cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5hqbzkh3h
title: Data from: Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land

description: Stable isotope composition of plants and soil animals in abandoned arable
 land Dataset provides raw data on stable isotope composition of C and N of
 plants and soil meso- and macrofauna. Dominating animal groups were
 collected in arable fallow systems 3 and 14-16 years after
 abandonment. Animals were sampled from the rhizosphere of three plant
 species of different functional groups: a legume (Medicaco sativa), a
 non-legume herb (Taraxacum officinale) and a grass (Bromus sterilis). More
 information can be found in the associated paper.
description: Soil fauna was collected using conventional method of heat
 extraction (Kempson). Fauna was collected non-quantitatively, targeting
 the rizosphere of the sertain plant species. Fauna was identified mostly
 to species or genus level. All dominating taxa were dried and analysed for
 stable isotope composition of carbon and nitrogen using IRMS at the
 Kompetenzzentrum Stabile Isotopen, University of Goettingen. Plant shoots
 and roots were collected, dried and milled before the stable isotope
 analysis.
description: Plant isotopic composition was used as the isotopic baseline in
 the study (shoots and roots).
DOI: 10.5061/dryad.h44j0zph0
title: Data from: Contrasting species decline but high sensitivity to increasing water stress on a mixed pine-oak ecotone

description: 1. Forest decline under environmental stress is expressed by regeneration
 failure and accelerated mortality in all ontogenic stages at the
 population level. Characterizing functional traits and mechanisms that
 best capture species decline and mortality is essential to assess forest
 dynamics. 2. We analyzed sensitivity to increasing water stress in two
 species with different water-use strategies on a mixed Quercus pyrenaica -
 Pinus sylvestris forest where adult pines express vulnerability to climate
 change but oaks do not. We compared dynamics of radial growth, wood δ13C
 and sapwood nonstructural carbohydrates (NSC) in response to drought at
 different time scales in both species and two age-cohorts in pine. 3. Both
 species were very sensitive to water stress, which influenced trait
 phenotypic plasticity at short- and long-time scales. Water-use strategy
 in pines of both ages was more conservative than in the more
 drought-tolerant oak. Both species showed negative growth trends despite
 increasing iWUE. Recent growth of pines is slower than it was in the past.
 Carbon isotope discrimination trends in young pines suggested increasing
 leaf gas exchange constraints. NSC were far from depletion in both species
 and all pine ages. Intra- and inter-annual NSC variability was higher in
 oaks than in pines and in soluble sugars (SS) than in starch. SS were
 lowest in young pines. Sensitivity of NSC to contrasting climatic years
 was low in pines, which NSC mostly remained homeostatic. The sensitivity
 to climate expressed suggests different C-allocation strategies, with less
 coupling between radial growth and current year photosynthesis in young
 pines. 4. Synthesis. Pines expressed negative responses to increased water
 stress regardless of age, showing rising gas-exchange constraints through
 tighter stomatal control of water losses than oaks. Young pines showed
 similar functional responses to water stress than old pines in decline,
 which suggests species-level vulnerability and could be regarded as
 early-warning signals anticipating mortality in pines. Yet, given the high
 sensitivity to drought also expressed by the non-declining oak, it would
 have been difficult to unequivocally disentangle species decline based
 only on the traits analysed.
DOI: 10.5061/dryad.c866t1g4f
title: Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)

