cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mcvdnck1g
title: Transcriptional response of mushrooms to artificial sun exposure

description: Climate change causes increased tree mortality leading to canopy loss and
 thus sun-exposed forest floors. Sun exposure creates extreme temperatures
 and radiation, with potentially more drastic effects on forest organisms
 than the current increase in mean temperature. Such conditions might
 potentially negatively affect the maturation of mushrooms of forest fungi.
 A failure of reaching maturation would mean no sexual spore release and,
 thus, entail a loss of genetic diversity. However, we currently have a
 limited understanding of the quality and quantity of mushroom-specific
 molecular responses caused by sun exposure. Thus, to understand the
 short-term responses towards enhanced sun exposure, we exposed mushrooms
 of the wood-inhabiting forest species Lentinula edodes, while still
 attached to their mycelium and substrate, to artificial solar light (ca.
 30 °C and 100.000 lux) for 5, 30, and 60 minutes. We found significant
 differentially expressed genes at 30 and 60 minutes. Eukaryotic
 Orthologous Groups (KOG) class enrichment pointed to defense mechanisms.
 The 20 most significant differentially expressed genes showed the
 expression of heat-shock proteins, an important family of proteins under
 heat stress. Although preliminary, our results suggest mushroom-specific
 molecular responses to tolerate enhanced sun exposure as expected under
 climate change. Whether mushroom-specific molecular responses are able to
 maintain fungal fitness under opening forest canopies remains to be
 tested.
description: Experiment subjecting mushrooms to solar heating while still
 attached to the substrate. Here attached are data and R
 Script to run core analyses performed in this article.
DOI: 10.5061/dryad.g1jwstqrb
title: Thermal adaptation in a holobiont accompanied by phenotypic changes in an endosymbiont

description: How and if organisms can adapt to changing temperatures has drastic
 consequences for the natural world. Thermal adaptation involves finding a
 match between temperatures permitting growth and the expected temperature
 distribution of the environment. However, if and how this match is
 achieved, and how tightly linked species change together, are poorly
 understood. Paramecium bursaria is a ciliate that has a tight
 physiological interaction with endosymbiotic green algae (zoochlorellae).
 We subjected a wild population of P. bursaria to a cold and warm climate
 (20℃ and 32℃) for ~300 generations. We then measured the thermal
 performance curve (TPC) for intrinsic rate of growth (rmax ) for these
 evolved lines across temperatures. We also evaluated number and size of
 the zoochlorellae populations within paramecia cells. TPCs for
 warm-adapted populations were shallower and broader than TPCs of
 cold-adapted populations, indicating that the warm populations adapted by
 moving along a thermal generalist/specialist trade off rather than
 right-shifting the TPC. Zoochlorellae populations within cold-adapted
 paramecia had fewer and larger zoochlorellae than hot-adapted paramecia,
 indicating phenotypic shifts in the endosymbiont accompany thermal
 adaptation in the host. Our results provide new and novel insight into how
 species involved in complex interactions will be affected by continuing
 increasing global temperatures.
DOI: 10.5061/dryad.ksn02v74g
title: Grassland Hemiptera and Coleoptera collected from Teagasc Grange, Ireland between 2002 and 2005

