cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8x331
title: Vulnerability of grassland seed banks to resource-enhancing global changes

description: Soil seed banks represent reservoirs of diversity in the soil that may
 increase resilience of communities to global changes. Two global change
 factors that can dramatically alter the composition and diversity of
 aboveground communities are nutrient enrichment and increased rainfall. In
 a full-factorial nutrient and rainfall addition experiment in an annual
 Californian grassland, we asked whether shifts in aboveground composition
 and diversity were reflected in belowground seed banks. Nutrient and
 rainfall additions increased exotic and decreased native abundances, while
 rainfall addition increased exotic richness, both in aboveground
 communities and seed banks. Under nutrient addition, forbs and
 short-statured plants were replaced by grasses and tall-statured species,
 both above and below ground, and whole-community responses to the
 treatments were similar. Structural equation models indicated that
 especially nutrient addition effects on seed banks were largely indirect
 via aboveground communities. However, rainfall addition also had a direct
 negative effect on native species richness and abundance of species with
 high specific leaf area (SLA) in seed banks, showing that seed banks are
 sensitive to the direct effects of temporary increases in rainfall. Our
 findings highlight the vulnerability of seed banks in annual,
 resource-poor grasslands to shifts in compositional and trait changes in
 aboveground communities and show how invasion of exotics and depletion of
 natives are critical for these above-belowground compositional shifts. Our
 findings suggest that seed banks have limited potential to buffer
 resource-poor annual grasslands from the community changes caused by
 resource enrichment.
DOI: 10.5061/dryad.44j0zpcdq
title: Evaluating species delimitation methods in radiations: The land snail Albinaria cretensis complex on Crete

description: Delimiting species in radiations is notoriously difficult because of the
 small differences between the incipient species, the star-like tree with
 short branches between species, incomplete lineage sorting, and the
 possibility of introgression between several of the incipient species.
 Next generation sequencing data may help to overcome some of these
 problems. We evaluated methods for species delimitation based on
 genome-wide markers in a land snail radiation on Crete. Species
 delimitation in the Albinaria cretensis group was based exclusively on
 shell characters until now and resulted in classifications distinguishing
 3–9 species. We generated sequences of 4270 loci for 140 specimens of the
 Albinaria cretensis group from 48 populations by double-digest restriction
 site-associated DNA sequencing. We evaluated three methods for species
 discovery. The multispecies coalescent approach implemented in the program
 Bayesian Phylogenetics and Phylogeography resulted in a drastic
 overestimating of the number of species, whereas Gaussian clustering
 resulted in an overlumping. Primary species hypotheses based on the
 maximum percentage of the genome of the individuals derived from ancestral
 populations as estimated with the program ADMIXTURE moderately
 overestimated the number of species, but this was the only approach that
 provided information about gene flow between groups. Two of the methods
 for species validation that we applied, BFD* and delimitR, resulted in an
 acceptance of almost all primary species hypotheses, even such based on
 arbitrary subdivisions of hypotheses based on ADMIXTURE. In contrast,
 secondary species hypotheses, resulting from an evaluation of primary
 species hypotheses based on ADMIXTURE with isolation by distance tests,
 approached the morphological classification, but also uncovered two
 cryptic species and indicated that some of the previously delimited units
 should be combined. Thus, we recommend this combination of approaches that
 provided more detailed insights in the distinctness of barriers between
 the taxa of a species complex and the spatial distribution of admixture
 between them than the other methods. The recognition and delimitation of
 undersampled species remained a major challenge.
DOI: 10.5061/dryad.cfxpnvx5g
title: Historical warming consistently decreased size, dispersal and speciation rate of fish

description: There is ongoing debate as to whether fish body size will decrease with
 global warming and how these changes may impact dispersal ability and
 speciation rate. Theory predicts that, under warmer temperatures, fish
 grow to a smaller size, undergo a reduction in dispersal ability and
 increase speciation rates. However, evaluations of such predictions are
 hampered owing to the lack of empirical data spanning both wide temporal
 and geographical scales. Here, using phylogenetic methods, we show that
 smaller clupeiform fish (anchovies and herrings) occurred historically in
 warmer waters, moved the shortest distances at low speed and displayed the
 lowest speciation rates. Furthermore, fish moved faster and evolved
 rapidly under higher rates of temperature change but these historical
 rates are far lower than current warming rates. Our results predict a
 future where smaller clupeiform fish that have reduced ability to move
 will be more prevalent; this, in turn, may reduce future speciation.
DOI: 10.5061/dryad.9cnp5hqj5
title: Social group size influences pathogen transmission in salamanders

