cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c2fqz6149
title: Data from: Human-dominated land uses favour species affiliated with more extreme climates, especially in the tropics

description: The data are derived from the PREDICTS Project database
 (https://data.nhm.ac.uk/dataset/902f084d-ce3f-429f-a6a5-23162c73fdf7) used
 within the paper titled "Human-dominated land uses favour species
 affiliated with more extreme climates, especially in the tropics"
 (DOI: 10.1111/ecog.04806). If using this data, please make sure that the
 PREDICTS Project is also cited.
 For Williams_et_al_Ecography_data_CWM -&gt; These data
 include, for the species assemblages in the analyses, the raw community
 weighted means (CWMs) for the extreme (maximum or minimum) and range-wide
 variation (standard deviations) for each climatic niche property. The
 columns for the CWMs of the extremes are headed CWM_MAXTmax, CWM_MINTmin,
 CWM_MAXPpmax and CWM_MINPpmin to match the terms used in the paper. The
 columns for the CWMs of range-wide variation are headed CWM_STDTmax,
 CWM_STDTmin, CWM_STDPpmax and CWM_STDPpmin. The columns headed
 'Total_abundance' and 'Species_richness' were
 calculated during data preparation. The other columns included are details
 about each site, unchanged from the PREDICTS Project database.
 For Williams_et_al_Ecography_data_Abundance_Tmax_Tropics, Williams_et_al_Ecography_data_Abundance_Tmax_Temperate, Williams_et_al_Ecography_data_Abundance_Ppmin_Tropics and Williams_et_al_Ecography_data_Abundance_Ppmin_Temperate -&gt; These are the data used for the abundance analyses. There are four files within each of these files, one for each species group (formed by splitting around the medians of the exteme and standard deviation of the climatic variable in question, i.e. either maximum temperature of the hottest month or precipitation of the driest month). 'Tropics' or 'Temperate' within the file name denote whether the data are from from tropical or temperate latitudes, respectively. The column headed 'LogAbund' includes the log(x+1) transformation of the abundance measures, used within the models. The columns headed 'Simpson_diversity', 'ChaoR', 'Richness_rarefied', 'UseIntensity' and 'UI' are other variables we calculated along the way, but did not use in these analyses. The column 'LandUse' contains our slight alterations (e.g. changing vegetation to Vegetation) of the 'Predominant_land_use' column found within the PREDICTS Project database. The columns headed 'Total_abundance' and 'Species_richness' were calculated by us using the PREDICTS Project database. The other columns include unchanged species-level data from the PREDICTS Project database.
DOI: 10.5061/dryad.tqjq2bvtq
title: Data from: Genetic evaluation of migratory fish: implications for conservation and stocking programs

description: Fish stocking programs have been implemented to mitigate the blockage of
 original riverbeds by the construction of hydropower dams, which affects
 the natural migration of fish populations. However, this method raises
 concerns regarding the genetic rescue of the original populations of
 migratory fish species. We present the first study to investigate the
 genetic diversity, population structure, and gene flow (migration) of the
 Neotropical migratory fish Prochilodus costatus in the Três Marias dam in
 São Francisco River basin, Brazil, using high-throughput genotyping and
 population genetics approaches. In total, 1,017 specimens were sampled
 from 12 sites during 4 hydrological years and from broodfish used in a
 fish stocking program, and genotyped with 8 microsatellite loci. The
 samples showed low genetic variability, with inbreeding and the presence
 of only four genetic pools; three pools were observed throughout the study
 region and the fourth was exclusive to one area in the Paraopeba River.
 Additionally, we identified high unidirectional gene flow between regions,
 and a preferred route between the Pará river and the upper portion of the
 São Francisco River. The fish stocking program succeeded in transposing
 the genetic pools from downstream to upstream of the Três Marias dam, but,
 regrettably, promoted genetic homogenization in the upper São Francisco
 River basin. Moreover, our data show the fragility of this species at the
 genetic level, and through these strategic methods of monitoring that
 could be as model for migratory fish populations that are consumed by
 humans to develop conservation and management measures.
DOI: 10.5061/dryad.hdr7sqvcx
title: Parasitoids of leaf herbivores enhance plant fitness and do not alter caterpillar-induced resistance against seed beetles

