cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4xgxd255j
title: Exploring the use of environmental DNA (eDNA) to detect animal taxa in the mesopelagic zone

description: Animal biodiversity in the ocean’s vast mesopelagic zone is relatively
 poorly studied due to technological and logistical challenges.
 Environmental DNA (eDNA) analyses show great promise for efficiently
 characterizing biodiversity and could provide new insight into the
 presence of mesopelagic species, including those that are missed by
 traditional net sampling. Here, we explore the utility of eDNA for
 identifying animal taxa. We describe the results from an August 2018
 cruise in Slope Water off the northeast United States. Samples for eDNA
 analysis were collected using Niskin bottles during 5 CTD casts. Sampling
 depths along each cast were selected based on the presence of biomass as
 indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the
 18S V9 gene region was used to assess taxonomic diversity. Environmental
 DNA metabarcoding results were compared with those from net-collected
 (MOCNESS) plankton samples. We found that the MOCNESS sampling recovered
 more animal taxa, but the number of taxa detected per liter of water
 sampled was significantly higher in the eDNA samples. Environmental DNA
 was especially useful for detecting delicate gelatinous animals which are
 undersampled by nets. We also detected eDNA changes in community
 composition with depth, but not with sample collection time (day vs.
 night). We provide recommendations for applying eDNA-based methods in the
 mesopelagic including the need for studies enabling interpretation of eDNA
 signals and improvement of barcode reference databases.
description: <strong>Environmental DNA fastq.gz sequences</strong>
 - fastq.gz files for forward and reverse reads for the 18S V9 barcode
 marker <strong>Environmental DNA metadata
 file</strong> - list of eDNA samples sequenced with their lab sample
 names (corresponding to fastq.gz sample names) and collecting information
 (cast, depth, time of day). <strong>MOCNESS
 zooplankton metabarcoding fastq.gz </strong>- fastq.gz files for
 forward and reverse reads for the 18S V9 barcode marker
 <strong>MOCNESS metadata file</strong> - list of
 MOCNESS samples sequenced including lab sample names (corresponding to
 fastq.gz file names), collecting information (net number and depth range),
 and size fraction (333-1000 um and &gt;1000 um).
 <strong>MOC7-Sanger fasta file</strong> - 18S V9 DNA
 sequences in fasta format for large individuals and fragments removed from
 the MOCNESS samples.
DOI: 10.6084/m9.figshare.31164304
title: Data and Scripts for Metadynamics Simulations of Crystallizing Yukawa Fluids

description: LAMMPS and PLUMED scripts that run metadynamics simulations of crystallizing Yukawa plasmas. Also contains processes free energy surfaces.
DOI: 10.6084/m9.figshare.31164304.v1
title: Data and Scripts for Metadynamics Simulations of Crystallizing Yukawa Fluids

description: LAMMPS and PLUMED scripts that run metadynamics simulations of crystallizing Yukawa plasmas. Also contains processes free energy surfaces.
DOI: 10.5061/dryad.wdbrv15js
title: Molding 3D curved structures by selective heating

description: It is of interest to fabricate curved surfaces in three dimensions from
 homogeneous material in the form of flat sheets. The aim is not just to
 obtain a surface which has a desired intrinsic Riemannian metric, but to
 get the desired embedding in R^3 up to translations and rotations. In this
 paper, we demonstrate three generic methods of molding a flat sheet of
 thermo-responsive plastic by selective contraction induced by targeted
 heating. These methods do not involve any cutting and gluing, which is a
 property they share with origami. The first method is inspired by
 tailoring, which is the usual method for making garments out of plain
 pieces of cloth. Unlike usual tailoring, this method produces the desired
 embedding in R^3. The second method just aims to bring about the desired
 new Riemannian metric via an appropriate pattern of local contractions,
 without directly controlling the embedding. The third method is based on
 triangulation, and seeks to induce the desired local distances. This
 results in getting the desired embedding in R^3. The second and the third
 methods, and also the first method for the special case of surfaces of
 revolution, are algorithmic in nature. We explain these methods, and show
 examples.
description: Matlab codes to generate patterns. We present Matlab codes to
 implement algorithms to convert a plane sheet to any surface by only
 contracting (and not expanding) some parts of it.
DOI: 10.5061/dryad.z612jm686
title: Data from: Exploratory and confirmatory research in the open science era

