cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h7790
title: Data from: Cytology and sexuality of 11 species of Elatostema (Urticaceae) in limestone karsts suggests that apomixis is a recurring phenomenon

description: Limestone karsts across southern China to southeastern Asia are renowned
 biodiversity hotspots. The karst are characterized by exposed calcareous
 rocks, seasonal droughts and thin soils that are deficient in N and P but
 with high Ca and Mg content. The stressful habitat may result in high
 biodiversity through mechanisms such as niche differentiation,
 hybridization, polyploidy and apomixis. The genus Elatostema (Urticaceae)
 has particularily high species diversity in this area and can be used a
 model genus to explore the mechanisms of speciation. We conducted
 cytological studies on 11 species of Elatostema from 12 populations in
 Guangxi, China. We found five populations to be diploid (2n = 26), and
 seven triploid populations (2n = 39). We infer x = 13 as the basic
 chromosome number of Elatostema. The chromosome numbers 2n = 26 and 2n =
 39 were both found in populations of E. longistipulum, indicating that
 this species comprise both diploids and triploids. Both male and female
 plants of Elatostema were found to be diploid. In contrast, the triploids
 found were all female plants, and these produce seeds, presumably by
 apomixis. We found no clear relationship between ploidy level or
 reproductive pathway and endemism in Elatostema which might be because
 Elatostema species are wind-pollinated and independent of biotic
 pollinators. However, a random sample of 11 karst species revealed that ca
 2/3 appeared to be apomictic, suggesting that it is a widespread
 reproductive strategy of Elatostema in the limestone karsts of Guangxi.
 Apomixis enables plants to reproduce and disperse from a single
 individual, allowing ‘hopeful monsters’ adapted to a new habitat to form
 stable populations.
description: cytology
 imagescytology images of 11
 species
DOI: 10.5061/dryad.752kk
title: Data from: Climate warming and humans played different roles in triggering Late Quaternary extinctions in east and west Eurasia

description: Climate change and humans are proposed as the two key drivers of total
 extinction of many large mammals in the Late Pleistocene and Early
 Holocene, but disentangling their relative roles remains challenging owing
 to a lack of quantitative evaluation of human impact and climate-driven
 distribution changes on the extinctions of these large mammals in a
 continuous temporal–spatial dimension. Here, our analyses showed that
 temperature change had significant effects on mammoth (genus Mammuthus),
 rhinoceros (Rhinocerotidae), horse (Equidae) and deer (Cervidae). Rapid
 global warming was the predominant factor driving the total extinction of
 mammoths and rhinos in frigid zones from the Late Pleistocene and Early
 Holocene. Humans showed significant, negative effects on extirpations of
 the four mammalian taxa, and were the predominant factor causing the
 extinction or major extirpations of rhinos and horses. Deer survived both
 rapid climate warming and extensive human impacts. Our study indicates
 that both the current rates of warming and range shifts of species are
 much faster than those from the Late Pleistocene to Holocene. Our results
 provide new insight into the extinction of Late Quaternary megafauna by
 demonstrating taxon-, period- and region-specific differences in
 extinction drivers of climate change and human disturbances, and some
 implications about the extinction risk of animals by recent and ongoing
 climate warming.
description: Table S1. Dated fossil
 occurrence of the four megafauna species usedDated fossil occurrence
 of the four megafauna species usedTable S2. Data sheet of
 human sites and all survey sitesData sheet of human
 sites and all survey sites
DOI: 10.5061/dryad.777bn
title: Data from: Diversity in tropical ecosystems: the species richness and turnover of moths in Malaysian rainforests

