cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2547d7wvk
title: Data for: Ecological and evolutionary origin of Costus flammulus (Costaceae): A new species from the montane cloud forests of the volcanic cordilleras in northern Costa Rica

description: Costus flammulus is a new herbaceous species endemic to montane cloud
 forests of the volcanic cordilleras in northern Costa Rica. Costus
 flammulus has been mistaken for C. wilsonii, but phylogenetic evidence
 demonstrates that it is closely related to the widespread lowland species
 C. pulverulentus. Here, we used an integrated framework of species
 concepts to evaluate whether C. flammulus and C. pulverulentus are
 distinct species. First, we re-evaluate prior phylogenetic analyses to
 assess whether C. flammulus bifurcated from or budded off from within C.
 pulverulentus and whether C. flammulus is monophyletic. We then compare
 phenotypic traits to determine which diagnostic vegetative and
 inflorescence traits can be used to identify species in herbarium
 specimens and examine whether floral traits may confer floral isolation.
 We compare pollinator assemblages to examine whether pollinator
 specificity may contribute to reproductive isolation. Finally, we model
 species distributions and climatic niche overlap to assess ecogeographic
 isolation. We found that C. flammulus is a monophyletic species
 phenotypically, ecologically, and geographically distinct from C.
 pulverulentus and may have speciated as a peripheral isolate at the high
 elevation range edge of C. pulverulentus. Several lines of evidence, such
 as C. pulverulentus paraphyly, range size asymmetry, and C. flammulus’
 nested distribution and vegetative traits, suggest that C. flammulus
 budded off from a C. pulverulentus‐like progenitor species, evolving to
 tolerate a colder and more seasonal montane environment.
description: README.md lists and describes all the files:
 This file describes the supplementary data accompanying: Juarez
 P., O.M. Vargas, and K.M.Kay. 2023. Ecological and evolutionary origin of
 <em>Costus</em> <em>flammulus</em> (Costaceae): a
 new species from the montane cloud forests of the volcanic cordilleras in
 northern Costa Rica. <br><br>Supplementary
 Tables:<br><br>(Table S1) Phenotypic vegetative measurements
 and <em>Costus</em> herbarium specimens.
 <br><br>(Table S2) Phenotypic floral measurements and
 <em>Costus</em> locations. <br><br>(Table S3)
 <em>Costus</em> occurrences. <br><br>(Table S4) 29
 Neotropical plant genera occurrences of targeted background pseudo-absence
 data within the terrestrial political borders of Costa Rica
 <br><br>Supplementary Figure:<br><br>(Fig S1) Map
 of the occurrences of targeted background pseudo-absence data within the
 terrestrial political borders of Costa Rica (08° to 11° latitude and -86°
 to -82° longitude).
DOI: 10.5061/dryad.cvdncjt7k
title: Data for: Combined effects of GBH residues and phosphate fertilizers on endophytic microbiota and plant performance of garden strawberry

description: Aims: In a field study, the effects of treatments of glyphosate-based
 herbicides (GBHs) in soil, alone and in combination with phosphate
 fertilizer, were examined on the performance and endophytic microbiota of
 garden strawberry.  Methods and results: The root and leaf
 endophytic microbiota of garden strawberries grown in GBH-treated and
 untreated soil, with and without phosphate fertilizer were analyzed. Next,
 bioinformatics analysis on the type of 5-enolpyruvylshikimate-3-phosphate
 synthase enzyme was conducted to assess the potential sensitivity of
 strawberry-associated bacteria and fungi to glyphosate, and to compare the
 results with field observations. GBH treatments altered the abundance
 and/or frequency of several operational taxonomic units (OTUs), especially
 those of root-associated fungi and bacteria. These changes were partly
 related to their sensitivity to glyphosate. Still, GBH treatments did not
 shape the overall community structure of strawberry microbiota or affect
 plant performance. Phosphate fertilizer increased the abundance of both
 glyphosate-resistant and glyphosate-sensitive bacterial OTUs, regardless
 of the GBH treatments. Conclusions: These findings demonstrate that
 although the overall community structure of strawberry endophytic microbes
 is not affected by GBH use, some individual taxa are. Significance and
 impact of study: Agrochemical residues in soil can shape the endophytic
 microbiota in crop plants.
description: Strawberry plantlets grown in greenhouse were planted to the
 experimental fields three weeks after glyphosate-based herbicide
 application in June 2019. The number of leaves and length of produced
 runners were measured in mid-August 2019. Samples for micobiome studies
 were collected in August 2019 from root and leaves of garden strawberry
 grown in glyphosate, phosphate fertilizer and glyphosate combined with
 phosphate fertilizer treated fields. The tissue samples were then
 processed for DNA extraction, PCR and high-throughput
 sequencing.
DOI: 10.5061/dryad.xsj3tx9kc
title: Data for: Earlier leaf senescence dates are constrained by soil moisture

