cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q83bk3jkb
title: Data from: Effective specialist or jack of all trades? Experimental evolution of a crop pest in fluctuating and stable environments

description: Understanding pest evolution in agricultural systems is crucial for
 developing effective and innovative pest control strategies. Types of
 cultivation, such as crop monocultures versus polycultures or crop
 rotation, may act as a selective pressure on pests’ capability to exploit
 the host’s resources. In this study, we examined the herbivorous mite
 Aceria tosichella (commonly known as wheat curl mite), a widespread wheat
 pest, to understand how fluctuating versus stable environments influence
 its niche breadth and ability to utilize different host plant species. We
 subjected a wheat-bred mite population to replicated experimental
 evolution in a single-host environment (either wheat or barley), or in an
 alternation between these two plant species every three mite generations.
 Next, we tested the fitness of these evolving populations on wheat,
 barley, and on two other plant species not encountered during experimental
 evolution, namely rye and smooth brome. Our results revealed that the
 niche breadth of A. tosichella evolved in response to the level of
 environmental variability. The fluctuating environment expanded the niche
 breadth by increasing the mite’s ability to utilize different plant
 species, including novel ones. Such an environment may thus promote
 flexible host-use generalist phenotypes. However, the niche expansion
 resulted in some costs expressed as reduced performances on both wheat and
 barley as compared to specialists. Stable host environments led to
 specialized phenotypes. The population that evolved in a constant
 environment consisting of barley increased its fitness on barley without
 the cost of utilizing wheat. However, the population evolving on wheat did
 not significantly increase its fitness on wheat, but decreased its
 performance on barley. Altogether, our results indicated that, depending
 on the degree of environmental heterogeneity, agricultural systems create
 different conditions that influence pests’ niche breadth evolution, which
 may in turn affect the ability of pests to persist in such systems.
DOI: 10.5061/dryad.ghx3ffbr1
title: Data from: Land-based climate solutions for the United States

description: Meeting end-of-century global warming targets requires aggressive action
 on multiple fronts. Recent reports note the futility of addressing
 mitigation goals without fully engaging the agricultural sector, yet no
 available assessments combine both nature-based solutions (reforestation,
 grassland and wetland protection, and agricultural practice change) and
 cellulosic bioenergy for a single geographic region. Collectively, these
 solutions might offer a suite of climate, biodiversity, and other benefits
 greater than either alone. Nature-based solutions are largely constrained
 by the duration of carbon accrual in soils and forest biomass; each of
 these carbon pools will eventually saturate. Bioenergy solutions can last
 indefinitely but carry significant environmental risk if carelessly
 deployed. We detail a simplified scenario for the U.S. that illustrates
 the benefits of combining approaches. We assign a portion of non-forested
 former cropland to bioenergy sufficient to meet projected mid-century
 transportation needs, with the remainder assigned to nature-based
 solutions such as reforestation. Bottom-up mitigation potentials for the
 aggregate contributions of crop, grazing, forest, and bioenergy lands are
 assessed by including in a Monte Carlo model conservative ranges for
 cost-effective local mitigation capacities, together with ranges for (a)
 areal extents that avoid double counting and include realistic adoption
 rates and (b) the projected duration of different carbon sinks. The
 projected duration illustrates the net effect of eventually saturating
 soil carbon pools in the case of most strategies, and additionally
 saturating biomass carbon pools in the case of reforestation. Results show
 a conservative end-of-century mitigation capacity of 110 (57 – 178) Gt
 CO2e for the U.S., ~50% higher than existing estimates that prioritize
 nature-based or bioenergy solutions separately. Further research is needed
 to shrink uncertainties but there is sufficient confidence in the general
 magnitude and direction of a combined approach to plan for deployment now.
description: The dataset is a synthesis of literature values selected based on
 criteria described in the parent paper’s narrative.
description: The files can be opened in Microsoft Excel or any other
 spreadsheet that can load Excel-format files.
DOI: 10.5061/dryad.8w9ghx3pb
title: Range expansion and contraction of Tillandsia landbeckii lomas in hyperarid Chilean Atacama Desert indicate ancient introgression and geneflow

