cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9s4mw6mgm
title: Data from: A new solution to an old riddle: elongate dinosaur tracks explained as deep penetration of the foot, not plantigrade locomotion

description: The dinosaur track record features numerous examples of trackways with
 elongate metatarsal marks. Such “elongate tracks” are often highly
 variable and characterised by indistinct outlines and abbreviated or
 missing digit impressions. Elongate dinosaur tracks are well-known from
 the Paluxy River bed of Texas, where some had been interpreted as “man
 tracks” by creationists due to their superficially human-like appearance.
 The horizontal orientation of the metatarsal marks led to the now widely
 accepted idea of a facultative plantigrade, or “flat-footed”, mode of
 locomotion in a variety of dinosaurian trackmakers small to large. This
 hypothesis, however, is at odds with the observation that elongate tracks
 do not indicate reduced locomotion speeds and increased pace angulation
 values, but instead are correlated with low anatomical fidelity. We here
 interpret elongate tracks as deep penetrations of the foot in soft
 sediment. Sediment may collapse above parts of the descending foot,
 leaving a shallow surface track that preserves a metatarsal mark. The
 length of a metatarsal mark is determined by multiple factors and is not
 necessarily correlated with the length of the metatarsus. Other types of
 posterior marks in dinosaur footprints, such as drag and slip marks, are
 reviewed.
description: Literature review; first-hand observations; photogrammetry
DOI: 10.5061/dryad.zpc866t8f
title: Biochar increases tree biomass in a managed boreal forest, but does not alter N2O, CH4, and CO2 emissions

description: Biochar soil amendment may provide the forestry sector with a formidable
 tool to simultaneously sequester carbon (C) in the soil and aboveground by
 enhancing plant productivity, yet several key uncertainties remain.
 Crucially, empirical evidence of long-term effects of biochar management
 on vegetation and on greenhouse gas emissions in forest ecosystems is
 scarce. Using a large field experiment in a young managed boreal forest in
 northern Sweden, we investigated the effects of biochar (applied either on
 the soil surface or mixed in the soil 8–9 years prior to this study) on
 supply rates of soil nutrients, on survival and growth of planted Pinus
 sylvestris, on community composition of the understory vegetation, and on
 forest floor fluxes of N2O, CH4 and CO2. We found that biochar promoted P.
 sylvestris survival only when biochar was applied on the soil surface.
 Conversely, biochar enhanced P. sylvestris growth overall, resulting in a
 19 % increase in C stored in biomass. Biochar also altered the composition
 of the understory vegetation, especially when mixed into the soil, and
 promoted a more resource-conservative community (i.e., with more
 ericaceous shrubs and less graminoids and forbs). Meanwhile, supply rates
 of the main soil nutrients were largely unaffected by biochar. Finally, we
 found that biochar did not alter overall N2O and CO2 emissions and CH4
 uptake from the forest floor. Our findings show that biochar amendment
 increased the net C input to the system, since, besides directly
 increasing soil C stocks, biochar enhanced biomass growth without
 increasing soil C losses. Therefore, our study suggests that biochar could
 potentially be used for emissions abatement in intensively managed boreal
 forests.
DOI: 10.5061/dryad.nvx0k6dsh
title: Thiamethoxam as an inadvertent anti-aphrodisiac in male bees