description: 1. Applied ecological research is increasingly inspired by the Open
 Science movement. However, new challenges about how we define our science
 when biodiversity data is being shared and re-used are not solved. Among
 these challenges is the risk associated with blurring the distinction
 between research that mainly seeks to explore patterns with no a-priori
 articulated hypotheses (exploratory research), and research that
 explicitly tests a-priori formulated hypotheses (confirmatory research).
 2. A rapid screening of a random selection of peer-reviewed articles
 suggests that neither experimental protocols nor hypothesis-testing sensu
 stricto are common in applied ecological research. In addition, most
 experiments are carried out on small spatial scales, which contrast with
 current global policy needs and research trends towards addressing large
 spatial and temporal scales. This latter trend make it unfeasible for
 policy to rely mainly on insights gained from experimental research. 3. To
 solve fundamental local, regional and global societal challenges, we need
 both exploratory and confirmatory research, and the fundamental (but
 different) role that hypothesis-testing and prediction play in applied
 ecological research should be revaluated. 4. A clearer distinction between
 exploratory and confirmatory research could be facilitated by allocating
 journal sections to different types of research; embracing new tools
 offered by the open science era, such as pre-registration of hypothesis;
 establishing new systems where post-hoc hypotheses emerging through
 exploration can also be registered for later testing; and more broad
 adoption of causal inference methods that foster more structured testing
 of hypotheses about causal mechanisms from observational biodiversity
 data. 5. Synthesis and applications. To gain the full benefits from the
 open science era, researchers, funding bodies and journal editors should
 explicitly consider incentives that encourage openness about methods and
 approaches, as well as value the full plurality of scientific approaches
 needed to address questions in conservation science.
description: A full description of the dataset, including data collection and
 the procedures for random selection of papers to include, is given in
 Appendix 1 accompanying in the paper. There is also additional
 suppelementary information available at the OSF registration located
 at https://doi.org/10.17605/OSF.IO/W3S49.
DOI: 10.5068/d1w37t
title: Data from: Physical and social cues shape nest-site preference and prey capture behavior in social spiders

description: Animals often face conflicting demands when making movement decisions. To
 examine the decision process of social animals, we evaluated nest site
 preferences of the social spider Stegodyphus dumicola. Colonies engage in
 collective web building, constructing three-dimensional nests and
 two-dimensional capture webs on trees and fences. We examined how
 individuals and groups decide where to construct a nest based on habitat
 structure and conspecific presence. Individuals had a strong preference
 for three dimensional-substrates and conspecific presence. Groups were
 then provided with conflicting options of three-dimensional substrates vs.
 two-dimensional substrates with a conspecific. Groups preferred the
 three-dimensional structures without pre-settled conspecifics over a
 two-dimensional substrate with conspecifics. When a group fragmented and
 individuals settled on both substrates, the minority group eventually
 joined the majority. Before rejoining, the collective prey capture
 behavior of divided groups improved with the size of the majority
 fragment. The costs of slow responses to prey for split groups and weak
 conspecific attraction may explain why dispersal is rare in these spiders.
description: Dataset contents overview 
 <b>Sheet
 name:</b> 
 <b>Content:</b> 
 
 Indiv_Choice Decisions made by individual
 spiders between closed and open structures. Column A is the source colony,
 column B is the individual ID and column C is the decision made.
 
 Paired_Choice Decisions made by individual
 spiders between open structure with a conspecific, and open structure
 without a conspecific. Column A is the source colony, Column B is the
 individual choice Trial_Groups 
 Foraging aggressiveness for
 each group. Column A is the trial number, Column B is the Group Number,
 Column C is the number of individuals on the open structure, Column D is
 the number of individuals on the closed strucure, Column E is the
 proportion of individuals on the structure with the majority of
 individuals, Column F is the foraging aggressiveness, Column G is the
 total number of attackers, Column H is the number of attackers that came
 from the closed structure, Column I is the number of attackers that came
 from the open structure, Column J is the day the trial took
 place.
DOI: 10.5061/dryad.ncjsxksr0
title: Data from: The arboreal ants of a Neotropical rainforest show high species density and comprise one third of the ant fauna

description: In tropical rainforests, the ant community can be divided into ground and
 arboreal faunas. Here we report a thorough sampling of the arboreal ant
 fauna of La Selva Biological Station, a Neotropical rainforest site.
 Forty-five canopy fogging samples were centered around large trees.
 Individual samples harbored an average of 35 ant species, with up to 55
 species in a single sample. The fogging samples yielded 163 observed
 species total, out of a statistically estimated 199 species. We found no
 relationship between within-sample ant richness and focal tree species,
 nor were the ant faunas of nearby trees more similar to each other than
 the faunas of widely spaced trees. Species density was high and beta
 diversity was low: a single column of vegetation typically harbors at
 least a fifth of the entire arboreal ant fauna. Considering the entire
 fauna, based on 23,326 species occurrence records using a wide variety of
 collecting methods, 182 of 539 observed species (196 of 605, estimated
 statistically) were entirely arboreal. The arboreal ant fauna is thus
 about a third of the total La Selva ant fauna, a robust result because
 inventory completeness was similar for ground and arboreal ants. The
 taxonomic history of discovery of the species that make up the La Selva
 fauna reveals no disproportionately large pool of undiscovered ant species
 in the canopy. The "last biotic frontier" for tropical ants has
 been the rotten wood, leaf litter, and soil of the forest floor.
description: canopy fogging
description: Three datasets are provided that are the basis of analyses in
 "The arboreal ants of a Neotropical rainforest show high species
 density and comprise one third of the ant fauna," in Biotropica. One
 dataset is ant species occurrences in a set of canopy fogging samples. One
 dataset is individual specimen records for the entire La Selva ant fauna.
 One dataset is a species list for the entire fauna, with information on
 frequency and microhabitat (mostly ground vs. canopy).
DOI: 10.5061/dryad.ffbg79cqt
title: Data from: Sleep, major depressive disorder and Alzheimer’s disease: a Mendelian randomisation study