description: Here we hypothesise that interspecies geneflow as well as secondary
 contact of formerly isolated clusters of T. landbeckii may have
 contributed to maintain, restore or even enhance the species´ genetic
 diversity through space and time. We employed genotyping-by sequencing
 (GBS) to obtain genetic variation largely retrieved from the nuclear
 genome on population level, and used the same data to extract sequence
 information to define maternally inherited plastid types. Reference
 plastomes from different plastid types via a genome-wide short read
 sequencing approach (genome skimming) were assembled. Plastome data were
 analysed in order to provide a robust phylogenetic and temporal framework
 of the maternal perspective including various epiarenic species of
 particular interest for the evolutionary history of T. landbeckii. The
 spatiotemporal scale of our study covers the entire Chilean Atacama Desert
 with a focus on one population form the central cluster. The aim of our
 study is to provide reasonable explanations for orphan genetic clusters on
 different spatial scales, while highlighting the idea of evolutionary
 significant secondary genetic contact on and between species level, which
 may have also fostered the evolution of epiarenic growth in Tillandsia.
 This study should pave the way for future comparative evolutionary studies
 across epiarenic Tillandsia species to unravel the co-evolution of the
 Atacama Desert system and biological life.
DOI: 10.5061/dryad.r7sqv9sdv
title: Molecular data of Sphagnum majus ssp. majus and ssp. norvegicum (Bryophyta: Sphagnaceae) relative to taxonomy and geography

description: Species delimitation is problematic in many plant groups and among the
 mosses, Sphagnum is one of the more contentious genera because of high
 levels of morphological variation. The allopolyploid species, Sphagnum
 majus, comprises one such problematic complex. Two morphologically
 differentiated but overlapping subspecies have been described. We
 conducted morphometric and molecular analyses with samples from around the
 Northern Hemisphere to test for phenotypic and phylogenetic
 differentiation between the subspecies. Although field collections of the
 two species can be statistically differentiated morphologically, there is
 substantial overlap. Genome-scale molecular data do not suggest any
 differentiation between S. majus ssp. majus and ssp. norvegicum, including
 samples assigned to the two taxa from sympatric sites. Sequence data from
 the plastid genome were employed to infer parentage of allopolyploid S.
 majus. Our results support the hypothesis that S. annulatum is the
 paternal parent and S. cuspidatum is the maternal parent.  We
 conclude that the morphological differences between them are either
 plastic responses to habitat heterogeneity or segregating genetic
 variation within a single taxon. Formal taxonomic recognition of two taxa
 is not supported by our molecular data.
description: Zipped folder with 88 files of demultiplexed Illumina reads for
 Sphagnum samples included in the analyses. Phylip
 format alignment of 6692 RADseq loci generated by ipyrad for 88 Sphagnum
 samples. Loci format file of 6692 RADseq loci generated
 by ipyrad for 88 Sphagnum samples. Fasta format
 alignment of 8 plastid concatenated loci generated by ipyrad and
 identified them by mapping to Sphagnum angustifolium reference genome (76
 samples). Structure format file (two lines per samples,
 considering S. majus samples as diploid and the remain species as haploid)
 with one randomly selected SNP per locus generated by ipyrad for 78
 ingroup S. majus and putative parental species.
 Structure format file (two lines per samples, considering S.
 majus samples as diploid) with one randomly selected SNP per locus
 generated by ipyrad for 63 ingroup S. majus.
DOI: 10.5061/dryad.7wm37pvvx
title: The Bug in a teacup – Monitoring arthropod-plant associations with environmental DNA from dried plant material

description: Environmental DNA analysis has revolutionized the field of biomonitoring
 in the past years. Various sources have been shown to contain eDNA of
 diverse organisms, for example water, soil, gut content and plant
 surfaces. Here we show that dried plant material is a highly promising
 source for arthropod community eDNA. We designed a metabarcoding assay to
 enrich diverse arthropod communities, while preventing amplification of
 plant DNA. Using this assay, we analyzed various commercially produced
 teas and herbs. These samples recovered ecologically and taxonomically
 diverse arthropod communities, a total of over a thousand species in more
 than 20 orders, many of them specific to their host plant and its
 geographic origin. Atypically for eDNA, arthropod DNA in dried plants
 shows a very high temporal stability, opening up plant archives as a
 source for historical arthropod eDNA. Considering these results, dried
 plant material appears excellently suited as a novel tool to monitor
 arthropods and arthropod-plant interactions, detect agricultural pests,
 and identify the geographic origin of imported plant material. The ability
 to detect highly diverse arthropod communities from all over the world in
 tea bags also highlights the utility of our approach for outreach purposes
 and to raise awareness about biodiversity.
DOI: 10.5061/dryad.f1vhhmgzq
title: Exposure to urban heavy metal contamination diminishes bumble bee colony growth

