cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m37pvmd13
title: Using multiple seedlots in restoration planting enhances genetic diversity compared to natural regeneration in fragmented tropical forests

description: Catastrophic degradation of forests is ongoing worldwide and leads to
 severe forest fragmentation. Restoration plantings are often necessary to
 restore fragmented forests, complementing the limited natural
 regeneration. High genetic diversity is critical for the long-term
 viability of restored forests. However, there is limited knowledge of
 whether planted populations capture a genetic variation comparable to
 natural populations. We measured the efficiency of two forest restoration
 strategies using the common tropical oak Quercus bambusifolia. The
 multi-seedlot planting was established over ten years by collecting seeds
 from several locations in fragmented secondary forests of Hong Kong, while
 the single seedlot planting was established in just one year with seeds
 from a single natural location. We analysed the genetic diversity and
 genetic structure from both plantings and compared them with natural
 populations. The multi-seedlot planting exhibited a higher rate of genetic
 recovery, greater genetic diversity (He = 0.69), and higher effective
 population size (Ne_p = 86.5) compared to natural populations (He = 0.66,
 Ne_p = 64.3, on average) and the single seedlot planting (He = 0.50, Ne_p
 = 30.8). The multi-seedlot planting erased the effect of seed shadows
 which was detected in natural populations while the single seedlot
 planting strengthened the effect. We conclude that capturing high levels
 of genetic diversity in the collection of propagules is a standard
 requirement to ensure the long-term viability of forest restoration.
 Propagule collection over multiple years is required when only a few
 parental trees are available to avoid founder effects.
DOI: 10.5061/dryad.vdncjsxsw
title: Data from: Diverse and complex muscle spindle afferent firing properties emerge from multiscale muscle mechanics

description: Despite decades of research, we lack a mechanistic framework capable of
 predicting how movement-related signals are transformed into the diversity
 of muscle spindle afferent firing patterns observed experimentally,
 particularly in naturalistic behaviors. Here, a biophysical model
 demonstrates that well-known firing characteristics of mammalian muscle
 spindle Ia afferents – including movement history dependence, and
 nonlinear scaling with muscle stretch velocity – emerge from first
 principles of muscle contractile mechanics. Further, mechanical
 interactions of the muscle spindle with muscle-tendon dynamics reveal how
 motor commands to the muscle (alpha drive) versus muscle spindle (gamma
 drive) can cause highly variable and complex activity during active muscle
 contraction and muscle stretch that defy simple
 explanation. Depending on the neuromechanical conditions, the
 muscle spindle model output appears to “encode” aspects of muscle force,
 yank, length, stiffness, velocity, and/or acceleration, providing
 an extendable, multiscale, biophysical framework for understanding and
 predicting proprioceptive sensory signals in health and disease.
DOI: 10.5061/dryad.4tmpg4f8c
title: Roles of the ClC chloride channel CLH-1 in food-associated salt chemotaxis behavior of C. elegans

description: The ability of animals to process dynamic sensory information facilitates
 foraging in an ever changing environment. However, molecular and neural
 mechanisms underlying such ability remain elusive. The ClC anion
 channels/transporters play a pivotal role in cellular ion homeostasis
 across all phyla. Here we find a ClC chloride channel is involved in salt
 concentration chemotaxis of C. elegans. Genetic screening
 identified two altered-function mutations of clh-1 that
 disrupt experience-dependent salt chemotaxis. Using genetically encoded
 fluorescent sensors, we demonstrate that CLH-1 contributes to regulation
 of intracellular anion and calcium dynamics of salt-sensing neuron, ASER.
 The mutant CLH-1 reduced responsiveness of ASER to salt stimuli in terms
 of both temporal resolution and intensity, which disrupted navigation
 strategies for approaching preferred salt concentrations. Furthermore,
 other ClC genes appeared to act redundantly in salt chemotaxis. These
 findings provide insights into the regulatory mechanism of neuronal
 responsivity by ClCs that contribute to modulation of navigation behavior.
description: Each dataset are collected by appropriate methods. For detailed
 methods related to these data, please refer to "Materials and
 methods" of the article "Roles of the ClC chloride channel CLH-1
 in food-associated salt chemotaxis behavior of <em>C.
 elegans</em>".
description: For statistic analysis data, please refer to "Supplementary
 File 5 statistics" of the supplementary file of the
 article.
DOI: 10.5061/dryad.pnvx0k6kv
title: Predator-based selection and the impact of edge sympatry on components of coral snake mimicry

