cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3r2280gjp
title: Enemy exclusion effects on biodiversity-productivity relationship in subtropical forest experiment

description: This data set is described in full detail in Huang et al. (2022) Journal
 of Ecology XXX. In brief, we used a large tree biodiversity experiment
 (BEF-China), established in 2009-2010, to test whether the application of
 fungicide or insecticide changes observed tree species richness effects on
 tree growth. We used a subset of plots in which tree species numbers
 ranged from 1 to 8. To these plots, a factorial split-plot treatment was
 added in April 2014. The new treatments (I: insecticide; F: fungicide; C:
 untreated control) were applied to subplots located along one side of the
 main plots. Each subplot contained 4 × 4 = 16trees. We further used the
 central 4 × 4 trees of the main plot for additional measurements (central
 control subplot). Insecticide and fungicide solutions (4 L per subplot)
 were sprayed over tree crowns every 4 weeks, but only on days with no or
 very little wind. During the rainy season, applicationintervals were
 halved to 2 weeks to compensate for more rapid leaching. The insecticide
 solution contained 10 mL dimethoate (an organophosphate) and 10 mL
 deltamethrin (apyrethroid). The fungicide solution contained 8 g of
 mancozeb (a dithiocarbamate) and 25 mL of myclobutanil (a triazole).
 Control subplots were sprayed with 4 L of water.
description: In September 2014 and 2016, we measured basal diameter and height
 of all trees in the subplots. We further measured the central 16 trees in
 each main plot because these are the trees that are censored as part of
 the regular inventories of all 566 BEF-China plots. Tree growth was
 estimated as increase in basal diameter from 2014 to 2016. We also used
 the product of basal diameter and height as a proxy for tree volume, and
 calculated volume growth as increment from 2014 to 2016. To obtain
 species-level basal area and volume, we added the values for all tree
 individuals of the same species per subplot. Community-level basal
 diameter and volume were than obtained by summing all the species-level
 values per subplot. We quantified leaf damage in all
 monocultures in September 2016. We randomly chose five individuals per
 species from the central 6×6 trees of each main plot. Then, for each tree,
 we randomly picked three branches from different canopy layers and sampled
 seven young, fully expanded leaves per branch. The damage of these leaves
 was classified based on the fraction of leaf area affected (0, &lt;5,
 &lt;25, &lt;50, &lt;75, and &gt;75%), separately for
 herbivory and fungal damage. Species mean leaf damage was calculated for
 each subplot by averaging the center of these damage classes over all
 leaves (e.g. 15% for the 5–25% class).
description: Data are in stored as comma-separated plain text files with utf-8
 encoding. The data can be read with most software, including R (www.r-project.org).
 For further details of use, see the comments included  in the R
 scripts.
DOI: 10.5061/dryad.hmgqnk9kh
title: Data condition dependence in biosynthesized chemical defenses of an aposematic and mimetic Heliconius butterfly

description: Aposematic animals advertise their toxicity or unpalatability with bright
 warning coloration. However, acquiring and maintaining chemical defenses
 can be energetically costly, and consequent associations with other
 important traits could shape chemical defense evolution. Here, we have
 tested whether chemical defenses are involved in energetic trade-offs with
 other traits, or whether the levels of chemical defenses are condition
 dependent, by studying associations between biosynthesized cyanogenic
 toxicity and a suite of key life-history and fitness traits in a
 Heliconius butterfly under a controlled laboratory setting. Heliconius
 butterflies are well known for the diversity of their warning color
 patterns and widespread mimicry, and can both sequester the cyanogenic
 glucosides of their Passiflora host plants and biosynthesize these toxins
 de novo. We find energetically costly life-history traits to be either
 unassociated or to show a general positive association with biosynthesized
 cyanogenic toxicity. More toxic individuals developed faster, had higher
 mass as adults, and a tendency for increased lifespan and fecundity. These
 results thus indicate that toxicity level of adult butterflies may be
 dependent on individual condition, influenced by genetic background or
 earlier conditions, with maternal effects as one strong candidate
 mechanism. Additionally, toxicity was higher in older individuals,
 consistent with previous studies indicating accumulation of toxins with
 age. As toxicity level at death was independent of lifespan, cyanogenic
 glucoside compounds may have been recycled to release resources relevant
 for longevity in these long-living butterflies. Understanding the origins
 and maintenance of variation in defenses is necessary in building a more
 complete picture of factors shaping the evolution of aposematic and
 mimetic systems.
description: Please refer to the Methods section of the article.
description: ReadMe files are provided.
DOI: 10.5061/dryad.47d7wm3gt
title: Importance of invasion mechanisms varies with abiotic context and plant invader growth form

