cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w0vt4b8np
title: Comparative analysis of genetic and morphological variation within the Platanthera hyperborea complex (Orchidaceae)

description: Species complexes present considerable problems for a working taxonomy due
 to the presence of intraspecific variation, hybridization, polyploidy, and
 phenotypic plasticity. Understanding evolutionary patterns using molecular
 markers can allow for a more thorough assessment of evolutionary lineages
 than traditional morphological markers. In this study, we evaluated
 genetic diversity and phylogenetic patterns among taxa of the Platanthera
 hyperborea (Orchidaceae) complex, which includes diploid (Platanthera
 aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, P.
 convallariifolia) taxa spanning North America, Greenland, Iceland, and
 Asia. We found that three floral morphological characters overlap among
 the polyploid taxa, but the diploid species has smaller flowers. DNA
 sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker
 indicated that at least three diploid species have contributed to the
 genomes of the polyploid taxa, suggesting all are of allopolyploid origin.
 Platanthera convallariifolia is most like P. dilatata and P. stricta,
 whereas P. huronensis and P. hyperborea appear to have originated from
 crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is
 found across North America, has multiple origins and reciprocal maternal
 parentage from the diploid species. By contrast, P. hyperborea, restricted
 to Greenland and Iceland, appears to have originated from a small founding
 population of hybrids in which P. dilatata was the maternal parent.
 Geographic structure was found among polyploid forms in North America. The
 area of Manitoba, Canada appears to be a contact zone among geographically
 diverse forms from eastern and western North America. Given the geographic
 and genetic variation found, we recommend continued recognition of four
 green-flowered species within this complex, but caution that there may be
 additional cryptic taxa within North America.
description: Sequences of ITS and rpl16 were collected by PCR and Sanger
 sequencing.  Morphological data was measured on herbarium specimens under
 a stereomicroscope.  Sequences were edited and aligned using Sequencher
 and Se-AL. 
description: Files are self-explanatory. Sequences are aligned.
DOI: 10.5061/dryad.w3r2280ng
title: Data from: Chemical novelty facilitates herbivore resistance and biological invasions in some introduced plant species

description: Ecological release from herbivory due to chemical novelty is commonly
 predicted to facilitate biological invasions by plants, but has not been
 tested on a community scale. We used metabolomics based on mass
 spectrometry molecular networks to assess the novelty of foliar secondary
 chemistry of 15 invasive plant species compared to 46 native species at a
 site in eastern North America. Locally, invasive species were more
 chemically distinctive than natives. Among the 15 invasive species, the
 more chemically distinct were less preferred by insect herbivores and less
 browsed by deer. Finally, an assessment of invasion frequency in 2,505
 forest plots in the Atlantic coastal plain revealed that, regionally,
 invasive species that were less preferred by insect herbivores, less
 browsed by white-tailed deer, and chemically distinct relative to the
 native plant community occurred more frequently in survey plots. Our
 results suggest that chemically-mediated release from herbivores
 contributes to many successful invasions.
description: Methods are described in: Sedio, B. E., J. L.
 Devaney, J. Pullen, G. G. Parker, S. J. Wright, and J. D. Parker.
 Accepted. Chemical novelty facilitates herbivore resistance and biological
 invasions in some introduced plant species. Ecology and
 Evolution. Lind, E. M., and J. D. Parker. 2010. Novel
 weapons testing: are invasive plants more chemically defended than native
 plants? PLOS One 5(5): e10429. doi:10.1371/journal.pone.0010429
DOI: 10.5061/dryad.hdr7sqvfj
title: Data from: Crop production in the USA is frequently limited by a lack of pollinators