description: Mimicry is a vivid example of how predator-driven selection can impact
 phenotypic diversity, which itself can be influenced by the presence
 (sympatry) or absence (allopatry) of a dangerous model. However, the
 impact of sympatry and allopatry on predation on mimicry systems at fine
 spatial scales (e.g., edge sympatry, allopatry) is not well understood. We
 used a clay model study in a montane tropical site in Honduras to test the
 impact of edge sympatry on 1) overall attack rates, 2) the fitness benefit
 of mimetic coloration, 3) predation on specific mimetic signal components,
 and 4) temporal variation in predator-based selection on mimicry
 components. Unlike previous research, we found that mimetic phenotypes
 received significantly more attacks than cryptic replicas in edge
 sympatry, suggesting that mimetic phenotypes might not confer a fitness
 benefit in areas of edge sympatry. Additionally, we documented temporal
 variation in predator-based selection, as the impacts of allopatry on
 predatory attacks varied among years. Our results imply that the effect of
 sympatry and allopatry on predator-based selection in mimicry systems may
 be more complex than previously thought for species-rich assemblies of
 coral snakes and their mimics in the montane tropics.
description: Methods on how our data were collected, processed and analysed
 are described in the associated paper.
description: Readme file for raw attack data: README_attack_data.txt
DOI: 10.15468/dl.g6ftr6
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Dolichandrone spathacea"
 ]
}

 The dataset includes 70 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002693-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9ghx3ffg5
title: Trait-similarity and trait-hierarchy jointly determine fine-scale spatial associations of resident and invasive ant species

description: Interspecific competition, a dominant process structuring ecological
 communities, is influenced by species' phenotypic differences.
 Limiting similarity theory holds that species with similar traits should
 compete intensely ("trait-similarity"). In contrast, competing
 theories including modern coexistence theory emphasize that species with
 traits conferring competitive advantages should outcompete others
 ("trait-hierarchy"). Either or both of these mechanisms may
 drive competitive exclusion, but their relative importance and interacting
 effects are rarely studied. Here, we explore empirically whether
 trait-similarity and trait-hierarchy can explain fine-scale spatial
 associations observed between invasive and native ant species in a
 tropical assemblage. We find that pairwise co-occurrences between the
 invasive red imported fire ant Solenopsis invicta and 28 other species
 across relatively homogenous grasslands can be explained largely by an
 interaction of trait-similarity and trait-hierarchy in a single
 morphological trait, relative pronotum width. Specifically, higher
 trait-hierarchy values are associated with negative co-occurrences;
 however, these effects are counteracted when species are increasingly
 dissimilar in their trait ranges. These findings are consistent with the
 notion that limiting similarity and competitive hierarchies are
 interactive rather than discrete mechanisms driving competitive exclusion.
description: See Methods in the paper.
DOI: 10.5061/dryad.m0cfxpp2g
title: Heat shock improves random spore analysis in diverse strains of Saccharomyces cerevisiae

