cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n5tb2rbrh
title: Origin and adaptive radiation of the exceptional and threatened bembidiine beetle fauna of St Helena (Coleoptera: Carabidae)

description: The central peaks of the isolated island of St Helena (in the south
 Atlantic Ocean) are home to an extraordinary set of ground beetles of the
 tribe Bembidiini, and belong to three endemic genus-group taxa. These
 beetles are strikingly different in overall body form from the many
 bembidiines found elsewhere in the world. At least some of the St Helena
 species are likely extinct, and all are threatened by habitat destruction
 and invasive species. Through next-generation sequencing of old museum
 specimens, we examine the phylogenetic relationships of the St Helena
 fauna. We find that, in spite of their morphological disparities, the
 endemic St Helena bembidiines form a clade of genetically very similar
 species, their sister group is Bembidion alsium from the
 island of La Réunion (east of Madagascar), and the sister group of this
 pair is the African subgenus Omotaphus.  We
 propose that the St Helena Peaks Bembidion are an
 adaptive radiation that arose from a single dispersal event to St Helena
 from a now-extinct African lineage (sister to Omotaphus), and
 that this extinct lineage also served as the ancestral source
 of Bembidion alsium.  As the St Helena
 Peaks Bembidion are deeply nested within the
 genus Bembidion, we move the three taxa back within that genus as
 subgenera, and provide a new name (Bembidion shepherdae) for the
 now-homonymous Bembidion wollastoni. 
description: Genome skimming using an Illumina sequencer from DNA extracted
 from pinned specimens that were 46-130 years old.  Sequences obtained by
 de novo and reference-based assembly.  Matrix of seven genes analyzed
 using maximum likelihood estimation using IQ-TREE.
DOI: 10.6078/d1x97d
title: Data from: Genome-wide epigenetic isolation by environment in a widespread Anolis lizard

description: Epigenetic changes can provide a pathway for organisms to respond to local
 environmental conditions by influencing gene expression. 
 However, we still know little about the spatial distribution of epigenetic
 variation in natural systems, how it relates to the distribution of
 genetic variation and the environmental structure of the landscape, and
 the processes that generate and maintain it.  Studies examining
 spatial patterns of genetic and epigenetic variation can provide valuable
 insights into how ecological and population processes contribute to
 epigenetic divergence across heterogeneous landscapes.  Here, we
 perform a comparative analysis of spatial genetic and epigenetic variation
 based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single
 methylation variants (SMVs) from eight populations of the Puerto Rican
 crested anole, Anolis cristatellus, an abundant lizard in the adaptive
 radiations of anoles on the Greater Antilles that occupies a diverse range
 of habitats.  Using generalized dissimilarity modeling and
 multiple matrix regression, we found that genome-wide epigenetic
 differentiation is strongly correlated with environmental divergence, even
 after controlling for the underlying genetic structure.  We also
 detected significant associations between key environmental variables and
 96 SMVs, including 42 located in promoter regions or gene
 bodies.  Our results suggest an environmental basis for
 population-level epigenetic differentiation in this system and contribute
 to better understanding how environmental gradients structure epigenetic
 variation in nature.
description: Environmental PC Rasters Principal component
 rasters for the bioclimate data from the WorldClim database are provided
 in GeoTIFF format.  The extent of each raster covers the whole island of
 Puerto Rico. SNP Data SNP data are
 provided in structure format, with samples on two rows.
 SMV Data Single methylation variant (SMV)
 data are provided in CSV format.  Samples are on two rows; C calls are the
 first row, and T calls are the second row.  The first column is the sample
 number.
DOI: 10.5061/dryad.dv41ns1tg
title: Ms3 dominant genetic male sterility for wheat improvement with molecular breeding