description: 1. Organisms of the third trophic level can indirectly interact with
 plants. However, whether parasitoids of herbivores have a positive effect
 on plant fitness has been controversial. In addition to possible effects
 on plant fitness, parasitoid-mitigated herbivory can modify plant
 physiological responses and thereby alter the plant-mediated indirect
 interactions between different herbivore species. These types of indirect
 multitrophic interactions remain largely unexplored. Thus, to understand
 the full effect of the third trophic level on plants, it is necessary to
 consider the context of the community of interacting species, both
 herbivores and their enemies. 2. Here, we investigated if parasitoids of
 leaf-feeding caterpillars affect plant fitness (seed quantity and quality)
 and the consequences for seed-dwelling insects at the second and third
 trophic levels through plant mediated effects. To test this, we exposed
 lima bean plants (Phaseolus lunatus), under controlled field conditions,
 to unparasitized caterpillars (Spodoptera latifascia) or caterpillars that
 were parasitized by the parasitoid species Cotesia marginiventris. Later
 in the season, we measured seed production and infestation by seed beetles
 and their parasitoids. 3. We found that parasitoids significantly reduced
 the leaf damage inflicted by the caterpillars, such that the plants
 suffered no loss in seed production. Yet, parasitoids had no effect on the
 emergence of seed beetles (Zabrotes subfasciatus and Acanthoscelides
 obtectus), which was equally reduced in plants attacked by unparasitized
 and by parasitized caterpillars. Seeds from undamaged plants were
 significantly more attacked by Z. subfasciatus beetles. Parasitism rates
 of seed beetle larvae were similar for all treatments. 4. Although
 parasitized caterpillars did not damage the plants enough to reduce seed
 production (unlike unparasitized caterpillars), the damage they inflicted
 induced resistance against other herbivores. Taken together, these results
 reveal how parasitoids can indirectly enhance plant fitness in the context
 of the local ecological networks. These findings have significant
 implications for natural and agricultural systems since they reveal that
 the indirect interaction between plants and parasitoids can be beneficial
 in communities with multiple herbivore species.
DOI: 10.5068/d1rq2w
title: Empirically estimated electron lifetimes in the Earth's radiation belts: 1. Observations

description: These data are provided as supporting information for
 the manuscript "Empirically estimated electron lifetimes in
 the Earth's radiation belts: 1. Observations" by Claudepierre et
 al. These data include electron flux measurements in the
 Earth's radiation belt obtained with the MagEIS instrument
 on the NASA Van Allen Probe B satellite, along with the empirical
 decay timescale estimates described in the manuscript. The contents of the
 data files are described in greater detail in the corresponding
 "readme" files.
DOI: 10.15468/dl.v9u4mp
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.1_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Antrodiaetus unicolor"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002021-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63xsj3tzd
title: Data from: Preservation-induced morphological change in salamanders and failed DNA extraction from a decades-old museum specimen: implications for Plethodon ainsworthi

description: Natural history collections are important data repositories, but different
 chemical treatments of specimens can influence morphological measurements
 and DNA extraction, complicating taxonomic and conservation decisions
 dependent upon these data. One such example is the Bay Springs Salamander
 (Plethodon ainsworthi), the only United States amphibian categorized as
 Extinct by the IUCN. Recent research has proposed that P. ainsworthi is an
 invalid taxon, arguing that the 55-year-old type specimens’ morphological
 distinctiveness from syntopic P. mississippi is a preservation artifact.
 To address this controversy, we tested for morphological changes across
 five experimental treatments in proxy P. shermani specimens, and we
 re-examined the datasets used to support the invalidity of P. ainsworthi.
 We also tested recently developed DNA extraction techniques on the
 putatively formalin-fixed P. ainsworthi holotype. We used Bayesian models
 to demonstrate that preservation method can differentially bias
 morphological measurements, with most methods causing lower estimates of
 mass and modestly higher estimates of snout-vent-length:head width ratio.
 These results are broadly consistent with previous studies of other
 vertebrates, but inconsistent with the hypothesis that P. ainsworthi type
 specimens are actually poorly preserved P. mississippi. Attempts to
 extract DNA from the P. ainsworthi holotype unfortunately proved
 unsuccessful, preventing conclusive resolution of its status and
 emphasizing the limitations of promising new methods. Nonetheless, we
 tentatively recommend continued recognition of P. ainsworthi as a valid
 but possibly extinct taxon. More generally, we invite all authors who
 study preserved specimens to recognize and report how certain chemical
 treatments might impact their results.
description: These files include: 1) our raw morphological measurements; 2)
 our R scripts; and 3) our Stan file.
DOI: 10.5061/dryad.qfttdz0cb
title: A model of the optimal selection of crypto assets - simulation code

