cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.866t1g1vx
title: Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement

description: Background During domestication and subsequent improvement, plants were
 subjected to intensive positive selection for desirable traits.
 Identification of selection targets is important with respect to the
 future targeted broadening of diversity in breeding programmes. Rye
 (Secale cereale L.) is a cereal that is closely related to wheat, and it
 is an important crop in Central, Eastern and Northern Europe. The aim of
 the study was (i) to identify diverse groups of rye accessions based on
 high-density, genome-wide analysis of genetic diversity within a set of
 478 rye accessions, covering a full spectrum of diversity within the
 genus, from wild accessions to inbred lines used in hybrid breeding, and
 (ii) to identify selective sweeps in the established groups of cultivated
 rye germplasm and putative candidate genes targeted by selection. Results
 Population structure and genetic diversity analyses based on high-quality
 SNP (DArTseq) markers revealed the presence of three complexes in the
 Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a
 relatively narrow diversity of S. sylvestre, very high diversity of S.
 strictum, and signatures of strong positive selection in S. vavilovii.
 Within cultivated ryes, we detected the presence of genetic clusters and
 the influence of improvement status on the clustering. Rye landraces
 represent a reservoir of variation for breeding, and especially a distinct
 group of landraces from Turkey should be of special interest as a source
 of untapped variation. Selective sweep detection in cultivated accessions
 identified 133 outlier positions within 13 sweep regions and 170 putative
 candidate genes related, among others, to response to various
 environmental stimuli (such as pathogens, drought, cold), plant fertility
 and reproduction (pollen sperm cell differentiation, pollen maturation,
 pollen tube growth), and plant growth and biomass production. Conclusions
 Our study provides valuable information for efficient management of rye
 germplasm collections, which can help to ensure proper safeguarding of
 their genetic potential and provides numerous novel candidate genes
 targeted by selection in cultivated rye for further functional
 characterisation and allelic diversity studies.
description: GBS genotyping (DArTseq) was
 performed at Diversity Array Technology Pty Ltd., Bruce ACT, Australia
 (http://diversityarrays.com) on DNA isolated from leaf tissue. Genome complexity reduction involved PstI-HpaII digestion. Two adaptors corresponding to two different restriction enzyme (RE) overhangs were used in ligation. The PstI-compatible adapter was designed to include Illumina flowcell attachment sequence, sequencing primer sequence and ‘‘staggered’’, varying length barcode region. Sequences generated from each lane were processed using proprietary DArT analytical pipelines.
description: Excel, text editor
DOI: 10.7910/dvn/p0d3nb
title: Replication Data for "White Americans’ “Loser” Perceptions and Redistributive Policy Preferences"

description: The enclosed files contain the data, outputs, and syntax file for the Research and Politics article titled "White Americans’ “Loser” Perceptions and Redistributive Policy Preferences"
DOI: 10.6086/d1sq4z
title: Cryptic behaviour and activity cycles of a small mammal keystone species revealed through accelerometry: a case study of Merriam’s kangaroo rats

description: Kangaroo rats are among the most abundant vertebrates in many terrestrial
 ecosystems in Western North America and are considered both keystone
 species and ecosystem engineers, providing linkages to other species as
 both consumers and resources. We developed an integrative miniaturized
 animal-borne accelerometry/radiotelemetry approach to quantify the cryptic
 behaviour and activity cycles of kangaroo rats. Our study highlights a
 method of attachment and retrieval for deploying accelerometers, a
 non-disruptive method of gathering observational validation datasets for
 acceleration data on free-ranging nocturnal small mammals, and a case
 study for analyzing how behavioural patterns relate to abiotic factors. We
 found that Merriam’s kangaroo rats are only active during later light
 phases of the night, show no reduction in activity or foraging associated
 with moonlight (indicating that kangaroo rats are actually more
 lunarphilic than lunarphobic) and increased foraging effort on more humid
 nights (most likely as a mechanism to avoid cutaneous water loss). Our
 work represents the first continuous detailed quantitative description of
 fine-scale behavioural activity budgets in kangaroo rats and lays out a
 general framework of how to use miniaturized biologging devices to examine
 behavioural responses of nocturnal small mammals to environmental factors.
description: We used these files to create our machine-learning models in the
 open-access software Accelerater.
DOI: 10.5061/dryad.s1rn8pkd9
title: Deep learning unmasks the ECG signature of Brugada Syndrome

