cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pr096
title: Data from: The role of topography and plant functional traits in determining tropical reforestation success

description: 1.Early establishment and sapling growth is a key phase in ensuring
 cost-effective reforestation success in relation to biodiversity outcomes.
 Therefore species selection must consider the interaction between plant
 functional traits and the often-challenging and heterogeneous biophysical
 environment of degraded landscapes. 2.In this study, we examine how
 microtopography (slope) results in spatial heterogeneity of soil
 nutrients, especially phosphorus (P) in a degraded tropical pasture
 landscape in Queensland, Australia. We then explore how this small-scale
 heterogeneity influences the growth of two native tree species, Cardwellia
 (C.) sublimis (Proteaceae) and Flindersia (F.) brayleyana (Rutaceae),
 which differ in key nutrient-acquisition strategies. 3.The proteaceous C.
 sublimis was found to be buffered from possible P limitation in degraded
 soils due to its effective P acquisition by cluster roots. In contrast to
 C. sublimis, which showed no difference in growth after 5 years across a
 range of soil conditions, F. brayleyana was found to be highly responsive
 to soil conditions with increased growth in low-slope, higher P
 availability areas. The ability of F. brayleyana to take advantage of high
 soil P levels, including the development of leaves with higher P
 concentrations, resulted in an apparent switch in competitive fitness
 between these two species across a landscape gradient. 4.Synthesis and
 applications. In a detailed study of a landscape reforestation experiment
 in North Queensland, Australia, we demonstrate that site edaphic factors
 can vary within tens of meters due to topographic relief, and that species
 respond differently to these conditions. We therefore show the need to
 consider both the spatial heterogeneity of edaphic factors and the
 belowground functional traits of potential reforestation species when
 planning reforestation programs.
description: Tree growth, plot slope,
 leaf, and soil biochemical analysisExcel file containing
 metadata descriptors and 5 data sheets derived from the Thiaki
 reforestation experiment used in Journal of Applied Ecology paper. Tree
 census data collected in field in July 2013 and Sep 2015. Average plot and
 row slope information extracted from digital elevation model, and leaf and
 soil biochemical results from bulked samples collected in Sep 2015. See
 paper for methods.JAPPL-2017-00489.xlsx
DOI: 10.5061/dryad.m1j24tf
title: Data from: Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers

description: Copy number variation (CNV) is a major part of the genetic diversity
 segregating within populations, but remains poorly understood relative to
 single nucleotide variation. Here, we report on a tRNA ligase gene (RLG1a)
 exhibiting unprecedented, and fitness-relevant, CNV within an annual
 population of the yellow monkeyflower Mimulus guttatus. Variation at RLG1a
 was associated with multiple traits in pooled population resequencing
 (PoolSeq) scans of phenotypic and phenological cohorts. Five of 35 (14%)
 of resequenced inbred lines carried three-copy variants of RLG1a (trip+),
 and trip+ lines exhibited elevated RLG1a expression. trip+ carriers, in
 addition to being over-represented in late-flowering and large-flowered
 PoolSeq populations, flowered later under stressful conditions in a
 greenhouse experiment (P &lt; 0.05). In early-flowering wild cohorts,
 we discovered an additional rare variant (high+) that carries 250-300
 copies of RLG1a totaling ~5.7Mb, equivalent to 20-40% of a chromosome.
 Mendelian segregation of diagnostic alleles and qPCR-based copy counts In
 the progeny of a high+ carrier, indicate that high+ is a single tandem
 array unlinked from the single copy RLG1a locus in the reference genome.
 In the wild, high+ carriers had highest fitness in two dry and/or hot
 years (2015 and 2017; both P &lt; 0.01), while single copy individuals
 were twice as fecund as either CNV genotype in a lush year (2016: p
 &lt; 0.005). Our results demonstrate fluctuating selection on CNVs
 affecting phenological traits in a wild population, suggest that plant
 tRNA ligases mediate stress-responsive life-history traits, and introduce
 a novel system for investigating the molecular mechanisms of gene
 amplification.
description: Data from: Extreme copy
 number variation at a tRNA ligase gene affecting phenological and fitness
 traits in yellow monkeyflowerThis xlsx file includes
 (after a brief readme sheet) 7 spreadsheets, each with
 genotype-phenotype-fitness or qpcr datasets presented in this paper. All
 plants in these datasets were derived from a single population of Mimulus
 guttatus (yellow monkeyflower) from Iron Mountain Oregon. Datasets are in
 the order they were presented in the paper.N2091genphendata.xlsx
DOI: 10.15468/dl.pe2nzj
title: Occurrence Download