description: Most of the world’s crops depend on pollinators, so declines in both
 managed and wild bees raise concerns about food security. However, the
 degree to which insect pollination is actually limiting current crop
 production is poorly understood, as is the role of wild species (as
 opposed to managed honey bees) in pollinating crops, particularly in
 intensive production areas. We established a nation-wide study to assess
 the extent of pollinator limitation in seven crops at 131 locations
 situated across major crop-producing areas of the USA. We found that five
 out of seven crops showed evidence of pollinator limitation. Wild bees and
 honey bees provided comparable amounts of pollination for most crops, even
 in agriculturally-intensive regions. We estimated the nation-wide annual
 production value of wild pollinators to the seven crops we studied at over
 $1.5 billion; the value of wild bee pollination of all
 pollinator-dependent crops would be much greater. Our findings show that
 pollinator declines could translate directly into decreased yields or
 production for most of the crops studied, and that wild species contribute
 substantially to pollination of most study crops in major crop-producing
 regions.
DOI: 10.25338/b83p6k
title: Pesticide and resource stressors additively impair wild bee reproduction

description: Bees and other beneficial insects experience multiple stressors within
 agricultural landscapes that act together to impact their health and
 diminish their ability to deliver the ecosystem services on which human
 food supplies depend. Disentangling the effects of coupled stressors is a
 primary challenge for understanding how to promote their populations and
 ensure robust pollination and other ecosystem services. We used a crossed
 design to quantify the individual and combined effects of food resource
 limitation and pesticide exposure on the survival, nesting, and
 reproduction of the blue orchard bee Osmia lignaria. Nesting
 females in large flight cages accessed wildflowers at high or low
 densities, treated with or without the common insecticide, imidacloprid.
 Pesticides and resource limitation acted additively to dramatically reduce
 reproduction in free-flying bees. Our results emphasize the importance of
 considering multiple drivers to inform population persistence, management,
 and risk assessment for the long-term sustainability of food production
 and natural ecosystems.
DOI: 10.5061/dryad.cvdncjt1x
title: Data from: Greater agility increases probability of survival in the endangered northern quoll

description: Introduced predators combined with habitat loss and modification are
 threatening biodiversity worldwide, particularly the ‘critical weight
 range’ (CWR) mammals of Australia. In order to mitigate the impacts of
 invasive predators on native species in different landscapes, we must
 understand how the prey's morphology and performance determine their
 survival. Here we evaluate how phenotypic traits related to escape
 performance predict the probability of survival for an endangered CWR
 mammal, the northern quoll (Dasyurus hallucatus). We measured mass, body
 size, body shape, body condition, and age, as well as maximum sprint
 speed, acceleration, and agility of female quolls over two consecutive
 years. Those with higher body condition and agility around a 135° corner
 were more likely to survive their first 21 months of life but were not
 more likely to survive after this period. No other morphological or
 performance traits affected survival. Heavier second-year individuals were
 more agile than first-years but second-years experienced higher mortality
 rates throughout the year. Females with higher body condition and agility
 around a 135° corner tended to have shorter limbs and feet but larger
 heads. Our findings suggest that higher body condition and agility are
 advantageous for survival in female northern quolls. These results can be
 used to develop predictive models of predator-prey interactions based on
 performance capacities and how performance is affected by habitat, aiding
 conservation efforts to predict and manage the impacts of introduced
 predators on native species.
DOI: 10.7291/d1d96q
title: Physical and biogeochemical drivers of alongshore pH and oxygen variability in the California Current System

