cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cjsxksn63
title: Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands

description: This dataset contains data and code that support the results in Weil,
 S.-S., Martinez-Almoyna, C., Piton, G., Renaud, J., Boulangeat, L.,
 Foulquier, A., ... & Thuiller, W. (2021) Strong links between
 plant traits and microbial activities but different abiotic drivers in
 mountain grasslands. Journal of Biogeography, 48(11), 2755-2770. We used
 an extensive plant-soil dataset that covers 14 elevational gradients
 (between 1500 and 2800 m of elevation) distributed over the whole
 French Alps to analyse the spatial co-dependencies between the plant and
 soil compartments. We ran a Graphical Lasso that extracts the direct and
 indirect linkages between plant functional composition, soil microbial
 activities, and environmental conditions (local climate and soil
 properties). Our main results are 1) that plant traits are tightly
 associated with microbial activities, the former being driven by climate
 and the latter by soil properties; 2) that the dominance of specific plant
 traits was more important than their diversity to determine plant-soil
 linkages; and 3) that soil microbes invested strongly in nutrient
 acquisition in sites with conservative plant traits and reduced organic
 matter quality.
description: Most of the data was collected in the field on plots of the
 ORCHAMP observation network in the French Alps. Community-weighted means
 on functional plant traits were calculated based on species-level data of
 traits that were measured in multiple populations across the whole French
 Alps between 2008 and 2018. Values of the integrated normalized difference
 vegetation index (NDVI) were based on the surface spectral reflectance at
 a resolution of 250 m derived from MODIS (Moderate Resolution Imaging
 Spectroradiometer) bands 1 and 2; MOD09Q1: MODIS/Terra Surface Reflectance
 8-Day L3 Global 250 m SIN Grid V006 satellite MODIS (Terra), available
 online: https://lpdaac.usgs.gov/products/mod09q1v006/. Climatic variables
 were calculated using data from the SAFRAN-Crocus (S2M) reanalyses. Please
 refer to the manuscript for more information on data collection, protocols
 and calculations.
description: This dataset contains data for 41 plots across the ORCHAMP
 observation network and an R script that can be used to run Graphical
 Lasso on the data. The ReadMe file contains information about the origin
 of the data and explanations of the variables as well as their
 units.
DOI: 10.15468/dl.rzswaf
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Fossil, Living Specimen, Occurrence evidence)",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (January, February, March, April, May, June, July, August, September, October, November, December)",
 "TaxonKey is Polygonatum sibiricum"
 ]
}

 The dataset includes 42 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002888-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18396795
title: HHHHHydrography30

description: AAA
DOI: 10.5061/dryad.gtht76hmr
title: Bird strikes at commercial airports explained by citizen science and weather radar data

description: 1. Aircraft collisions with birds span the entire history of human
 aviation, including fatal collisions during some of the first powered
 human flights. Much effort has been expended to reduce such collisions,
 but increased knowledge about bird movements and species occurrence could
 dramatically improve decision support and proactive measures to reduce
 them. Migratory movements of birds pose a unique, often overlooked, threat
 to aviation that is particularly difficult for individual airports to
 monitor and predict: the occurrence of birds vary extensively in space and
 time at the local scales of airport responses. 2. We use two publicly
 available datasets, radar data from the US NEXRAD network characterizing
 migration movements and eBird data collected by citizen scientists to map
 bird movements and species composition with low human effort expenditures
 but high temporal and spatial resolution relative to other large scale
 bird survey methods. As a test case we compare these results from weather
 radar distributions and eBird species composition with detailed bird
 strike records from three major New York airports. 3. We show that weather
 radar based estimates of migration intensity can accurately predict
 probability of bird strikes, with 80% of the variation in bird strikes
 across the year explained by the average amount of migratory movements
 captured on weather radar. We also show that eBird based estimates of
 species occurrence can, using species’ body mass and flocking propensity,
 accurately predict when most damaging strikes occur. 4. Synthesis and
 applications: Our results highlight the power of federating datasets with
 movement and distribution data for developing better and more
 taxonomically and ecologically tuned models of likelihood of strikes
 occurring and severity of strikes. By better understanding when, and
 where, different species occur, airports across the world can predict
 seasonal periods of collision risks with greater temporal and spatial
 resolution; such predictions include potential to predict when the most
 severe and damaging strikes may occur.
DOI: 10.5061/dryad.gxd2547mj
title: Physiological data and R script for running physiology combined model for Drosophila suzukii