description: As a result of their industrial past, legacy cites often have elevated
 concentrations of soil heavy metal contamination. Metal pollution can have
 negative and prolonged ecosystem impacts, and bees that forage in these
 urban ecosystems are at risk of exposure. Legacy cities are known to
 support species rich bee communities, which highlights the importance of
 determining the impact of heavy metal contamination on wild bee health. We
 examined how oral exposure to concentrations of four metals found within
 the provisions of bees foraging within Cleveland, Ohio, USA influenced
 colony growth of Bombus impatiens Cresson (Hymenoptera: Apidae), a common
 species within legacy cities across the eastern United States. Colony
 weight and brood survivorship were compared among hives fed uncontaminated
 sucrose solution (hereafter nectar), nectar spiked with one metal
 (arsenic, cadmium, chromium, or lead), and nectar containing all metals,
 after 15 or 30 d of exposure within flight tents. Across both exposure
 periods, we found a significantly higher proportion of dead brood in metal
 exposed hives. Additionally, colonies fed all four metals had a
 significantly higher proportion of dead brood than those fed a single
 metal. Our findings illustrate that even low, environmentally relevant
 concentrations of metals collected by B. impatiens in legacy cities can
 negatively influence bee colony growth. We highlight the need to identify
 metal exposure routes for bees in contaminated landscapes to minimize risk
 and bolster conservation habitat initiative success.
description: Data was collected upon completion of each tent experiment.
 Colonies were dissected and the number of each life stage and status was
 tallied and summarized. 
description: Colonies 2 and 10 were removed from the dataset due to missing
 data values from recording error, and colonies 37- 48 were removed from
 analysis due to total control colony death, likely due to atmospheric
 conditions outside of bumble bee colony tolerance ranges. TENT_README file
 includes descriptions of column names.
DOI: 10.5061/dryad.rn8pk0pcj
title: Smaller species experience mild adversity under shading in an old-field plant community

description: Background: Plant competition experiments commonly suggest that larger
 species have an advantage, primarily in terms of light acquisition.
 However, within crowded natural vegetation, where competition evidently
 impacts fitness, most resident species are relatively small. It remains
 unclear, therefore, whether the size-advantage observed in controlled
 experiments is normally realized in habitats where competition is most
 intense. Methods: We characterized the light environment and tested for
 evidence of a size-advantage in competition for light in an old-field
 plant community composed of herbaceous perennial species. We investigated
 whether larger species contributed to reduced light penetration (i.e.,
 greater shading), and examined the impact of shade on smaller species by
 testing whether the abundance and richness of smaller species were lower
 in plots with less light penetration. Results: Light penetration in plots
 ranged from 0.3-72.4%. Plots with a greater mean species height had
 significantly lower light penetration. Plots with lower light penetration
 had significantly lower small species abundance and richness. However, the
 impact of shade on small species abundance and richness was relatively
 small (R2 values between 8% and 15%) and depended on how we defined “small
 species”. Significant effects were more common when analyses focused on
 small plant species that reached reproduction; focusing on only flowering
 plants can clarify patterns. Synthesis: Our results confirm that light
 penetration in herbaceous vegetation can be comparable to levels seen in
 forests, that plots with taller species cast more shade, and that smaller
 species are less abundant and diverse in plots where light penetration is
 low. However, variation in mean plot height explained less than 10% of
 variation in light penetration, and light penetration explained between
 5-15% of variation in small species abundance and richness. Coupled with
 the fact that reproductive small species were present even within the most
 heavily shaded plots, our results suggest that any advantage in light
 competition by large species is limited. One explanation is that at least
 some small species in these communities are shade tolerant. Shade
 tolerance in predominantly herbaceous communities, particularly among
 small plant species, requires further research.
description: See manuscript for full details.
description: Please consult the README.csv file; if you are unsure whether
 these data are applicable to your work, please ask the authors for
 clarification via email.
DOI: 10.5061/dryad.866t1g1sf
title: Calcium concentration regulates interspecific interaction of algae along the nutrient gradient