description: Genetic dominant male sterility (DMS) has not been widely used as a
 breeding tool in wheat (Triticum aestivum L.), although DMS-facilitated
 backcross, mass selection, half-sib selection, and S1 family recurrent
 selection strategies have been described, and Ms2-facilitated recurrent
 selection has been used in China. Our objective was to revisit these
 strategies using the tools of molecular breeding. Development of a
 mechanism for seedling identification of sterile progeny was a key
 component of designing practical DMS-facilitated molecular breeding
 systems. The DMS gene Ms3 was previously localized to the centromeric
 region of chromosome 5A. The centromeric location is an advantage because
 recombination rates are very low. Once identified, a broadly informative
 marker would reliably predict the male-sterile phenotype. A set of 429
 hybrids incorporating Ms3 were constructed, both within US hard winter
 wheats, and between these winter wheats and Asian spring wheats.
 Association of the male-sterile phenotype with those polymorphic DNA
 sequence tags that localized to chromosome 5A was tested using
 case-control association analysis. Two highly significant (logarithm of
 odds [LOD] &gt; 30) single nucleotide polymorphism (SNP)–trait
 associations were obtained. One SNP was developed into a highly sensitive,
 reliable molecular marker for the Ms3-associated male-sterile. Previously
 described breeding strategies using DMS were updated for trait-targeted
 marker-assisted backcrossing and gene pyramiding, S1 recurrent selection,
 and early-generation genomic selection. Application of DMS to association
 mapping, with the particular use case of the multiparent advanced
 generation intercross population, is also described.
description: The SNPs were called by TASSEL 5.0 (Bradbury et al.,
 2007) using the
 reference sequence of the bread wheat landrace Chinese Spring
 (International Wheat Genome Sequencing Consortium [IWGSC] RefSeq 1.0)
 (Alaux et al.,
 2018). The 197,543 SNPs called were
 filtered in TASSEL to the 5666 SNPs that aligned to chromosome 5A and had
 minor allele frequency &gt;0.05. Genotyping data thus subsetted were
 imported to JMP Genomics 9.0 (SAS Institute) using the TASSEL GBS Import
 Engine. Further filtering using the Subset and Reorder Genetic Data
 utility in JMP Genomics filtered the markers to those with &lt;40%
 missing data and filtered the genotypes to those with a minimum proportion
 of nonmissing genotypes of 20%.
description: Files are SAS datasets, genotype and annotation, used for
 association analysis.
DOI: 10.5061/dryad.866t1g1m1
title: Weighing the cost: the impact of serial heatwaves on body mass in a small Australian passerine

description: Rising temperatures pose a grave risk to arid zone birds because they are
 already living close to their physiological limits and must balance water
 conservation against the need for evaporative cooling. We assess how
 extreme temperatures affect a wild population of small passerines by
 monitoring daily mass change in individual Jacky Winters (a small
 Australasian robin; Microeca fascinans) across a series of severe
 heatwaves that afflicted southern Australia in the summer of 2018-19.
 Daily maximum temperature and duration of heat exposure were negatively
 related to the birds’ ability to maintain body mass. At maximum
 temperatures ≥42oC, birds lost 2.0% of their body mass daily and at ≥45oC,
 2.6%. Apparent mortality increased almost three-fold, and all breeding
 birds abandoned their nests. Nevertheless, net daily mass loss was less
 than might be expected from laboratory-based findings, presumably because
 wild Jacky Winters undertook behavioural thermoregulation. The birds also
 regained some mass between heatwave events and suffered no long-term
 reduction in body condition.
DOI: 10.5061/dryad.bnzs7h461
title: Disruptive selection of shell colour in land snails: a mark–recapture study of Euhadra peliomphala simodae

description: Many theoretical studies have suggested that disruptive
 selection plays an important role in phenotypic divergence, but
 few studies have determined the action of disruptive selection on
 phenotypic divergence via field studies. This study
 investigated the effect of disruptive selection
 on shell colour polymorphism in the Japanese
 land snail Euhadra peliomphala simodae to
 determine whether extreme phenotypes of snail shell
 colour are favored over intermediate
 phenotypes. We conducted field surveys on an
 oceanic island with black, yellow,
 and intermediate-coloured E. p. simodaesnails, capturing
 and marking approximately
 1,800 individual snail
 and monitoring their survival over 18 months.
 We quantified their shell colours
 against images and examined the frequency distribution of shell
 colour variation. The variation exhibited a
 bimodal distribution with a far lower frequency of
 intermediate-coloured snails than of black oryellow snails. The
 population sizes of the three snail
 groups fluctuated synchronously with the changing
 seasons.
 Bayesian estimates showed lower survival rates for the juvenile intermediate-coloured snails than for juvenile black and yellow snails, implying there was disruptive selection associated with shell colour. We suggest this disruptive selection may have resulted in the evolutionary divergence of the snail’s shell colour within the lineage having high shell colour variations.
DOI: 10.5061/dryad.b5mkkwh89
title: Data from: Tracking ice phenology by migratory waterbirds: settling phenology and breeding success of species with divergent population trends

