cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8cz8w9gqs
title: Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot-study from an invaded alpine streambed

description: An important focus of community ecology, including invasion biology, is to
 investigate functional trait diversity patterns to disentangle the effects
 of environmental and biotic interactions. However, a notable limitation is
 that studies usually rely on a small and easy to measure set of functional
 traits, which might not immediately reflect ongoing ecological responses
 to changing abiotic or biotic conditions, including those that occur at a
 molecular or physiological level. We explored the potential of using the
 diversity of expressed genes—functional genomic diversity (FGD)—to
 understand ecological dynamics of a recent and ongoing alpine invasion. We
 quantified FGD based on transcriptome data measured for 26 plant species
 occurring along adjacent invaded and pristine streambeds. We used an
 RNA-seq approach to summarize the overall number of expressed transcripts
 and their annotations to functional categories, and contrasted this with
 functional trait diversity (FTD) measured from a suite of characters that
 have been traditionally considered in plant ecology. We found greater FGD
 and FTD in the invaded community, independent of differences in species
 richness. However, the magnitude of functional dispersion was greater from
 the perspective of FGD than from FTD. Comparing FGD between congeneric
 alien-native species pairs, we did not find many significant differences
 in the proportion of genes whose annotations matched functional
 categories. Still, native species with a greater relative abundance in the
 invaded community compared with the pristine tended to express a greater
 fraction of genes at significant levels in the invaded community,
 suggesting that changes in FGD may relate to shifts in community
 composition. Comparisons of diversity patterns from the community- to the
 species-level offer complementary insights into processes and mechanisms
 driving invasion dynamics. FGD has the potential to illuminate cryptic
 changes in ecological diversity, and we foresee promising avenues for
 future extensions across taxonomic levels and macro-ecosystems. 
description: Assembled transcriptomes from RNA-seq data for 38 samples
 representing 26 unique plant species, as well as reference transcriptome
 assemblies for differential expression analysis of 10 native species
 (indicated in the README.txt file). See publication for detailed
 methods.
DOI: 10.5061/dryad.rfj6q57b6
title: Large and small herbivores have strong effects on tundra vegetation in Scandinavia and Alaska

description: Large and small mammalian herbivores are present in most vegetated areas
 in the Arctic, and often have large impacts on plant community composition
 and ecosystem functioning. The relative importance of different herbivores
 and especially how their specific impact on the vegetation varies across
 the Arctic is however poorly understood. Here, we investigate how large
 and small herbivores influence vegetation density and plant community
 composition in four arctic vegetation types in Scandinavia and Alaska. We
 used a unique set of exclosures, excluding only large (reindeer and
 muskoxen) or all mammalian herbivores (also voles and lemmings) for at
 least 20 years. We found that mammalian herbivores in general decreased
 Leaf Area Index, NDVI and abundance of vascular plants in all four
 locations, even though the strength of the effect and which herbivore type
 caused these effects differed across locations. In three locations,
 herbivore presence caused contrasting plant communities, but not in the
 location with lowest productivity. Large herbivores had a negative effect
 on plant height, whereas small mammalian herbivores increased species
 diversity by decreasing dominance of the initially dominating plant
 species. Above- or belowground disturbances caused by herbivores were
 found to play an important role in shaping the vegetation in all
 locations. Synthesis: Based on these results, we conclude that both small
 and large mammalian herbivores influence vegetation in Scandinavia and
 Alaska in a similar way, some of which can mitigate effects of climate
 change. We also see important differences across locations, but these
 depend rather on local herbivore- and plant community composition than
 large biogeographical differences among continents.
DOI: 10.5061/dryad.bnzs7h4bn
title: The role of individual behavioral traits on fishway passage attempt behavior

