweed. We used field surveys around Ottawa,
 Canada to determine monarch oviposition preference on common milkweed
 (Asclepias syriaca) plants and the seasonal availability of these plants.
 To determine the potential fitness consequences when females oviposit on
 non-preferred plants, we conducted a field experiment to assess the effect
 of milkweed size on monarch larval performance (e.g., development time,
 final size). 4. Preferred oviposition plants (earlier stages of
 development, better condition) were consistently available in large
 proportion over the summer season. We also found that declines in leaf
 quality (more latex, thicker leaves) with plant size did not translate
 into decreases in larval performance. 5. Our results suggest that even if
 asynchrony of the monarch-milkweed interaction occurs due to climate
 change, the larval stage of the eastern monarch may not face negative
 consequences. Future studies should determine how the relative timing of
 the interaction will change in the region.
description: Field surveys and field experiments (mowing)
DOI: 10.5061/dryad.w3r2280tm
title: Data and code for: A healthy but depleted herd: predators decrease prey disease and density

description: The healthy herds hypothesis proposes that predators can reduce parasite
 prevalence and thereby increase density of their prey. However, evidence
 for such predator-driven reductions in prevalence in prey remains mixed.
 Furthermore, even less evidence supports increases in prey density during
 epidemics. Here, we used a planktonic predator-prey-parasite system to
 experimentally test the healthy herds hypothesis. We manipulated density
 of a predator (the phantom midge, Chaoborus punctipennis) and parasitism
 (the virulent fungus Metschnikowia bicuspidata) in experimental
 assemblages. Because we know natural populations of the prey (Daphnia
 dentifera) vary in susceptibility to both predator and parasite, we
 stocked experimental populations with nine genotypes spanning a broad
 range of susceptibility to both enemies. Predation significantly reduced
 infection prevalence, eliminating infection at the highest predation
 level. However, lower parasitism did not increase densities of prey;
 instead, prey density decreased substantially at the highest predation
 levels (a major density cost of healthy herds predation). This density
 result was predicted by a model parameterized for this system. The model
 specifies three conditions for predation to increase prey density during
 epidemics: (i) predators selectively feed on infected prey, (ii) consumed
 infected prey release fewer infectious propagules than unconsumed prey,
 and (iii) sufficiently low infection prevalence. While the system
 satisfied the first two conditions, prevalence remained too high to see an
 increase in prey density with predation. Low prey densities caused by high
 predation drove increases in algal resources of the prey, fueling greater
 reproduction, indicating that consumer-resource interactions can
 complicate predator-prey-parasite dynamics. Overall, in our experiment,
 predation reduced prevalence of a virulent parasite but, at the highest
 levels, also reduced prey density. Hence, while healthy herds predation is
 possible under some conditions, our empirical results make it clear that
 manipulation of predators to reduce parasite prevalence may harm prey
 density.
description: There are two components to this study:
 Empirical work: The data was collected during an experiment run
 in Summer 2019. It has been processed as noted in the Rmd and README
 files.  Theoretical work: These analyses were done in
 2021 and 2022. More information is in the associated README
 file.
description: The empirical work has all datasets in csv files and is analyzed
 in R/RStudio. The theoretical work is in
 Matlab.
DOI: 10.5061/dryad.9w0vt4bjd
title: Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding

description: The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an
 endangered species endemic to the coastal wetlands of the San Francisco
 Estuary, California. RERA are specialized to saline coastal wetlands, and
 their historical range has been severely impacted by landscape conversion
 and the introduction of non-native plant and rodent species. A better
 understanding of their diet is needed to assess habitat quality,
 particularly in relation to potential competitors. We investigated three
 questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA
 specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do
 RERA consume non-native plants, and (3) What is the dietary niche breadth
 and overlap with three sympatric native and non-native rodents? RERA diet
 was dominated by two plants, native Salicornia and non-native salt bush
 (Atriplex spp.), but included 48 plant genera. RERA diet breadth was
 narrowest in fall, when they consumed the highest frequencies of
 Salicornia and Atriplex, and broadest in spring when the frequencies of
 these two plants were lowest. Diet breadth was slightly lower for RERA
 than for co-occurring species in pairwise comparisons. All four species
 consumed similarly high frequencies of wetland plants, but RERA consumed
 fewer grasses and upland plants, suggesting that it may be less suited to
 fragmented habitats than sympatric rodents. Diet overlap was lowest
 between RERA and the native California vole (Microtis californicus). In
 contrast, RERA diet overlapped substantially with the native western
 harvest mouse (R. megalotis) and non-native house mouse (Mus musculus),
 suggesting potential for competition if these species become sufficiently
 abundant.
DOI: 10.5061/dryad.cnp5hqc74
title: eDNAssay: a machine learning tool that accurately predicts qPCR cross-amplification