description: Sexual reproduction is common to almost all multi-cellular organisms and
 can be compromised by environmental pollution, thereby affecting entire
 populations. Even though there is consensus that neonicotinoid
 insecticides can impact non-target animal fertility, their possible impact
 on male mating success is currently unknown in bees. Here, we show that
 sublethal exposure to a neonicotinoid significantly reduces both mating
 success and sperm traits of male bumblebees. Sexually mature male
 Bombus terrestris exposed to a field-realistic concentration of
 thiamethoxam (20 ng g-1) or not (controls) were mated with virgin gynes in
 the laboratory. The results confirm sublethal negative effects of
 thiamethoxam on sperm quantity and viability. While the latency to mate
 was reduced, mating success was significantly impaired in
 thiamethoxam-exposed males by 32% probably due to female choice. Gynes
 mated by exposed males revealed impaired sperm traits compared to their
 respective controls, which may lead to severe constraints for colony
 fitness. Our laboratory findings demonstrate for the first time that
 neonicotinoid insecticides can negatively affect male mating success in
 bees. Given that holds true for the field, this provides a plausible
 mechanism contributing to declines of wild bee populations globally. The
 widespread prophylactic use of neonicotinoids may therefore have
 previously overlooked inadvertent anti-aphrodisiac effects on non-target
 animals, thereby limiting conservation efforts.
DOI: 10.5061/dryad.4j0zpc8bk
title: Pollen-chemistry variations along elevation gradients and their implications for a proxy for UV-B radiation in the plant-fossil record

description: 1. Research indicates that the phenolic compounds (e.g. para-coumaric
 acid) found within pollen grains may be useful as a proxy to reconstruct
 the UV-B radiation received at the Earth’s surface in the geological past.
 However, application of this method to the plant-fossil record currently
 relies on a series of untested assumptions surrounding the ecological
 factors driving the response of pollen grains in the contemporary
 environment. 2. Here, we investigate the relationship of Pinus spp. pollen
 to UV-B radiation using individuals of five populations sampled from three
 elevation gradients across Europe. We develop a novel radiation-modelling
 approach, which allows us to estimate the UV-B-radiation dose of
 individual trees, weighted by different UV-B action spectra. We then use
 linear mixed-effects modelling to investigate: (i) whether the variations
 in UV-B-absorbing compounds in Pinus pollen are best described by models
 using coarser (subgenus) or finer (population) taxonomic levels; and (ii)
 the duration of the period of accumulation of UV-B-absorbing compounds in
 pollen, ranging from 8-28 days. 3. Our results demonstrate an overall
 positive relationship between para-coumaric acid and UV-B radiation, best
 described by applying a UV-B accumulation period spanning 12-19 days.
 However, we also show clear evidence for population-level factors
 influencing this relationship across the study locations. 4. Synthesis.
 Our multidisciplinary approach, which combines expertise from
 palaeoecology, plant physiology and atmospheric physics, provides clear
 evidence that pollen-grain chemistry is subject to population-level
 variations. We suggest that quantitative reconstructions of long-term
 changes in springtime UV-B radiation are still achievable using fossil
 reconstructions, but only with careful consideration of the factors
 leading to pollen representation in sediments. Future improvements are
 dependent on mechanistic understanding of the local factors which mediate
 the UV-B response across different populations, and on upscaling knowledge
 at the plant level to incorporate longer-term chemical variations
 represented within sediment samples. --
description: An RStudio project, including the input data, scripts and
 manuscript files, are included in the entry. A read-me document is also
 included in the directory to explain usage.
DOI: 10.5061/dryad.fbg79cnv5
title: Data from: Direct and indirect effects of global change on mycorrhizal associations of savanna plant communities