description: In the modelling we assume that crypto assets differ by two essential
 features: security (technological)
 and stability (governance). Investors make choices over
 crypto assets similarly to how they make choices by using a recommender
 app: the app presents each investor with a pair of crypto assets with
 certain security-stability characteristics to be compared. Each investor
 submits its preference for adopting one of the two assets to the app. The
 app, in turn, provides a recommendation on whether the proposed adoption
 is sensible given the assets’ essential features, information about the
 adoption choices of all other investors, and expected future economic
 benefits of adoption. Investors continue making their adoption choices
 over all pairs of crypto assets until their expected future economic
 benefits can no longer be improved upon. This constitutes an optimal
 selection decision. We simulate optimal selection decisions considering
 the behaviour of different types of investors, driven by their attitudes
 towards assets’ features. We find a variety of possible emergent outcomes
 for the investments in the crypto-ecosystem and the future adoption of the
 crypto assets.
description: This repository contains the Matlab code for the simulations of a
 process of crypto assets optimal selection.
DOI: 10.5061/dryad.95x69p8fd
title: Intraspecific mating system evolution and its effect on complex male secondary sexual traits: does male-male competition increase selection on size or shape?

description: Sexual selection is generally held responsible for the exceptional
 diversity in secondary sexual traits in animals. Mating system evolution
 is therefore expected to profoundly affect the covariation between
 secondary sexual traits and mating success. While there is such evidence
 at the interspecific level, data within species remain scarce. We here
 investigate sexual selection acting on the exaggerated male fore femur and
 the male wing in the common and widespread dung flies Sepsis punctum and
 S. neocynipsea (Diptera: Sepsidae). Both species exhibit intraspecific
 differences in mating systems and variation in sexual size dimorphism
 (SSD) across continents that correlates with the extent of male-male
 competition. We predicted that populations subject to increased male-male
 competition will experience stronger directional selection on the sexually
 dimorphic male foreleg. Our results suggest that fore femur size, width
 and shape were indeed positively associated with mating success in
 populations with male-biased SSD in both species, which was not evident in
 conspecific populations with female-biased SSD. However, this was also the
 case for wing size and shape, a trait often assumed to be primarily under
 natural selection. After correcting for selection on overall body size by
 accounting for allometric scaling, we found little evidence for
 independent selection on any of these size or shape traits in legs or
 wings, irrespective of the mating system. Sexual dimorphism and (foreleg)
 trait exaggeration is therefore unlikely to be driven by direct
 precopulatory sexual selection, but more so by selection on overall size
 or possibly selection on allometric scaling.
DOI: 10.5061/dryad.bcc2fqz7m
title: Data from: Picoplankton carbon biomass assessments and distribution of Prochlorococcus ecotypes linked to Loop Current Eddies during summer in the southern Gulf of Mexico

description: Assessments of picoplankton carbon biomass in the pelagic ecosystem over
 the deep region of the southern Gulf of Mexico were conducted during three
 consecutive summer cruises. Notably, the relationship between carbon
 distribution of Prochlorococcus (PRO) and Loop Current (LC) dynamics was
 evaluated. Seawater samples were collected from the euphotic zone (~150 m)
 for estimating the abundance of the picoplankton populations using flow
 cytometry analyses. Carbon biomass estimates were based on cell abundance
 and variable conversion factors computed across stations and depths. On
 average, about half of the total depth-integrated carbon biomass of
 picoplankton was attributed to heterotrophic bacteria (HB, 54%) and three
 autotrophic populations (Prochlorococcus, Synechococcus, and
 pico-eukaryotes, 46%). In agreement with previous winter assessments, PRO
 was the dominant component of abundance (~90%) and picophytoplankton
 community biomass (&gt;70%). Based on molecular analyses, distinct
 ecotypes of high-light PRO and low-light (LL) PRO were found within the
 euphotic zone, vertically distributed along light and nutrient gradients.
 Also, PRO distributions were related to hydrographic conditions strongly
 modulated by mesoscale dynamics. LL-PRO subgroups, located close to the
 nutricline under LL conditions, were associated with the westward
 propagation of anticyclonic eddies that episodically detach from the LC.
 This study highlights the role of the LC and its eddies in the transport
 and distribution of carbon biomass into the Gulf of Mexico, as represented
 by the deep subgroups of the dominant, tiniest autotroph within this
 oligotrophic ecosystem.
DOI: 10.5061/dryad.4f4qrfj7f
title: Age of first infection across a range of parasite taxa in a wild mammalian population