description: Various methods have been used to divide communities into core species and
 occasional or satellite species. Some methods are somewhat arbitrary and
 there is evidence that many communities are more multi-modal than bimodal.
 They also tend to rely on having multiple years of data. A completely
 novel method is presented that not only has no requirement for long-term
 datasets but can divide communities into multiple groups. It is based on
 probability a species is present, calculated using Simpson's index
 and the sequential removal of species from the data. The sequential
 Simpson’s index method was applied to species data from a grassland insect
 community. It was also applied to eleven other datasets that had been
 divided into core and occasional species in previously published studies.
 The new method was found not only to be consistent with previous
 core-occasional assessments but was able to identify multimodality in
 species-abundance distributions. Although ideally used with a measure of
 persistence (frequency of occurrence) to rank species, community structure
 is consistently described even with only species abundance data. The
 method can be applied to short or long-term datasets, help identify
 multimodality and provide a valuable insight into how communities change
 in time or space.
description: The dataset was collected between 2002 and 2005, as part of the
 Ag-Biota Project. Samples of Hemiptera and Coleoptera were collected using
 a Vortis suction sampler from a cattle grazed grassland at Teagasc Grange,
 Ireland. Specimens were identified to species level in most cases,
 although some to genus level, or morphospecies. The dataset consists of
 numbers of individuals of each species collected. Rows represent separate
 samples, with each row having a unique combination of sample reference
 number, experiment reference number and date. Further details of sampling
 can be found in: Helden, A. J., Anderson, A., Finn, J.,
 & Purvis, G. (2015). The response of sward-dwelling arthropod
 communities to reduced grassland management intensity in pastures.
 <i>Irish Journal of Agricultural and Food Research</i>,
 <b>54</b>(2), 107–120.
 https://doi.org/10.1515/ijafr-2015-0012
DOI: 10.5061/dryad.4mw6m909k
title: Data from: The non-coding RNA CcnA modulates the master cell cycle regulators CtrA and GcrA in Caulobacter crescentus

description: Bacteria are powerful models for understanding how cells divide and
 accomplish global regulatory programs. In Caulobacter crescentus, a
 cascade of essential master regulators supervises the correct and
 sequential activation of DNA replication, cell division and development of
 different cell types. Among them, the response regulator CtrA plays a
 crucial role coordinating all those functions. Here, for the first time we
 describe the role of a novel factor named CcnA, a cell cycle regulated
 ncRNA located at the origin of replication, presumably activated by CtrA
 and responsible for the accumulation of CtrA itself. In addition, CcnA may
 be also involved in the inhibition of translation of the S-phase
 regulator, GcrA, by interacting with its 5’ untranslated region (5’-UTR).
 Performing in vitro experiments and mutagenesis, we propose a mechanism of
 action of CcnA based on liberation (ctrA) or sequestration (gcrA) of their
 ribosome-binding site (RBS). Finally, its role may be conserved in other
 alphaproteobacterial species, such as Sinorhizobium meliloti, representing
 indeed a potentially conserved process modulating cell cycle in
 Caulobacterales and Rhizobiales. 
description: # Data from: The non-coding RNA CcnA modulates the master cell cycle
 regulators CtrA and GcrA in Caulobacter crescentus
 [https://doi.org/10.5061/dryad.4mw6m909k](https://doi.org/10.5061/dryad.4mw6m909k) ## Description of the data and file structure Fastq files included. See `metadata.txt` for details on which file relates to which sample.  ## Sharing/Access information n/a
DOI: 10.5061/dryad.s1rn8pk83
title: Datasets and scripts from: Sensory-based quantification of male colour patterns in Trinidadian guppies reveals no support for parallel phenotypic evolution in multivariate trait space

description: Parallel evolution, in which independent populations evolve along similar
 phenotypic trajectories, offers insights into the repeatability of
 adaptive evolution. Here, we revisit a classic example of parallelism,
 that of repeated evolution of brighter males in the Trinidadian guppy
 (Poecilia reticulata). In guppies, colonisation of low predation habitats
 is associated with emergence of ‘more colourful’ phenotypes since
 predator-induced viability selection for crypsis weakens while sexual
 selection by female preference for conspicuousness remains strong. Our
 study differs from previous investigations in three respects. First, we
 adopt a multivariate phenotyping approach to characterise parallelism in
 multi-trait space. Second, we use ecologically-relevant colour traits
 defined by the visual systems of the two selective agents (i.e. guppy,
 predatory cichlid). Third, we estimate population genetic structure to
 test for adaptive (parallel) evolution against a model of neutral
 phenotypic divergence. We find strong phenotypic differentiation that is
 inconsistent with a neutral model but very limited support for the
 predicted pattern of greater conspicuousness at low predation. Effects of
 predation regime on each trait were in the expected direction, but weak,
 largely non-significant, and explained little among-population variation.
 In multi-trait space, phenotypic trajectories of lineages colonising low
 from high predation regimes were not parallel. Our results are consistent
 with reduced predation risk facilitating adaptive differentiation,
 potentially by female choice, but suggest that this proceeds in
 independent directions of multi-trait space across lineages.
 Pool-sequencing data also revealed SNPs showing greater differentiation
 than expected under neutrality, among which some are found in genes
 contributing to colour pattern variation, presenting opportunities for
 future genetic study.
DOI: 10.15468/dl.anzkgb
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus decacuspidatus"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002862-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t4b8gtj28
title: Competition alters species' plastic and genetic response to environmental change