description: A dataset containing 988 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Drymarchon melanurus",
 "Year 1960-2026"
 ]
}

 The dataset includes 988 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000759-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0rp52
title: Data from: A phylogenetically controlled meta-analysis of biologging device effects on birds: deleterious effects and a call for more standardized reporting of study data

description: 1.The use of biologging devices continues to increase, with technological
 advances yielding remarkable ecological insights and generating new
 research questions. However, as devices develop and are deployed more
 widely, there is a need to update our knowledge of the potential ethical
 impacts to allow scientists to balance these against the knowledge gained.
 2.We employed a suite of phylogenetically controlled meta-analyses on a
 dataset comprising more than 450 published effect sizes across 214
 different studies to examine the effects of biologger tagging on five key
 traits in birds. 3.Overall, we found small but significant negative
 effects of tagging on survival, reproduction, parental care. In addition,
 tagging was positively associated with foraging trip duration, but had no
 effect on body mass. Meta-regressions revealed that flying style,
 migration distance and proportional tag mass were significant influences
 producing these deleterious effects, with attachment type and position
 additionally important covariates influencing survival- and
 reproduction-based effect sizes. 4.There was a positive correlation
 between the effects of tagging on survival and reproduction, highlighting
 that effects may be cumulative, with the full effects of tagging not
 necessarily apparent in studies focused on single traits. We discuss the
 tradeoff between these negative effects and the advances gained through
 the use of biologgers. 5.Finally, given the number of studies from our
 initial literature search that lacked sufficient data for inclusion in
 analyses, we provide recommendations on the essential information that all
 biologging studies should report in order to facilitate future assessments
 of impacts on animals.
description: PhylogeniesPhylogenies used for each analysisDataZr_DryList of studies with Effect Sizes
DOI: 10.5061/dryad.5f3f0
title: Data from: Sperm variation within a single ejaculate affects offspring development in Atlantic salmon

description: It is generally believed that variation in sperm phenotype within a single
 ejaculate has no consequences for offspring performance, because sperm
 phenotypes are thought not to reflect sperm genotypes. We show that
 variation in individual sperm function within an ejaculate affects the
 performance of the resulting offspring in the Atlantic salmon Salmo salar.
 We experimentally manipulated the time between sperm activation and
 fertilization in order to select for sperm cohorts differing in longevity
 within single ejaculates of wild caught male salmon. We found that
 within-ejaculate variation in sperm longevity significantly affected
 offspring development and hence time until hatching. Whether these effects
 have a genetic or epigenetic basis needs to be further evaluated. However,
 our results provide experimental evidence for transgenerational effects of
 individual sperm function.
description: Immler et al_Biol
 Lett_dataDataset containing the
 data for analysis on time from fertilisation until hatching, larval size
 at hatching and growth rate for all experiments described in the
 article.
DOI: 10.15468/dl.777zm2
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Records of Reptilia and Amphibia within the territory of Chornobyl Exclusion Zone, Ukraine, during 2020-2023"
 ]
}