description: The unprecedented warming that has occurred in recent decades has led to
 later autumn leaf senescence dates (LSD) throughout the Northern
 Hemisphere. Yet, great uncertainties still exist regarding the strength of
 these delaying trends, especially in terms of how soil moisture affects
 them. Here we show that changes in soil moisture in 1982–2015 had a
 substantial impact on autumn LSD in one fifth of the vegetated areas in
 the Northern Hemisphere (&gt;30° N), and how it contributed more to
 LSD variability than either temperature, precipitation or radiation. We
 developed a new model based on soil-moisture-constrained cooling degree
 days (CDDSM) to characterize the effects of soil moisture on LSD and
 compared its performance with the cooling degree days (CDD), Delpierre
 (DM) and spring-influenced autumn (SIAM) models. We show that the CDDSM
 model with inputs of temperature and soil moisture outperformed the three
 other models for LSD modelling and had an overall higher correlation
 coefficient (R), a lower root mean square error (RMSE) and lower Akaike
 information criterion (AIC) between observations and model predictions.
 These improvements were particularly evident in arid and semi-arid
 regions. We studied future LSD using the CDDSM model under two scenarios
 (SSP126 and SSP585) and found that predicted LSD was 4.1±1.4 days and
 5.8±2.8 days earlier under SSP126 and SSP585, respectively, than other
 models for the end of this century. Our study therefore reveals the
 importance of soil moisture in regulating autumn LSD and, in particular,
 highlights how coupling this effect with LSD models can improve
 simulations of the response of vegetation phenology to future climate
 change.
description: See the Methods section in the original paper.
DOI: 10.5061/dryad.4j0zpc8gn
title: Data from: Savanna resilience to droughts increases with proportion of browsing wild herbivores and plant functional diversity

description: 1. Maintaining the resilience and functionality of savannas is key to
 sustaining the ecosystem services they provide. This maintenance is
 largely dependent on the resilience of savannas to stressors, such as
 prolonged droughts. The resilience to drought is largely determined by the
 interaction of herbivores and the functional composition of vegetation. So
 far, our understanding and ability to predict the response of savannas to
 drought under different types of rangeland use and as a function of
 vegetation composition are still limited. 2. In this study, we used the
 ecohydrological, spatially-explicit savanna model EcoHyD to determine if
 the resilience of a savanna rangeland towards prolonged droughts can be
 enhanced by the choice of rangeland use type (grazer-dominated,
 mixed-feeders or browser-dominated) and animal density. We evaluated the
 ability of a Namibian savanna system to withstand droughts and to recover
 from droughts based on its perennial grass cover and the overall species
 composition. 3. Generally, we determined a low resilience under high
 grazer densities. Most importantly, we found that functional
 diversification of herbivores and plants acted as resilience insurance
 against droughts, leading to greater resistance and recovery of perennial
 grasses. In particular, a higher proportion of herbivores allowed for
 higher resilience, probably also due to a short-term switch to more
 drought-resistant or unpalatable species.  4. In this case,
 herbivore diversification was of high self-regulatory value by
 reestablishing trophic complexity, reducing the need for additional
 management interventions.  5. Synthesis and applications. Savanna
 systems will be more resistant to drought if (i) a dense perennial grass
 cover is maintained, protecting the topsoil from heat-induced water losses
 and erosion, encompassing functionally important species that are
 particularly well adapted to water stress and that are palatable, if (ii)
 the grazing pressure is adjusted to the productivity of the system, and
 (iii) the herbivore community includes browsers. 
description: Model code (C++), simulation data and R scripts to reproduce the
 results and figures of the manuscript "Savanna resilience to droughts
 increases with proportion of browsing wild herbivores and plant functional
 diversity" by Katja Irob et al.
DOI: 10.5061/dryad.gmsbcc2s7
title: The size of a smell: assessment of rival’s size from femoral secretions in the common wall lizards