description: Individuals within animal societies are expected to mitigate the costs and
 enhance the benefits associated with group living. For example, sociality
 can facilitate the sharing of beneficial microbes among individuals, but
 can also increase transmission of pathogens, representing a major cost of
 group living.  We examine the costs of sociality in the
 California slender salamander (Batrachoseps attenuatus), a
 terrestrial salamander which naturally forms close social
 aggregations.  We investigate whether innate sociality
 (e.g., skin-to-skin contact) increases an individual’s transmission risk
 of Batrachochytrium dendrobatidis (Bd), a fungal
 pathogen that emerged throughout the salamander’s range over the last 50
 years and has decimated hundreds of amphibian species
 globally. We found that in captivity, B.
 attenuatus exhibit random mixing within social groups, resulting
 in high contact rates and high potential
 for Bd transmission. Our experimental infection trials
 resulted in 50% mortality after one month in moist
 conditions.  In order to test how group size affects
 pathogen transmission, we manipulated social group size and found a marked
 effect on the spread Bd among individuals; a single,
 uninfected individual contracted Bd much more rapidly in
 larger groups of infected individuals. Surprisingly, this did not
 translate into a more rapid death rate or higher pathogen infection
 loads.  Our results show that the innate behavior of
 group formation represents a per-individual risk of socially acquired
 directly transmissible pathogens and is magnified in larger social groups.
 This study highlights one important cost of sociality in terrestrial
 salamanders and underscores the general susceptibility of social animals
 to novel invasive pathogens.
DOI: 10.5061/dryad.wstqjq2mk
title: Number of seeds recorded from the feces of different species of mammals during the study

description: Senna spectabilis, a native tree of tropical America is rapidly colonizing
 the forests of Western Ghats. We identified the Asian elephant (Elephas
 maximus) as the major disperser of Senna, with the dung
 facilitating germination of the species. The study provides
 critical information for the management of Senna in tropical Asia,
 elephants, Western Ghats, Senna spectabilis, and seed dispersal.
DOI: 10.5061/dryad.q2bvq83k3
title: Predictability of temporal variation in climate and the evolution of seasonal polyphenism in tropical butterflies

description: Phenotypic plasticity in heterogeneous environments can provide tight
 environment-phenotype matching. However, the pre-requisite is a reliable
 environmental cue(s) that enables organisms to use current environmental
 information to induce the development of a phenotype with high fitness in
 a forthcoming environment. Here we quantify predictability in the timing
 of precipitation and temperature change to examine how this is associated
 with seasonal polyphenism in tropical Mycalesina butterflies. Seasonal
 precipitation in the tropics typically results in distinct selective
 environments, the wet- and dry seasons, and changes in temperature can be
 a major environmental cue. We sampled communities of Mycalesina
 butterflies from two seasonal and one aseasonal location. Quantifying
 environmental predictability using wavelet analysis and Colwell’s indices
 confirmed a strong periodicity of precipitation over a 12-month period at
 both seasonal locations compared to the aseasonal one. However,
 temperature seasonality and periodicity differed between the two seasonal
 locations. We further show that: (1) most females from both seasonal
 locations synchronise their reproduction with the seasons by breeding in
 the wet season but arresting reproduction in the dry season. In contrast,
 all species breed throughout the year in the aseasonal location, and (2)
 species from the seasonal locations, but not those from the aseasonal
 location, exhibited polyphenism in wing pattern traits (eyespot size). We
 conclude that seasonal precipitation and its predictability are primary
 factors shaping the evolution of polyphenism in Mycalesina butterflies,
 and populations or species secondarily evolve local adaptations for cue
 use that depend on the local variation in the environment.
description: The data represented in this manuscript were obtained both from
 the climate database (CRU database) and traits were quantified from the
 field-collected samples. From the climate database, we downloaded data
 from 2001-2019 on Mean Precipitation and Mean Temperature for three
 locations that were sampled in this study. This time series climate data
 was used for quantifying the predictability of the precipitation and
 temperature using wavelet analysis. From the field-collected samples, we
 measured the eyespot size of several species represented from all three
 locations and also dissected females to detect the reproductive activity
 of the female based on the presence/absence of spermatophores and
 eggs.
DOI: 10.5061/dryad.nk98sf7tc
title: Genotypic variation in an ecologically important parasite is associated with host species, lake, and spore size