description: Species react to environmental change via plastic and evolutionary
 responses. While both of them determine species’ survival, most studies
 quantify these responses only individually. As species occur in
 communities, competing species may further influence their respective
 response to environmental change. Yet, how environmental change and
 competing species combined shape plastic and genetic responses to
 environmental change remains unclear. Quantifying how species interactions
 such as competition alter plastic and genetic responses of species to
 environmental change requires integrating approaches from trait-based,
 community and evolutionary ecology. We exposed unicellular aquatic
 organisms to long-term selection of increasing salinity—representing a
 common and relevant environmental change. Then, we assessed plastic and
 genetic contributions to phenotypic change in biomass, cell shape, and
 dispersal ability along increasing levels of salinity in the presence and
 absence of competition. Species differed in their response to salinity and
 to competition. The observed trait changes during selection were mainly
 due to mean trait evolution, and differed whether species evolved in the
 presence or absence of competition. Moreover, our results show that
 species’ evolutionary and plastic responses to environmental change
 depended both on the presence of competing species and the magnitude of
 the environmental change, ultimately determining species persistence. Our
 results suggest that understanding plastic and genetic responses to
 environmental change within a community will improve predictions of
 species’ persistence to environmental change.
DOI: 10.5061/dryad.12jm63xz4
title: A Peristaltic Pump and Filter-Based Method for Aqueous Microplastic Sampling and Analysis

description: Sampling the aquatic environment for microplastic concentration is
 inherently difficult because of variations in microplastic concentration,
 shape, and density and the potential for contamination. We present an
 assessment of a method for microplastic sampling that uses a peristaltic
 pump to pump water through a series of in-line stainless-steel mesh
 filters. Following filtration, the stainless-steel filters were treated
 using previously published methods to isolate microplastics, adjusted for
 the stainless-steel mesh filters. Microplastics were identified using
 micro-Fourier Transform Infrared (µFTIR) spectroscopy in transmission
 mode. This method was tested in the laboratory using standard polyethylene
 beads and was applied to two sample sites at the Las Vegas Wash in Nevada.
 The results showed 70% of the polyethylene beads were recovered after the
 peristaltic pump and laboratory steps with minimal blank contamination.
 The advantages of the peristaltic pump sampling method are it (1) supports
 a range of sample volumes, (2) reduces sample handling, (3) reduces the
 potential for contamination, (4) provides flexibility in sampling
 locations, and (5) supports a variety of filter types. Using
 stainless-steel mesh filters allows for (1) streamlined and direct
 field-to-laboratory sample processing, (2) µFTIR transmission mode
 analysis of filter-mounted microplastics, and (3) reduced filter and
 sample processing costs.
description: A 
 Microplastic polymer type was identified using a Thermo Nicolet iN10 MX
 instrument housed at DRI. We analyzed the SS mesh mounted samples in
 transmission mode using the imaging detector MCT cooled array with an
 aperture size of 25 µm x 25 µm and 25 µm step size, spectral resolution of
 8 cm<sup>-1</sup> (from 4000 to 715
 cm<sup>-1</sup>), and 64 scans. Background spectra using the
 same settings were automatically collected every 60 minutes. Results were
 corrected for baseline drift and data were exported and processed using
 siMPle<sup>40–42</sup> The publicly available standard
 dataset<sup>43</sup> was imported into siMPle and was used to
 compare and identify the collected spectra. We tested the siMPle program
 using known standard plastic materials and adjusted the threshold match
 accordingly (Supplementary Table S2). One randomly selected area of the
 VMPS25 standard (Table 1) with PE beads was analyzed for method testing
 and two randomly selected areas of each LVW SS filter were
 analyzed.
DOI: 10.5061/dryad.pzgmsbcmb
title: A lightweight backpack harness for tracking hummingbirds