description: Random spore analysis (RSA) is a classic method in yeast genetics that
 allows high-throughput purification of recombinant haploid spores
 following specific crosses. RSA typically involves a number of steps to
 induce sporulation, purge vegetative cells that fail to sporulate, and
 disrupt the ascus walls of sporulated cells to release
 haploid spores. These steps generally require expensive chemicals
 and/or enzymes that kill diploid cells but have few effects on
 spores. In the fission yeast Schizosaccharomcyes pombe, heat shock has
 been reported as an effective addition to RSA protocols, but to
 our knowledge heat shock not been used for this purpose in the
 budding yeast Saccharomyces cerevisiae. Here, we evaluate the
 effects of heat shock on vegetative and sporulated cultures of
 four diverse yeast strains: a European wine strain (DBVPG6765), a
 Japanese sake strain (Y12), a West African palm wine
 strain (DBVPG6044) and a North American strain isolated from the
 soil beneath an oak tree (YPS128). We characterize this phenotype
 under multiple combinations of temperature and incubation time, and find
 specific conditions that lead to the exclusion of
 vegetative cells and an enrichment in spores, which differ by
 strain. We also collected genome sequence data from a recombinant
 population that experienced multiple rounds of RSA, including one
 round with a heat shock treatment. These data suggest that
 when incorporated into an RSA protocol, heat shock leads to
 increased genetic diversity among the cells that survive and
 mate. Ultimately, our work provides evidence that short heat
 treatments can improve existing RSA protocols, though in a
 strain-specific manner. This result informs applications of
 high-throughput RSA protocols, such as QTL mapping and
 experimental evolution research.
DOI: 10.5061/dryad.hhmgqnkfr
title: Data from: Leaf litter decomposition in tropical freshwater swamp forests is slower in swamp than non-swamp conditions

description: Decomposition is a key ecosystem function, and the rate of decomposition
 in forests affects their carbon storage potentials. Processes and factors
 determining leaf litter decomposition rates in dry-land and temperate
 forests are well understood, but these are generally poorly studied in
 tropical wetland forests, especially freshwater swamp forests (FSF). The
 home-field advantage (HFA) hypothesis predicts that soil microbes
 specialize in decomposing leaf litter produced by the tree species in
 their immediate vicinity. However, empirical support for the HFA is
 equivocal, and the HFA has never been tested in the highly heterogeneous
 and biodiverse ecosystems of tropical FSFs. We collected leaf litter from
 swamp and non-swamp tree species in a tropical FSF in Singapore and
 monitored the decomposition rates of these in swamp and non-swamp plots
 for a period of eight months. Leaf litter decomposed 3.7 times more slowly
 in swamp plots. Leaf litter from swamp tree species were significantly
 poorer in quality (higher C:N ratio) than those of non-swamp FSF tree
 species, but this had only a weak effect on decomposition rates. There was
 also only weak evidence for the HFA and only in non-swamp conditions. Our
 results show that while the leaf litter of tropical FSF swamp and
 non-swamp tree species differ significantly in chemical traits, litter
 decomposition rate is ultimately determined by local abiotic conditions,
 such as hydrology. Additionally, the high FSF tree diversity may prevent
 decomposer communities from specializing on any group of leaf litter types
 and thus limit the extent of HFA observed in such heterogeneous forests.
DOI: 10.5061/dryad.8cz8w9gp4
title: Data from: Life-history dimensions indicate non-random assembly processes in tropical island tree communities

description: Community assembly processes on islands are often non-random. The
 mechanisms behind non-random assembly, however, are generally difficult to
 disentangle. Functional diversity in combination with a null model
 approach that accounts for differences in species richness among islands
 can be used to test for non-random assembly processes, but has been
 applied rarely to island communities. By linking functional diversity of
 trees on islands with a null model approach, we bridge this gap and test
 for the role of stochastic vs. non-random trait-mediated assembly
 processes in shaping communities by studying functional diversity-area
 relationships. We measured 11 plant functional traits linked to species
 dispersal and resource acquisition strategies of 57 tree species on 40
 tropical islands. We grouped traits into four life-history dimensions
 representing (i) dispersal ability, (ii) growth strategy, (iii) light
 acquisition, and (iv) nutrient acquisition. To test for non-random
 assembly processes, we used null models that account for differences in
 species richness among the islands. Our results reveal contrasting
 responses of the four life-history dimensions to island area. The
 dispersal and the growth strategy dimensions were underdispersed on
 smaller islands, whereas the light acquisition dimension was
 overdispersed. The nutrient acquisition dimension did not deviate from
 null expectations. With increasing island area, shifts in the strength of
 non-random assembly processes increased the diversity of dispersal and
 acquisition strategies in island communities. Our results suggest that
 smaller islands may be more difficult to colonize and provide more limited
 niche space compared to larger islands, whose tree communities are likely
 determined by stochastic processes and higher niche diversity. Our null
 model approach highlights that analysing the functional diversity of
 different life-history dimensions provides a powerful framework to unravel
 community assembly processes on islands. These complex, non-random
 assembly processes are masked by measures of functional diversity that do
 not account for differences in species richness between islands.
description: Study design, data collection, processing and analysis is
 described in detail in the article (doi: 10.1111/ecog.05363 ).
DOI: 10.5281/zenodo.18348700
title: Global Major Water Transfer Projects Dataset
DOI: 10.5281/zenodo.18348701
title: Global Major Water Transfer Projects Dataset
DOI: 10.5061/dryad.xgxd254ff
title: PPIMT measurement data