 The dataset includes 25 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000760-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.502
title: Data from: Ontogeny and phylogeny in the northern swordtail clade of Xiphophorus

description: It has been hypothesized than morphological diversity within clades can be
 generated by simple alterations of shared developmental programs. However,
 few studies have examined changes in heterochrony, the rate and timing of
 developmental events, in an explicitly phylogenetic context. We studied
 how developmental patterns have changed phylogenetically in the northern
 swordtail clade of Xiphophorus. We reared individuals of an outgroup and
 seven of nine species in the clade and followed their development for ~300
 days. For each individual, we used nonlinear regression to estimate three
 growth parameters: growth rate, adult body size, and age of cessation of
 growth. We estimated sword growth rates in males by linear regression. We
 then used the means of these growth parameters to construct standard
 growth curves for each species and to study growth patterns in a
 phylogenetic context. A combined phylogeny was constructed from both
 phenotypic and DNA sequence data. The phenotypic data set, compiled from
 the literature, consisted of 86 morphological, pigmentation, behavioral,
 and random amplified polymorphic DNA characters, many of which had not
 been used before for phylogenetic analysis. DNA sequence data from three
 genes for a total of 1284 bases were also obtained from the literature and
 included in the analysis. Relationships between growth parameters were
 examined by phylogenetically independent contrasts in relation to seven
 different phylogenies based on the most-parsimonious trees generated from
 the phenotypic, DNA sequence, and combined data sets; this allowed us to
 identify relationships between variables that were not sensitive to
 ambiguities in Xiphophorus phylogeny. Our analysis revealed statistically
 significant correlations between female body size and male body size, and
 between female growth rate and male sword growth rate, for all seven
 phylogenies. Marginally statistically significant relationships were also
 identified between female body size and female growth rate, and between
 female growth rate and male body size. We relate these relationships to
 what is known about the ecology, genetics, and behavior of Xiphophorus to
 better understand the evolution of growth patterns of both the body as a
 whole and the sword in particular. The relationship of these data to the
 evolution of swords is discussed.
description: Marcus and McCune Data
 SetMarcus.txt
DOI: 10.5061/dryad.s3np654
title: Data from: Variation in three community features across habitat types and scales within a 15-ha subtropical evergreen-deciduous broadleaved mixed forest dynamics plot in China

description: The evergreen and deciduous broadleaved mixed forests (EDBMFs) belong to
 one of the ecosystems most sensitive to environmental change, however,
 little is known about the environmental determinants for their plant
 diversity and forest structure at different habitat types and spatial
 scales. Here, we used data from a 15-ha (300×500 m) forest dynamic plot
 (FDP) of an old-growth EDBMF to examine the patterns and determinants of
 the three community features (stem abundance, rarefied species richness
 and basal area) in three habitat types (ridge, hillside and foothill) and
 at three spatial scales (20×20 m, 50×50 m and 100×100 m). We found that
 the three community features significantly changed with habitat type, but
 only one of them (rarefied richness) changed with scale. Among spatial
 scales, the principle environmental factors that widely affected community
 features were pH, SOM and TP, while these effects only taken place at
 certain habitat. Variations in the three community features explained by
 soil conditions were generally greater than those explained by
 topographical conditions. With changes in habitat type, the proportion of
 variations explained by environmental conditions was 31-53%, 8-25%, and
 18-26% for abundance, rarefied richness and basal area (BA), respectively.
 With increasing spatial scale, the variations explained by environmental
 conditions were 44-75% for abundance, 28-95% for rarefied richness, and
 18-86% for BA. Our study demonstrated that environmental factors had great
 impacts on the plant diversity and forest structure in the EDBMFs,
 especially the soil factors such as pH. In addition, the importance of the
 environmental determinants on these community features was highly related
 to the spatial scale.
description: Diversity and
 environmental properties in MLZ 15 ha plotThis file includes the
 coordinate of each subplot in different grain size, environmental
 properties (elevation, convexity,slope, pH, SOM, AP, TP, AN, TN) and
 community characteristics (basal area, rarefied richness,
 abundance).Data-S1.xlsx
DOI: 10.5061/dryad.3q0mk00
title: Data from: Evolution of transmission mode in conditional mutualisms with spatial variation in symbiont quality