description: Newborn mammals have an immature immune system that cannot sufficiently
 protect them against infectious diseases. However, variation in the
 effectiveness of maternal immunity against different parasites may couple
 with temporal trends in parasite exposure to influence disparities in
 timing of infection risk. Determining the relationship between age and
 infection risk is critical in identifying the portion of a host population
 that contributes to parasite dynamics, as well as the parasites that
 regulate host recruitment. While age-prevalence curves have been used as a
 rough estimation of timing of infection, there are no data directly
 identifying timing of first infection among parasites in wildlife. Here,
 we took advantage of a longitudinal dataset, tracking infection status in
 a herd of African buffalo, with a number of individuals born during the
 study or immediately prior to the start of the study, to ask: (1) How does
 age of first infection differ amongst parasite taxa? and (2) Are buffalo
 parasite communities age-structured? We found distinct differences in age
 of first infection among parasites that aligned with mode of transmission
 and parasite taxonomy. Furthermore, we found parasite community
 composition differs between animals &lt;1.5 years and animals &gt;
 1.5 years of age. These results emphasize the importance of understanding
 infection risk in juveniles, especially in host species where young
 animals are purported to sustain parasite persistence and / or where
 mortality rates of juveniles strongly influence population dynamics.
DOI: 10.5061/dryad.4j0zpc871
title: Leaf litter quality drives the feeding by invertebrate shredders in tropical streams

description: Amazon and Cerrado forested streams show natural fluctuations in
 leaf-litter quantity along the time and space, suggesting a change on
 litter quality input. These natural fluctuations of leaf-litter have
 repercussion on the organic matter cycling and 
 consequentlyeffects on leaf decomposition in forested streams. The effects
 of the quantity of leaf litter with contrasting traits on consumption by
 larvae of shredder insects from biomes with different organic matter
 dynamics have still been an understudied question. The Trichoptera
 Phylloicus spp. is a typical shredder in tropical headwater streams and
 keep an important role in leaf-litter decomposition. Here, we assessed the
 consumption by shredder Phylloicus spp., from Amazonia and Cerrado biomes,
 on higher (Maprounea guianensis) and lower quality leaves (Inga laurina)
 in different proportions and quantities. Experiments were performed
 concomitantly in microcosms approaches, simulating Cerrado and Amazonian
 streams. Higher leaf consumption occurred in Cerrado microcosms. Litter
 quantity influenced negatively leaf consumption by shredders in Cerrado,
 in opposition to Amazonia, where consumption was not affected by leaf
 quantity. In both sites we observed higher consumption by shredders in
 treatment with only M. guianensis and no difference between other
 treatments with mixture of leaves. In treatment with litter of I. laurina,
 we noted the use of substrate for case building (due to the higher leaf
 toughness), affecting the fragmentation process. Therefore, our results
 indicate that leaf-litter quality drives the preference of consumption by
 Phylloicus larvae in Cerrado and Amazonia streams.
DOI: 10.15468/dl.q36enm
title: Occurrence Download

description: A dataset containing 7293 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polyporus ciliatus"
 ]
}

 The dataset includes 7293 records from 259 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002022-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4b8gtht7z
title: Burrowing behavior and burrowing energetics of a bioindicator under human disturbance

description: Bioindicator species are extensively used for rapid assessment of
 ecological changes. Their use commonly focuses on changes in population
 abundance and individual sizes in response to environmental change. These
 numerical and demographic shifts likely have behavioral
 and physiological mechanistic drivers that, if understood, could
 provide additional insights into the use of these species as bioindicators
 of habitat health. The Atlantic ghost crab, Ocypode quadrata, is
 a global bio-indicator species of human disturbance on sandy
 shores. Individual size and population abundance of O. quadrata decline
 dramatically at sites with human disturbance, and the causes of
 this phenomenon remain unclear. Here, we test the hypothesis that
 individual and population-level changes at disturbed sites
 reflect changes in burrowing behavior and energetics.
 Specifically, we examine whether or not the burrowing behavior
 (e.g. burrow fidelity and longevity) of O. quadrata changes because of
 human disturbance. We also examine energy required for burrowing by O.
 quadrata across different levels of human
 disturbance. We show that O. quadrata has the highest burrow
 fidelity and longevity at sites with low level of human impact,
 and weakest burrow fidelity and longevity at pristine sites. O. quadrata
 reduce the burrowing energy allocation by manipulating the burrow
 dimension and increasing the burrow longevity even under low
 levels of human disturbance. Overall, this study shows that human
 disturbances not only change the behavior of organisms, but also
 shift energetic balance. Our results support the use of a bioenergetic
 approach to better understand how human disturbances influence
 natural populations, and the specific use of this approach with this
 bioindicator species.
DOI: 10.6078/d1b974
title: Pretrained model for UCBShift

description: UCBShift is a program for predicting chemical shifts for backbone atoms
 and β-carbon of a protein in solution. It utilizes a machine learning
 module that makes predictions from features extracted from the 3D
 structures of the proteins. Provided here are the pre-trained machine
 learning models for making the predictions. The instructions for
 downloading UCBShift and use these .sav format pretrained models can be
 found at https://github.com/THGLab/CSpred