cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c2fqz6156
title: Data from: Consumer responses to experimental pulsed subsidies in isolated vs. connected habitats

description: Increases in consumer abundance following a resource pulse can be driven
 by diet shifts, aggregation, and reproductive responses, with combined
 responses expected to result in faster response times and larger numerical
 increases. Previous work in plots on large Bahamian islands has shown that
 lizards (Anolis sagrei) increased in abundance following pulses of seaweed
 deposition, which provide additional prey (i.e., seaweed detritivores).
 Numerical responses were associated with rapid diet shifts and
 aggregation, followed by increased reproduction. These dynamics are likely
 different on isolated small islands where lizards cannot readily immigrate
 or emigrate. To test this, we manipulated the frequency and magnitude of
 seaweed resource pulses on whole small islands and in plots within large
 islands, and monitored lizard diet and numerical responses over four
 years. We found that seaweed addition caused persistent increases in
 lizard abundance on small islands regardless of pulse frequency or
 magnitude. Increased abundance may have occurred because the initial pulse
 facilitated population establishment, possibly via enhanced overwinter
 survival. In contrast with a previous experiment, we did not detect
 numerical responses in plots on large islands, despite lizards consuming
 more marine resources in subsidized plots. This lack of a numerical
 response may be due to rapid aggregation followed by disaggregation, or
 stronger suppression of A. sagrei by their predators on
 large islands in this study. Our results highlight the importance of
 habitat connectivity in governing ecological responses to resource pulses
 and suggest that disaggregation and changes in survivorship may be
 underappreciated drivers of pulse-associated dynamics. 
description: Carbon stable isotope and percent marine contribution to diet
 data set diet.data.csv Lizard
 abundance index data (number seen per person-minute during
 surveys) abundance.data.csv R code
 to re-create analyses in the manuscript submitted
 script 2020-03-16.R
DOI: 10.5061/dryad.4j0zpc880
title: Non-invasive monitoring of multiple wildlife health factors by fecal microbiome analysis

description: Fecal microbial biomarkers represent a less invasive alternative for
 acquiring information on wildlife populations than many traditional
 sampling methodologies. Our goal was to evaluate linkages between fecal
 microbiome communities in Rocky Mountain elk (Cervus canadensis) and four
 host factors including sex, age, population, and physical condition
 (body-fat). We paired a feature-selection algorithm with an LDA-classifier
 trained on elk differential bacterial abundance (16S-rRNA amplicon survey)
 to predict host health factors from 104 elk microbiomes across four elk
 populations. We validated the accuracy of the various classifier
 predictions with leave-one-out cross-validation using known measurements.
 We demonstrate that the elk fecal microbiome can predict the four host
 factors tested. Our results show that elk microbiomes respond to both the
 strong extrinsic factor of biogeography and simultaneously occurring, but
 more subtle, intrinsic forces of individual body-fat, sex, and age class.
 Thus, we have developed and described herein a generalizable approach to
 disentangle microbiome responses attributed to multiple host factors of
 varying strength from the same bacterial sequence data set. Wildlife
 conservation and management presents many challenges, but we demonstrate
 that non-invasive microbiome surveys from scat samples can provide
 alternative options for wildlife population monitoring. We believe that,
 with further validation, this method could be broadly applicable in other
 species and potentially predict other measurements. Our study can help
 guide the future development of microbiome-based monitoring of wildlife
 populations and supports hypothetical expectations found in
 host-microbiome theory.
description: Fecal sampling of Rocky Mountain elk from Montana, USA. Elk were
 sampled in winter 2014. Sequence data: This data
 includes 16S rRNA raw sequences produced on a MiSeq with 300bp paired-end
 chemistry. Samples (elk) were demultiplexed and samples are provided as
 separate files. Files are paired with forward files ending in “R1” and
 reverse reads with “R3”. There are 4 populations of elk in this 16S
 survey, and the first letter of the filename denotes this: T = Tobacco
 Root, S = Sapphire, B = Bitterroot, F = Black’s Ford.
 Metadata for each elk: For a complete description of associated
 data collected for each animal please review the csv file named
 “elk_meta_data.csv”. All metadata that was collected by MT Fish Wildlife
 and Parks is included and any data that was not collected (not sampled) is
 denoted with “n/a”. Variables include: Elk (ID), Population, Sex, Age,
 Pregnant, IFBF (body fat), TT4, FT4, TT3, color.
DOI: 10.5061/dryad.4f4qrfj8d
title: Lower St. Lawrence Estuary bacterial 16S rRNA gene diversity