description: One in ten cases of sudden cardiac death strikes without warning as the
 result of an inherited arrhythmic cardiomyopathy, such as Brugada
 Syndrome (BrS). Normal physiological variations often obscure visible
 signs of this and related life-threatening channelopathies in conventional
 electrocardiograms (ECGs). Sodium channel blockers can reveal
 previously hidden diagnostic ECG features, however, their use
 carries the risk of life-threatening proarrhythmic side effects. The
 absence of a non-invasive test places a grossly underestimated fraction of
 the population at risk of SCD. Here, we present a machine
 learning algorithm that extracts, aligns, and classifies ECG waveforms for
 the presence of BrS. This protocol, which succeeds without the
 use of a sodium channel blocker (88.4% accuracy, 0.934 AUC in validation),
 can aid clinicians everywhere to identify the presence of this
 potentially life-threatening heart disease more easily.
DOI: 10.5061/dryad.p2ngf1vwj
title: Data for: Early radial positional information in the cochlea is optimized by a precise linear BMP gradient and enhanced by SOX2

description: Positional information encoded in signaling molecules is essential for
 early patterning in the prosensory domain of the developing cochlea. The
 sensory epithelium, the organ of Corti, contains an exquisite repeating
 pattern of hair cells and supporting cells. This requires precision in the
 morphogen signals that set the initial radial compartment boundaries, but
 this has not been investigated. To measure gradient formation and
 morphogenetic precision in developing cochlea, we developed a quantitative
 image analysis procedure measuring SOX2 and pSMAD1/5/9 profiles in mouse
 embryos at embryonic day (E)12.5, E13.5, and E14.5. Intriguingly, we found
 that the pSMAD1/5/9 profile forms a linear gradient up to the medial ~75%
 of the PSD from the pSMAD1/5/9 peak in the lateral edge during E12.5 and
 E13.5. This is a surprising activity readout for a diffusive BMP4 ligand
 secreted from a tightly constrained lateral region since morphogens
 typically form exponential or power-law gradient shapes. This is
 meaningful for gradient interpretation because while linear profiles offer
 the theoretically highest information content and distributed precision
 for patterning, a linear morphogen gradient has not yet been observed.
 Furthermore, this is unique to the cochlear epithelium as the pSMAD1/5/9
 gradient is exponential in the surrounding mesenchyme. In addition to the
 information-optimized linear profile, we found that while pSMAD1/5/9 is
 stable during this timeframe, an accompanying gradient of SOX2 shifts
 dynamically. Last, through joint decoding maps of pSMAD1/5/9 and SOX2, we
 see that there is a high-fidelity mapping between signaling activity and
 position in the regions that will become Kölliker's organ and the
 organ of Corti. Mapping is ambiguous in the prosensory domain precursory
 to the outer sulcus. Altogether, this research provides new insights into
 the precision of early morphogenetic patterning cues in the radial cochlea
 prosensory domain.
DOI: 10.5061/dryad.9p8cz8wn3
title: Sirtuin3 ensures the metabolic plasticity of neurotransmission during glucose deprivation

description: Neurotransmission is an energetically expensive process that underlies
 cognition. During intense electrical activity or dietary restrictions,
 glucose levels in the brain plummet, forcing neurons to utilize
 alternative fuels. However, the molecular mechanisms of neuronal metabolic
 plasticity remain poorly understood. Here, we demonstrate that
 glucose-deprived neurons activate the CREB and PGC1α transcriptional
 program that induces the expression of the mitochondrial deacetylase
 Sirtuin 3 (Sirt3) both in vitro and in vivo. We show that Sirt3 localizes
 to axonal mitochondria and stimulates mitochondrial oxidative capacity in
 hippocampal nerve terminals. Sirt3 plays an essential role in sustaining
 synaptic transmission in the absence of glucose by powering the retrieval
 of synaptic vesicles after release. These results demonstrate that the
 transcriptional induction of Sirt3 ensures the metabolic plasticity of
 synaptic transmission.
description: We examined the transcriptional rewiring of neuronal metabolism
 during glucose deprivation by performing RNA sequencing on primary
 cultures of rat cortical neurons maintained in glucose-rich or
 glucose-depleted (and serum-free) media.
DOI: 10.5061/dryad.cc2fqz6bp
title: Mesopelagic fish reference specimen photographic library