description: As a contribution to accurate estimation of arthropod alpha and beta
 diversities in tropical forests, we present results of some of the largest
 moth samples ever collected in the Malaysian region. To estimate alpha
 diversity, light traps were run at three geographically distinct
 locations. We generated individual-based and coverage-based rarefaction
 curves to estimate sampling sufficiency and alpha diversity of the
 locations. Despite a large number of moths collected (67 282 individuals,
 from three locations), none of the rarefaction curves reached asymptote.
 The species accumulation curves based on the Chao1 richness estimator at
 each location suggested that, even when sampling yielded over 30 000
 individuals, Chao1 could not reliably estimate the observed number of
 species. In one of the three locations, moths were collected
 systematically by light traps in 1979–1980 and 2000–2001. Despite over 160
 trapping nights and 16 500 individuals collected in total, the estimated
 total number of species (2262) was well below the general collection
 conducted at the same location over a 35-year period [3921 species
 (1975–2013)]. Beta diversity was investigated using the samples collected
 at one location on two occasions over a 20-year period. The faunal
 composition has changed over the 20-year period, possibly as a result of
 extensive land-use change around the study location. We estimated the
 minimum sampling effort required to detect such changes by calculating
 type II errors. Unlike alpha diversity estimation, we found that only four
 replicate samples, each with only two trapping nights, would be sufficient
 to reliably detect changes in assemblage composition.
description: Borneo Rainforest Lodge
 moth samples 1998Moth samples collected
 at Borneo Rain forest Lodge 1997-1998Halong Moth samples 1994
 trap one and twoMoth samples collected
 in Halong, Malaysia 1993-94Genting Tea Estate moth
 samples 1980Moth samples collected
 at Genting Tea Estate, Malaysia 1979-80Genting Tea Estate moth
 samples 2000Moth samples collected
 at Genting Tea Estate, Malaysia 2000-01GTE Lepidoptera List as
 of 2011Checklist of Lepidoptera
 collected at Genting Tea Estate between 1975-2011GTE Lepidoptera
 List_10-2-17Checklist of Lepidoptera
 collected at Genting Tea Estate between 1975-2017
DOI: 10.6084/m9.figshare.29365349.v1
title: Exploring curiosity, surprise, and interest: validating the MagicCATs dataset in Italy

description: This study validated the Magic Curiosity Arousing Tricks (MagicCATs) dataset, a collection of 166 short magic trick videos designed to elicit epistemic emotions such as curiosity, surprise, and interest. Involving 654 Italian participants aged 18 to 86, we assessed emotional and cognitive responses to the stimuli using both binary and Likert-scale measures. The results confirm the dataset’s effectiveness in eliciting epistemic emotions even in a cultural context different from the original. This work provides evidence of ecological validity and experimental utility, opening new opportunities for its application in psychology, neuroscience, education, and cognitive aging research.
DOI: 10.5061/dryad.d1h97
title: Data from: Conventional oil and natural gas infrastructure increases brown-headed cowbird (Molothrus ater) relative abundance and parasitism in mixed-grass prairie

description: The rapid expansion of oil and natural gas development across the Northern
 Great Plains has contributed to habitat fragmentation, which may
 facilitate brood parasitism of ground-nesting grassland songbird nests by
 brown-headed cowbirds (Molothrus ater), an obligate brood parasite,
 through the introduction of perches and anthropogenic edges. We tested
 this hypothesis by measuring brown-headed cowbird relative abundance and
 brood parasitism rates of Savannah sparrow (Passerculus sandwichensis)
 nests in relation to the presence of infrastructure features and proximity
 to potential perches and edge habitat. The presence of oil and natural gas
 infrastructure increased brown-headed cowbird relative abundance by a
 magnitude of four times, which resulted in four times greater brood
 parasitism rates at infrastructure sites. While the presence of
 infrastructure and the proximity to roads were influential in predicting
 brood parasitism rates, the proximity of perch sites was not. This
 suggests that brood parasitism associated with oil and natural gas
 infrastructure may result in additional pressures that reduce productivity
 of this declining grassland songbird.
description: BHCO_Brooks for
 DryadBrown-headed cowbird
 relative abundance and brood parasitism data collected at mixed-grass
 prairie and conventional oil and natural gas infrastructure lease sites
 near Brooks, Alberta, Canada, 2013-2014.
DOI: 10.5061/dryad.9rd5f
title: Data from: Patterns of phenotypic plasticity and local adaptation in the wide elevation range of the alpine plant Arabis alpina