description: 1. Many invasion hypotheses propose biotic interactions as the main
 mechanism to explain non-native species' success.  Despite
 the evidence that the strength of biotic interactions varies with abiotic
 context, it remains unclear whether the importance of the different
 mechanisms proposed to explain invasion predictably varies with abiotic
 context and whether this variation is consistent across different growth
 forms. 2. We reviewed studies at a global scale to evaluate whether
 evapotranspiration, latitude, precipitation, and temperature influence the
 importance of disturbance, enemy release, facilitation, and novel weapons
 mechanisms to explain non-native plant invasions.  In total, we
 calculated 171 effect sizes for ~300 non-native plant species covering a
 wide range of environmental conditions and growth forms. 3. Environmental
 context and plant growth form influenced the role played by each invasion
 mechanism.  The importance of disturbance in facilitating
 invasion exhibited a quadratic relationship with latitude and temperature
 and decreased with increasing precipitation.  In mixed
 communities and trees, disturbance was mediated by either
 evapotranspiration, latitude, precipitation, or temperature. 
 Enemy release exhibited a quadratic relationship with evapotranspiration,
 latitude, and precipitation, and was positively related to temperature.
  The importance of enemy release was also contingent on growth
 form and was highly context-dependent, enemy release responses for
 grasses, and trees were modulated by either evapotranspiration, latitude,
 precipitation, or temperature.  The importance of facilitation
 decreased with increasing temperature.  In forbs, facilitation
 decreased with evapotranspiration and temperature.  The
 importance of novel weapons was more strongly confirmed for studies
 conducted at lower evapotranspiration, precipitation, and higher
 latitudes, and exhibited a quadratic relationship with temperature. 4.
 Synthesis. Our results show that environmental conditions not only filter
 non-native species depending on physiological tolerances but may also
 influence the importance of invasion mechanisms.
description: Dataset used in meta-analyses and meta-regression models in
 Chiuffo et al. (2022). Columns A-G contain study and invasion mechanisms
 information. Columns H-W contains effect sizes and variance estimates.
 Full citations for each publication can be found in Appendix S4. Columns
 X-AA contains the four explanatory predictor variables used.
DOI: 10.5061/dryad.2547d7wsv
title: Associations of self-compassion with shame, guilt, and training motivation after sport-specific daily stress – a smartphone study

description: By applying a diary study design, we investigated the role of
 selfcompassion during sport-specific daily stress (SSDS) with regard to
 the negative self-conscious emotions of shame and guilt and training
 motivation. We hypothesised that self-compassion would protect athletes
 from certain self-conscious emotions, namely shame, after SSDS. We also
 predicted that self-compassion would either increase or decrease the
 relationship between stress and motivation. Ninety-six athletes (Mage =
 22.14, SD = 5.92) reported their level of self-compassion and evaluated
 their trainings and/or competitions over three weeks in terms of
 experienced stress, guilt, shame and subsequent training motivation on
 their smartphones. Multilevel analyses showed that SSDS was associated
 with more negative self-conscious emotions and reduced training
 motivation. Moreover, self-compassion weakened the effect of SSDS on shame
 and was not correlated with training motivation. We discuss the results
 with regard to sport psychology practice and future research.
DOI: 10.5061/dryad.5x69p8d5s
title: Crotalaria pallida chemical defence and ant attendance