description: Hummingbirds and other lightweight bird species are challenging to track
 because they have limited capacity to carry devices for data-logging. We
 present a simple and customizable three-loop ‘backpack’ harness for
 studying hummingbird migration and movement, with step-by-step
 instructions for harness construction and attachment. The harness has
 negligible weight and cost (&lt; $0.50 USD/each), is easy for a single
 person to make and apply in the field, and it requires no complicated
 setup or equipment. We have field-tested this harness on 74 Giant
 Hummingbirds (Patagona gigas) with three different types of tracking
 devices (geolocators, GPS tags, and satellite transmitters) in Chile and
 Peru from 2017–2020. Based on recaptures to date, we report that harnesses
 last at least two years, even under high UV-light conditions. We found no
 evidence of adverse effects of the harnesses on birds after one to two
 years and apparent survival of geolocator-tracked Giant Hummingbirds was
 in line with published estimates for other hummingbird species. This
 harness method is a practical and effective option for mounting
 ultra-light devices on hummingbirds, and it can be readily modified for
 other species with short legs, prominent sternal keels, and long wings.
description: We designed a harness for tracking hummingbirds and field-tested
 this harness on 74 Giant Hummingbirds (<i>Patagona gigas</i>)
 with three different types of tracking devices (geolocators, GPS tags, and
 satellite transmitters) in Chile and Peru from 2017–2020. All collected
 data are original. We additionally conducted a literature review of
 temperate and tropical hummingbird survival and capture probability and
 used capture-mark-recapture models (Cormack-Jolly-Seber models) to
 estimate survival and capture probabilities of geolocator-tracked Giant
 Hummingbirds. Source code for reproducing analyses can be found at https://github.com/jlwilliamson/Hummingbird_Harness_Methods.
description: See README.txt file for description of all files included in this
 data publication and see fully-annotated code on GitHub for further
 details. All data files are also stored on GitHub for completeness of
 repository. We provide .csv files, which were read into R for analysis,
 and we additionally provide corresponding .xlsx files (see .xlsx files for
 metadata and descriptions; tab 2 in each file).
DOI: 10.25349/d97w3t
title: Analyzing environmental and social impacts of urban forestry practices in Tacoma, WA with PlanIT Geo

description: Urban forestry encompasses street trees, residential trees, park trees and
 greenbelt vegetation. Despite local groups’ efforts and trends in better
 forest management practices, there is an unequal distribution of urban
 forests and their associated ecosystem services across most of the United
 States. Evaluating canopy distribution is the first step to enable cities
 to better devote limited resources to marginalized communities, which
 often have additional equity concerns. Our project will help the urban
 forestry nonprofit, PlanIT Geo™, and their future clients in their urban
 forestry management plan recommendations and could increase the equitable
 dispersal of environmental benefits.  In addressing the equity of
 Tacoma’s urban forests, we assessed trees' impacts on air quality and
 human health. We designed an equity index model to compare census block
 groups based on five indicators: canopy coverage, demographic, climate,
 air quality, and health. The air quality and health indicators were
 derived by analyzing PM2.5 reduction through the amount of canopy coverage
 and the associated health benefits from improved air quality in Tacoma,
 WA. We then calculated individual indicator scores and a composite
 environmental equity score for each census block group in Tacoma.
 Conclusions reveal that there is an overall unequal tree canopy
 distribution in Tacoma and considering additional indicators broadens
 PlanIT Geo’s awareness of the most vulnerable communities in Tacoma.
 Through this analysis, we identified priority areas in need of
 intervention and environmental considerations to maximize socio-economic
 and environmental benefits while minimizing harm
 post-intervention.
DOI: 10.5061/dryad.f7m0cfxwc
title: Three sex phenotypes in a haploid algal species give insights into the evolutionary transition to a self-compatible mating system