description: Local adaptation and phenotypic plasticity are two important
 characteristics of alpine plants to overcome the threats caused by global
 changes. Among alpine species, Arabis alpina is characterised by an
 unusually wide altitudinal amplitude, ranging from 800 to 3,100 m of
 elevation in the French Alps. Two non‐exclusive hypotheses can explain the
 presence of A. alpina across this broad ecological gradient: adaptive
 phenotypic plasticity or local adaptation, making this species especially
 useful to better understand these phenomena in alpine plant species. We
 carried out common garden experiments at two different elevations with
 maternal progenies from six sites that differed in altitude. We showed
 that (1) key phenotypic traits (morphotype, total fruit length, growth,
 height) display significant signs of local adaptation, (2) most traits
 studied are characterised by a high phenotypic plasticity between the two
 experimental gardens and (3) the two populations from the highest
 elevations lacked morphological plasticity compared to the other
 populations. By combining two genome scan approaches (detection of
 selection and association methods), we isolated a candidate gene
 (Sucrose‐Phosphate Synthase 1). This gene was associated with height and
 local average temperature in our studied populations, consistent with
 previous studies on this gene in Arabidopsis thaliana. Synthesis. Given
 the nature of the traits involved in the detected pattern of local
 adaptation and the relative lack of plasticity of the two most extreme
 populations, our findings are consistent with a scenario of a locally
 adaptive stress response syndrome in high elevation populations. Due to a
 reduced phenotypic plasticity, an overall low intra‐population genetic
 diversity of the adaptive traits and weak gene flow, populations of high
 altitude might have difficulties to cope with, e.g. a rise of temperature.
description: Phenotypic
 dataPhenotypic data from
 common gardens in Vercors and Lautaretdata.odsEnvironmental data (all years)Environmental data averaged over each yearallyears.odsEnvironmental data (total averaged)Environmental data averaged over all yearsenv2.odsRAD haplotypesData corresponding to the RAD-tags ("RAD haplotypes" in the article)haplotypes.txtSNP data from ddRADseqSNP data from ddRADseqsnp.txtPosition of the loci in the genomePosition of the different loci (haplo: RAD haplotypes; snp: SNP) within the genome.position.zip
DOI: 10.5061/dryad.pk50t
title: Data from: Susceptibility to type 2 diabetes may be modulated by haplotypes in G6PC2, a target of positive selection

description: Background: The endoplasmic reticulum enzyme glucose-6-phosphatase
 catalyzes the common terminal reaction in the gluconeogenic/glycogenolytic
 pathways and plays a central role in glucose homeostasis. In most mammals,
 different G6PC subunits are encoded by three paralogous genes (G6PC,
 G6PC2, and G6PC3). Mutations in G6PC and G6PC3 are responsible for human
 mendelian diseases, whereas variants in G6PC2 are associated with fasting
 glucose (FG) levels. Results: We analyzed the evolutionary history of
 G6Pase genes. Results indicated that the three paralogs originated during
 early vertebrate evolution and that negative selection was the major force
 shaping diversity at these genes in mammals. Nonetheless, site-wise
 estimation of evolutionary rates at corresponding sites revealed weak
 correlations, suggesting that mammalian G6Pases have evolved different
 structural features over time. We also detected pervasive positive
 selection at mammalian G6PC2. Most selected residues localize in the
 C-terminal protein region, where several human variants associated with FG
 levels also map. This region was re-sequenced in ~560 subjects from Saudi
 Arabia, 185 of whom suffering from type 2 diabetes (T2D). The frequency of
 rare missense and nonsense variants was not significantly different in T2D
 and controls. Association analysis with two common missense variants
 (V219L and S342C) revealed a weak but significant association for both
 SNPs when analyses were conditioned on rs560887, previously identified in
 a GWAS for FG. Two haplotypes were significantly associated with T2D with
 an opposite effect direction. Conclusions: We detected pervasive positive
 selection at mammalian G6PC2 genes and we suggest that distinct haplotypes
 at the G6PC2 locus modulate susceptibility to T2D.
description: Mammalian G6PC2
 alignmentG6PC2_alignG6PC2_chimpanzee_gammaMapG6PC2_gorilla_gammaMapG6PC2_human_gammaMapG6PC2_outgroupMammalian G6PC3 alignmentG6PC3_alignG6PC3_chimpanzee_gammaMapG6PC3_gorilla_gammaMapG6PC3_human_gammaMapG6PC3_outgroupMammalian G6PC alignmentG6PC_alignG6PC_chimpanzee_gammaMapG6PC_gorilla_gammaMapG6PC_human_gammaMapG6PC_outgroupMetazoans alignMetazoans_alignG6PC, G6PC2 and G6PC3 phylogenetic treestreesplink_ped_fileplink.pedplink_map_fileplink.mapplink_covariates_fileplinkCOVAR.txtSKAT_covariates_fileskatCOVARSKAT_phenotype_fileskatPHENOSKAT_all_genotype_fileVariant genotypes are ordered as follows: rs560887, rs492594, rs2232328, rs2232323, rs146779637, rs2232326, rs540914059, rs16856162, rs2232321, rs181737385 , rs77719485, rs10166439, rs189856873skatGENOall
DOI: 10.5061/dryad.48963
title: Data from: The early-life environment of a pig shapes the phenotypes of its social partners in adulthood