description: In the California Current System (CCS), the nearshore environment
 experiences natural exposure to low pH and reduced oxygen in response to
 coastal upwelling. Anthropogenic impacts further decrease pH and oxygen
 below biological thresholds, making the CCS particularly vulnerable to
 ocean acidification and hypoxia. Results from a coupled
 physical-biogeochemical model reveal a strongly heterogeneous alongshore
 pattern of nearshore pH and oxygen in the central CCS, both in their
 long-term means and trends. This spatial structuring is explained by an
 interplay between alongshore variability in local upwelling intensity and
 subsequent primary production, as well as changes in the vertical density
 structure modulated by meanders in the regional ocean circulation. The
 model solution suggests that the progression of ocean acidification and
 hypoxia will not be spatially homogeneous, thereby highlighting the need
 to consider sub-regional processes when assessing natural and
 anthropogenic impacts on coastal ecosystems in eastern boundary current
 upwelling regions.
description: This dataset is a subset of a coupled physical-biogeochemcial
 model for the central California Current upwelling system. The physical
 model is an implementation of the Regional Ocean Modelling System (ROMS;
 www.myroms.org) coupled to NEMUCSC, a customized version of the North
 Pacific Ecosystem Model for Understanding Regional Oceanography (NEMURO).
 The NEMUCSC biogeochemical model includes three limiting macro-nutrients,
 two phytoplankton functional groups, three zooplankton size-classes, and
 three detritus pools. To better represent the combined effects of regional
 circulation patterns and local upwelling intensity on alongshore
 biophysical properties, the model downscales a data-assimilative physical
 reanalysis at 1/10° (~10 km) resolution for the broader California Current
 system to a higher 1/30° (~3 km) resolution domain for the central
 California Current region. A subset of variables were extracted from the
 full daily model output at various depths and subsequently averaged
 monthly for 1988-2010 using Ferret V7.1
 (http://ferret.pmel.noaa.gov/Ferret). The dataset is in NetCDF4 format
 (CF-1.4 compliant) with metadata describing each variable name and
 associated units on the native ROMS grid.
description: All necessary information to use this dataset is contain in the
 metadata (variable name, units, missing value flag, etc).
DOI: 10.5061/dryad.mkkwh70ws
title: Data from: Foraging by an avian ecosystem engineer extensively modifies the litter and soil layer in forest ecosystems

description: Ecosystem engineers physically modify their environment, thereby altering
 habitats for other organisms. Increasingly, ‘engineers’ are recognised as
 an important focus for conservation and ecological restoration because
 their actions affect a range of ecosystem processes and thereby influence
 how ecosystems function. The superb lyrebird Menura novaehollandiae is
 proposed as an ecosystem engineer in forests of south-eastern Australia
 due to the volume of soil and litter it turns over when foraging. We
 measured the seasonal and spatial patterns of foraging by lyrebirds and
 the amount of soil displaced in forests in the Central Highlands,
 Victoria. We tested the effects of foraging on litter, soil nutrients and
 soil physical properties by using an experimental approach with three
 treatments: lyrebird exclusion, lyrebird exclusion with simulated
 foraging, and non-exclusion reference plots. Treatments were replicated in
 three forest types in each of three forest blocks. Lyrebirds foraged
 extensively in all forest types in all seasons. On average, lyrebirds
 displaced 155.7 t/ha of litter and soil in a 12-month period. Greater
 displacement occurred where vegetation complexity (&lt;50 cm height)
 was low. After two years of lyrebird exclusion, soil compaction (top 7.5
 cm) increased by 37% in exclusion plots compared with baseline measures,
 whilst in unfenced plots it decreased by 22%. Litter depth was almost
 three times greater in fenced than unfenced plots. Soil moisture, pH and
 soil nutrients showed no difference between treatments. The enormous
 extent of litter and soil turned over by the superb lyrebird is
 unparalleled by any other vertebrate soil engineer in terrestrial
 ecosystems globally. The profound influence of such foraging activity on
 forest ecosystems is magnified by its year-round pattern and widespread
 distribution. The disturbance regime that lyrebirds impose has
 implications for diverse ecosystem processes including decomposition and
 nutrient cycling, the composition of litter- and soil-dwelling
 invertebrate communities, the shaping of ground-layer vegetation patterns,
 and fire behavior and post-fire ecosystem recovery. Maintaining lyrebird
 populations as a key facilitator of ecosystem function is now timely and
 critical as unprecedented wildfires in eastern Australia in summer
 2019/2020 have severely burned ~12 million ha of forest, including ~30% of
 the geographic range of the superb lyrebird.
description: Excel worksheets
 contain a primary tab with the raw data and a secondary tab that contains
 the measured variables' descriptions for each analysis. Soil nutrient
 measures were provided by CSBP Soil and Plant Analysis Laboratory (Bibra
 Lakes, Western Australia). All other data were measured by the
 authors.
DOI: 10.6086/d1667n
title: California grid electrical energy storage requirements for select renewables integration and fleet electrification scenarios