description: The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is among the
 largest and most productive coastal ecosystems in the world. Very little
 information on bacterial diversity exists, hampering our understanding of
 the relationships between bacterial community structure and biogeochemical
 function in the EGSL. During the productive spring period, we investigated
 free-living and particle-associated bacterial communities across the
 stratified waters of the Lower St. Lawrence Estuary, including the
 particle-rich surface and bottom boundary layers. Modeling of community
 structure based on 16S rRNA gene and transcript diversity identified
 bacterial assemblages specifically associated with four habitat types
 defined by water mass (upper water or lower water column) and size
 fraction (free-living or particle-associated). Assemblages from the upper
 waters represent sets of co-occurring bacterial populations that are
 widely distributed across Lower St. Lawrence Estuary surface waters., and
 likely key contributors to organic matter degradation during the spring.
 In addition, we provide strong evidence that particles in deep hypoxic
 waters and the bottom boundary layer support a metabolically-active
 bacterial community that is compositionally distinct compared to surface
 particles and the free-living communities. Among the distinctive features
 of the bacterial assemblage associated with lower water particles was the
 presence of uncultivated lineages of Deltaproteobacteria, including marine
 Myxobacteria. Overall, these results provide an important ecological
 framework for further investigations of the biogeochemical contributions
 of bacterial populations in this important coastal marine ecosystem.
description: The full methods is available in the published article. The
 article has been accepted for publicaiton.
description: The dataset consists of two files. The first
 file (LSLE_16S.fasta) is the nucleotide algnment of all 16S rRNA amplicons
 and the second file (LSLE_16S.groups) maps each amplicon to its sample of
 origin. FD is free-living DNA fraction, FR is free-living RNA fraction, PD
 is particle-associated DNA fraction, PR is particle-associated RNA
 fraction.
DOI: 10.5066/p13ksoac
title: Survey of sites for the presence of the nonindigenous benthic foraminifera Trochammina hadai along the west coast of North America from 1930 to 2022

description: Results of a survey of samples collected from 1930 to 2022 along the west coast of the United States from Alaska to San Diego, California as well as Honolulu, Hawaii for the presence of the Asian nonindigenous benthic foraminifera Trochammina hadai.
DOI: 10.5061/dryad.866t1g1nc
title: UPLC-MS/MS Method for quantitation of the recently FDA approved combination of vaborbactam and meropenem in human plasma

description: A parenteral medical combination containing vaborbactam (VBR) and
 meropenem (MRP) is used mainly to treat complicated urinary tract
 infections. A novel ultra-performance liquid chromatography (UPLC)- tandem
 mass spectrometric (MS/MS) method was developed for the sensitive
 determination of both compounds in human plasma. Sample preparation was
 performed by precipitation technique. The chromatographic separation was
 accomplished using the Acquity C18-BEH column, 0.01 M ammonium formate:
 acetonitrile (47:53, v/v) as a mobile phase with a flow rate of 0.2
 mL/min. Analytes were monitored by applying multiple reaction monitoring
 (MRM). The bioanalytical validation criteria were conducted following the
 FDA recommendations. The method was linear within range 0.5 to 50 µg/mL,
 for both drugs. The intra-day and inter-day precision, as coefficient
 variation (%CV) and the accuracy, as % bias not exceed than 15% for both
 drugs. The percentage recovery of targeted analytes was not less than 77
 %, calculated at three QC levels. The proposed method showed a suitable
 LLOQ value of 0.5 µg/mL for both analytes, which is far lower than the
 expected Cmax, which permits the use of this method for pharmacokinetic
 studies. The proposed method proved to be useful for the evaluation of
 this combination in both human plasma and pharmaceutical formulation.
DOI: 10.5061/dryad.hqbzkh1cj
title: Data from: Mating preference for novel phenotypes can be explained by general neophilia in female guppies

description: Understanding how genetic variation is maintained in
 ecologically-important traits is a fundamental question in evolutionary
 biology. Male Trinidadian guppies (Poecilia reticulata) exhibit extreme
 genetic diversity in color patterns within populations, which is believed
 to be promoted by a female mating preference for rare or novel patterns.
 However, the origins of this preference remain unclear. Here, we test the
 hypothesis that mating preference for novel phenotypes is a by-product of
 general neophilia that evolved in response to selection in non-mating
 contexts. We measured among-female variation in preference for eight
 different, novel stimuli that spanned four ecological contexts: mate
 choice, exploration, foraging, and social (but non-sexual) interactions.
 Females exhibited preference for novelty in 6 out of 8 tests. Individual
 variation in preference for novelty was positively correlated among all 8
 types of stimuli. Furthermore, factor analysis revealed a single axis of
 general neophilia that accounts for 61% of individual variation in
 preference for novel color patterns. The single-factor structure of
 neophilia suggests that interest in novelty is governed primarily by
 shared processes that transcend context. Because neophilia likely has a
 sizable heritable component, our results provide evidence that mating
 preference for novel phenotypes may be a non-adaptive by-product of
 natural selection on neophilia.
DOI: 10.5061/dryad.zgmsbcc7p
title: Mutant sequences of OsGSTU17