description: Mesopelagic fishes are a crucial component of the world’s oceans in terms
 of their abundance, biomass, and ecosystem function. These fishes are
 important contributors to the biological carbon pump via their feeding and
 behaviors, whereby they facilitate the transfer of carbon from shallow
 waters to the deep sea. Several species undertake diel vertical migration,
 feeding in shallower waters at night and moving to deeper waters during
 the day. This process actively expedites the downward flux of carbon.
 However, carbon budgets and climate models require accurate information
 regarding the depth distributions and migration patterns of these fishes,
 and environmental DNA (eDNA) analyses can provide this information. Here,
 we utilize eDNA approaches, generating taxonomically-informative COI and
 12S reference barcodes for 80 species of mesopelagic fishes, which can be
 used to for species-level identification of eDNA sequences. Using these,
 along with a publicly available barcode database, we compare results from
 eDNA analysis with traditional net sampling and explore the ability of
 eDNA techniques to detect diel vertical migration in fishes from samples
 collected in Northwest Atlantic Slope Water. We found that eDNA and net
 samples often resulted in different species identifications, demonstrating
 that eDNA can detect species that would otherwise be missed with
 traditional methods. In our eDNA samples, we also detected more species
 (12) in our shallowest depth category (0–100 m) from nighttime samples
 than from daytime samples (3). This is consistent with increased diversity
 in shallow waters at night due to diel vertical migration. Based on the
 variability observed in sample duplicates, we suggest that future
 mesopelagic eDNA studies incorporate larger sample volumes and scaled-up
 sampling efforts. We also note the potential for eDNA analysis to address
 ecological questions such as predator-prey relationships and
 identification of foraging hotspots, yielding insights into carbon flow
 through the ocean’s midwaters.
description: The data are photographs of mesopelagic fish specimens that were
 used to obtain COI and 12S DNA barcodes. The barcodes have been deposited
 in GenBank and the GenBank accession numbers are provided in a
 supplementary metadata file. The file name includes the
 fish species and the source identification numbers, which are also
 provided in the associated manuscript supplementary data, as well as in
 the GenBank records.
description: The images are .jpg files that can be opened with any standard
 image software.
DOI: 10.5061/dryad.bvq83bkfd
title: Low genetic diversity and shallow population structure in the broom hare, Lepus castroviejoi (Lagomorpha:Leporidae)

description: Microsatellite dataset of 322 hare samples from five species: 76 samples
 from the broom hare (Lepus castroviejoi);  81 for the European
 hare (L. europaeus); 68 for the Iberian hare (L. granatensis); 77 for the
 mountain hare (L. timidus); and 20 for the Italian hare (L. corsicanus).
description: For the broom hare
 (<em>Lepus castroviejoi</em>), a total of 54 consensus
 genotypes were obtained from 185 genetic
 non-invasive samples
 (gNIS) (i.e.,
 feces)
 collected between 2019 and 2021 across
 the entire species distribution range
 in the
 Cantabrian mountains
 (Spain). In addition to the
 gNIS, 22 specimens
 were collected from hunting and
 road-kills, in
 an opportunistic
 manner and
 with no special
 regard
 for the locality of the specimens,
 between 2003 and
 2007.  Samples from
 populations of
 the European hare (<em>L.
 europaeus</em>), mountain
 hare (<em>L. timidus</em>), Iberian hare (<em>L.
 granatensis</em>) and Italian hare
 (<em>L. corsicanus</em>) from the
 CIBIO-InBIO tissue bank to accurately
 were collected between 2002 and 2020 in the
 scope of previous studies, with help of researchers and
 collaborators. The sampled populations were: Alava
 (EUR1,
 n=20),
 Germany (EUR2,
 n=15),
 Austria (EUR3,
 n=19) and Northeast Spain
 (EUR4,
 n=27) for the European
 hare (n=81 in total); Southern Spain
 (GRA1,
 n=15),
 Pancas
 (GRA2,
 n=29) and
 Soria (GRA3,
 n=24) for the Iberian
 hare (n=68 in total); Sweden (TIM1,
 n=20) and
 Switzerland (TIM2,
 n=57) for the
 mountain hare (n=77
 in
 total); and mainland
 Italy for the Italian hare (COR1,
 n=20). 
description: Microsoft Excel or similar.
DOI: 10.5061/dryad.7sqv9s4xc
title: A nationwide collapse of a priority grassland bird related to livestock conversion and intensification