description: Many symbioses have costs and benefits to their hosts that vary with the
 environmental context, which itself may vary in space. The same symbiont
 may be a mutualist in one location and a parasite in another. Such
 spatially conditional mutualisms pose a dilemma for hosts, who might
 evolve (higher or lower) horizontal or vertical transmission to increase
 their chances of being infected only where the symbiont is beneficial. To
 determine how transmission in hosts might evolve, we modeled transmission
 evolution where the symbiont had a spatially conditional effect on either
 host lifespan or fecundity. We found that over ecological time, symbionts
 that affected lifespan but not fecundity led to high frequencies of
 infected hosts in areas where the symbiont was beneficial and low
 frequencies elsewhere. In response, hosts evolved increased horizontal
 transmission only when the symbiont affected lifespan. We also modeled
 transmission evolution in symbionts, which evolved high horizontal and
 vertical transmission, indicating a possible host-symbiont conflict over
 transmission mode. Our results suggest an eco-evolutionary feedback where
 the component of host fitness affected by a conditionally mutualistic
 symbiont in turn determines its distribution in the population, and,
 through this, the transmission mode that evolves.
description: Code for analyzing
 analytical model and for running simulationsSimulation_code_and_model.zip
DOI: 10.5061/dryad.8s75g
title: Data from: Transgenerational effects of nutrition are different for sons and daughters

description: Food shortage is an important selective factor shaping animal life-history
 trajectories. Yet, despite its role, many aspects of the interaction
 between parental and offspring food environments remain unclear. In this
 study, we measured developmental plasticity in response to food
 availability over two generations and tested the relative contribution of
 paternal and maternal food availability to the performance of offspring
 reared under matched and mismatched food environments. We applied a
 cross-generational split-brood design using the springtail Orchesella
 cincta, which is found in the litter layer of temperate forests. The
 results show adverse effects of food limitation on several life-history
 traits and reproductive performance of both parental sexes. Food
 conditions of both parents contributed to the offspring phenotypic
 variation, providing evidence for transgenerational effects of diet.
 Parental diet influenced sons’ age at maturity and daughters’ weight at
 maturity. Specifically, being born to food-restricted parents allowed
 offspring to alleviate the adverse effects of food limitation, without
 reducing their performance under well-fed conditions. Thus, parents raised
 on a poor diet primed their offspring for a more efficient resource use.
 However, a mismatch between maternal and offspring food environments
 generated sex-specific adverse effects: female offspring born to well-fed
 mothers showed a decreased flexibility to deal with low-food conditions.
 Notably, these maternal effects of food availability were not observed in
 the sons. Finally, we found that the relationship between age and size at
 maturity differed between males and females and showed that offspring
 life-history strategies in O. cincta are primed differently by the
 parents.
description: DatasetThe effects of diet on parental life-history traits, the effects of mating partner on resource allocation and the effects of parental diet on offspring life-history traits, are organized in four worksheets. Please, note that the shortcuts H and L in the dataset, denote the high and low diet, respectively.
DOI: 10.5061/dryad.9pv5625
title: Data from: Controlled clinical trial of canine therapy versus usual care to reduce patient anxiety in the emergency department

description: Objective: Test if therapy dogs can reduce anxiety in emergency department
 (ED) patients. Methods: In this controlled clinical trial (NCT03471429),
 medically stable, adult patients were approached if the physician believed
 that the patient had “moderate or greater anxiety.” Patients were
 allocated on a 1:1 ratio to either 15 min exposure to a certified therapy
 dog and handler (dog), or usual care (control). Patient reported anxiety,
 pain and depression were assessed using a 0-10 scale (10=worst). Primary
 outcome was change in anxiety from baseline (T0) to 30 min and 90 min
 after exposure to dog or control (T1 and T2 respectively); secondary
 outcomes were pain, depression and frequency of pain medication. Results:
 Among 98 patients willing to participate in research, 7 had aversions to
 dogs, leaving 91 (93%) were willing to see a dog; 40 patients were
 allocated to each group (dog or control). No data were normally
 distributed. Median baseline anxiety, pain and depression were similar
 between groups. With dog exposure, anxiety decreased significantly from T0
 to T1: 6 (IQR 4-9.75) to T1: 2 (0-6) compared with 6 (4-8) to 6 (2.5-8) in
 controls (P&lt;0.001, for T1, Mann-Whitney U). Dog exposure was
 associated with significantly lower anxiety at T2 and a significant
 overall treatment effect on two-way repeated measures ANOVA for anxiety,
 pain and depression. After exposure, 1/40 in the dog group needed pain
 medication, versus 7/40 in controls (P=0.056, Fisher’s). Conclusions:
 Exposure to therapy dogs plus handlers significantly reduced anxiety in ED
 patients.
description: CANINE_DATA_LABELS_2018-12-07 public deidentified V2Data used for manuscriptCANINE_DATA_LABELS_2018-12-07 public deidentified V3.xls
DOI: 10.5061/dryad.49sk0
title: Data from: Connecting the sun to flowering in sunflower adaptation