description: Variations in behavioural traits are widely recognised to drive animal
 behaviours exhibited within a population. However, information on how
 behaviour traits influence behaviour in anthropogenically modified
 habitats is lacking. Many habitats have become highly fragmented as a
 result of human processes. To mitigate this and improve habitat
 connectivity, wildlife passes are increasingly employed, with the aim of
 enabling animals to move freely between habitats. However, wildlife passes
 (e.g. fishways) are not always effective in achieving passage and it
 remains uncertain what factors play a role in an individual’s likelihood
 of passing successfully. This study measured three behavioural traits
 (boldness, exploration and activity) in juvenile brown trout (Salmo
 trutta; n =78) under field conditions within a river, and tested whether
 these behaviour traits influenced both the passage success and the
 behaviours exhibited during upstream fishway passage attempts. Although
 behavioural traits were found and collapsed into two behavioural trait
 dimensions, behavioural traits had low repeatability and so did not
 contribute to a personality spectrum. Boldness was found to negatively
 influence the number of passage attempts carried out by an individual and
 to positively influence passage success, with bolder individuals carrying
 out fewer attempts and having an increased probability of passage success.
 No behavioural traits were found to be related to other passage metrics
 (passage success, time until first attempt, and passage duration) during
 the first passage. But all three behavioural traits were significantly
 negatively related to the changes in passage behaviours at consecutive,
 successful passage attempts, with bolder, more exploratory and more active
 individuals passing through a fishway quicker on the second passage than
 on the first. This study suggests that bolder and more active individuals
 may perform better during fishway passage attempts, particularly within
 rivers where multiple barriers to movement exist.
DOI: 10.5061/dryad.0vt4b8h09
title: Recruitment limitation for three tree species in BCI, Panama

description: Recruitment limitation – the failure of a species to establish recruits at
 an available site – is a potential determinant of plant communities’
 structure, causing local communities to be a limited subset of the
 regional species pool. Recruitment limitation results from three
 mechanisms: i) lack of seed sources (i.e., source limitation), ii) failure
 of available seeds to reach recruitment sites (i.e., dispersal
 limitation), and iii) failure of arrived seeds to establish at a location
 (i.e., establishment limitation). Here, we evaluated the relative
 importance of these mechanisms in three co-occurring tree species
 (Dipteryx oleifera, Attalea butyracea, and Astrocaryum standleyanum) that
 share seed dispersers/predators. The study was set up on Barro Colorado
 Island (Panama) at 62 1-ha sites with varying tree densities. Source
 limitation was estimated as the proportion of sites that would be reached
 by seeds if seeds were distributed uniformly. Dispersal limitation was
 estimated from the number of sites with seeds in the soil bank.
 Establishment limitation was evaluated by measuring germination and 1-year
 survival in seed addition experiments. The effect of conspecific and
 heterospecific densities on the mechanisms was evaluated at three spatial
 scales (1, 5 and 9 ha). For all species, seed predation was the most
 important recruitment component (~80% decrease in seed survival).
 Establishment varied among species and was affected by conspecific and
 heterospecific species densities across spatial scales. Given that species
 identity, distribution and seed dispersal/predation affect recruitment at
 multiple scales, multiscale studies are required to understand how
 recruitment limitation determines community structure in tropical forests.
description: Extent: 62 1ha site located at Barro Colorado Island
 (Panama) Species: Attalea butyracea, Astrocaryum
 standleyanum and Dipteryx oleifera Tree
 mapping using aerial imagery and ground surveys Seed
 density and predation: soil survey in the first 10cm of soil looking for
 seeds of the species studied Seed germination: Seed
 addition experiment and survey after 4 months and 12 months to record
 germination and survival.
DOI: 10.5061/dryad.s7h44j172
title: Elevated temperature increases reproductive investment in less preferred mates in the invasive European corn borer moth