description: The efficiency of different plant defences is expected to vary depending
 on the combination and abundance of herbivores. Effectiveness of
 ant-mediated defences can also depend on ant activity and local ant
 assemblage, which can vary due to human activities such as intensive
 grazing. We used the plant Crotalaria pallida (Fabaceae), its two
 pod-boring herbivores and the ants that visit the extrafloral nectaries
 (EFNs) to understand how chemical defence and ant-plant associations
 affect plant damage. We hypothesised causal relationships between plant
 chemical defence, ant presence on plants and herbivore damage in scenarios
 of constitutive and induced plant defences and tested the different
 possible relationships using path analysis. The constitutive model
 explained the data more adequately, and each plant defence had different
 effects on each herbivore species. First, chemical defence significantly
 reduced damage by the generalist pod borer Etiella zinckenella but not by
 the specialist Utetheisa ornatrix. Second, ant presence reduced damage by
 the generalist, but had no effect on damage by the specialist. Third, a
 larger number of pods on the plant increased ant presence, as expected
 since more pods results in more EFNs. Finally, we show that these
 density-dependent responses by ants mediate indirect cascades on herbivory
 and generate context-specific responses reducing damage by E. zinckenella
 in sites with cattle grazing. In synthesis, we highlight that plant
 defences have distinct effects on co-occurring herbivores and that
 indirect defences can mediate ecological cascades that generate context
 dependency in the efficiency of different defences.
description: See Pareja & Rezende (2022)
 Direct and indirect plant defences
 reduce damage by a generalist but not by a specialist pod borer.
 Biotropica.
DOI: 10.5061/dryad.zkh1893cj
title: Data from: Hybrid incompatibility between D. virilis and D. lumei is stronger in the presence of transposable elements

description: Mismatches between parental genomes in selfish elements are frequently
 hypothesized to underlie hybrid dysfunction and drive speciation. However,
 because the genetic basis of most hybrid incompatibilities is unknown,
 testing the contribution of selfish elements to reproductive isolation is
 difficult. Here we evaluated the role of transposable elements (TEs) in
 hybrid incompatibilities between Drosophila virilis and D. lummei by
 experimentally comparing hybrid incompatibility in a cross where active
 TEs are present in D. virilis (TE+) and absent in D. lummei, to a cross
 where these TEs are absent from both D. virilis (TE-) and D. lummei
 genotypes. Using genomic data, we confirmed copy number differences in TEs
 between the D. virilis (TE+) strain and the D. virilis (TE-) strain and D.
 lummei. We observed F1 postzygotic reproductive isolation exclusively in
 the interspecific cross involving TE+ D. virilis but not in the cross
 involving TE- D. virilis. This precisely mirrors the intraspecies dysgenic
 phenotype where teste atrophy only occurs when TE+ D. virilis is the
 paternal parent. A series of backcross experiments, designed to account
 for alternative models of hybrid incompatibility, showed that both F1
 hybrid incompatibility and intrastrain dysgenesis is consistent with the
 action of TEs rather than other, genic, interactions. A further Y-autosome
 interaction contributes to additional, sex-specific, inviability in one
 direction of this cross combination. These experiments demonstrate that
 TEs that cause intraspecies dysgenesis can increase reproductive isolation
 between closely related lineages, thereby adding to the processes that
 consolidate speciation.
DOI: 10.57724/cndp_20250113_microant_cnie
title: C and N stable isotopes in excrements, 2025
DOI: 10.5061/dryad.0gb5mkm3r
title: The impacts of host association and perturbation on symbiont fitness