description: Objective To explore the causal relationships between sleep, major
 depressive disorder (MDD), and Alzheimer’s disease (AD). Methods We
 conducted bi-directional two-sample Mendelian randomisation analyses.
 Genetic associations were obtained from the largest genome-wide
 association studies currently available in UK Biobank (N=446,118), the
 Psychiatric Genomics Consortium (N=18,759), and the International Genomics
 of Alzheimer’s Project (N=63,926). We used the inverse variance weighted
 Mendelian randomisation method to estimate the causal effects,
 and the weighted median and MR-Egger for sensitivity analyses to
 test for pleiotropic effects. Results We found that higher risk of AD was
 significantly associated with being a “morning person” (odds ratio
 (OR)=1.01, P=0.001), shorter sleep duration (self-reported: β=-0.006,
 P=1.9×10-4; accelerometer-based: β=-0.015, P=6.9×10-5), less likely to
 report long sleep (β=-0.003, P=7.3×10-7), earlier timing of the least
 active 5 hours (β=-0.024, P=1.7×10-13), and a smaller number of sleep
 episodes (β=-0.025, P=5.7×10-14) after adjusting for multiple comparisons.
 We also found that higher risk of AD was associated with lower risk of
 insomnia (OR=0.99, P=7×10-13). However, we did not find evidence that
 these abnormal sleep patterns were causally related to AD or a significant
 causal relationship between MDD and risk of AD. Conclusion We found that
 AD may causally influence sleep patterns. However, we did not find
 evidence supporting a causal role of disturbed sleep patterns in AD or
 evidence for a causal relationship between MDD and AD risk.
DOI: 10.5061/dryad.stqjq2c0c
title: Consumption of red maple in anticipation of beech mast-seeding drives reproduction in Eastern chipmunks

description: 1. Understanding the determinants of reproduction is a central question in
 evolutionary ecology. In pulsed resources environments, the reproduction
 and population dynamics of seed consumers is driven by pulsed production
 of seeds by trees, or mast-seeding. In Southern Québec, eastern chipmunks
 (Tamias striatus) exclusively reproduce during the summer before and the
 spring after a mast-seeding event of American beech. They thus seem to
 anticipate beech mast by reproducing during early summer, so that
 juveniles can emerge at the time of maximum beechnut abundance during late
 summer. 2. However, the cues allowing chipmunks to anticipate beech mast
 remain unknown, and the existence of the anticipation process itself has
 been questioned. To tackle those issues, we investigated the links between
 the nutritional ecology and reproduction of adult chipmunks and compared
 their spring diet in mast- vs post-mast years. 3. We monitored female’s
 reproductive status (N=446), analyzed cheek pouch contents at capture
 (n=3761 captures), and recorded seed production by deciduous trees on
 three different sites in Mont-Sutton from 2006 to 2018. 4. Results
 revealed a systematic shift in chipmunk diet towards red maple seeds in
 springs preceding a beech mast, with red maple seeds composing more than
 77% of chipmunk diet. However, red maple consumption was unrelated to red
 maple production, but was related to beech seed production in the upcoming
 fall. We also found that red maple consumption best predicted the
 proportion of females in summer estrus. 5. Our results confirm that
 chipmunks anticipate beech mast-seeding and suggest a key role of red
 maple consumption in that anticipation. Results also suggest that red
 maple seeds may contain nutrients or secondary-plant components essential
 to sustain or trigger the summer reproduction in chipmunks, which allow
 them to remain synchronized with pulsed productions of both red maple and
 beech and improve their fitness. 08-Jan-2020
DOI: 10.5061/dryad.n5tb2rbrz
title: Local adaptation constrains drought tolerance in a tropical foundation tree