description: Significant electrification of the transportation sector is necessary for
 the State to achieve several important greenhouse gas (GHG) reduction and
 renewable energy targets. The State’s electricity generation and
 transmission capabilities must increase in order to meet the demand
 generated by increasing levels of fleet electrification. The increased
 demand, combined with the Renewables Portfolio Standard (RPS) targets will
 require significantly increased energy storage capabilities that can
 accommodate demand while integrating renewable power sources into the
 grid. This project evaluated the mid to long-term energy storage needs of
 the electric grid for select fleet electrification scenarios. The analysis
 was conducted using Resolve, a power systems planning model, for RPS
 targets of 60% and 80% by 2030 and 2042 respectively. The results show
 that Electrical Energy Storage (EES) capacity requirements depend on a
 number of parameters, including Demand Response (DR), Electric Vehicle
 (EV) charging flexibility, and total EV population. The EES requirements
 for the 60% RPS scenarios range from 3.9 to 4.3 GW while for the 80% RPS
 scenarios, the range is from 18.5 to 20.4 GW.
description: The dataset was collected from the results of simulations
 performed using the Resolve model
 (https://www.cpuc.ca.gov/General.aspx?id=6442462824) to assess the
 Electrical Energy Storage requirements of California's electricity
 grid under select scenarios. The Resolve model results have been processed
 to create the dataset.
description: The datasets are self explanatory within the context of the main
 report. Each individual tab in the Excel spreadsheets are assigned a
 descriptive name and the Tables and Figures have descriptive title
 columns.
DOI: 10.5061/dryad.gb5mkkwms
title: Data from: High rates of carbon and dinitrogen fixation suggest a critical role of benthic pioneer communities in the energy and nutrient dynamics of coral reefs

description: 1. Following coral mortality in tropical reefs, pioneer communities
 dominated by filamentous and crustose algae efficiently colonize
 substrates previously occupied by coral tissue. This phenomenon is
 particularly common after mass coral mortality following prolonged
 bleaching events associated with marine heatwaves. 2. Pioneer communities
 play an important role for the biological succession and reorganization of
 reefs after disturbance. However, their significance for critical
 ecosystem functions previously mediated by corals, such as the efficient
 cycling of carbon (C) and nitrogen (N) within the reef, remains uncertain.
 3. We used 96 carbonate tiles to simulate the occurrence of bare
 substrates after disturbance in a coral reef of the central Red Sea. We
 measured rates of C and dinitrogen (N2) fixation of pioneer communities on
 these tiles monthly over an entire year. Coupled with elemental and stable
 isotope analyses, these measurements provide insights into macronutrient
 acquisition, export, and the influence of seasonality. 4. Pioneer
 communities exhibited high rates of C and N2 fixation within 4 – 8 weeks
 after the introduction of experimental bare substrates. Ranging from 13 to
 25 μmol C cm−2 d−1 and 8 to 54 nmol N cm−2 d−1, respectively, C and N2
 fixation rates were comparable to reported values for established Red Sea
 coral reefs. This similarity indicates that pioneer communities may
 quickly compensate for the loss of benthic productivity by corals.
 Notably, between 40 and 85% of fixed organic C was exported into the
 environment, constituting a vital source of energy for the coral reef food
 web. 5. Our findings suggest that benthic pioneer communities may play a
 crucial, yet overlooked role in the C and N dynamics of oligotrophic coral
 reefs by contributing to the input of new C and N after coral mortality.
 While not substituting other critical ecosystem functions provided by
 corals (e.g. structural habitat complexity and coastal protection),
 pioneer communities likely contribute to maintaining coral reef nutrient
 cycling through the accumulation of biomass and import of macronutrients
 following coral loss.
description: This is the raw data to "High rates of carbon and dinitrogen
 fixation suggest a critical role of benthic pioneer communities in the
 energy and nutrient dynamics of coral reefs". All information on how
 the dataset was collected can be found in the manuscript. Missing values
 are represented by NA (not available).
DOI: 10.15468/dl.mkeeu3
title: Occurrence Download