description: Mating systems of haploid species such as fungi, algae, and bryophytes are
 either heterothallic (self-incompatible) with two sex phenotypes (male and
 female, or mating type minus and plus in isogamous species) or homothallic
 (self-compatible) with only a bisexual phenotype producing zygotes within
 a clone. The anisogamous volvocine green alga Pleodorina starrii is a
 haploid species previously reported to have a heterothallic mating system.
 Here, we found that two additional culture strains originating from the
 same water system of P. starrii were taxonomically identified as P.
 starrii and produced male and female gametes and zygotes within a clone
 (bisexual). Sequences of rapidly evolving plastid genome regions were
 identical between the bisexual and unisexual (male or female) P. starrii
 strains. Intercrossings between the bisexual and unisexual strains
 demonstrated normal thick-walled zygotes and high survivability of F1
 strains. Thus, these strains belong to the same biological species. P.
 starrii has a new haploid mating system that is unique in having three sex
 phenotypes; namely, male, female, and bisexual. Genetic analyses suggested
 the existence of autosomal “bisexual factor” locus independent of
 volvocine male and female determining regions. The present findings
 increase our understanding of the initial evolutionary step of transition
 from heterothallism to homothallism.
description: The dataset was composed of the rbcL gene alignment used for the
 construction of the tree in Figure 1B and the results of three
 phylogenetic analyses. Supplementary pdf files are DIC
 and DAPI images of <em>Pleodorona starrii</em> strain P85
 (NIES-4479) showing a male nucleus within a female gametic
 cytoplasm.
description: rbcL_tree.nexus: the rbcL gene alignment
 rbcL_Baysiantree.tre: results of Baysian inference
 rbcL_MLtree.tre: results of ML analysis
 rbcL_MPtree.tre: results of MP analysis
 Supplementary Information (published on Zenodo)
 DIC-P85.pdf: DIC image DAPI-P85.pdf: DAPI
 image
DOI: 10.5061/dryad.mkkwh710x
title: Habitat alteration facilitates the dominance of invasive species through disrupting niche partitioning in floodplain wetlands

description: Aim: Exotic species invasion often leads to declines in local and regional
 biodiversity, particularly in freshwater ecosystems. This biodiversity
 loss is generally facilitated by human activities such as land cover
 change and hydrological alternation. Recent advances in stable isotope
 analysis (SIA) have been highlighted in many studies addressing
 fundamental issues in invasion ecology, especially in quantifying
 competition for resources between native and exotic species. However, how
 anthropogenic disturbance influences trophic relationships among invasive
 and native species remains poorly understood. Location: Middle-lower
 Yangtze River region, China Methods: To investigate the effects of human
 disturbance on interspecific trophic interactions, this study compared
 isotopic niche space and overlap of the introduced red swamp crayfish
 (Procambarus clarkii) and the native oriental river shrimp (Macrobrachium
 nipponense) and freshwater snail (Bellamya aeruginosa) in natural and
 modified wetlands. Results: Based on carbon and nitrogen SIA, we found
 ubiquitous niche shifts in macroinvertebrates with increased competition,
 which might lead to significant niche contraction in modified habitats at
 both community and population scales. Moreover, the isotopic niche width
 of the exotic crayfish was twice as larger as that of natives at both
 habitats, suggesting that the exotic P. clarkii had great competitive
 superiority over the native species. However, the effects of habitat
 modification on niche overlap were inconsistent. While the niche overlap
 between crayfish and shrimp was significantly higher in modified habitats
 than in natural open waters, niche overlap between crayfish and the snail
 was significantly reduced. Main conclusions: Collectively, our findings
 highlight that the competitive outcomes of interspecific trophic
 interactions can be dependent on the prey availability and diversity,
 which embraces both the classic optimal foraging theory and competition
 theory to understand how environmental change, such as habitat
 alternation, affects the biological invasion processes.
description: The dataset was  δ<sup>13</sup>C,
 δ<sup>15</sup>N and environmental data of the crayfish, shrimp
 and snail collected at natural and modified habitats.
description: id=sample
 id,  species=crayfish, shrimp or snail, site=sample
 location, 13C=δ<sup>13</sup>C,
 15N=δ<sup>15</sup>N, Hab=natural
 or modified sample site. Information on how the measurements
 were done can be found in the associated manuscript referenced
 above.