description: 1. Plant species with broad climatic ranges might be more vulnerable to
 climate change than previously appreciated due to intraspecific variation
 in climatic stress tolerance. In tropical forests, drought is increasingly
 frequent and severe, causing widespread declines and altering community
 dynamics. Yet, little is known about whether foundation tropical trees
 vary in drought tolerance throughout their distributions, and how
 intraspecific variation in drought tolerance might contribute to their
 vulnerability to climate change. 2. We tested for local adaptation in
 seedling emergence and establishment with a full-factorial reciprocal
 transplant experiment including 27 populations and 109,350 seeds along a
 3500 mm precipitation gradient for a widespread tropical foundation tree,
 Metrosideros polymorpha, in Hawaii. To more precisely relate seedling
 performance to soil moisture, we conducted a complementary greenhouse
 experiment to test responses of the same focal populations to simulated
 drought. 3. In the reciprocal transplant experiment, we observed
 significant variation among populations and sites in germination and
 seedling establishment rates. Overall, there was a significant link
 between historical rainfall of populations and their performance under
 current rainfall at the study sites consistent with local adaptation. In
 particular, populations from historically wet sites demonstrated lower
 germination rates in currently dry sites compared to wet field sites,
 while populations from historically dry sites germinated well across all
 sites, with particularly high germination in dry sites. In the greenhouse,
 seedlings from wet populations survived fewer days without water, and
 succumbed at wetter soil conditions than populations from historically dry
 sites, corroborating results from the field experiment. 4.
 Synthesis. While climate change models project the greatest
 drying trends for historically dry areas in Hawaii, even moderate drying
 of wet sites could significantly reduce M. polymorpha recruitment given
 the sensitivity of seedlings to slight changes in water regimes. Thus,
 although M. polymorpha demonstrates high seedling drought tolerance in
 some populations, providing evidence of resilience at the species-scale,
 there are nonetheless vulnerable populations likely to decline under
 climate change. Our approach demonstrates that even trees with high
 dispersal can show significant clines in drought tolerance, and suggests
 that similar intraspecific variation might be an important consideration
 for other tropical tree species.
description: Field data are seedling counts in reciprocal transplant
 experiment, with the greatest number of seedlings observed at any census
 (germinate) and the total number of seedlings left at the end of the
 experiment (establish). Greenhouse data are performance
 metrics for focal populations used in the field experiment, subjected to
 simulated drought.
description: See READMe file
DOI: 10.5061/dryad.ffbg79cqv
title: The biogeography of thermal risk for terrestrial ectotherms: scaling of thermal tolerance with body size and latitude

description: 1. Many organisms are shrinking in size in response to global warming.
 However, we still lack a comprehensive understanding of the mechanisms
 linking body size and temperature of organisms across their geographical
 ranges. Here we investigate the biophysical mechanisms determining the
 scaling of body temperature with size across latitudes in terrestrial
 ectotherms. 2. Using biophysical models, we simulated operative
 temperatures experienced by lizard-like ectotherms as a function of
 microclimatic variables, body mass and latitude and use them to generate
 null predictions for the effect of size on temperature across geographical
 gradients. We then compared model predictions against empirical data on
 lizards’ field body temperature (Tb), and thermal tolerance limits (CTmax
 and CTmin). 3. Our biophysical models predicted that the allometric
 scaling of operative temperatures with body size varies with latitude,
 with a positive relationship at low latitudes that vanishes with
 increasing latitude. The analyses of thermal traits of lizards show a
 significant interaction of body size and latitude on Tb and CTmax and no
 effect of body mass on CTmin, consistent with model’s predictions. The
 estimated scaling coefficients are within the ranges predicted by the
 biophysical model. The effect of body mass, however, becomes
 non-significant after controlling for the phylogenetic relatedness between
 species. 4. We propose that large-bodied terrestrial ectotherms exhibit
 higher risk of overheating at low latitudes, while size differences in
 thermal sensitivity vanish towards higher latitudes. 5. Our work
 highlights the potential of combining mechanistic models with empirical
 data to investigate the mechanisms underpinning broad-scale patterns and
 ultimately provide a null model to develop baseline expectations for
 further empirical research. 08-Jan-2020
DOI: 10.15468/dl.5umry4
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus cantralli",
 "Year 1900-2026"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002146-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d9v2tk
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Datisca cannabina",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 129 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002145-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.69p8cz8xq
title: Data from: Egg mass polymorphism in Ambystoma maculatum is not associated with larval performance or survival, or with cell density of the algal symbiont Oophila amblystomatis

description: These data are from a 2018 study of larval morphology, performance, and
 survival in the spotted salamander (Ambystoma maculatum). We examined
 larvae of two egg mass color morphs: clear and white. We also quantified
 the density of algal (Oophila amblystomatis) cells on the egg capsules of
 embryos. The data correspond to our publication in Evolutionary Ecology.
description: Details can be found in the manuscript. Additional information
 can be obtained by contacting R. Hale at rhale@unca.edu.
description: Data files are described in the
 DErricoKennedyHale_polymorphism_data2018 readme.txt file.