description: Social interactions among individuals are abundant, both in natural and
 domestic populations, and may affect phenotypes of individuals. Recent
 research has demonstrated that the social effect of an individual on the
 phenotype of its social partners may have a genetic component, known as an
 Indirect Genetic Effect (IGE). Little is known, however, of non-genetic
 factors underlying such social effects. Early life environments often have
 large effects on phenotypes of the individuals themselves later in life.
 Offspring development in many mammalian species, for example, depends on
 interactions with the mother and siblings. In domestic pigs, individuals
 sharing the same juvenile environment develop similar body weight later in
 life. We, therefore, hypothesized that offspring originating from the same
 early-life environment also develop common social skills, which generate
 Early-Life Social Effects (ELSE) that affect the phenotypes of their
 social partners later in life. We, therefore, quantified IGEs and ELSEs on
 growth in domestic pigs. Results show that individuals from the same
 early-life environment express similar social effects on the growth of
 their social partners, and that such ELSE shape the growth rate of social
 partners more than IGE. Thus, the social skills that individuals develop
 in early-life have a long-lasting impact on the phenotypes of social
 partners. Early-life and genetic social effects were independent of the
 corresponding direct effects of offspring on their own growth, indicating
 that individuals may enhance the growth of their social partners without a
 personal cost. Our findings also illustrate how research devoted to
 quantifying IGEs may miss non-genetic and potentially confounded social
 mechanisms, which may bias the estimates of IGEs.
description: Data_Dryad_HDY-16-OR0297RPhenotypic data used for the statistical analyses of this paper. Head lines describe the different traits and factors of variation.Pedigree_Dryad_HDY-16-OR0297RPedigree information related to the genetic analyses carried out for this publication.
DOI: 10.5061/dryad.s91p4
title: Data from: Interaction rewiring and the rapid turnover of plant-pollinator networks

description: Whether species interactions are static or change over time has
 wide-reaching ecological and evolutionary consequences. However, species
 interaction networks are typically constructed from temporally aggregated
 interaction data, thereby implicitly assuming that interactions are fixed.
 This approach has advanced our understanding of communities, but it
 obscures the timescale at which interactions form (or dissolve) and the
 drivers and consequences of such dynamics. We address this knowledge gap
 by quantifying the within-season turnover of plant–pollinator interactions
 from weekly censuses across 3 years in a subalpine ecosystem. Week-to-week
 turnover of interactions (1) was high, (2) followed a consistent seasonal
 progression in all years of study and (3) was dominated by interaction
 rewiring (the reassembly of interactions among species). Simulation models
 revealed that species’ phenologies and relative abundances constrained
 both total interaction turnover and rewiring. Our findings reveal the
 diversity of species interactions that may be missed when the temporal
 dynamics of networks are ignored.
description: CaraDonna_Interaction_Turnover_All_Years_RMBLData from Table S4. Beta-diversity (turnover) values for each week-to-week transition for all turnover metrics (including Bray-Curtis interaction turnover) for each year of study. All notation is included in the main text of the manuscript.CaraDonna_Interaction_Turnover_simulation_models_and_observed_All_Years_RMBLData generated from probability-based simulation models to explore potential ecological factors that may constrain within-season interaction turnover. Details of simulation models and subsequent analyses are provided in the main text of the manuscript.
DOI: 10.5061/dryad.6g7j6
title: Data from: Naturally-occurring changes in social-cognitive factors modify change in physical activity during early adolescence