description: Symbiosis benefits hosts in numerous ways, but much less is known about
 how host-association affects symbionts. While symbiont fitness can be
 mediated by host, symbiont, and/or environmental factors, recent works
 indicate that symbiont performance can depend on whether the symbiont is
 needed by the host, suggesting that symbiosis is not always beneficial for
 symbionts. To determine the impact of symbiosis on symbionts across the
 Tree of Life, we conducted a meta-analysis across 83 unique host-symbiont
 pairings under a range of spatial and temporal contexts. Specifically, we
 asked how symbiont fitness is altered outside of symbiosis, when
 host-symbiont interaction is under suboptimal conditions, or as hosts age.
 We found that intracellular symbionts associated with protists tend to
 have greater fitness outside of symbiosis, with the opposite trend for
 animal hosts. This result suggests that animals may be better at
 maintaining symbionts. Symbiont fitness also generally increased as hosts
 grow older. Moreover, symbionts that can proliferate in- and outside host
 cells performed better than those found exclusively inside or outside
 cells, suggesting that flexibility in growing location may help symbionts
 thrive. We discuss these fitness patterns in light of host-driven factors,
 where hosts exert influence over symbionts to suit their needs.
DOI: 10.5061/dryad.wwpzgmsmv
title: Kenya heel prick and cord blood sample data

description: Using data from Ontario Canada, we previously developed machine
 learning-based algorithms incorporating newborn screening metabolites to
 estimate gestational age (GA). The objective of this study was to evaluate
 the use of these algorithms in a population of infants born in Siaya
 county, Kenya.  Cord and heel prick samples were collected from
 newborns in Kenya and metabolic analysis was carried out by Newborn
 Screening Ontario in Ottawa, Canada. Postnatal GA estimation models were
 developed with data from Ontario with multivariable linear regression
 using ELASTIC NET regularization. Model performance was evaluated by
 applying the models to the data collected from Kenya and comparing
 model-derived estimates of GA to reference estimates from early pregnancy
 ultrasound.  Heel prick samples were collected from 1,039
 newborns from Kenya. Of these, 8.9% were born preterm and 8.5% were small
 for GA. Cord blood samples were also collected from 1,012 newborns. In
 data from heel prick samples, our best-performing model estimated GA
 within 9.5 days overall of reference GA [mean absolute error (MAE) 1.35
 (95% CI 1.27, 1.43)]. In preterm infants and those small for GA, MAE was
 2.62 (2.28, 2.99) and 1.81 (1.57, 2.07) weeks, respectively. In data from
 cord blood, model accuracy slightly decreased overall (MAE 1.44 (95% CI
 1.36, 1.53)). Accuracy was not impacted by maternal HIV status and
 improved when the dating ultrasound occurred between 9 and 13 weeks of
 gestation, in both heel prick and cord blood data (overall MAE 1.04 (95%
 CI 0.87, 1.22) and 1.08 (95% CI 0.90, 1.27), respectively). Compared to
 internal validation performance using Ontario data and to our previously
 published external validations, model performance was diminished in the
 Kenya cohort, suggesting that reference ultrasound timing is an important
 factor in model performance. Our study highlights the challenges in
 reliably estimating GA in low resource settings, even those with access to
 dating ultrasound, given that the timing of dating ultrasound is critical
 to develop algorithms for accurate estimation of GA based on metabolic
 analysis of blood obtained at birth.
DOI: 10.5061/dryad.pnvx0k6qd
title: Supplementary datasets for: Prodigious polyphyly in Pleuroceridae (Gastropoda: Cerithioidea)