description: Species living in seasonal environments often adaptively time their
 reproduction in response to photoperiod cues. We characterized the
 expression of genes in the flowering-time regulatory network across wild
 populations of the common sunflower, Helianthus annuus, that we found to
 be adaptively differentiated for photoperiod response. The observed clinal
 variation was associated with changes at multiple hierarchical levels in
 multiple pathways. Paralog-specific changes in FT homolog expression and
 tissue-specific changes in SOC1 homolog expression were associated with
 loss and reversal of plasticity respectively, suggesting that redundancy
 and modularity are gene network characteristics easily exploited by
 natural selection to produce evolutionary innovation. Distinct genetic
 mechanisms contribute to convergent evolution of photoperiod responses
 within sunflower, suggesting regulatory network architecture does not
 impose strong constraints on the evolution of phenotypic plasticity.
description: BlackmanME2011_DataArchive of seven data files. Includes: Fig1Data_BlackmanME2011, Fig2_S2Data_BlackmanME2011, Fig3_S2Data_BlackmanME2011, FigS1Data_BlackmanME2011, FigS2_4_5_6_LD_BlackmanME2011, FST_genotypes_BlackmanME2011, QstData_BlackmanME2011
DOI: 10.5061/dryad.sq35b
title: Data from: Inbreeding depression at the sapling stage and its genetic consequences in a population of the outcrossing dominant tree species, Castanopsis sieboldii

description: Highly frequent pollination at short distances combined with spatial
 genetic structure (SGS) among reproductive individuals, as observed in
 populations of many forest tree species, may lead to highly frequent
 pollinations between genetically related individuals located close to each
 other. This could increase frequencies of biparental inbreeding and
 strengthen the degree of SGS across generations. However, the degree of
 SGS observed in forest tree populations is not usually strong, suggesting
 that such processes are restricted by other factors, which may include
 inbreeding depression. To test this hypothesis, we examined inbreeding
 depression in Castanopsis sieboldii saplings in a population known to have
 significant SGS and high frequencies of short-distance pollination. We
 determined genotypes at eight microsatellite loci of 125 adult trees and
 899 saplings in a 4-ha plot. The neighborhood model approach, assuming an
 exponential power function, showed highly frequent pollination at short
 distance among parents of saplings. SGS was significantly stronger among
 saplings than among adults. The average value of F is (individual
 inbreeding coefficient based on kinship coefficients between genes within
 individuals) was also significantly higher among saplings than among
 adults. Furthermore, average values for saplings were relatively high
 (0.036–0.052) in 30–50 to 90–110 cm height classes and rapidly decreased
 to 0.006 for the ≥110-cm class. Analysis of covariance, taking into
 account the canopy state, showed that inbreeding depression had a
 significant negative effect on the saplings’ height. Thus, the level of
 inbreeding in saplings decreased with size classes increasing, probably
 due to pronounced inbreeding depression resulting in mortality or reduced
 growth of inbred saplings, and hence, the inbreeding depression may
 prevent increasing of the level of inbreeding and the degree of SGS in
 subsequent generations.
description: Data of Nakanishi et al.
 2015DB_Nakanishi et al.
 2015.xlsx