description: This is the dataset that accompanies an article entitled "The use of
 insect life tables in optimizing invasive pest distributional models"
 that would be published in Ecography. The dataset include two R script
 that used to generate physical model and the physiology combined model
 respectively. Our paper shows that the physiology combined model show good
 performance when applying ecological niche model in risk assessment. We
 addressed this by determining whether incorporating physiological data
 from life table analyses of an invasive insect, Drosophila suzukii,
 improved predictions of ecological niche models. The dataset also include
 the physiology data D. suzukii that we assembled for running our
 physiology combined model.
DOI: 10.5061/dryad.9s4mw6mh3
title: GARD 1.5 range shapefiles used in: Global diversity patterns are explained by diversification rates at ancient, not shallow, timescales

description: Explaining global species richness patterns is a “Holy Grail” of ecology
 and evolution. These richness patterns are often attributed to spatial
 variation in diversification rates (speciation minus extinction).
 Surprisingly, prominent studies of birds, fish, and angiosperms reported
 higher diversification rates at higher latitudes (mismatched with
 richness). Yet these studies only examined diversification rates at
 relatively recent timescales. Here, we quantify global richness patterns
 among lizard and snake species (10,213; 94%) and explore their underlying
 causes. We found that diversification rates at more recent timescales in
 squamates also show mismatched patterns of rates and richness. However,
 diversification rates at deeper timescales were positively related to
 richness. These observations may help resolve the paradoxical results of
 previous studies. Remarkably, these diversification patterns are largely
 unrelated to climate. Instead, higher tropical richness is related to
 ancient occupation of tropical regions. Thus, these large-scale diversity
 patterns are only understood by considering climate, deep-time
 diversification rates, and the time spent in different regions.
description: This data set contains range shapefiles for the majority of
 terrestrial squamates globally.  It is an update to GARD 1.0.  Range
 shapefiles for new species were created using the same methods as version
 1.0, described fully in: Roll, U., Feldman, A., Novosolov, M., Allison, A., Bauer, A., Bernard, R., Bohm, M., Chirio, L., Collen, B., Colli, G.R., Dabul, L., Das, I., Doan, T., Grismer, L., Herrera, F.C., Hoogmoed, M., Itescu, Y., Kraus, F., LeBreton, M., Lewin, A., Martins, M., Maza, E., Meirte, D., Nagy, Z., Nogueira, C.C., Pauwels, O.S.G., Pincheira-Donoso, D., Powney, G., Sindaco, R., Tallowin, O., Torres-Carvajal, O., Trape, J.F., Uetz, P., Vidan, E. Wagner, P., Wang, Y.Z., Orme, D., Grenyer, R. and Meiri, S. 2017. The global distribution of tetrapods reveals a need for targeted reptile conservation. Nature Ecology & Evolution 1: 1677-1682. doi.org/10.1038/s41559-017-0380-7.
DOI: 10.6076/d1mk58
title: Data from: Precisely timed theta oscillations are selectively required during the encoding phase of memory