description: Dependence on climate-driven environmental cues in the initiation of life
 cycle stages is a critical attribute when assessing vulnerability of
 species to climate change impacts. This study focused on spring ice
 phenology as a cue to the settling of migratory waterbirds, asking whether
 there is an asynchrony between ice phenology and setting phenology that
 could affect breeding success of six species with divergent population
 trends. In the 37 study lakes in southeastern Finland, the ice-out date
 not only varied considerably between years, but became progressively
 earlier during the study period, 1991–2018. Settling phenology of all
 species tracked inter-annual variation in ice phenology. However, the
 degree of asynchrony between ice phenology and settling phenology varied
 between species, allowing discrimination between early and late settlers.
 Considerable inter-annual variation also occurred within species, but in
 only one species did the degree of asynchrony correlate with the ice-out
 date: for the horned grebe Podiceps auritus an earlier ice-out date meant
 greater asynchrony between settling phenology and ice phenology. The
 degree of asynchrony between settling phenology and ice phenology did not
 affect breeding success in any species. However, ice phenology per se
 affected breeding success of horned grebes: earlier ice-out was associated
 with lower annual breeding success. Breeding numbers of horned grebe
 showed a long-term decline. Results suggest that short-distance migratory
 birds are able to respond to climate change-driven phenological changes in
 their breeding environments, and that this ability may not depend on the
 relative timing of breeding.
description: For variable abbreviations, see the article.
DOI: 10.5061/dryad.c59zw3r3h
title: Cross-activity of honeybee queen pheromones in bumblebees provides evidence for sensory exploitation

description: The evolutionary origin of queen pheromones, which regulate reproductive
 division of labor in insect societies, has been explained by two
 evolutionary scenarios: the sender-precursor hypothesis and the sensory
 exploitation hypothesis. These scenarios differ in terms of whether the
 signaling system was built on preadaptations on the part of either the
 sender queens or the receiver workers. While some social insect queen
 pheromones – such as cuticular hydrocarbons – were likely derived from
 ancestral fertility cues and evolved according to the former theory, the
 honeybee’s queen mandibular pheromone (QMP) has been suggested to act
 directly on pre-existing gene-regulatory networks linked with
 reproduction. This is evidenced by the fact that QMP has been shown to
 also inhibit ovary activation in fruit flies, thereby implying
 exploitation of conserved physiological pathways. To verify whether QMP
 has similar effects on more closely related eusocial species, we here
 tested for QMP cross-activity in the bumblebee Bombus terrestris.
 Interestingly, we found that the non-native QMP blend significantly
 inhibited egg-laying in both worker and queen bumblebees and caused
 accompanying shifts in ovary activation. The native bumblebee queen
 pheromone pentacosane, by contrast, only inhibited the reproduction of the
 workers. Overall, these findings support the hypothesis that honeybee QMP
 likely evolved via a route of sensory exploitation. We argue that such
 exploitation could allow social insect queens to produce compounds that
 manipulate the workers to remain sterile, but that a major hurdle would be
 that the queens themselves would have to be immune to such compounds.
DOI: 10.6086/d10m3d
title: PTV VISSIM simulation data for efficient eco-ramp control project funded by NCST 18-19