description: Endangered species are grouped into genetically discrete populations to
 direct conservation efforts. Mitochondrial Control Region (mtCR)
 haplotypes are used to elucidate deep divergences between populations, as
 compared to nuclear microsatellites that can detect recent structuring.
 When prior populations are unknown, it is useful to subject microsatellite
 data to clustering and/or ordination population inference. Olive ridley
 sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet
 few studies have characterized olive ridley population structure.
 Recently, clustering results of olive ridleys in the Eastern Tropical
 Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and
 Central America. We analyzed mtCR haplotypes, new microsatellite genotypes
 from Costa Rica, and pre-existing microsatellite genotypes from olive
 ridleys across the Eastern Tropical Pacific, to further explore population
 structuring in this region. We subjected inferred populations to multiple
 analyses to explore the mechanisms behind their structuring. We found 10
 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but
 did not detect divergence between Costa Rican sites, or between Central
 America and Mexico. In Costa Rica, clustering suggested one population
 with no structuring, but ordination suggested four cryptic clusters with
 moderate structuring (FST=0.08, p&lt;0.001). Across the Eastern
 Tropical Pacific, ordination suggested nine cryptic clusters with moderate
 structuring (FST=0.103, p&lt;0.001) that largely corresponded to
 Mexican and Central American populations. All ordination clusters
 displayed significant internal relatedness relative to global relatedness
 (p&lt;0.001) and contained numerous sibling pairs. This suggests that
 broadly dispersed family lineages have proliferated in Eastern Tropical
 Pacific olive ridleys and corroborates previous work showing basin-wide
 connectivity and shallow population structure in this region. The
 existence of broadly dispersed kin in Eastern Tropical Pacific olive
 ridleys has implications for management of olive ridleys in this region,
 and adds to our understanding of sea turtle ecology and life-history,
 particularly in light of the natal-homing paradigm.
description: Sampling, PCR, and genotyping as described in Silver-Gorges et
 al. 2020.
description: This dataset contains all 8 loci genotyped for Costa Rican olive
 ridleys. Three loci (OR7, OR16, OR22) appear to be in linkage
 disequilibrium, and OR7 and OR22 were excluded from analyses in the
 publication. Data are formatted for population analysis in GenAlex.
 Populations are as follows: P1=Playa Grande, P2=Playa Ostional Arribada,
 P3=Playa Ostional Solitary, and P4=Playa Nancite Arribada.
DOI: 10.5061/dryad.q573n5tg8
title: Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies

description: For social animals, the genotypes of group members affect the social
 environment, and thus individual behavior, often indirectly. We used
 genome-wide association studies (GWAS) to determine the influence of
 individual vs. group genotypes on aggression in honey bees. Aggression in
 honey bees arises from the coordinated actions of colony members,
 primarily nonreproductive “soldier” bees, and thus, experiences
 evolutionary selection at the colony level. Here, we show that individual
 behavior is influenced by colony environment, which in turn, is shaped by
 allele frequency within colonies. Using a population with a range of
 aggression, we sequenced individual whole genomes and looked for
 genotype–behavior associations within colonies in a common environment.
 There were no significant correlations between individual aggression and
 specific alleles. By contrast, we found strong correlations between colony
 aggression and the frequencies of specific alleles within colonies,
 despite a small number of colonies. Associations at the colony level were
 highly significant and were very similar among both soldiers and foragers,
 but they covaried with one another. One strongly significant association
 peak, containing an ortholog of the Drosophila sensory gene dpr4 on
 linkage group (chromosome) 7, showed strong signals of both selection and
 admixture during the evolution of gentleness in a honey bee population. We
 thus found links between colony genetics and group behavior and also,
 molecular evidence for group-level selection, acting at the colony level.
 We conclude that group genetics dominates individual genetics in
 determining the fatal decision of honey bees to sting.
DOI: 10.5061/dryad.z34tmpg9q
title: Early Stuart sockeye salmon metapopulation data