description: Rapidly changing environments may weaken sexual selection and lead to
 indiscriminate mating by interfering with the reception of mating signals
 or by increasing the costs associated with mate choice. If temperature
 alters sexual selection, it may impact population response and adaptation
 to climate change. Here, we examine how differences in temperature of the
 mating environment influence reproductive investment in the European corn
 borer moth (Ostrinia nubilalis). Mate preference in this species is known
 to be related to pheromone usage, with assortative mating occurring
 between genetically distinct E- and Z-strains that differ in the
 composition of female and male pheromones. We compared egg production
 within and between corn borer lines derived from four different
 populations that vary in pheromone composition and other traits. Pairs of
 adults were placed in a mating environment that matched the pupal
 environment (ambient temperature) or at elevated temperature (5ºC above
 the pupal environment). At ambient temperature, we found that within-line
 pairs produced eggs sooner and produced more egg clusters than
 between-line pairs. However, at elevated temperature, between-line pairs
 produced the same number of egg clusters as within-line pairs. These
 results suggest that elevated temperature increased investment in matings
 with typically less preferred, between-line mates. This increased
 investment could result in changes in gene flow among corn borer
 populations in warming environments.
DOI: 10.5061/dryad.mgqnk990f
title: Data supplement for: Disrupting cortico-cerebellar communication impairs dexterity

description: This dataset, along with the corresponding code, is a supplement to
 “Disrupting cortico-cerebellar communication impairs dexterity” (Guo*,
 Sauerbrei* et al., eLife 2021). It consists of single-unit
 electrophysiology data from the pontine nuclei, Purkinje cells, cerebellar
 nuclei, and motor cortex of awake mice, along with measurements of the
 hand position of mice performing reaching movements. These data address
 the question of how the dynamics of motor cortex and cerebellum interact
 to control skilled reaching. First, we recorded from neurons in the
 pontine nuclei (PN), the bridge between cerebral cortex and the
 cerebellum, as mice reached to and grasped food pellets. Most PN neurons
 were strongly modulated by an acoustic go cue, by movement onset, or by
 both. Optogenetic stimulation of the PN strongly entrained spiking in
 Purkinje cells and the cerebellar nuclei, and induced transients in some
 motor cortical neurons. PN stimulation during a reach-to-grasp task
 induced a range of deficits, including decreases in success rate,
 increases in the standard deviation of hand position, increases in
 movement duration, and overreaching of the target. During movement, PN
 stimulation altered neural activity in the cerebellar nuclei and motor
 cortex, and a velocity decoding analysis revealed that these shifts in
 activity were consistent with the kinematic effects of stimulation. Our
 findings suggest that interaction between motor cortex and the cerebellum
 is essential for fine-tuning movements to enable accurate and precise
 behavior. Code required to generate the figures is available in the
 companion repository on Zenodo, and a list of which scripts generate which
 figure panels is contained in /docs/README.
description: Experimental and data processing methods are described in detail
 in Guo*, Sauerbrei* et al. (eLife 2021).
DOI: 10.7291/d1310w
title: Data for: The coevolutionary dynamics of cryptic female choice

description: In contrast to sexual selection on traits that affect interactions between
 the sexes before mating, little theoretical research has focused on the
 coevolution of post-mating traits via cryptic female choice (when females
 bias fertilization toward specific males). We used simulation models to
 ask (1) whether and if so how non-directional cryptic female choice
 (female-by-male interactions in fertilization success) causes deviations
 from models that focus exclusively on male-mediated post-mating processes
 and (2) how the risk of sperm competition, the strength of cryptic female
 choice, and tradeoffs between sperm number and sperm traits interact to
 influence the coevolutionary dynamics between cryptic female choice and
 sperm traits. We found that incorporating cryptic female choice can result
 in males investing much less in their ejaculates than predicted by models
 with sperm competition only. We also found that cryptic female choice
 resulted in the evolution of genetic correlations between cryptic female
 choice and sperm traits, even when the strength of cryptic female choice
 was weak, and the risk of sperm competition was low. This suggests that
 cryptic female choice may be important even in systems with low multiple
 mating. These genetic correlations increased with the risk of sperm
 competition and as the strength of cryptic female choice increased. When
 the strength of cryptic female choice and risk of sperm competition was
 high, extreme co-divergence of sperm traits and cryptic female choice
 preference occurred even when the sperm trait traded off with sperm
 number. We also found that male traits lagged behind the evolution of
 female traits; this lag decreased with increasing strength of cryptic
 female choice and risk of sperm competition. Overall, our results suggest
 that cryptic female choice deserves more attention theoretically and may
 be driving trait evolution in ways just beginning to be explored.
description: Contains Julia code related to running the model and R code
 related to processing the data/generating figures, and creating the
 supplemental web app. Contains data used in the paper.
DOI: 10.5061/dryad.1zcrjdfsj
title: Gene presence absence in Serratia plymuthica strains