description: This data set contains a very detailed information on a field manipulative
 experiment of rainfall exclusion and increased temperature aimed to
 evaluate the impact of forecasted warming and drying on mycorrhizal
 associations of savanna plant communities subjected to different grazing
 history. Additionally, we compiled detailed information on the abiotic and
 biotic environment with the final aim of disentangling the direct and
 indirect effects of climate change on this widespread mycorrhizal
 symbiosis. Our results suggest that climate change could induce relevant
 changes in mycorrhizal associations, primarily promoted by warming, which
 decreased the abundance of mycorrhizae but induced higher activity of
 nutrient exchange between the host-plant and the mycosymbiont. Temperature
 did not only affect this symbiosis in a direct way, but also exerted
 relevant indirect effects via changes in soil functioning and other
 root-colonizing microorganisms such as dark septate endophytes. Grazing
 history influenced the allocation of fungal structures inside the
 host-root, but its effect differed as a function of the climatic
 treatment. Results from this study suggest that mycorrhizal fungi might
 become less prevalent in plant communities inhabiting savanna ecosystems
 under future scenarios of increasing aridity. In agreement with this
 finding, higher temperatures also promoted the predominance of plants with
 root traits that favour efficient resource acquisition by themselves
 without the help of a mycorrhizal partner. Our results provide new
 insights into the interactive effects of the two main threats facing
 Mediterranean savanna ecosystems, as well as potentially useful
 information to be applied in ecologically-based management strategies
 aimed at attenuating the potential impact of global change on mycorrhizal
 fungi.
description: A detailed explanation on how this dataset was collected is
 provided in the "Material and Methods" section of our
 manuscript.
DOI: 10.5061/dryad.00000003q
title: Sharks surf the slope: current updrafts reduce energy expenditure for aggregating marine predators

description: An animal’s energy landscape considers the power requirements associated
 with residing or moving through habitats. Within marine environments,
 these landscapes can be dynamic, as water currents will influence animal
 power requirements and can change rapidly over diel and tidal cycles. In
 channels and along slopes with strong currents, updraft zones may reduce
 energy expenditure of negatively buoyant fishes that are also obligate
 swimmers. Despite marine predators often residing within high-current
 area, no study has investigated the potential role of the energetic
 landscape in driving such habitat selectivity. Over 500 grey reef sharks
 (Carcharhinus amblyrhinchos) reside in the southern channel of Fakarava
 Atoll, French Polynesia. We used diver observations, acoustic telemetry,
 and biologging to show that sharks use regions of predicted updrafts and
 switch their core area of space use based on tidal state (incoming vs
 outgoing). During incoming tides, sharks form tight groups and display
 shuttling behavior (moving to the front of the group and letting the
 current move them to the back) to maintain themselves in these potential
 updraft zones. During outgoing tides, group dispersion increases, swimming
 depths decrease, and shuttling behaviors cease. These changes are likely
 due to shifts in the nature and location of the updraft zones, as well as
 turbulence during outgoing tides. Using a biomechanical model, we estimate
 that routine metabolic rates for sharks may be reduced by 10-15 % when in
 updraft zones. Grey reef sharks save energy by using predicted updraft
 zones in channels and ‘surfing the slope’. Analogous to birds using
 wind-driven updraft zones, negatively buoyant marine animals may use
 current-induced updraft zones to reduce energy expenditure. Updrafts
 should be incorporated into dynamic energy landscapes and may partially
 explain the distribution, behavior, and potentially abundance of marine
 predators.
description: Sharks were tagged with acoustic transmitters which are detected
 by fixed listening stations. Tags include sensors that also measure
 swimming depth and animal activity. Data has been separated out based on
 tidal state.
DOI: 10.5061/dryad.b8gtht7cm
title: Raw data, code, and derived data from: Nonchalant neighbors: space-use and overlap of the critically endangered Elongated Tortoise