description: There is a need to explicitly consider metapopulation dynamics in the
 development of conservation strategies for spatially-structured
 populations. We examined the spatial dynamics of sockeye salmon
 (Oncorhynchus nerka) that spawn in 36 streams of the Stuart River
 watershed in British Columbia, Canada, using a 69-year record of spawner
 abundance and a demographically-based Bayesian dynamic occupancy model. We
 identified a set of 12 streams with good habitat conditions that were
 occupied &gt;90% of years despite large year-to-year changes in
 abundance. Over 85% of spawners were concentrated in these streams. Many
 other streams with poorer habitat had small populations that were not
 persistent over time and were periodically recolonized by dispersers from
 other streams. Although it is often assumed population diversity and
 resiliency is maximized when all available habitats are used, for this
 salmon metapopulation, resiliency is due to the core streams of higher
 habitat quality. Currently other streams make only small contributions to
 population abundance, however, some may have conservation value if their
 habitats become more suitable for spawning in the future.
description: Data is comprised of observations of spawning salmon made by
 Fisheries and Oceans Canada. Details of the data collected are provided in
 the Supplement to Bradford and Braun.
description: See Readme file
DOI: 10.5061/dryad.7d7wm37s8
title: Data from: Snow-mediated plasticity does not prevent camouflage mismatch

description: Global reduction in snow cover duration is one of the most consistent and
 widespread climate change outcomes. Declining snow duration has severe
 negative consequences for diverse taxa including seasonally color molting
 species, which rely on snow for camouflage. However, phenotypic plasticity
 may facilitate adaptation to reduced snow duration. Plastic responses
 could occur in the color molt phenology or through behavior that minimizes
 coat color mismatch or its consequences. We quantified molt phenology of
 200 wild snowshoe hares (Lepus americanus), and measured microhabitat
 choice and local snow cover. Similar to other studies, we found that hares
 did not show behavioral plasticity to minimize coat color mismatch via
 background matching; instead they preferred colder, snow free areas
 regardless of their coat color. Furthermore, hares did not behaviorally
 mitigate the negative consequences of mismatch by choosing resting sites
 with denser vegetation cover when mismatched. Importantly, we demonstrated
 plasticity in the initiation and the rate of the molt and established the
 direct effect of snow on molt phenology; greater snow cover was associated
 with whiter hares and this association was not due to whiter hares
 preferring snowier areas. However, despite the observed snow-mediated
 plasticity in molt phenology, camouflage mismatch with white hares on
 brown snowless ground persisted and was more frequent during early
 snowmelt. Thus, we find no evidence that phenotypic plasticity in snowshoe
 hares is sufficient to facilitate adaptive rescue to camouflage mismatch
 under climate change.
description: Using VHF radio-telemetry, we tracked individual snowshoe hares
 and obtained locations during the fall brown-to-white and the spring
 white-to-brown molts. We followed a standardized protocol of visual
 observation and photography to estimate hare percent white: (0%, 5%, 20%,
 40%, 60%, 80%, 95%, and 100%) and snow cover at each hare location in 20%
 increments. At both available sites and sites used by hares we recorded
 snow cover, temperature and the total number of stems (&gt;1m tall and
 &gt;2.5 cm diameter at breast height).
description: See uploaded ReadME file.
DOI: 10.5061/dryad.q2bvq83gq
title: Potential short-term earthquake forecasting by farm animal monitoring

description: Whether changes in animal behavior allow for short-term earthquake
 predictions has been debated for a long time. Before, during and after the
 2016/2017 earthquake sequence in Italy, we deployed bio-logging tags to
 continuously observe the activity of farm animals (cows, dogs, sheep)
 close to the epicenter of the devastating magnitude M6.6 Norcia earthquake
 (Oct-Nov 2016) and over a subsequent longer observation period (Jan-Apr
 2017). Relating 5304 (in 2016) and 12948 (in 2017) earthquakes with a wide
 magnitude range (0.4 ≤ M ≤ 6.6) to continuously measured animal activity,
 we detected how the animals collectively reacted to earthquakes. We also
 found consistent anticipatory activity prior to earthquakes during times
 when the animals were in a building (stable), but not during their time on
 a pasture. We detected these anticipatory patterns not only in periods
 with high, but also in periods of low seismic activity. Earthquake
 anticipation times (1-20hrs) are negatively correlated with the distance
 between the farm and earthquake hypocenters. Our study suggests that
 continuous bio-logging of animal collectives has the potential to provide
 statistically reliable patterns of pre-seismic activity that could yield
 valuable insights for short-term earthquake forecasting. Based on a-priori
 model parameters we provide empirical threshold values for pre-seismic
 animal activities to be used in real-time observation stations.
description: We used 3D acceleration sensors to measure the activity of
 animals on a farrm (cows, dogs, and sheep). For each of the individuals of the
 three species, we computed the 15 min average of their ODBA
 (overall dynamic body acceleration), that is, the average acceleration and
 the average over all tagged animals of the respective species.
 