description: Glutathione S-transferases (GSTs) are a family of phase II detoxification
 enzymes whose main function is to improve plant resistance to stresses. To
 understand the structural effects of tau class GSTs on their function,
 using OsGSTU17 as an example, we predicted three pairs of residues
 involving in the interactions between its domains and linker region, and
 obtained the corresponding single mutation sequences through site-directed
 mutating Arg20, Glu74 and Asp77 which involved the hydrogen bonds and salt
 bridges between domains.
DOI: 10.25934/pr00012478.0
title: Available datapackage for study 'Communities Fighting COVID!'

description: To create and evaluate effective COVID-19 testing uptake strategies that focus on underserved individuals who are exposed but have not accessed testing, and underserved individuals who are not routinely tested because they are unaware of their exposure or risk status in order to increase testing among these populations and reduce Covid-19 related disparities.
DOI: 10.5061/dryad.5mkkwh72s
title: Data from: Brain size does not predict learning strategies in a serial reversal learning test

description: Reversal learning assays are commonly used across a wide range of taxa to
 investigate associative learning and behavioural flexibility. In serial
 reversal learning, the reward contingency in a binary discrimination is
 reversed multiple times. Performance during serial reversal learning
 varies greatly at the interspecific level, as some animals adapt a
 rule-based strategy that enables them to switch quickly between reward
 contingencies. Enhanced learning ability and increased behavioural
 flexibility generated by a larger relative brain size has been proposed to
 be an important factor underlying this variation. Here we experimentally
 test this hypothesis at the intraspecific level. We use guppies (Poecilia
 reticulata) artificially selected for small and large relative brain size,
 with matching differences in neuron number, in a serial reversal learning
 assay. We tested 96 individuals over ten serial reversals and found that
 learning performance and memory were predicted by brain size, whereas
 differences in efficient learning strategies were not. We conclude that
 variation in brain size and neuron number is important for variation in
 learning performance and memory, but these differences are not great
 enough to cause the larger differences in efficient learning strategies
 observed at higher taxonomic levels.
DOI: 10.5061/dryad.w6m905qmj
title: Data from: Spatial heterogeneity of tree diversity changes in montane forests under climate warming

description: Many studies reported biotic change along a continental warming gradient.
 The temporal and spatial change of tree diversity and their sensitivity to
 climate warming might differ from region to region. however, understanding
 of the variation among studies with regard to the magnitude of such biotic
 changes is minimal, especially for montane ecosystems. To better
 understand spatial heterogeneity and temporal dynamics of mountain trees
 community change under climate warming over the past four decades. We
 re-surveyed and recorded all tree species from 107 long-term monitoring
 plots since 1974 in 2017 to study the changes of tree community
 composition of montane forests in the Giant Panda National Park. Our
 results showed that spatial differences were found in tree species
 diversity changes in response to climate warming over the past four
 decades. Tree species richness and abundance of montane forests increased
 over time in all our study area, except Liangshan (LS), especially in
 XiaoXiangLing with the highest warming rate. However, beta diversity
 underwent a significantly higher change rate at LS than in other mountains
 which indicated that plant species that do not belong to these four
 mountains entered LS in those year. Moreover, the beta diversities of tree
 between sample plots in the LS regions were homogenized. So, LS may become
 risk regions under continuing climatic warming, and should thus receive
 priority protection in the next conservation plan of the Giant Panda
 National Park (GPNP). We provide a explanation for the large variation
 among studies in warming-related biotic changes and recommend that the
 GPNP should implement a regional-specific conservation policy to
 strengthen conservation in at-risk regions (i.e., LS) under climate
 warming.
DOI: 10.15468/dl.d5p4n8
title: Occurrence Download

description: A dataset containing 2363 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphausia vallentini",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 2363 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002348-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qz612jmbf
title: Data from: Belowground-mediated and phase-dependent processes drive nitrogen-evoked community changes in grasslands