description: Grassland birds are among the most threatened and fastest declining
 terrestrial vertebrate species in Europe, principally due to agricultural
 intensification and transformation. The little bustard is a priority
 grassland bird under the European Directive (2009/147/CE) that led to the
 classification of a network of Special Protected Areas (SPAs) in Portugal.
 A third national survey carried out in 2022 reveals a worsening of an
 ongoing population collapse at a national scale. The population declined
 by 77% and 56% compared to the previous surveys in 2006 and 2016,
 respectively. We found that the little bustard has greatly disappeared
 outside SPAs, while the remaining breeding population concentrated within
 the protected area network is showing a steep decline rate of 9% a year.
 This decline is now twice as fast when compared to the period 2006-2016.
 Analysis of the variation of the breeding densities between 2006 and 2022
 at 49 survey sites revealed that those that initially had higher bustard
 densities and shifted toward a higher proportion of cattle among the total
 stocking rate experienced steeper declines. Areas where the density of
 roads increased also experienced declines over the course of the study
 period. Agricultural areas converted to or dominated by beef production
 likely relate to low breeding success and mortality of nesting females in
 fodder crops. Still, major habitat conversion outside SPAs to permanent
 crops led to overall habitat destruction, which contributed to the species
 decline and range contraction. Other threats are likely acting
 synergistically such as fragmentation, climate change and anthropogenic
 mortality. The extinction of the little bustard in Portugal is expected in
 the short term if no conservation actions are put in place.
description: The data collection protocol is described in the methods section
 of the manuscript.
DOI: 10.5061/dryad.ncjsxkt0x
title: Woodland wildfire enables fungal colonization of encroaching Douglas-fir

description: Self-reinforcing differences in fire frequency help closed-canopy forests,
 which resist fire, and open woodlands, which naturally burn often, to
 co-occur stably at landscape scales. Forest tree seedlings, which could
 otherwise encroach and overgrow woodlands, are killed by regular fire, yet
 fire has other effects that may also influence these feedbacks. In
 particular, many forest trees require symbiotic ectomycorrhizal fungi in
 order to establish. By restructuring soil fungal communities, fire might
 affect the availability of symbionts or the potential for symbiont sharing
 between encroaching trees and woodland vegetation. To investigate this
 possibility, we performed a soil bioassay experiment using inoculum from
 burned and unburned oak woodlands and Douglas-fir forests. We examined how
 fire, ecosystem type, and neighboring heterospecific seedlings affect
 fungal root community assembly of Douglas-firs and oaks. We asked whether
 heterospecific seedlings facilitated fungal colonization of seedling roots
 in non-native soil, and if so, whether fire influenced this interaction.
 External fungal colonization of oak roots was more influenced by fire and
 ecosystem type than by the presence of a Douglas-fir, and oaks increased
 the likelihood that Douglas-fir roots would be colonized by fungi in oak
 woodland soil. Yet fire increased colonization of Douglas-fir in oak soil,
 diminishing the otherwise crucial role played by oak facilitation. Fire
 also strengthened the positive effect of Douglas-firs on oak
 root-associated fungal diversity in Douglas-fir forest soil. Prior work
 shows that fire supports woodland ecosystems by stemming recruitment of
 encroaching seedlings. Here, we find evidence that it may contrastingly
 reduce fungal limitation of invasive seedling growth and establishment,
 otherwise relieved only by facilitation. Future work can investigate how
 these opposing effects might contribute to the net impact of changes in
 fire regime on landcover stability.
DOI: 10.5061/dryad.rv15dv4cx
title: The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems

description: Circadian clocks are pervasive throughout nature, yet only recently has
 this adaptive regulatory program been described in non-photosynthetic
 bacteria. Here, we describe an inherent complexity in the Bacillus
 subtilis circadian clock. We find that B. subtilis entrains to blue and
 red light and that circadian entrainment is separable from masking through
 fluence titration and frequency demultiplication protocols. We identify
 circadian rhythmicity in constant light, consistent with Aschoff’s Rule,
 and entrainment aftereffects, both of which are properties described for
 eukaryotic circadian clocks. We report that circadian rhythms occur in
 wild isolates of this prokaryote, thus establishing them as a general
 property of this species, and that its circadian system responds to the
 environment in a complex fashion that is consistent with multicellular
 eukaryotic circadian systems.
description: Luminometry datasets White, 96-well plates (Nunclon
 Delta, Thermo Fisher Scientific) were used, with each well inoculated with
 5 × 10<sup>5</sup> cells. Plates were sealed with a
 transparent, evaporation-free cover (Optical Adhesive Covers, Applied
 Biosystems, Life Technologies). Cultures were exposed to light-darkness
 cycles as indicated in the manuscript, after which the cultures were
 released to constant conditions (either constant darkness or light). The
 temperature was kept constant at 27 °C. We measured bioluminescence
 (Berthold Centro LB960 XS3 or Berthold Mithras LB 940 Multimode Plate
 Reader) for 1 s each hour. All experiments were carried out in
 temperature-controlled incubators (MIR-154, Panasonic, Japan or Percival
 Intellus, Percival, USA). In entrainment experiments, the plates were
 ejected from the machine between readings for exposure to
 light. Datasets uploaded correspond to
 unprocessed, raw data. Luminometry data have been collected every hour and
 data analysis has been performed on detrended, normalised data as
 described in the manuscript. 
description: Data uploaded are in XLSX format.
DOI: 10.5061/dryad.v41ns1s25
title: Mismatches between phenotype and environment shape fitness at hyperlocal scales (Agama atra)

description: In the era of human-driven climate change, understanding whether
 behavioural buffering of temperature change is linked with organismal
 fitness is essential. According to the “cost-benefit” model of
 thermoregulation, animals that live in environments with high frequencies
 of favourable thermal microclimates should incur lower thermoregulatory
 costs, thermoregulate more efficiently and shunt the associated savings in
 time and energy towards other vital tasks such as feeding, territory
 defence, and mate acquisition, increasing fitness. Here, we explore how
 thermal landscapes at the scale of individual territories, physiological
 performance, and behaviour interact and shape fitness in the southern rock
 agama lizard (Agama atra). We integrated laboratory assays of whole
 organism performance with behavioural observations in the field,
 fine-scale estimates of environmental temperature, and paternity
 assignment of offspring to test whether fitness is predicted by territory
 thermal quality (i.e., the number of hours that operative temperatures in
 a territory fall within individual’s performance breadth). Male lizards
 that occupied territories of low thermal quality spent more time
 behaviourally compensating for suboptimal temperatures and displayed less.
 Further, display rate was positively associated with lizard fitness,
 suggesting that there is an opportunity cost to engaging in
 thermoregulatory behaviour that will increase as climate change
 progresses.
DOI: 10.25345/c5sq8qx35
title: MassIVE MSV000100617 - Mycosporine-like amino acid from the marine cyanobacterium Capilliphycus salinus ALCB114379
title: Lyophilized cyanobacterial biomass (5 mg; n=3) was extracted with 0.1% (v/v) formic acid and 0.2 mM ammonium formate (pH ~2.55), followed by cell disruption via sonication and bead beating. Extracts were clarified by centrifugation and PVDF filtration (0.45 um), spiked with acyclovir as an internal standard, and quantified for shinorine, porphyra-334, and palythine using external standards by LC ESI TQMS.