description: Our current transportation system faces a variety of issues in terms of
 safety, mobility, and environmental sustainability. The emergence of
 innovative intelligent transportation system (ITS) technologies such as
 connected and automated vehicles (CAVs) and transportation electrification
 unfold unprecedented opportunities to address aforementioned issues. In
 this project, we propose a hierarchical ramp control system that
 not only allows microscopic cooperative maneuvers for connected and
 automated electric vehicles (CAEVs) on the ramp to merge into mainline
 traffic flow under certain controlled ramp inflow rate,  but
 also enables macroscopic corridor-level traffic flow control
 (i.e., coordinated ramp metering rate determination). A centralized
 optimal control-based approach is proposed to both smooth the merging flow
 and improve the system-wide mobility of the network. Linear quadratic
 trackers in both finite horizon and receding horizon forms are developed
 to solve the optimization problem in terms of path planning and sequence
 determination, and a microscopic electric vehicle (EV) energy consumption
 model is applied to estimate the energy consumption. Finally, traffic
 simulation is conducted through PTV VISSIM to evaluate the impact of the
 proposed system on a highway segment. The results confirm that under the
 regulated inflow rate, the proposed system can avoid potential traffic
 congestion and improve mobility significantly up to 102% compared to the
 conventional ramp metering and the ramp without any control approach.
DOI: 10.5061/dryad.9cnp5hqdc
title: Data from: Sampling effects drive the species-area relationship in lake zooplankton

description: The Island Species-Area relationship (ISAR) describes how the numbers of
 species increases with increasing size of an island (or island-like
 habitat, such as lakes), and is one of the oldest laws in ecology. Despite
 its conceptual importance, there remains a great deal of ambiguity
 regarding the ISAR and its underlying processes. We compiled data from
 sampled zooplankton assemblages from several hundred lakes in North
 America and Europe to examine the influence of the three main hypothesized
 mechanisms leading to ISARs - passive sampling, disproportionate effects,
 and habitat heterogeneity. We compiled data on lake zooplankton
 assemblages that reported sample-level and lake level species richness
 estimates, as well as relative abundance data. In both North American and
 European lakes, we found a consistent and strong increase in total species
 richness with increasing lake area. However, when we compared the number
 of species standardized by number of individuals, there was no
 relationship between lake area and sample-level species richness or an
 estimate of species relative abundances, calculated as the Probability of
 Interspecific Encounter (PIE; a measure of evenness). This was true even
 when multiple samples were taken across lakes and combined, reducing the
 likelihood that habitat heterogeneity was driving the results. Overall,
 our results suggest that the ISAR of zooplankton in these lakes was most
 likely determined by sampling effects rather than disproportionate effects
 or habitat heterogeneity leading to more species in larger lakes.
 Understanding the mechanisms driving ISAR results such as ours can also
 help us develop predictions for biodiversity change when the area of these
 habitats changes. 
description: <b id="docs-internal-guid-bce1e8ab-7fff-7783-9e68-473fe5da6a08">We searched the literature for studies on freshwater zooplankton having abundance and/or richness data in European and North American lakes using Google Scholar and a variety of open access online databases (e.g., Dryad, FigShare, LTER) with the following keywords: “zooplankton”, “abundance”, “richness”, “species”, “freshwater”, and “lakes”. The list of datasets used as well as their references is included in the file "dataset_references". The main file "</b><b>all_data_diversity_metrics" contains the different biodiversity metrics calculated (i.e., rarefied richness, S<sub>n</sub> and a measure of evenness, S<sub>PIE</sub>) as well as the corresponding lake areas (given in hectares, ha). </b>
description: Variables in "all_data_diversity_metrics":
 study_id : Unique ID given to datasets
 lake_name : Name of different lakes Continent
 : either North America or Europe total_sample :
 "Total " for lakes with total species richness and
 "Sample" for lakes that had sample data
 lake_area : Area of lakes given in hectares (ha)
 S_PIE : Measure of evenness  S_total : Total
 species richness in lakes S_n : Rarefied species
 richness
DOI: 10.15468/dl.f7zkea
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Poland",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Trichorhina tomentosa, Armadillidium arcangelii, Porcellio dilatatus)"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001963-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k0p2ngf42
title: Cryo-EM Structure of Actin Filaments from Zea mays Pollen