description: Although many studies have focused on the influence of abiotic stress
 gradients on biological interactions, few studies explained the effects of
 both resource and non-resource stress gradients on the facilitation
 between species. We conducted a controlled experiment to study the effects
 of nutrient stress gradient on the interspecific relationship between
 Phormidium corium and Scenedesmus quadricauda under different calcium
 concentration. The results showed that when the calcium concentration was
 high, the change of interspecific relationship between the two algae along
 the nutrient stress gradient accorded with the SGH theory, that is, the
 competitive interaction changed into positive interaction. The reason for
 this phenomenon may be that in the stress environment, the population
 density is low and the encounter rate is low; secondly, facilitation may
 improve the harsh environment and make it more beneficial to the
 beneficiary species, which may enable the beneficiary species to survive
 in the environment that they could not survive before. When the calcium
 concentration was low, the change of interspecific relationship along
 resource stress was in line with the "Hump hypothesis", that is,
 facilitation reached the peak under medium resource stress. This
 phenomenon may be caused by the interaction between salt stress and
 nutrient. When calcium stress was high, it may not be conducive to the
 absorption of nutrients by algae, resulting in the fierce competition for
 limited resources in the harsh environment. While the facilitation effect
 may be strongest in the medium stress environment due to the relatively
 sufficient resource. These results emphasized the joint effects of various
 stress factors on interspecific relationships, especially the importance
 of non-resource stress in the study of community composition, pointed out
 a new direction for the study of facilitation, and provided theoretical
 guidance for the prevention and control of freshwater blooms.
DOI: 10.5061/dryad.g1jwstqsv
title: MADS2 regulates priming defence in postharvest peach through combined salicylic acid and abscisic acid signaling

description: MADS-box genes play well-documented roles in plant development, but
 relatively little has been recorded regarding their involvement in the
 defence response. Herein, the treatment of peach fruit with BABA activated
 resistance against Rhizopus stolonifer, leading to a significant delay in
 the symptomatic appearance of Rhizopus rot disease. This protection was
 greatly potent in R. stolonifer-inoculated peaches and equipped the
 intertwined defence response containing H2O2 burst, ABA accumulation and
 callose deposition. Moreover, nucleus-localized PpMADS2 was identified as
 a PpNPR1 interacting partner via cDNA library screening. Y2H, LCI and
 co-IP assays further verified the interaction between PpNPR1 and PpMADS2.
 The DNA binding activity of PpNPR1 conferred by the PpNPR1-PpMADS2 complex
 was required for the transcription of SA-dependent PR and ABA-inducible
 PpCalS genes to gain the augmented BABA-IR, in which the PpMAPK1-induced
 posttranslational modification of PpMADS2 simultaneously was involved.
 Accordingly, PpMADS2 overexpression potentiated the transcription of a
 group of PR genes and fungal resistance in transgenic Arabidopsis.
 Conversely, mads2 knockout lines showed high sensitivity to fungal
 pathogen. Therefore, the results indicate that PpMADS2 positively
 participates in the BABA-elicited defence in peaches through the
 collaboration of SA-dependent NPR1 activation and ABA-signaling callose
 accumulation, which is also related to the posttranslational modification
 of PpMADS2 by PpMAPK1 for signal amplification.
description: The method were carefully recorded in MS.
DOI: 10.5061/dryad.1rn8pk0w9
title: Data from: Retinoic acid-induced protein 14 controls dendritic spine dynamics associated with depressive-like behaviors