description: Background: The Serratia plymuthica UBCF_13 is a phylloplane associated
 plant bacterium showing antifungal activity. Whole genome sequence
 provides information to get more insight about evolutionary study, unique
 traits in the genome and possibility to explore potential of this
 microorganism for future study. Here, we report the genome sequence of S.
 plymuthica UBCF_13 and the comparison with other seventeen strains.
 Methods: A pan-genome based method was used to identify the
 core-genome and the the gene
 presence or absence in of the S.
 plymuthica strains Results: The pan-genome
 idenfied the gene presence and absence
 in the S. plymuthica strains. The total genes was
 10455. Comparative genomics analysis revealed 3.315 core
 proteins/ genes shared among 18 strains. The genome of the
 UBCF_13 harbors 488 unique genes, of which 300 genes are only contained by
 this strain.
description: Comparative
 genomics analysis was carried out using genome sequences of UBCF_13 from
 this research and 17 whole sequenced genomes of other <i>Serratia
 plymuthica </i>strains retrieved from NCBI’s GenBank. The genomes
 were reannotated using Prokaryotic genome annotation (Prokka, Galaxy
 Version 1.14.6+galaxy0) (Prokka, RRID:SCR_014732). Identification of genes
 shared between the strains, and presence-absence gene set were carried out
 using Roary ((Galaxy Version 3.13.0+galaxy1) (Roary, RRID:SCR_018172) with
 minimum percentage identity for blastp was 70%.
DOI: 10.34740/kaggle/dsv/14646652
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.3886/e244704
title: Skilled Nursing Facility Cost Report

description: The Skilled Nursing Facility (SNF) Cost Report dataset is a public use 
file that provides select measures from the skilled nursing 
facility annual cost report. This data includes provider information 
such as facility characteristics, utilization data, cost and charges by 
cost center (in total and for Medicare), Medicare settlement data, and 
financial statement data organized by CMS Certification Number.
DOI: 10.3886/e244704v1
title: Skilled Nursing Facility Cost Report

description: The Skilled Nursing Facility (SNF) Cost Report dataset is a public use 
file that provides select measures from the skilled nursing 
facility annual cost report. This data includes provider information 
such as facility characteristics, utilization data, cost and charges by 
cost center (in total and for Medicare), Medicare settlement data, and 
financial statement data organized by CMS Certification Number.
DOI: 10.5061/dryad.zpc866t8v
title: Mineral nitrogen nutrition of Fagus sylvatica L roots colonized by ectomycorrhizal fungi in native forest soil