description: Phylogenomic studies with hundreds or thousands of loci are rare for most
 invertebrate groups, including freshwater gastropods. This can prevent
 understanding of phylogeny, which hinders many areas of research.
 Pleuroceridae is a family of freshwater snails that is highly imperiled
 and plays an essential role in the ecology of many freshwater systems of
 the eastern United States. However, the evolutionary history of the family
 is not understood, and the systematics of the family has not been revised
 in a modern framework. Pleurocerids display a variety of egg-deposition
 behaviors and shell shapes, making the family an ideal system for studying
 evolution of invertebrate life history and morphology. However, past
 mitochondrial-based phylogenetic analyses have failed to produce
 meaningful phylogenetic hypotheses, preventing conclusions about
 pleurocerid systematics and evolution. Here, we generated a novel anchored
 hybrid enrichment probe set with phylogenetic utility for Pleuroceridae.
 We sampled pleurocerids from across their range to test the probe set and
 generated a backbone phylogeny. Our analyses uncovered striking levels of
 polyphyly among currently accepted genera. Numerous species were also
 polyphyletic, indicative of unrecognized diversity. Phylogenetic patterns
 also revealed considerable convergence of shell morphologies. In contrast,
 anatomical and life history features appeared to be much less homoplastic.
 Despite generic paraphyly, high support for most major clades and
 phylogenetic cohesiveness of non-shell characters indicate utility of the
 AHE probe set for studying pleurocerid evolution.
description: Please see Whelan et al. (2022) doi: 10.18061/bssb.v1i2.8419 for
 details
DOI: 10.5061/dryad.76hdr7t05
title: Integrating methylome and transcriptome signatures expands the molecular classification of the pituitary tumors

description: Purpose: To explore pituitary
 tumors by methylome and transcriptome signatures in a
 heterogeneous ethnic population.  Design: Retrospective
 cross-sectional study. Patients and Methods: Clinicopathological features,
 methylome, and transcriptome were evaluated in pituitary tumors
 from 77 patients (61% women, age: 12-72 years)followed
 due to functioning (FPT: GH-secreting n=18, ACTH-secreting
 n=14) and non-functioning pituitary tumors (NFPT, n=45) at
 Ribeirao Preto Medical School, University of Sao Paulo. 
 Results: Unsupervised hierarchical clustering analysis
 (UHCA) of methylome (n=77) and
 transcriptome (n=65 out of 77) revealed three clusters
 each: one enriched by FPT, other by NFPT, and another
 by ACTH-secreting and NFPT. Comparison between each omics-derived
 cluster identified 3,568 and 5,994 differentially
 methylated and expressed genes, respectively, which were
 associated with each other, with tumor clinical presentation, and with
 2017 and 2022 WHO classifications. UHCA considering 11
 transcripts related to pituitary development/differentiation
 also supported three clusters: POU1F1-driven
 somatotroph, TBX19-driven corticotroph,
 and NR5A1-driven gonadotroph adenomas, with rare exceptions
 (NR5A1 expressed in few GH-secreting and corticotroph-silent
 adenomas; POU1F1 in few ACTH-secreting adenomas;
 and TBX19 in few NFPTs).  Conclusions: This
 large heterogenic ethnic Brazilian cohort confirms that
 integrated methylome and transcriptome signatures classify FPT
 and NFPT, which are associated with clinical presentation and tumor
 invasiveness. Moreover, the cluster NFPT/ACTH-secreting adenomas raises
 interest regarding tumor heterogeneity, supporting the challenge raised by
 the 2017 and 2022 WHO definitions regarding the discrepancy, in rare
 cases, between clinical presentation and pituitary lineage
 markers. Finally, making our data publicly available
 enables further studies to validate genes/pathways involved in
 pituitary tumor pathogenesis and prognosis.
DOI: 10.57707/fmi-b2share.4hr6v-3bq79
title: Fluxes and plant diversity data in urban grasslands

description: Files that were used in Justine et al.'s manuscript, entitled 'Lawns and meadows in urban green space - A comparison from greenhouse gas, drought resilience and biodiversity perspectives'. CO2, CH4 and N2O fluxes, C/N content in soil and plant diversity were measured in urban grasslands around Helsinki Metropolitan Area. Twelve of the sites (6 control lawns and 6 meadows) belong to the Lawns into Meadows experiment measured from 2020-2022, and provide crucial data (respiration, CH4 and N2O and plant diversity) about conversion from a lawn into a meadow. The 4 other sites includes a mesic meadow, a dry meadow, an irrigated lawn and a non-irrigated lawn, where respiration, GPP, green cover and plant diversity were recorded from 2021-2022.