description: Recent research in empirical moral psychology attempts to understand
 (rather than place judgment on) the salient normative differences that
 laypeople have when making moral decisions by using survey methodology
 that is based on the operationalized principles from moral
 theories. The PPIMT is the first measure designed to assess
 respondents’ preference for the precepts implied in the three dominant
 moral theories: virtue ethics, deontology, and consequentialism. The
 current study used a latent modeling approach to determine the most
 theoretically-sound and psychometrically-acceptable model for the PPIMT
 using a combined sample of college students from a southeastern university
 in U.S. and MTurk respondents. The PPIMT model fit was acceptable (χ2=
 84.125, df= 40, p= 0.001; RMSEA = 0.052, 90%CI = 0.037
 to 0.068; CFI = 0.980; SRMR = 0.035) with four items for Virtue, four
 items for Deontology, and three items for Consequentialism.
DOI: 10.5061/dryad.bcc2fqzbd
title: Body temperature is a repeatable trait in a free-ranging passerine bird

description: Body temperature (Tb) affects animal function through its influence on
 rates of biochemical and biophysical reactions, the molecular structures
 of proteins and tissues, metabolic rate, and ultimately, organismal
 performance. Despite its importance in driving physiological processes,
 there are few data on how much variation in Tb exists within populations
 of organisms, and whether this variation consistently differs among
 individuals over time (i.e., repeatability of a trait). Understanding the
 repeatability of Tb is important for predicting how animal populations
 will respond to climatic warming, given that endotherms maintain Tb that
 are close to the upper lethal threshold.  Here, we quantified the
 repeatability of Tb, both in the context of a fixed average
 environment (~21°C) environment and across ambient temperatures, in a
 free-living population of tree swallows (Tachycineta bicolor). by
 experimentally trimming the ventral plumage of a subset of female
 swallows, we also asked whether the repeatability of Tb is
 influenced by the capacity to dissipate body heat. We found that the
 Tb of both female and male tree swallows was highly repeatable
 at 21°C, and with increasing ambient temperatures. The
 repeatability of female Tb did not differ as a function of heat
 dissipation capacity, thereby supporting the hypothesis that individual
 performance is limited by the capacity to dissipate body heat. To our
 knowledge, our study is the first to provide evidence that Tb is
 a repeatable trait in a free-living bird, and that avian Tb could
 therefore be responsive to natural selection.
description: The attached files contain the necessary descriptions for
 understanding and working with data used in the construction of Tapper et
 al. 2020, "Body temperature is a repeatable trait in a free-ranging
 passerine bird" (submitted to Journal of Experimental Biology). The
 Repeatability_dryad_readme.docx file contains descriptions of each file
 name attached to this data repository, and descriptions of the data
 contained within each column of a data file. Information pertaining to the
 R code, which has been provided in this data repository as a .Rmd (R
 Markdown) file, has not been provided within this readme file, because
 necessary descriptions for understanding our code are provided within the
 R code file itself.
DOI: 10.5061/dryad.stqjq2c2c
title: Toxin or medication? Immunotherapeutic effects of nicotine on a specialist caterpillar