description: Dendritic spines are the central postsynaptic machinery that determines
 synaptic function. The F-actin within dendritic spines regulates their
 dynamic formation and elimination. Rai14 is an F‑actin-regulating protein
 with a membrane‑shaping function. Here, we identified the roles of Rai14
 for the regulation of dendritic spine dynamics associated with
 stress-induced depressive-like behaviors. Rai14-deficient neurons failed
 to maintain a proper dendritic spine density in
 the Rai14+/- mouse brain, resulting in impaired
 functional synaptic activity. Rai14 was protected from degradation by
 complex formation with Tara, and accumulated in the dendritic spine neck,
 thereby enhancing spine maintenance. Concurrently, Rai14 deficiency in
 mice altered gene expression profile relevant to depressive conditions and
 increased depressive-like behaviors. Moreover, Rai14 expression was
 reduced in the prefrontal cortex of the mouse stress model, which was
 blocked by antidepressant treatment. Thus, we propose that Rai14-dependent
 regulation of dendritic spines may underlie the plastic changes of
 neuronal connections relevant to depressive-like behaviors.
description: The brains from two 9-week-old male Rai14+/- mice and two male
 wild-type littermate controls and two 9-week-old female Rai14+/- mice and
 two female wild-type littermate controls were used for RNA sequencing. The
 mice were deeply anesthetized with isoflurane inhalation and
 transcardially perfused with PBS. Then brains except the cerebellum and
 pons (left cerebral hemispheres) were isolated and kept in RNAlaterTM
 Solution (Invitrogen) with dry ice and subjected for further RNA-Seq
 library construction and transcriptome sequencing.
 RNA-Seq library construction, transcriptome sequencing, and
 expression profiling were performed by Macrogen (Macrogen, Inc., Seoul,
 Korea, http://www.macrogen.com/). Briefly, the mRNA from each brain sample
 was pooled for RNA-Seq library construction using TruSeq Stranded mRNA LT
 Sample Prep Kit (Illumina, San Diego, CA, USA). The mRNA library was
 subjected to paired-end transcriptome sequencing (Illumina
 platform).
DOI: 10.5061/dryad.2bvq83bs3
title: Beak lengths of young laying hens (pullets) from flocks provided with potential beak-blunting materials and from control flocks

description: Injurious Pecking, commonly controlled by beak trimming (BT) is a
 widespread issue in laying hens associated with thwarted foraging. This
 controlled study compared the effect in intact and beak-trimmed pullets of
 providing pecking pans to 8 treatment flocks from 6 weeks of age. Flocks
 (mean size 6,843) comprised 8 British Blacktail, 6 Lohmann Brown and 2
 Bovans Brown. All young birds (6-7 weeks) pecked more frequently at the
 pecking pans (mean 40.4) than older pullets (mean 26.0, 23.3
 pecks/bird/minute at 10-11 weeks and 14-15 weeks respectively)
 (p&lt;0.005).  There was no effect on feather pecking or
 plumage cover. Mean side-beak length and mean top-beak lengths were
 shorter in treatment flocks at 6-7 weeks and 10-11 weeks (p
 &lt;0.001). Intact-beak treatment flocks had shorter mean side-beak
 length at 10-11 weeks (p &lt; 0.001) and at 14-15 weeks
 (p&lt;0.05) and mean top-beak length at 6-7 weeks (p &lt; 0.05)
 and at 10-11 weeks (p &lt; 0.05). BT treatment flocks had shorter
 side-beak and top-beak lengths at 6-7 weeks and at 10-11 weeks
 (p&lt;0.001).  Beak lengths showed linear growth, with
 individual bird variation indicating a potential for genetic selection.
 The study demonstrated that abrasive material can reduce beak length in
 pullets.
description: Sixteen UK commercial rearing flocks were studied between
 September 2015 and December 2016. Half of the 16 flocks were infra-red
 beak trimmed (IRBT) at day old at the hatchery and the other half were
 intact-beak flocks (i.e. not trimmed) Strains were British Blacktail
 (n=8), Lohmann Brown (n=6) and Bovans Brown (n=2). Eight treatment flocks
 were randomly allocated and supplied with pecking pans containing an
 abrasive material, and 8 were paired control flocks reared on the same
 farm. Thus there were 4 intact treatment, 4 intact control, 4 trimmed
 treatment, and 4 trimmed control flocks. At each visit
 (when birds were 6-7 weeks, 10-11 weeks and 14-15 weeks of age) 45 birds
 were randomly selected from different areas of the rearing house for beak
 measurement. Beak length was measured using Vernier callipers.
 Measurements of beak side-length and top-length were taken three times in
 succession to provide a mean length with an estimated accuracy of +/-
 0.5mm. Top-length was measured from the frontal feather tract margin to
 beak tip. Side-length was measured on the right side, from nares to the
 tip of the beak. 
description: Individual birds were treated as independent datapoints in
 analysis. Analysis used the average of the 3 measurements. Data were not
 normally distributed and data were analysed using non-parametric
 tests.