description: To prevent population extirpations we need to understand a species’
 requirements, especially for critically endangered species inhabiting
 biodiversity hotspots. Studying animal movement provides necessary
 insights and gauges protected area effectiveness. Southeast Asian
 protected areas are becoming isolated, stressing the need for maintaining
 population viability. We used radio-telemetry with the critically
 endangered Elongated Tortoise (Indotestudo elongata) to assess: movements,
 space-use, and conspecific overlap in a small protected area –Sakaerat
 Biosphere Reserve, Thailand. Movements were weakly seasonal, higher in hot
 and wet seasons than the dry season, and annual space-use varied
 (4.24–55.57 ha), with conspecifics frequently overlapping. Conspecific
 comparisons revealed males (n = 5) moved similarly to females (n = 12) but
 used larger areas. Despite more instances of conspecific attraction over
 avoidance (20:8), avoidance/attraction behaviour appeared disconnected
 from individual size; therefore, interaction patterns may result from
 resources locations (mates or food) rather than competition (i.e., no
 evidence of smaller individuals avoiding larger individuals).
 Female-female attraction suggests no resource exclusion tactics at our
 temporal resolution. Male-female attraction may indicate seasonal
 reproductive movements, but we couldn’t detect significant interactive
 effects linking conspecific attraction or step length to breeding
 activity. Our observations of annual space-use and overlap present
 critical components when designing robust population assessments
 underlining any successful I. elongata conservation effort. In the context
 of previous work connecting space overlap with population viability, our
 results suggest the biosphere population of I. elongata to be
 reproductive, with enough resources to be viable, emphasising the
 importance of relatively small protected natural areas.
description: A basic explanation of the data contents can be found alongside
 the data in a metadata file. A warning for those
 re-using movement data: there are instances where two locations where
 recorded for an animal on a given day. These days with two locations do
 not have timestamps and so will cause issues with time-using
 analyses.
DOI: 10.5061/dryad.80gb5mkr0
title: Rate of formation of caustics in heavy particles advected by turbulence

description: The rate of collision and the relative velocities of the colliding
 particles in turbulent flows is a crucial part of several natural
 phenomena, e.g., rain formation in warm clouds and planetesimal formation
 in a protoplanetary disks. The particles are often modeled as passive, but
 heavy and inertial. Within this model, large relative velocities emerge
 due to formation of singularities (caustics) of in the gradient matrix of
 the velocities of the particles. Using extensive direct numerical
 simulations of heavy particles in both two (direct and inverse cascade)
 and three dimensional turbulent flows we calculate the rate of formation
 of caustics,  as a function of the Stokes number. The two
 directories contains tar file of run directories for two different
 Reynolds number (90 and 180). The corresponding taueta are 0.41 and 1.54
 respectively.   The data can be read and analyzed with
 the python files included in the python directory.
description: The dataset is generated from direct numerical simulation of
 turbulent flows using the pencil-code.
description: The two directories contains tar file of run directories for two
 different Reynolds number (90 and 180). The corresponding taueta are 0.41
 and 1.54 respectively. A brief description of the files
 and directory structure: These are raw data from direct
 numrical simulations using the pencil-code
 (http://pencil-code.nordita.org/). The code is open-source. You can also
 reproduce the data from the input files in these run directories and the
 pencil-code. The directory structure is typical of pencil-code runs. An
 example is given below : Consider the directory
 Relam180/512kf2hiRe-5 This means that this is a run
 with 512^3 grid points, with a forcing wavenumber kf = 2 . The suffix 5
 does not imply that they Reynolds number is 5 but is just a label.
   The input files are start.in, run.in (and so on). The
 CVS directory contains information about our private CVS repository and is
 irrelevant here. The slurm-xxx-.out files contains output from job
 scheduler in the computing cluster. This is also not relevant.
 The relevant data are in the subdirectory data/. Within the
 subdirectory the data are divided by the processors. It is best if you use
 the scripts we provide within the python directory to read these data. The
 scripts collate the data scattered over the directories. The python
 scripts assume that you have the pencil-code installed.
DOI: 10.5061/dryad.5hqbzkh61
title: Data from: Viral transmission and infection prevalence in a cannibalistic host–pathogen system