 Earthquake Data from the Nocia Region in Italy were collected from 17/01/2017 - 16/04/2017 Data are from INGV Rome, downloaded Sept 19, 2017 (by Laura Parise & Martin Mai, KAUST) Event specific parameters were computed by Martin Mai on Sept 20, 2017. Distances (in km) are calculated. with reference (= origin) to farm location: [LAT 43.0147, LON 13.0509, ELEV 0.580 km]
description: Please contact Prof. Martin Wikelski for further usage help,
 wikelski@ab.mpg.de
DOI: 10.5061/dryad.vdncjsxrb
title: Data from: Cell therapy for chronic TBI: interim analysis of the randomized, controlled, double-blind STEMTRA trial

description: Objective: To determine if chronic motor deficits secondary to traumatic
 brain injury (TBI) can be improved by implantation of allogeneic modified
 bone marrow-derived mesenchymal stromal/stem cells (SB623). Methods: This
 6-month interim analysis of the 1-year double-blind, randomized, surgical
 sham-controlled, Phase 2 STEMTRA trial (NCT02416492) evaluated safety and
 efficacy of the stereotactic intracranial implantation of SB623 in
 patients with stable chronic motor deficits secondary to TBI. Patients in
 this multi-center trial (N=63) underwent randomization in a 1:1:1:1 ratio
 to 2.5x106, 5.0x106, 10x106 SB623 cells or control. Safety was assessed in
 patients who underwent surgery (N=61), and efficacy in the modified
 intent-to-treat population of randomized patients who underwent surgery
 (N=61; SB623=46, control=15). Results: The primary efficacy endpoint of
 significant improvement from baseline of Fugl-Meyer Motor Scale score at 6
 months for SB623-treated patients was achieved. SB623-treated patients
 improved by (LS mean [SE]) +8.3 (1.4) versus +2.3 (2.5) for control at 6
 months, the LS mean difference was 6.0 (95% CI: 0.3-11.8); P=0.040.
 Secondary efficacy endpoints improved from baseline, but were not
 statistically significant versus control at 6 months. There were no
 dose-limiting toxicities or deaths, and 100% of SB623-treated patients
 experienced treatment-emergent adverse events versus 93.3% of control
 patients (P=0.25). Conclusions: SB623 cell implantation appeared to be
 safe and well tolerated, and patients implanted with SB623 experienced
 significant improvement from baseline motor status at 6 months compared to
 controls. Classification of Evidence: This study provides Class I evidence
 that implantation of SB623 was well tolerated and associated with
 improvement in motor status.
DOI: 10.5061/dryad.76hdr7sth
title: Vascular plant community data for Northwest Territories, Canada