description: The aim of this study was to examine the transcription-level response of a
 symbiotic system comformed by the host tree Fagus sylvatica L (European
 beech) and the root-associated mycobiota to fluctuations in ammonium and
 nitrate availability in the soil. The experiment was conducted with young
 trees grown at a natural regeneration forest. We used 15N stable isotopes
 in combination with DNA-based and RNA-based molecular methods and Illumina
 sequencing. We report data on the beech root-associated fungal community
 structure obtained by metabarcoding of the fungal ITS2 region,
 transcriptome data from the fungal community associated to the tree roots,
 and transcriptome data from Fagus sylvatica L in response to ammonium or
 nitrate application to the soil. We also report data from soil ammonium-N,
 soil-nitrate-N, tree and soil dry mass, root 15N, root N, root C, root
 carbohydrates, root ammonium-N, root nitrate-N, soil pH, and climate data
 from the experiment.
description: Young beech trees grown in a natural regeneration forest were
 excavated with the surrounding soil using cylinders. After nearly 21 weeks
 of adjustement period inside cosms, the tree roots were supplied with 15-N
 labeled ammonium, or 15N-labeled nitrate solutions, or demineralized water
 (control). DNA was isolated from the root tips and used for metabarcoding
 of the fungal ITS2 marker gene and sequenced by Illumina MiSeq. RNA was
 also isolated from the same root tip samples and used for transcriptome
 analyses of both the fungi and the host in response to nitrogen treatment
 relative to control conditions. Soil ammonium-N, Soil-nitrate-N, tree and
 soil dry mass, root 15N, root N, root C, root carbohydrates, root
 ammonium-N, root nitrate-N, soil pH, and climate data were
 measured.
DOI: 10.5061/dryad.bzkh18993
title: Population abundance data and species range maps

description: Aim – The abundant-center hypothesis (ACH) predicts a negative
 relationship between species abundance and the distance to geographic
 range center. Since its formulation, empirical tests of the ACH have
 involved different settings (e.g. the distance to the ecological niche or
 to the geographic range center), but studies found contrasting support for
 this hypothesis. Here, we evaluate whether these discrepancies might stem
 from differences regarding the context in which the ACH is tested
 (geographical or environmental), how distances are measured, how species
 envelopes are delineated, how the relationship is evaluated and which data
 are used. Location – Americas. Time Period – 1800-2017. Major taxa studied
 – mammal, bird, fish and tree seedlings. Methods – Using published
 abundance data for 801 species, together with species range maps, we
 tested the ACH using three distance metrics in both environmental and
 geographical spaces with range and niche envelopes delineated using two
 different algorithms, totaling 12 different settings. We then evaluated
 the distance-abundance relationship using correlation coefficients
 (traditional approach) and mixed-effect models to reduce the effect of
 sampling noise on parameter estimates. Results – Similar to previous
 studies, correlation coefficients indicated an absence of effect of
 distance on abundance for all taxonomic groups and settings. In contrast,
 mixed-effect models highlighted relationships of various strengths and
 shapes, with a tendency for more theoretically-supported settings to
 provide stronger support for the ACH. The relationships were however not
 consistent across taxonomic groups and settings, and were sometimes even
 opposite to ACH expectations. Main conclusions – We found mixed and
 inconclusive results regarding the ACH. These results corroborate recent
 findings, and suggest either that our ability to predict abundances from
 the location of populations within geographical or environmental spaces is
 low, or that the data used here have a poor signal-to-noise-ratio. The
 latter calls for further testing on other datasets using the same range of
 settings and methodological framework.
description: All the data used in this paper have either already been
 published (see Dallas et al., 2017 and Osorio-Olvera et al., 2020) or are
 freely available (range maps can be dowloaded
 here https://www.fs.fed.us/nrs/atlas/littlefia/ for trees and
 here https://www.iucnredlist.org/resources/spatial-data-download for
 mammals, fish and birds; climatic data can be downloaded here
 https://www.worldclim.org/data/worldclim21.html).
description: The R script showing how these data can be used to draw
 inferences is available on github
 (https://github.com/Mathieu-Chevalier/ACH-GEB). Requires R
 packages: raster, ade4, data.table, dplyr, boa, rgeos, ks, tidymv,
 ggplot2,
 robustbase, car, spatstat, ecospat, reshape2, mgcv, gratia, runjags, R2jags, qpcR, plyr, ggpubr, raptr, PBSmapping to load all RData files.