description: Environmental DNA (eDNA) sampling is a highly sensitive and cost-effective
 technique for wildlife monitoring, notably through the use of qPCR assays.
 However, it can be difficult to ensure assay specificity when many closely
 related species cooccur. In theory, specificity may be assessed in silico
 by determining whether assay oligonucleotides have enough base-pair
 mismatches with nontarget sequences to preclude amplification. However,
 the mismatch qualities required are poorly understood, making in silico
 assessments difficult and often necessitating extensive in vitro
 testing—typically the greatest bottleneck in assay development. Increasing
 the accuracy of in silico assessments would therefore streamline the assay
 development process. In this study, we paired 10 qPCR assays with 82
 synthetic gene fragments for 530 specificity tests using SYBR Green
 intercalating dye (n = 262) and TaqMan hydrolysis probes (n = 268). Test
 results were used to train random forest classifiers to predict
 amplification. The primer-only model (SYBR Green-based) and full-assay
 model (TaqMan probe-based) were 99.6% and 100% accurate, respectively, in
 cross-validation. We further assessed model performance using six
 independent assays not used in model training. In these tests the
 primer-only model was 92.4% accurate (n = 119) and the full-assay model
 was 96.5% accurate (n = 144). The high performance achieved by these
 models makes it possible for eDNA practitioners to more quickly and
 confidently develop assays specific to the intended target. Practitioners
 can access the full-assay model via eDNAssay
 (https://NationalGenomicsCenter.shinyapps.io/eDNAssay), a user-friendly
 online tool for predicting qPCR cross-amplification.
description: This dataset combines information on assay-template mismatch
 characteristics and the results of SYBR Green and TaqMan probe-based qPCR
 tests. These parameters can be used to train random forest classifiers to
 predict qPCR cross-amplification.
description: Usage of these data requires Microsoft Excel (or similar), MEGA
 (or similar), and R software.
DOI: 10.5061/dryad.9p8cz8wk6
title: Increasing synchrony opposes stabilizing effects of species richness on terrestrial communities

description: Aim: Ecological theory has predicted that species richness should
 stabilize communities, with mechanisms including species synchrony and
 population variability determining the net impacts. While these theories
 have been supported empirically, results can be sensitive to taxonomic
 bias as studies are often focused on plants. Trophic differences between
 consumers and primary producers can lead to varying stabilizing effects of
 species richness. Here, we compared the impact of species richness on
 community variability in four taxonomic groups: terrestrial birds,
 mammals, invertebrates, and plants. Location: Global Method: Using data
 from 6,763 time series globally (BioTIME) for four terrestrial taxa, we
 quantified community and population variability and species synchrony
 based on abundance fluctuations over time. Results: Species richness
 destabilized communities through increasing synchrony and stabilized
 communities through reducing population variability in all taxa. Such
 opposing effects weakened net impacts of species richness on communities.
 Population variability had higher importance relative to synchrony in
 plant communities. In contrast, synchrony had more comparable (or even
 higher) importance compared to population variability in animal
 communities. When synchrony and population variability were not
 controlled, stabilizing impacts of species richness were detected in plant
 communities only. Main conclusions: Our results highlight how species
 richness drives stabilizing and destabilizing mechanisms simultaneously
 across all taxa, with strong taxonomic variation in the relative
 importance of these mechanisms in regulating community variability. This
 questions the generality of previous findings on stabilizing impacts of
 species richness based on limited taxonomic coverage. Additionally, our
 results indicate the need to understand how the importance of stabilizing
 and destabilizing mechanisms differ in determining community variability
 across organisms and environments.
DOI: 10.5061/dryad.kwh70rz6j
title: Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers

description: Understanding the mechanisms underlying heterogeneous genomic divergence
 is of particular interest in evolutionary biology. Highly differentiated
 genomic regions, known as genomic islands, often evolve between diverging
 lineages. These genomic islands may be related to selection promoting
 adaptation or reproductive isolation. Based on whole genome assembly and
 genome-wide RAD sequencing in a pair of yellow croakers (genus:
 Larimichthys), we investigated the evolutionary processes shaping genomic
 landscapes of divergence. Demographic modelling indicated that the two
 species diverged following a secondary contact scenario, where
 differential introgression and linked selection were suggested to be
 involved in heterogeneous genomic divergence. We identified reduced
 recombination rate in genomic islands and a relatively good conservation
 of both genetic diversity and recombination landscapes between species,
 which highlight the roles of linked selection and recombination rate
 variation in promoting heterogeneous divergence in the common ancestral
 lineage of the two species. In addition, we found a positive correlation
 between differentiation (FST) and absolute sequence divergence (Dxy), and
 elevated Dxy in genomic islands, which were different from the patterns
 under linked selection. Restricted gene flow in highly differentiated
 regions has likely remodeled the landscape of heterogeneous genomic
 divergence. Moreover, genomic islands showed little evidence of
 overlapping within and between species, implying that high gene flow and
 divergent selection when colonizing new habitats have reshaped the
 patterns of intraspecific divergence. This study highlights that highly
 differentiated genomic regions can also be from linked selection and
 variation of recombination rate, and thus are not necessarily related to
 speciation islands or local adaptation.
DOI: 10.5061/dryad.931zcrjnx
title: Data from: Stable isotopes in the different trophic levels reveal regional divergence in dietary habits among Tibetan pastoralists

description: Understanding geographical variation and driving mechanisms of the dietary
 habits of Tibetan pastoralists is a key to improving their health status
 under climate change and globalization. Characterization of diet via
 isotopic signatures along the length of the local food chain could provide
 this information. We analyzed δ13C and δ15N of soil, plants, animals and
 pastoralists at different geographical sites ranging in a
 gradient of easily accessible to remote areas. The high δ15N
 values in soil and plants were not recovered in animals and pastoralists,
 indicating use of external feed and food
 resources respectively. The mean δ13C (-22.0‰) and δ15N
 values (6.9‰) of pastoralists indicated diets consisting mainly of native
 C3 plants and animal products. Pastoralists living in the
 remotest areas maintained more traditional dietary habits based on native
 animal products. However, dietary changes of pastoralists were
 triggered by external food resources and
 alterations in ecological chain of easily accessible
 areas.
description: This file includes isotopes data for five regions