description: Animal communication depends on signals conveying information to a
 receiver who must perceive and decode them. Signals involved in
 territoriality are usually complex stimuli that should be correctly
 interpreted to avoid unnecessary conflicts. Lacertids use both visual and
 chemical stimuli in modulating their aggressive response against
 conspecifics and the rival’s size is one of the most important
 information, affecting the success probability in a combat. To assess the
 actual ability of decoding information about rival’s size based on its
 chemical stimulus alone, 60 males of Podarcis muralis were tested for
 three consecutive days in an arena bearing a mirror (to simulate an
 equal-sized intruder), and the chemical cues (femoral secretions) from an
 unknown individual of different size. Significant differences were
 observed in tongue-flicks number, which grew as the size difference
 between the focal lizard and the secretion donor decreased. This can be
 interpreted as the need for the lizard to better evaluate the potential
 competitor’s characteristics. The size difference also affected the number
 of bites against the mirror, which increased when the size of the focal
 lizard was larger than the donor triggering the aggressive response with a
 higher probability of winning the contest, as expected if the focal lizard
 had correctly decoded the information about the opponent’s size by
 chemical stimulus. Although previous studies have shown that some
 components of the chemical signals are potentially informative about the
 signaller’s size, this is the first demonstration that male P. muralis are
 actually able to decode and use such information.
DOI: 10.5061/dryad.2ngf1vhst
title: Long-term ecological responses of a lowland dipterocarp forest to climate changes and nutrient availability at Bulusan Lake

description: This data publication encompasses the datasets generated in a study
 focusing on reconstructing ecological responses to climatic and nutrient
 availability changes during the late Holocene in northern Philippines. The
 data comes from samples taken from sediment cores retrieved from Bulusan
 Lake, located on Luzon Island, Philippines, in March 2013. In these
 samples, we analyzed fossil pollen and spores (a proxy for plant taxa
 abundance), charcoal (a proxy for fire activity), stable carbon isotopic
 composition of terrestrial-lipid biomarkers (a proxy for vegetation
 cover), stable nitrogen and phosphate isotope composition of bulk
 sediments, and elemental composition of sediment cores at a high
 resolution (proxies for nutrient availability and volcanic activity). The
 dataset also includes links to records generated in a previous study on
 the same sediments (Prohaska et al. 2023), where we measured the stable
 hydrogen isotopic composition of terrestrial-lipid biomarkers to
 reconstruct past hydrological conditions, as well as the magnetic
 susceptibility record and AMS dates of plant macrofossils to calculate
 sediment accumulation ages. The data generation spanned the period from
 April 2013 to September 2020, and the data files are provided in Excel
 spreadsheet format.
description: Information on how the data have been collected and processed is
 provided in the published article.
DOI: 10.15468/dl.xfpww7
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Rheum palmatum",
 "Year 1975-2026"
 ]
}