description: A dataset containing 178048 records in GBIF matching the query:
SELECT
 '434' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -75.5327771015545
 AND decimalLongitude &lt;= -65.93482227598784
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 178048 records were derived from 439 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002410-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s7h44j14r
title: RNA-sequencing endometrium intact, vasectomized, and control heifers

description: An appropriate female reproductive environment is essential for pregnancy
 success. In several species, including mice, pigs and horses, seminal
 plasma (SP) components have been shown to modulate this environment,
 leading to increased embryo viability and implantation. Due to the
 characteristics of mating in the aforementioned species, SP comes into
 direct contact with the uterus. However, it is questionable whether any SP
 reaches the uterus in species that ejaculate inside the vagina, such as
 humans and cattle. Hence, we hypothesized that sperm, perhaps acting as a
 vehicle for SP factors, play a more important role in the modulation of
 the maternal uterine environment in these species. In addition, changes
 elicited by SP and/or sperm may originate in the vagina and propagate to
 more distal regions of the female reproductive tract. To test these
 hypotheses, a bovine model in which heifers were mated to intact or
 vasectomized bulls or were left unmated was used. RNA-sequencing of
 endometrial samples collected 24 h after mating with a vasectomized bull
 did not reveal any differentially expressed genes (DEGs) in comparison
 with control samples. However, the endometrium of heifers mated with
 intact bulls exhibited 24 DEGs when compared to heifers mated with
 vasectomized bulls, and 22 DEGs when compared to unmated control heifers.
 The expression of a set of cytokines (IL6, IL1A, IL8, and TNFA) and
 candidate genes identified in the endometrial RNA-sequencing (PLA2G10,
 CX3CL1, C4BPA, PRSS2, BLA-DQB, and CEBPD) were assessed by
 RT-qPCR in the vagina and oviductal ampulla. No differences in expression
 of these genes were observed between treatments in any region. However,
 mating to both intact and vasectomized bulls induced an increase in IL1A
 and TNFA expression in the vagina compared to the oviduct. These data
 indicate that sperm, but not secretions from the accessory glands alone,
 induce modest changes in endometrial gene expression after natural mating
 in cattle. However, it is not clear whether this effect is triggered by
 inherent sperm proteins or SP proteins bound to sperm surface at the time
 of ejaculation.
DOI: 10.5061/dryad.hmgqnk9dm
title: Primary determinants of communities in deadwood vary among taxa but are regionally consistent

description: These data are the raw data for Figure 2 in "Primary determinants of
 communities in deadwood vary among taxa but are regionally
 consistent"
DOI: 10.5683/sp3/ylsggi
title: Using data from automated calf feeders to predict the weaning performance of dairy calves

description: Weaning from milk is a stressful phase for dairy calves affecting behaviors and growth. This study explored individual differences in feeding behaviors before weaning to predict calves’ grain intake and growth during and after gradual weaning. Specifically, we sought to predict average daily gain (ADG) and grain intake during and after weaning using measures of milk intake, grain intake, drinking speed, and visits to the grain feeder in the pre-weaning period. Group-housed Holstein heifers calves (n=92) were offered 12 L/d of milk and ad libitum grain using an automatic feeder from 8-51 days of age. Starting on day 52, milk allowance was reduced by 1.2L/d until reaching 6 L/d on day 57, and then reduced to 0 from day 72 to 77. Calves were weighed weekly until 97 days of age. Automated feeders recorded individual milk intake, drinking speed, grain intake, visits to the grain feeder. Calves with higher and more consistent milk intakes before weaning showed greater grain intakes later, and earlier grain consumption was associated with improved grain intakes and growth during and after weaning. Providing high milk allowances and early access to solid feed allows calves to express variability in feeding behaviors that may serve as indicators of weaning and post-weaning performance, creating opportunities for early intervention.