description: Genetic variation in parasites has important consequences for
 host-parasite interactions. Prior studies of the ecologically important
 parasite Metschnikowia bicuspidata have suggested low genetic variation in
 the species. Here, we collected M. bicuspidata from two host species
 (Daphnia dentifera and Ceriodaphnia dubia) and two regions (Michigan and
 Indiana, USA). Within a lake, outbreaks tended to occur in one host
 species but not the other. Using microsatellite markers, we identified six
 parasite genotypes grouped within three distinct clades, one of which was
 rare. Of the two main clades, one was generally associated with D.
 dentifera, with lakes in both regions containing a single genotype. The
 other M. bicuspidata clade was mainly associated with C. dubia, with a
 different genotype dominating in each region. Despite these associations,
 both D. dentifera- and C. dubia-associated genotypes were found infecting
 both hosts in lakes. However, in lab experiments, the D.
 dentifera-associated genotype infected both D. dentifera and C. dubia, but
 the C. dubia-associated genotype, which had spores that were approximately
 30% smaller, did not infect D. dentifera. We hypothesize that variation in
 spore size might help explain patterns of cross-species transmission.
 Future studies exploring the causes and consequences of variation in spore
 size may help explain patterns of infection and the maintenance of
 genotypic diversity in this ecologically important system.
description: MichiganField2015.txt and IndianaField2015.txt datasets give the
 prevalence of <em>Metschnikowia bicuspidata</em> through the
 season in <em>Daphnia dentifera</em> and
 <em>Ceriodaphnia dubia</em> host species at each sampling date
 in 2015 in the Michigan study lakes and the Indiana study lakes
 respectively. microsats.data.txt gives the fragment
 lengths for the microsatellites analyzed for each parasite
 sample BenefielInfections.csv and
 GooseInfections.csv contain the infection data from the cross infection
 experiments from each lake. BenefielSporeCounts.csv and
 GooseSporeCounts.csv give the number of spores per infected animal in the
 cross infection experiments from each lake.
 Spore_Measurements.txt gives the length of spores measured from
 the cross infection experiment.
 FragAnalysisResults.Experiment.csv gives the fragment lengths for
 the microsatellite loci analyzed in cross infection experiment and
 genotype assignment given to each genotyped animal.
description: Use the R code, 'SporeSizeCombinedCode.R', to analyze
 the data in the way it was analyzed for the manuscript.
 See Read me.doc for a description of the variables in each of the
 datasets.
DOI: 10.5061/dryad.0zpc866xq
title: Ontogeny, phylogeny, and mechanisms of adaptive changes in evaporative water loss in geckos

description: Body-size dependence of metabolic rate, body surface and scale morphology
 complicate disentangling the contribution of these characteristics to
 adaptive changes in total evaporative water loss (TEWL) of reptiles. To
 separate adaptive changes from size-related dependence, we compared intra-
 and interspecific scaling of several candidate traits in eyelid geckos
 (Eublepharidae), a group exhibiting large variation in body size and TEWL.
 The intraspecific allometry of TEWL of an eublepharid species fits the
 geometric surface-mass relationship. However, evolutionary shifts to both
 higher and lower evaporation were strongly correlated with habitat aridity
 and cannot be explained by shifts in body size alone. The intraspecific
 allometry of standard metabolic rate is nearly the same as the
 interspecific allometry. Unlike for mammals and birds, this pattern rules
 out respiratory water loss as a driver of the adaptive changes in TEWL
 among eublepharids. Scale morphology was independent of TEWL variation as
 well, but the correlation between cutaneous water loss and TEWL suggests a
 crucial role of skin permeability in adaptation to habitat aridity. Our
 analyses demonstrate how powerful a comparison of intra- and interspecific
 allometries can be for detecting body size-dependent mechanisms of
 adaptive changes in ecophysiological traits correlated with body size.
description: Data collected as described in the paper Hlubeň M., Kratochvíl
 L., Gvoždík L. & Starostová Z. (2021). Ontogeny, phylogeny, and
 mechanisms of adaptive changes in evaporative water loss in geckos.
 Journal of Evolutionary Biology, in press.
DOI: 10.7291/d1vh5f
title: Simulated wood duck maternity analysis results from COLONY and CERVUS