 The dataset includes 89 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003440-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r2280gbh9
title: Relatedness modulates reproductive competition among queens in ant societies with multiple queens

description: Reproductive sharing in animal groups with multiple breeders, insects and
 vertebrates alike, contains elements of both conflict and cooperation, and
 depends on both relatedness between co-breeders, as well as their internal
 and external conditions. We studied how queens of the ant Formica fusca
 adjust their reproductive efforts in response to experimental
 manipulations of the kin competition regime in their nest, as well as
 their own reproductive status. Queens respond to the presence of
 competitors by increasing their egg laying efforts, but only if the
 competitors are highly fecund and distantly related. Furthermore, queens
 only engage in cannibalism of eggs when the risk of erroneously destroying
 own offspring is absent. We demonstrate that queens of Formica fusca
 fine-tune their behaviours in response to kinship and fecundity of others
 as well as their own physiological state in a manner that is unusually
 precise for any cooperative breeder.
DOI: 10.15468/dl.sf9mfk
title: Occurrence Download

description: A dataset listing the 12 species recorded in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Xerochrysum bracteatum"
 ]
}

 The dataset's 12 records were derived from 175 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002766-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j0zpc86jj
title: Data for: Warming and hypoxia reduce performance and survival of northern bay scallops, Argopecten irradians irradians, amid a fishery collapse

description: Populations of the northern bay scallop, Argopecten irradians irradians,
 across the northeast US have recently experienced severe declines. Here we
 used high-resolution satellite-based temperature records, long-term
 temperature and dissolved oxygen records, field and laboratory
 experiments, and high-frequency measures of scallop cardiac activity in an
 ecosystem setting to quantify decadal summer warming and assess the
 vulnerability of northern bay scallops to thermal- and hypoxic-stress
 across their geographic distribution. This set of files contains the raw
 data analyzed for this study. The data are grouped into relevant
 subfolders: Commercial Landings Data; Field Deployment Data; Gonad Index
 Data; Laboratory Data; Optical Infrared Sensor Data; Remote Sensing Data.
DOI: 10.5061/dryad.9kd51c5n9
title: Data for: Spatial monitoring of flying insects over a Swedish lake using a CW lidar system

description: Data for a field experiment on remote sensing of flying insects are
 supplied. A bistatic CW lidar system of the Scheimpflug type was employed,
 and echoes from flying insects over and close to a Swedish lake were
 recorded as read-out files from an array detector making observations
 along the emitted laser beam. The activated pixels of the detector could
 be converted into range data by triangulation. With a high detector
 read-out frequency, data on numerous insects could be obtained. Special
 emphasis was put on distinguishing between large and small insects (from
 the intensities of the recorded echoes) and the insect positions with
 regard to the shores of the lake. 
description: Data were recorded by using a CW Scheimpflug lidar system
 equipped with a linear array detector. Insect echoes, recorded by the
 detector are read out at a high repetition rate. The provided material
 constitutes the raw data used to produce the evaluated material, which is
 displayed in the publication figures.
DOI: 10.5061/dryad.mcvdnck4m
title: Dataset: Effect of soil organic matter content and nutrient loading on productivity of Spartina patens (v.0.10)

description: River sediment diversions in the Mississippi River Delta have been planned
 as a keystone strategy for wetland restoration in coastal Louisiana. The
 introduction of mineral sediment and dissolved nutrients present in
 Mississippi River water could drastically alter the abiotic environment of
 the surrounding wetlands, and the effects on wetland vegetation are
 unclear. In this study, 50 sods were transplanted from a Spartina
 patens-dominated brackish marsh into a greenhouse and grown in either
 mineral or organic soil in combination with one of five levels of nutrient
 enrichment. The primary component of the mineral soil was silt collected
 from the bank of the Mississippi River, while that of the organic soil was
 peat collected from the aforementioned S. patens marsh. Nutrient
 treatments were based on a range of Mississippi River diversion discharge
 rates of nitrate, phosphate, sulfate, potassium, and iron as well as a
 control with no nutrient addition. After one summer, we found that total
 porewater conductivity increased with nutrient loading under both soil
 types. Under higher nutrient treatments the concentrations of porewater
 sulfide were elevated to phytotoxic levels, but this effect was only
 observed in the organic soil treatment. Nitrate and ammonium porewater
 concentrations were affected by both nutrient loading and soil type;
 however, nitrate was higher in the mineral soil while ammonium was higher
 in the organic soil. Porewater phosphorous and potassium concentrations
 were elevated in organic soil conditions and higher nutrient loading,
 while porewater iron was higher under mineral soil and lower nutrient
 loading. Aboveground standing crop, belowground biomass accumulation
 (i.e., ingrowth), and soil shear strength were also sampled at the end of
 the growing season with the goal of examining their relationships with
 nutrient and sediment enrichment and porewater chemistry.
DOI: 10.15468/dl.mvk4um
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gonocytisus pterocladus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 17 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003442-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mcvdnck4n
title: How well must surface vorticity be organized for tornadogenesis?