description: Enhanced deposition of atmospheric nitrogen (N) leads to loss of plant
 diversity in grassland ecosystems. Numerous theories have provided
 potential explanations for the negative effects of N enrichment on plant
 diversity. However, the relative importance of each mechanism and the time
 scales of responses for the different functional groups remain unclear. We
 investigated the temporal responses of plant community in a temperate
 steppe to N enrichment by linking aboveground to belowground processes
 using a series of field N-addition and greenhouse experiments. The N
 enrichment-induced declines in plant diversity of grasslands were
 phase-based, functional group-dependent, and driven by three belowground
 processes. The rapid accumulation of NH4+-N by N addition inhibited
 photosynthetic rates of broad-leaf-non-rhizomatous forbs, contributing to
 loss of these N-sensitive species  during early phase of N
 enrichment (≤3 years). The N-induced changes in this phase were
 independent of soil pH as evidenced by results from application lime to
 mitigate N-evoked soil acidification. With progression of N addition,
 manganese (Mn) toxicity to narrow-leaf-non-rhizomatous forbs due to soil
 acidification-induced Mn2+ mobilization in soil accounted for their loss
 in the second phase of N enrichment (~ 4-9 years). When N addition
 proceeded longer than ~10 years, N enrichment stimulated belowground
 meristem differentiation and rhizome growth of the rhizomatous species,
 leading to the dominance by rhizomatous sedges/grasses in the community at
 later phase of N enrichment. Synthesis: The hierarchical mechanisms not
 only provide a comprehensive explanation for the N enrichment-induced
 diversity decline in grasslands, but can also facilitate us to understand
 the differential sensitivities of ecosystems to chronic N enrichment, and
 predict future ecosystem dynamics.
description: The dataset was collected from both field and greenhouse
 experiments.
DOI: 10.5061/dryad.v6wwpzgs7
title: Data from: State-dependent decision-making by predators and its consequences for mimicry

description: The mimicry of one species by another provides one of the most celebrated
 examples of evolution by natural selection. Edible Batesian mimics deceive
 predators into believing they may be defended, whereas defended Müllerian
 mimics have evolved a shared warning signal, more rapidly educating
 predators to avoid them. However, it may benefit hungry predators to
 attack defended prey, while the benefits of learning about unfamiliar prey
 depends on the future value of this information. Previous energetic
 state-dependent models of predator foraging behaviour have assumed
 complete knowledge, while informational state-dependent models have
 assumed fixed levels of hunger. Here, we identify the optimal decision
 rules of predators accounting for both energetic and informational states.
 We show that the nature of mimicry is qualitatively and quantitatively
 affected by both sources of state dependence. Associative learning weakens
 the extent of parasitic mimicry by edible prey because naive predators
 often attack defended models. More importantly, mimicry among equally
 highly defended prey may be parasitic or mutualistic depending on the
 ecological context. Finally, mimicry by prey with intermediate defences
 corresponds to Batesian or Müllerian mimicry depending on whether the
 mimic is profitable to attack by hungry predators, but it is not a special
 case of mimicry.
description: Datasets are simulated using the computer code provided in the
 Repository.
description: Simulations are run using Julia (tested on version 1.0.1). The R
 code is used to analyse the outputs of the simulations. Please see the
 README.txt file for further information.
DOI: 10.5061/dryad.4b8gtht92
title: Data from: It’s not all about temperature: breeding success also affects nest design

description: There are numerous observational studies on intra-specific variation in
 avian nest building and a single experimental manipulation. The general
 consensus is that birds build nests in response to environmental
 conditions, but it is not clear whether such flexibility in nest building
 is reproductively advantageous. To test the relationship between building
 flexibility and reproductive success, we allowed captive zebra finches to
 build their first nest, using string, and to breed in
 temperature-controlled rooms held at 14oC or 30oC. Once the offspring had
 fledged, we returned half the pairs to breed at the same temperature while
 half the pairs were switched to the alternative temperature. We provided
 all pairs with string and left them to build and breed a second time. For
 their first nest, pairs that built at 14°C used more string than did pairs
 that built at 30°C, and pairs that bred successfully built a nest with
 more string than did unsuccessful pairs. When pairs built their second
 nest, however, temperature no longer explained the number of pieces of
 string they used; rather, irrespective of the ambient temperature, pairs
 that had successfully produced young from their first nest used the same
 amount of string for their second nest while those that had failed to
 reproduce with their first nest used more string. These latter pairs were
 then more likely to reproduce successfully. Ambient temperature,
 therefore, did affect the nest the pairs built, but only in the absence of
 reproductive experience.
DOI: 10.15468/dl.2vh3n8
title: Occurrence Download

description: A dataset containing 2595 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apios americana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2595 records from 158 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002350-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.