description: Brain oscillations have been hypothesized to support cognitive function by
 coordinating spike timing within and across brain regions, yet it is often
 not known when timing is either critical for neural computations or an
 epiphenomenon. The entorhinal cortex and hippocampus are necessary for
 learning and memory and exhibit prominent theta oscillations (6–9 Hz),
 which are controlled by pacemaker cells in the medial septal area. Here we
 show that entorhinal and hippocampal neuronal activity patterns were
 strongly entrained by rhythmic optical stimulation of parvalbumin-positive
 medial septal area neurons in mice. Despite strong entrainment, memory
 impairments in a spatial working memory task were not observed with pacing
 frequencies at or below the endogenous theta frequency and only emerged at
 frequencies ≥10 Hz and specifically when pacing was targeted to maze
 segments where encoding occurs. Neural computations during the encoding
 phase were therefore selectively disrupted by perturbations of the timing
 of neuronal firing patterns.
description: Electrophysiological data was collected from the hippocampus or
 the medial entorhinal cortex of mouse brains. Data has been appropriately
 filtered and downsampled for further analysis. 
description: See README for detailed descriptions of the dataset.
DOI: 10.5061/dryad.cvdncjt4n
title: Bioenergetic consequences of sex-specific mitochondrial DNA evolution

description: Doubly uniparental inheritance (DUI) represents a notable exception to the
 general rule of strict maternal inheritance (SMI) of mitochondria in
 metazoans. This system entails the coexistence of two mitochondrial
 lineages (F- and M-type) transmitted separately through oocytes and sperm,
 thence providing an unprecedented opportunity for the mitochondrial genome
 to evolve adaptively for male functions. In this study, we explored the
 impact of a sex-specific mitochondrial evolution upon gamete bioenergetics
 of DUI and SMI bivalve species, comparing the activity of key-enzymes of
 glycolysis, fermentation, fatty acid metabolism, tricarboxylic acid cycle,
 oxidative phosphorylation and antioxidant metabolism. Our
 findings suggest reorganized bioenergetic pathways in DUI gametes compared
 to SMI gametes. This generally results in a decreased enzymatic
 capacity in DUI sperm with respect to DUI oocytes, a limitation especially
 prominent at the terminus of the electron transport system. This
 bioenergetic remodelling fits a reproductive strategy that does not
 require a high energy input and could potentially link with the
 preservation of the paternally-transmitted mitochondrial genome in DUI
 species. Whether this phenotype may derive from positive or relaxed
 selection acting on DUI sperm is still uncertain.
DOI: 10.5061/dryad.95x69p8m1
title: Transcriptomic analysis reveals potential candidate pathways and genes involved in toxin biosynthesis in true toads

description: Synthesized chemical defenses have broadly evolved across countless taxa
 and are important in 30 shaping evolutionary and ecological interactions
 within ecosystems. However, the underlying 31 genomic mechanisms by which
 these organisms synthesize and utilize their toxins are relatively 32
 unknown. Herein, we use comparative transcriptomics to uncover potential
 toxin synthesizing 33 genes and pathways, as well as interspecific
 patterns of toxin synthesizing genes across ten 34 species of North
 American true toads (Bufonidae). Upon assembly and annotation of the ten
 35 transcriptomes, we explored patterns of relative gene expression and
 possible protein-protein 36 interactions across the species to determine
 what genes and/or pathways may be responsible for 37 toxin synthesis. We
 also tested our transcriptome dataset for signatures of positive selection
 to 38 reveal how selection may be acting upon potential toxin producing
 genes. We assembled high 39 quality transcriptomes of the bufonid parotoid
 gland, a tissue not often investigated in other 40 bufonid related RNAseq
 studies. We found several genes involved in metabolic and biosynthetic 41
 pathways (e.g. steroid biosynthesis, terpenoid backbone biosynthesis,
 isoquinoline biosynthesis, 42 glucosinolate biosynthesis) that were
 functionally enriched and/or relatively expressed across the 43 ten focal
 species that may be involved in the synthesis of alkaloid and steroid
 toxins, as well as 44 other small metabolic compounds that cause
 distastefulness in bufonids. We hope that our study 45 lays a foundation
 for future studies to explore the genomic underpinnings and specific
 pathways 46 of toxin synthesis in toads, as well as at the
 macroevolutionary scale across numerous taxa that 47 produce their own
 defensive toxins.
DOI: 10.5061/dryad.83bk3j9rx
title: Data from: Backfire effects after correcting misinformation are strongly associated with reliability