description: Climate change is altering disturbance regimes outside of historical
 norms, which can impact biodiversity by selecting for plants with
 particular traits. The relative impact of disturbance characteristics on
 plant traits and community structure may be mediated by environmental
 gradients. We aimed to understand how wildfire impacted understory plant
 communities and plant regeneration strategies along gradients of
 environmental conditions and wildfire characteristics in boreal forests.
 We established 207 plots (60m2) in recently burned stands and 133 plots in
 mature stands with no recent fire history in comparable gradients of stand
 type, site moisture (drainage), and soil organic layer (SOL) depth in two
 ecozones in Canada’s Northwest Territories. At each plot, we recorded all
 vascular plant taxa in the understory and measured the regeneration
 strategy (seeder, resprouter, survivor) in burned plots, along with
 seedbed conditions (mineral soil and bryophyte cover). Dispersal,
 longevity, and growth form traits were determined for each taxon. Fire
 characteristics measured included proportion pre-fire SOL combusted (fire
 severity), date of burn (fire seasonality), and pre-fire stand age (time
 following fire). Results showed understory community composition was
 altered by fire. However, burned and mature stands had similar plant
 communities in wet sites with deep SOL. In the burned plots, regeneration
 strategies were determined by fire severity, drainage, and pre- and
 post-fire SOL depth. Resprouters were more common in wet sites with deeper
 SOL and lower fire severity, while seeders were associated with drier
 sites with thinner SOL and greater fire severity. This led to drier burned
 stands being compositionally different from their mature counterparts and
 seedbed conditions were important. Our study highlights the importance of
 environment-wildfire interactions in shaping plant regeneration strategies
 and patterns of understory plant community structure across landscapes,
 and the overriding importance of SOL depth and site drainage in mediating
 fire severity, plant regeneration, and community structure.  
description: 207 plots were established with 5, 1 by 1 m quadrats within which
 vegetation data was recorded one year after fire
description: Each data file has a metadata sheet
DOI: 10.5061/dryad.qjq2bvqd4
title: Capacity for freshwater acclimation and differences in the transcription of ion transporter genes underlying different migratory life histories of Takifugu fish

description: The genus Takifugu is a group of approximately 20 species of puffer fishes
 living in a wide range of salinity environments around East Asian
 countries. This group presents a broad spectrum of evolutionary stages
 adapted to anadromy as a result of speciation that occurred a short time
 (2–5 million years) ago on an evolutionary timescale. This group thus can
 be considered as a model for studying the evolutionary mechanisms of
 anadromy. We firstly conducted a transfer experiment from seawater to
 low-salinity waters on five Takifugu species: two anadromous species T.
 obscurus and T. ocellatus, two euryhaline wanderer marine species T.
 rubripes and T. niphobles, and a strictly marine species T. snyderi, and
 confirmed that the capacity for acclimation to hypotonic environments was
 associated with their life history strategies. Next, transcriptomes of the
 gill and intestine of these species in hypotonic condition were compared
 to those under hypertonic condition for each species using RNA-Sequencing
 so as to determine possible candidate transporters playing an important
 role on freshwater adaptation. As this analysis suggested that cftr,
 encoding an important ion transporter for seawater acclimation in the
 gill, and ncc, encoding a transporter that is suggested to play important
 osmoregulatory roles in the intestine, are important candidates, their
 expression was validated by quantitative real-time PCR analysis.
 Expression of cftr was downregulated in the gills of the four euryhaline
 species under the hypotonic condition, but no change was detected in the
 gill of stenohaline T. snyderi, which may be one reason for the poor
 hypotonic acclimation capacity of T. snyderi. Expression of ncc was
 clearly upregulated in the intestines of the two anadromous species under
 the hypotonic condition, but not in other three species. Different ion
 transporter expression patterns between the five species indicate that the
 transcriptional regulation of cftr in the gill and ncc in the intestine
 may be important for the improvement of hypotonic acclimation capacity and
 evolution of anadromy in the Takifugu species.
description: Unique gene reads in RNA-seq data were used for fold change
 analysis.
description: "cftr_qPCR_result" and "ncc_qPCR_result" are
 the expression data obtained by q-PCR. Other files are RNA-seq data. For
 these data,  tn stands for T.niphobles, ts stands for T. snyderi, tr
 stands for T. rubripes, tob stands for T.obscurus, toc stands for
 T.ocellaus. The rest of file name show the salinity and organs from
 which data was obtained from. For example, tr-sal1-inte_1 (paired) (GE) is
 the data obtained from intestine (inte) of T. rubripes (tr) under sal.1
 condition.