description: This study investigates whether quasi-random surface vertical vorticity is
 sufficient for tornadogenesis when combined with an updraft typical of
 tornadic supercells. The viability of this pathway could mean that a
 coherent process to produce well-organized surface vertical vorticity is
 rather unimportant. Highly idealized simulations are used to establish
 random noise as a possible seed for the production of tornado-like
 vortices (TLVs). A number of sensitivities are then examined across the
 simulations. The most explanatory predictor of whether a TLV will form
 (and how strong it will become) is the maximal value of initial surface
 circulation found near the updraft. Perhaps surprisingly, sufficient
 circulation for tornadogenesis is often present even when the surface
 vertical vorticity field lacks any obvious organized structure. The other
 key ingredient for TLV formation is confirmed to be a large vertical
 gradient in vertical velocity close to the ground (to promote stretching).
 Overall, it appears that random surface vertical vorticity is indeed
 sufficient for TLV formation given adequate stretching. However, it is
 shown that longer-wavelength noise is more likely to be associated with
 substantial surface circulation (because it is the areal integral of
 vertical vorticity). Thus, coherent vorticity sources that produce longer
 wavelength structures are likely to be the most supportive of
 tornadogenesis.
description: The Cloud Model 1 (CM1)  is available from https://www2.mmm.ucar.edu/people/bryan/cm1/ This repository includes namelists and input files needed to recreate the simulations in the study using release 20.3 of CM1. (Dryad, as described in README.md) Post-processing of NetCDF output from CM1 was accomplished using Python scripts developed by the author, which are also included in this repository. (Zenodo, as described in README.md) The induced flow solver used in this study is the intellectual property of Dr. Johannes Dahl and may be available by contacting him (johannes.dahl@ttu.edu).  The induced flow fields it produces (which were used as initial conditions in this study) are included in this repository (binary form, with descriptive .ctl files).
description: The CM1 model requires a fortran compiler (see https://www2.mmm.ucar.edu/people/bryan/cm1/ for more information). The plotting scripts require access to NetCDF libraries and Python (including installation of several packages listed in the preamble to the attached Python scripts). The easiest way to view the contents of the induced_flow.dat files is to use the Gridded Analysis and Display Software (GrADS). All files are contained within tar archives, and the user will need to unpack them.
DOI: 10.5061/dryad.xpnvx0kkb
title: Dataset: Methane and carbon dioxide fluxes in an intermediate marsh in Barataria Bay, LA (v.0.10)

description: Methane and carbon dioxide fluxes were measured in August 2019 in an
 Intermediate salinity marsh in Barataria Bay, Louisiana. The flux chamber
 method was used to measure methane (CH4) and carbon dioxide (CO2) under
 light and dark conditions in an Intermediate salinity marsh in Barataria
 Bay, LA. Fluxes were measured in plots with the following treatments:
 Control and high nutrients. Treatments included: Control; Sediment
 deposition- 0 (control) and 5 cm (45 kg river silt); Nutrient- Low
 nutrients:  645.2 g of CaNO3 and 11.11g of P2O5 High
 nutrients:  6451.6 g of CaNO3 and 111.1 g of P2O5; and Low
 nutrients + Sediment and High nutrients + Sediment Measurements included
 methane flux (calculated from concentration regressions over time), carbon
 dioxide flux (calculated from concentration regressions over time), air
 temperature inside and outside of chambers, PAR inside and outside of
 chambers, salinity and water table depth.