description: The backfire effect is when a correction increases belief in the very
 misconception it is attempting to correct, and it is often used as a
 reason not to correct misinformation. The current study aimed to test
 whether correcting misinformation increases belief more than a
 no-correction control. Furthermore, we aimed to examine whether item-level
 differences in backfire rates were associated with test-retest reliability
 or theoretically meaningful factors. These factors included
 worldview-related attributes, namely perceived importance and strength of
 pre-correction belief, and familiarity-related attributes, namely
 perceived novelty and the illusory truth effect. In two nearly identical
 experiments, we conducted a longitudinal pre/post design with N = 388 and
 532 participants. Participants rated 21 misinformation items and were
 assigned to a correction condition or test-retest control. We found that
 no items backfired more in the correction condition compared to
 test-retest control or initial belief ratings. Item backfire rates were
 strongly negatively correlated with item reliability (⍴ = -.61 / -.73) and
 did not correlate with worldview-related attributes. Familiarity-related
 attributes were significantly correlated with backfire rate, though they
 did not consistently account for unique variance beyond reliability. While
 there have been previous papers highlighting the non-replicable nature of
 backfire effects, the current findings provide a potential mechanism for
 this poor replicability. It is crucial for future research into backfire
 effects to use reliable measures, report the reliability of their
 measures, and take reliability into account in analyses. Furthermore,
 fact-checkers and communicators should not avoid giving corrective
 information due to backfire concerns.
DOI: 10.5061/dryad.4xgxd259g
title: Using machine learning to model nontraditional spatial dependence in occupancy data

description: Spatial models for occupancy data are used to estimate and map the true
 presence of a species, which may depend on biotic and abiotic factors as
 well as spatial autocorrelation. Traditionally researchers have accounted
 for spatial autocorrelation in occupancy data by using a correlated
 normally distributed site-level random effect, which might be incapable of
 modeling nontraditional spatial dependence such as
 discontinuities and abrupt transitions. Machine learning approaches have
 the potential to model nontraditional spatial dependence, but these
 approaches do not account for observer errors such as false absences. By
 combining the flexibility of Bayesian hierarchal modeling and machine
 learning approaches, we present a general framework to model occupancy
 data that accounts for both traditional and nontraditional spatial
 dependence as well as false absences. We demonstrate our framework using
 six synthetic occupancy data sets and two real data sets. Our results
 demonstrate how to model both traditional and nontraditional spatial
 dependence in occupancy data which enables a broader class of spatial
 occupancy models that can be used to improve predictive accuracy and model
 adequacy.
description: The file 'Serengeti.csv' includes Thomson’s gazelle
 data used in our study. The original data file is obtained from Hepler et
 al. (2018), who reported the presence and absence of Thomson’s gazelle at
 195 sites within Serengeti National Park, Tanzania. The sites were sampled
 using a network of 179 motion-sensitive and thermally activated
 cameras. The file 'Sugarglider.csv' includes
 sugar glider data that is used in our study. The original data file is
 obtained from Stojanovic (2019), who reported the presence and absence of
 sugar gliders. The data were collected during four or five site visits
 made to 100 sites in the Southern Forest region of Tasmania.
 The zip file 'Serengeti.zip' includes the associated
 shapefile for the sampling grid in Serengeti National Park, Tanzania
 where Thomson’s gazelle data were collected. The zip
 file 'Sugarglider.zip' includes the associated shapefile for the
 Southern Forest region of Tasmania where the sugar glider data were
 collected.
DOI: 10.5061/dryad.w3r2280r6
title: Optic flow and odometry data from intelrealsense camera