description: Actins are among the most abundant and conserved proteins
 in eukaryotic cells, where they form filamentous structures that
 perform vital roles in key cellular processes. Although large amounts of
 data on the biochemical activities, dynamic behaviors, and important
 cellular functions of plant actin filaments have accumulated,
 their structural basis is elusive. Here, we report a 3.9 Å
 structure of the plant actin filament (ZMPA) from Zea mays pollen using
 cryo-electron microscopy. The structure shows a right-handed,
 double-stranded (two strands running parallel to each other) and staggered
 architecture that is stabilized by intra- and interstrand interactions.
 While the overall structure resembles that of other actin filaments, its
 DNase I-binding loop (D-loop) bends further outward, adopting an open
 conformation similar to that of the jasplakinolide- or Beryllium fluoride
 (BeFx)-stabilized rabbit skeleton muscle actin (RSMA) filament.
 Single-molecule magnetic tweezer analysis revealed that the ZMPA
 filament can resist a greater stretching force than the RSMA filament.
 Overall, these data provide evidence that plant actin filaments have
 greater stability than animal actin filaments, which is important for
 their roles as tracks for long-distance vesicle and organelle
 transportation.
description: The structural data (Supplemental Movies 1 and 2) were from the
 structure of <em>Zea mays</em> pollen actin filaments that we
 determined by cryo-electron microscopy. These movies were made by Chimera
 software. The stretching data (Supplemental Movies 3, 4, 5 and 6) were
 from the single-molecular magnetic tweezer analysis of actin filaments in
 our study. These movies were made by Wondershare and MATLAB.
DOI: 10.13012/b2idb-8802487_v1
title: Data for "Increased fire occurrence benefits early oak regeneration in temperate deciduous forests in part by disrupting an invasive grass-fire feedback"

description: This dataset includes data from a study conducted in southern Illinois, USA, which was published in the Journal of Applied Ecology. The study investigated the interactive effects of fire history and invasion by the non-native grass Microstegium vimineum on fire intensity and oak regeneration in central hardwood forests. The dataset includes data on environmental conditions, historical fire occurrence, experimental fire intensity and fuel load, seedling and juvenile oak characteristics, Microstegium cover, and plot descriptions.
DOI: 10.5061/dryad.7d7wm37qw
title: Data from: Resilience to changes in lake trophic state: nutrient allocation into Daphnia resting eggs

description: During past decades, many lakes underwent drastic human-caused changes in
 trophic state with strong implications for population dynamics and food
 web processes. We investigated the influence of trophic state on nutrient
 allocation into Daphnia resting eggs. The production of
 resting eggs is an important survival strategy,
 allowing Daphnia to cope with unfavorable environmental
 conditions. Allocation of essential nutrients into resting eggs may
 crucially influence embryonic development and offspring survival and thus
 is of great ecological and evolutionary interest. The capacity
 of Daphnia to adjust the allocation of nutrients into
 resting eggs may depend on the dietary nutrient supply, which may vary
 with trophic state-related changes in the phytoplankton community
 composition. Resting eggs were isolated from sediment cores taken from
 Lake Constance, a large pre-alpine lake with a distinct eutrophication and
 re-oligotrophication history, and analysed for elemental (carbon, nitrogen
 and phosphorus) and biochemical (sterols and fatty acids) nutrients.
 Carbon allocation into Daphnia resting eggs continuously
 decreased over time, irrespective of changes in trophic state. The
 allocation of nitrogen into Daphnia resting eggs
 followed the changes in trophic state, i.e. nitrogen concentrations in
 resting eggs increased with eutrophication and decreased again with
 re-oligotrophication. The allocation of phosphorus, sterols and long-chain
 polyunsaturated fatty acids (PUFA), such as eicosapentaenoic acid (EPA),
 into Daphnia resting eggs did not change significantly
 over time. Changes in trophic state strikingly influenced all trophic
 levels in Lake Constance. However, nutrient allocation
 into Daphnia resting eggs was mostly resilient to
 changes in lake trophic state.