description: Cannibalism, while prevalent in the natural world, is often viewed as
 detrimental to a cannibal’s health, especially when they consume
 pathogen-infected conspecifics. The argument stems from the idea that
 cannibalizing infected individuals increases the chance of coming into
 contact with a pathogen and subsequently becoming infected. Using an
 insect pest, the fall armyworm (Spodoptera frugiperda), that readily
 cannibalizes at the larval stage and its lethal pathogen, we
 experimentally examined how cannibalism affects viral transmission at both
 an individual and population level. Prior to death, the pathogen in the
 system stops the larval host from growing, resulting in infected
 individuals being smaller than healthy individuals. This leads to
 size-structured cannibalism of infected individuals with the larger
 healthy larvae consuming the smaller infected larvae, which is commonly
 observed. At the individual level, we show that the probability of
 cannibalism is relatively high for both infected and uninfected
 individuals especially when the cannibal is larger than the victim.
 However, the probability of the cannibal becoming infected given that a
 pathogen-infected individual has been cannibalized is relatively low. On a
 population level, when cannibalism is allowed to occur transmission rates
 decline. Additionally, by cannibalizing infected larvae, cannibals lower
 the infection risk for non-cannibals. Thus, cannibalism can decrease
 infection prevalence and, therefore, may not be as deleterious as once
 thought. Under certain circumstances, cannibalizing infected individuals,
 from the uninfected host’s perspective, may even be advantageous, as one
 obtains a meal and decreases competition for resources with little chance
 of becoming infected.
description: Please see associated manuscript and associated README file.
DOI: 10.5061/dryad.wstqjq2mb
title: Insect RTUs from the degraded forest fragments in the Attappady and Anaikatti landscapes.

description: Datasets were collected as part of the project titled "EVALUATING THE
 EFFICEINCY OF RESTORATION EFFORTS IN REVIVING TROPICAL FORESTS USING
 GROUND INSECTS AS INDICATORS."
description: Insects were collected through pitfall trapping (in January and
 May of 2008 and 2009) from the 24 degraded forest fragments of the
 Attappady hills along with four sites within the adjoining Anaikatti
 forests.
DOI: 10.5061/dryad.m905qfv1c
title: Datafile - In situ adaptation and ecological release facilitate the occupied niche expansion of an invasive Madagascan day gecko in Florida

description: Aim To investigate whether the frequently advocated climate-matching
 species distribution modelling approach could predict the
 well-characterized colonization of Florida by the Madagascar giant day
 gecko Phelsuma grandis. Location Madagascar and Florida, USA. Methods To
 determine the climatic conditions associated with the native range of P.
 grandis, we used native-range presence-only records and Bioclim climatic
 data to build a Maxent species distribution model and projected the
 climatic thresholds of the native range onto Florida. We then built an
 analogous model using Florida presence-only data and projected it onto
 Madagascar. We constructed a third model using native-range presences for
 both P. grandis and the closely related parapatric species P. kochi.
 Results Despite performing well within the native range, our Madagascar
 Bioclim model failed to identify suitable climatic habitat currently
 occupied by P. grandis in Florida. The model constructed using Florida
 presences also failed to reflect the distribution in Madagascar by
 over-predicting distribution, especially in western areas occupied by P.
 kochi. The model built using the combined P. kochi/P. grandis dataset
 modestly improved the prediction of the range of P. grandis in Florida,
 thereby implying competitive exclusion of P. grandis by P. kochi from
 habitat within the former’s fundamental niche. These findings thus suggest
 ecological release of P. grandis in Florida. However, because ecological
 release cannot fully explain the divergent occupied niches of P. grandis
 in Madagascar versus Florida, our findings also demonstrate some degree of
 in situ adaptation in Florida. Main conclusions Our models suggest that
 the discrepancy between the predicted and observed range of P. grandis in
 Florida is attributable to either in situ adaptation by P. grandis within
 Florida, or a combination of such in situ adaptation and competition with
 P. kochi in Madagascar. Our study demonstrates that climate-matching
 species distribution models can severely underpredict the establishment
 risk posed by non-native herpetofauna.
description: This datafile contains i) the datafiles used in this study, ii)
 the R script used to generate, project, and analyze the models presented
 in this paper, and iii) the output files associated with the models. It
 should be sufficient to recreate the model outputs as presented in the
 manuscript.
description: All necessary data and files supplied.