description: Insects rely on the perception of image motion, or optic flow, to estimate
 their velocity relative to nearby objects. This information provides
 important sensory input for avoiding obstacles. However, certain
 behaviors, such as estimating the absolute distance to a landing target,
 accurately measuring absolute distance travelled, and estimating the
 ambient wind speed require decoupling optic flow into its component parts:
 absolute ground velocity and distance to nearby objects. Behavioral
 experiments suggest that insects perform these calculations, but their
 mechanism for doing so remains unknown. Here we present a novel algorithm
 that combines the geometry of dynamic forward motion with known features
 of insect visual processing to provide a hypothesis for how insects might
 \textit{directly} estimate absolute ground velocity from a combination of
 optic flow and acceleration information. Our
 robotics-inspired-biology approach reveals three critical
 requirements. First, absolute ground velocity can only be
 directly estimated from optic flow during times of active acceleration and
 deceleration. Second, spatial pooling of optic flow across a receptive
 field helps to alleviate the effects of noise and/or low resolution visual
 systems. Third, averaging velocity estimates from multiple receptive
 fields further helps to reject noise. Our algorithm provides a
 hypothesis for how insects might estimate absolute velocity from vision
 during active maneuvers, and also provides a theoretical framework for
 designing fast analog circuitry for efficient state estimation that can be
 applied to insect-sized robots.   
description: Data was collected with an Intel Realsense camera, and an
 overhead tracking camera. See paper for detail.
description: Data is intended to be used by the code given
 at https://github.com/florisvb/flivver.
DOI: 10.5061/dryad.sqv9s4n4f
title: Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests

description: Background: The East Asian subtropical evergreen broad-leaved forests
 (EBLFs) harbor remarkable biodiversity. However, their historical assembly
 remains unclear. To gain new insights into the assembly of this biome, we
 generated a molecular phylogeny of one of its essential elements, the
 tribe Perseeae (Lauraceae). Results: Our plastid tree topologies were
 robust to analyses based on different plastid regions, data partitioning,
 nucleotide substitution saturation and gap handling strategies. We found
 that Perseeae comprised six major clades and started to colonize the
 subtropical EBLFs of east Asia in the early Miocene. The diversification
 rates of Perseeae accelerated twice in the late Miocene. Conclusions: Our
 findings suggest that the intensified precipitation in East Asia in the
 early Miocene might have facilitated range expansions of the
 drought-sensitive subtropical EBLFs and establishment of Perseeae within
 this biome. By the late Miocene, assembly and diversification within the
 EBLFs had become rapid.
DOI: 10.5061/dryad.b5mkkwhdm
title: Permian–Triassic phylogenetic and morphologic evolution of rhynchonellide brachiopods

description: The Rhynchonellida is a major group of brachiopods that survived the “big
 five” mass extinctions and flourished after the Permian-Triassic (P-Tr)
 crisis. However, phylogenetic and character evolution in the
 Rhynchonellida across the P-Tr transition is poorly understood. In view of
 the widespread homoplasy across this order, we employ a tip-dated Bayesian
 analysis to reconstruct phylogenetic relationships for Late
 Permian–Triassic rhynchonellides. The same data were also analyzed using
 three other methods: undated Bayesian, equal-weighting, and
 implied-weighting parsimony. Compared with trees generated by other
 methods, those constructed by tip-dating best account for the homoplasy in
 this group, and are closer to previous assumptions on the evolution of
 this group. Based on the analyses of multiple trees, the major increase in
 lineage richness occurred in the Early and early Middle Triassic, and the
 richness in the Anisian almost reached its highest level in the Triassic.
 According to fossil records, a pronounced reduction in shell size and in
 the development of ornamentation occurred after the P-Tr extinction, which
 is largely due to the loss of large and highly-sculptured genera, and the
 diversification of small-sized and weakly-ornamented genera. Ancestral
 state estimation of shell size and development of ornamentation, coupled
 with comparisons of other characters, indicate that the Early–Middle
 Triassic mature “small-sized taxa” may have characters displayed by
 juveniles of their ancestors. This suggests that for these genera,
 paedomorphosis was possibly a strategy to survive and diversify in the
 harsh environment after the P-Tr extinction.