description: Modern genetic parentage methods reveal that alternative reproductive
 strategies are common in both males and females. Under ideal conditions,
 genetic methods accurately connect the parents to offspring produced by
 extra-pair matings or conspecific brood parasitism. However, some breeding
 systems and sampling scenarios present significant complications for
 accurate parentage assignment. We used simulated genetic pedigrees to
 assess the reliability of parentage assignment for a series of challenging
 sampling regimes that reflect realistic conditions for many
 brood-parasitic birds: absence of genetic samples from sires, absence of
 samples from brood parasites, and female kin-structured populations. Using
 18 microsatellite markers and empirical allele frequencies from two
 populations of a conspecific brood parasite, the wood duck (Aix sponsa),
 we simulated brood parasitism and determined maternity using two widely
 used programs, CERVUS and COLONY. Errors in assignment were generally
 modest for most sampling scenarios but differed by program: CERVUS
 suffered from false assignment of parasitic offspring, whereas COLONY
 sometimes failed to assign offspring to their known mothers. Reducing the
 number of markers (9 loci rather than 18) caused the assignment error to
 slightly worsen with COLONY but balloon with CERVUS. One potential error
 with important biological implications was rare in all cases—few nesting
 females were incorrectly excluded as the mother of their own offspring, an
 error that could falsely indicate brood parasitism. We consider the
 implications of our findings for both a retrospective assessment of
 previous studies as well as suggestions for the best practices for future
 studies. 
description: Please refer to the publication for detailed methods on the data
 collection and processing.
description: Please contact the corresponding author, Bruce Lyon
 (belyon@ucsc.edu) for any questions regarding the use of this
 dataset.
DOI: 10.5061/dryad.h44j0zpkb
title: Health Friendly Activity Index

description: We developed the Health-Friendly Activity Index (HFAI) to comprehensively
 measure the health-friendly activities of corporations or organizations.
 We validated the developed tool and reported on its use as an assessment
 tool to improve consumers’ health-related outcomes. This was a
 cross-sectional study. Development of the HFAI questionnaire followed a
 three-phase process: item generation, item construction, and validation
 with field testing. Using relevance and feasibility criteria, we developed
 a 105-item questionnaire with six domains (Governance and Infrastructure,
 Needs Assessment, Planning, Implementation, Monitoring and Feedback, and
 Outcomes). To assess the sensitivity and validity of the questionnaire,
 the HFAI and Contribution Assessment Tool for Consumer’s Health (CATCH)
 were administered to 302 participants (151 employers and 151 employees)
 from 151 Korean companies. The CATCH measured the contribution of each
 company to the physical, mental, social, and spiritual health of its
 consumers. To estimate the reliability and validity of all five HFAI
 domains and their respective scales, Cronbach’s α coefficients and
 correlation coefficients were used. Each domain and scale of the HFAI
 exhibited a Cronbach’s α coefficient between 0.80 and 0.98 for the
 employers and employees. The overall HFAI and its six domains correlated
 significantly and positively with all health outcomes such as physical,
 mental, social, and spiritual status scores evaluated using the CATCH
 (Spearman’s correlation range: 0.37 to 0.68). The HFAI, a unique
 assessment tool with acceptable psychometric properties, can help
 corporate managers assess their health-friendly activities.
description: To test
 reliability and validity, both employers and employees were selected
 independently as participants from 1,500 eligible companies between July
 and August 2020. The inclusion criteria for employers were as
 follows: (1) are in charge of human resources, general affairs,
 management, finance, or labor, (2) are the chief executive officer or
 representative of the employer, and (3) voluntarily agreed to participate
 in the survey. The inclusion criteria for employees were as
 follows: (1) are in charge of development, planning, or marketing, (2) are
 representatives of employees, and (3) voluntarily agreed to participate in
 the survey.<b> </b>There were no exclusion
 criteria. Two web survey systems,
 Computer Assisted Web Interview (CAWI) and Computer Assisted
 Mobile Interview (CAMI) that enable online responses by sending survey
 <b>r</b>equests to participants’ email accounts and phone
 numbers, were applied. The companies were selected with consideration of
 the size, industry, and business type for obtaining a representative
 national sample; this sample was pooled for the web survey by the Hankook
 Research Co., Ltd., (Seoul, Korea) since 2015. A total of 151 companies
 (10% response rate) responded to the self-reported
 questionnaire.
DOI: 10.5061/dryad.prr4xgxmh
title: Scale-dependent shifts in functional and phylogenetic structure of Mediterranean island plant communities over two centuries