description: Purpose. To determine whether naturally-occurring changes in
 children's motives and beliefs are associated with the steep decline
 in physical activity observed from childhood to early adolescence.
 Methods. Latent growth modeling was applied in longitudinal tests of
 social-cognitive influences, and their interactions, on physical activity
 in a large cohort of boys and girls evaluated annually between 5th and 7th
 grades. Results. Measurement equivalence of motives and beliefs was
 confirmed between boys and girls. After adjustment for gender and maturity
 differences, physical activity declined less in children who reported the
 least decreases in self-efficacy for overcoming barriers to activity and
 perceived parental support. Physical activity also declined less in
 students who persistently felt they had more parental and friend support
 for activity compared to those who reported the largest decrease in
 support from friends. After further adjustment for race, the decline in
 physical activity was less in those who had the largest decrease in
 perceived barriers and maintained a favorable perception of their
 neighborhood environment. Changes in enjoyment and social motives were
 unrelated to change in physical activity. Conclusion. Using an objective
 measure of physical activity, we confirm that naturally-occurring changes
 in children's beliefs about barriers to physical activity and their
 ability to overcome them, as well as perceptions of their neighborhood
 environment and social support, are concurrent with age-related declines
 in children's physical activity. The longitudinal findings confirm
 these putative social-cognitive mediators as plausible, interacting
 targets of interventions designed to mitigate the marked decline in
 physical activity that occurs during the transition between elementary and
 middle schools.
description: TRACK COHORT 857 PLOS
 ONE shortCases are in rows.
 Repeated variables in columns. Variable names in row 1 (b indicates 6th
 grade variable assessment; c indicates 7th grade variable assessment).
 Variable labels and formatting are found in README
 file.
DOI: 10.5061/dryad.4g26c
title: Data from: Oviposition traits generate extrinsic postzygotic isolation between two pine sawfly species

description: Background: Although empirical data indicate that ecological speciation is
 prevalent in nature, the relative importance of different forms of
 reproductive isolation and the traits generating reproductive isolation
 remain unclear. To address these questions, we examined a pair of
 ecologically divergent pine-sawfly species: while Neodiprion pinetum
 specializes on a thin-needled pine (Pinus strobus), N. lecontei utilizes
 thicker-needled pines. We hypothesized that extrinsic postzygotic
 isolation is generated by oviposition traits. To test this hypothesis, we
 assayed ovipositor morphology, oviposition behavior, and host-dependent
 oviposition success in both species and in F1 and backcross females.
 Results: Compared to N. lecontei, N. pinetum females preferred P. strobus
 more strongly, had smaller ovipositors, and laid fewer eggs per needle.
 Additionally, we observed host- and trait-dependent reductions in
 oviposition success in F1 and backcross females. Hybrid females that had
 pinetum-like host preference (P. strobus) and lecontei-like oviposition
 traits (morphology and egg pattern) fared especially poorly. Conclusions:
 Together, these data indicate that maladaptive combinations of oviposition
 traits in hybrids contribute to extrinsic postzygotic isolation between N.
 lecontei and N. pinetum, suggesting that oviposition traits may be an
 important driver of divergence in phytophagous insects.
description: Parental_Oviposition_BehaviorThis folder contains the data for the "oviposition behavior" section of the manuscript. It includes oviposition willingness, oviposition preference, Average number of eggs per needle, preslit presence, and egg spacing for N. lecontei and N. pinetumHost_ Needle_WidthThis folder contains the data from the "Host needle width" section of the manuscript. It includes both mature and seedling measurementsParental_Ovipositor_MorphologyThis folder contains the data for the "Ovipositor Morphology" section of the manuscript. It includes the landmark coordinates and ovipositor size measurements for N. lecontei and N. pinetumInterspecific_crossThis folder contains the data for the "cross oviposition behavior and success" section of the manuscript. It includes oviposition willingness, oviposition preference, and oviposition success for the interspecific crosses.BC_Oviposition_successThis folder contains the data for the "Impact of oviposition traits on BCL oviposition success" section of the manuscript. It includes ovipositor landmark coordinates, ovipositor size measurements, oviposition pattern, and associated oviposition success for N. lecontei backcross females.