description: 1. A core tenant in the field of ecological immunology is that
 immune responses trade off with other physiological functions due to
 resource-allocation costs. Caterpillars, for example, tend to exhibit
 reduced immune responses when reared on more toxic food plants due to a
 cost from detoxifying or sequestering secondary metabolites, also known as
 the “vulnerable host hypothesis”. However, support for this hypothesis is
 mixed, and studies have not yet mechanistically isolated the relative
 contributions of total plant defenses, specific metabolites, or
 macro-nutritional
 quality.      2. We
 used the tobacco hornworm (Manduca sexta), a specialist herbivore on
 plants in the nightshade family (Solanaceae), to investigate tradeoffs in
 immune response. This system is ideal given the availability of
 solanaceous plant lines varying in general (i.e., jasmonate-induced) and
 specific (i.e., nicotine) resistance traits. We also applied a geometric
 diet stoichiometry approach to examine how phytochemical toxicity and
 nutritional quality interactively impact insect immunity and performance.
 We predicted that as plant toxicity increased immune activity and
 herbivore performance would decrease. 3. Increasing food plant
 toxicity reduced insect growth and development, as predicted, but contrary
 to our hypothesis, plant toxicity did not trade off with immune
 parameters. Surprisingly, specific plant chemicals, in this case nicotine,
 appeared immunotherapeutic, stimulating the phenoloxidase (PO) immune
 response of M. sexta. Available nutrients in artificial diets, mainly
 protein, also strongly impacted insect growth, but did not affect PO
 activity, while diets supplemented with nicotine enhanced the PO and
 melanization response. 4. This work highlights how specific secondary
 metabolites, and not overall plant toxicity, impact the immune response.
 Importantly, our data also suggest an alternative mechanism (i.e., immune
 enhancement) for reduced parasitoid performance when reared from hosts on
 toxic plants via tri-trophic interactions.
description: Data for all associated experiments to conduct the statistical
 anyalases in the paper are presented in the excel file with each tab
 coresponding to a different set of experiments.
description: Please contact the first auther if you have further questions on
 using this data set.
DOI: 10.5061/dryad.r4xgxd2b8
title: HemeLB input files for areteriovenous fistula simulation

description: This dataset contains the HemeLB input files used to run the blood flow
 simulations described in our manuscript "High fidelity physiological
 blood flow in patient-specific arteriovenous fistula for clinical
 applications". These work with the PressureCouplingBeds and
 ResistorCapacitorBeds branches of the source code available
 at https://github.com/UCL-CCS/HemePure_SelfCoupled. Provided in
 this dataset are four *.tar.gz files containing the necessary input files
 for the flow simulations through the arteries and veins of the left
 forearm discussed in our manuscript: 1) Healthy vessels, 2) Arteriovenous
 fistula via modified mapping, 3) End-to-Side arteriovenous fistula and 4)
 Side-to-Side arteriovenous fistula. The files for 1), 3) and 4) contain
 the *.gmy files, input *.xml files for arteries and veins, the *0to1.txt
 map files describing the mapping parameters for the capillaries beds of
 the models and the MESH* files used to construct velocity boundary
 conditions for the geometry inlets. The *.gmy and MESH* files for 1) are
 reused for 2) in conjunction with the input* and  *0to1.txt map
 files provided for 2). When launching the jobs, all relevant files are
 called from the input *.xml files - those labelled PCB are to be used with
 the PressurCoupling Beds branch and the those labelled RC with the
 ResistorCapacitorBeds branch.
description: Input files for simulations described in "High fidelity
 physiological blood flow in patient-specific arteriovenous fistula for
 clinical applications"<br> HealthyVessels<br> - Input
 files for simulation results described in Section 3.1
 MapFistula<br> - Input files for simulation results
 described in Section 3.2<br> - This model made use of many of the
 files provided in HealthyVessels. The files in MapFistula replace the
 respective input* files and the *_0to1.txt map files in
 HealthyVessels. EndToSideFistula<br> - Input
 files for simulation results described in Section
 3.3SideToSideFistula<br> - Input files for simulation results
 described in Section 3.4