description: 1. Since the Industrial Revolution, the rapid global population and
 economic expansion has had tremendous impacts on biodiversity across
 spatial scales, especially for islands. While changes in species richness
 are easily inferred, the impact of human activity on the underlying
 community assembly processes has been difficult to ascertain because of
 lack of long-term community data. 2. Here, we document how the
 manifestations of plant community assembly have changed over time and
 space in a Mediterranean archipelago, using a long-term dataset of plant
 species composition on 16 Tuscan islands sampled across two centuries. The
 community structure of Mediterranean island plant communities was assessed
 by integrating species’ trait and evolutionary distances. 3. We found
 that, with increasing island area, the functional and phylogenetic
 structure of plant communities shifted from clustered early (1830–1950) to
 overdispersed more recently (1951–2015). On large islands, extirpated
 species were generally more phylogenetically or functionally similar to
 remaining residents than expected by chance, while colonists were
 generally more distantly related to residents. The extinction of similar
 species and the colonization of dissimilar species drove plant communities
 towards overdispersion. 4. Synthesis. We provide evidence that plant
 community assembly on islands has dramatically changed following increased
 human impacts during the last two centuries, and that this change is
 shaped by the scale dependency of species extinctions and colonizations.
 Our results reveal accelerated species replacements of closely related
 residents by distant colonists on large islands over time, reflecting
 changes in community assembly and which could alter the functioning of
 island ecosystems in the future. 
description: These trait data were obtained from the Botanical Information and
 Ecology Network database (Enquist et al., 2016) using the R package BIEN
 (Maitner et al., 2018), TRY database (Kattge et al., 2020) and
 BROT 2.0 (Tavşanoğlu & Pausas 2018).
DOI: 10.5061/dryad.f7m0cfxw9
title: High-Throughput-Methyl-Reading (HTMR) assay: A solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases

description: Epigenetic therapy has significant potential for cancer treatment.
 However, few small potent molecules have been identified against DNA or
 RNA modification regulatory proteins. Current approaches for activity
 detection of DNA/RNA methyltransferases and demethylases are
 time-consuming and labor-intensive, making it difficult to subject them to
 high-throughput screening. Here, we developed a fluorescence
 polarization-based “High-Throughput Methyl Reading” (HTMR) assay to
 implement large-scale compound screening for DNA/RNA methyltransferases
 and demethylases-DNMTs, TETs, ALKBH5, and METTL3/METTL14. This assay is
 simple to perform in a mix-and-read manner by adding the methyl-binding
 proteins MBD1 or YTHDF1. The proteins can be used to distinguish
 FAM-labelled substrates or product oligonucleotides with different
 methylation statuses catalyzed by enzymes. Therefore, the extent of the
 enzymatic reactions can be coupled with the variation of FP binding
 signals. Furthermore, this assay can be effectively used to conduct a
 cofactor competition study. Based on the assay, we identified two natural
 products as candidate compounds for DNMT1 and ALKBH5. In summary, this
 study outlines a powerful homogeneous approach for high-throughput
 screening and evaluating enzymatic activity for DNA/RNA methyltransferases
 and demethylases that is cheap, easy, quick, and highly sensitive.