cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.724vn
title: Data from: Using ricelands to provide temporary shorebird habitat during migration

description: To help mitigate large wetland losses in California, The Nature
 Conservancy launched a dynamic conservation incentive program to create
 temporary wetland habitats in harvested and fallow rice fields for
 shorebirds migrating along the Pacific Flyway. Farmers were invited to
 participate in a reverse auction bidding process and winning bids were
 selected based on their cost and potential to provide high quality
 shorebird habitat. This was done in 2014 and 2015, for separate enrollment
 periods that overlapped with spring and fall migration, both before and
 after the traditional post-harvest flooding period. To assess the success
 of the program we monitored shorebird use of fields that were enrolled
 (treatments), and others that were subject to typical rice farm management
 (controls). To put these observations in context, we used satellites to
 simultaneously monitor the extent of shallow-water habitat across the
 ~215,000 hectares of ricelands in the area. Results showed that providing
 habitat during migration, when it is typically unavailable in rice fields,
 yielded the largest average shorebird densities ever reported for
 agriculture in the region. Treatment fields had significantly greater
 shorebird density, richness and diversity than control fields in both
 spring and fall (especially September – early October, and late March –
 early April), but in fall the difference was greater. Shorebird responses
 to habitat provisioning, and regional habitat conditions, were variable
 from year to year, and highly dynamic within a given season. Overall,
 shorebirds densities were found to be negatively related to the total
 amount of flooded habitat in the rice landscape. Factors that affected
 habitat availability included allocation schedules of water deliveries
 from reservoirs, and rainfall patterns, both of which were influenced by
 drought. Collectively, these results suggest that appropriately managed
 agricultural lands have great potential to provide high value habitat for
 shorebirds during times of habitat deficit, including migration, and that
 fall may be a particularly impactful time to create additional habitat.
 Migratory species face great challenges due to the climate change,
 conversion of historical stopover sites, and other factors, but dynamic
 conservation programs offer promise that, at least in certain instances,
 their needs can still be met.
description: DataS1Data file used for
 analyses of abundance, density, richness and diversity.AppendixS1Number of surveys and survey days during each week of monitoring in the four enrollment periods.
DOI: 10.5061/dryad.1619
title: Data from: Adaptation and plasticity of animal communication in fluctuating environments

description: Adaptations that facilitate the reception of long-range signals under
 challenging conditions are expected to generate signal diversity when
 species communicate in different habitats. While we have a general
 understanding of how individual communicating animals cope with conditions
 influencing signal detection, the extent to which plasticity and
 evolutionary changes in signal characteristics contribute to interspecific
 differences in signaling behavior is unclear. We quantified the visual
 displays of free-living lizards and environmental variables known to
 influence display detection for multiple species from two separate island
 radiations. We found evidence of both adaptive evolution and adaptive
 plasticity in display characteristics as a function of environmental
 conditions, but plasticity accounted for most of the observed differences
 in display behavior across species. At the same time, prominent
 differences between the two island radiations existed in aspects of
 signaling behavior, unrelated to the environment. Past evolutionary events
 have therefore played an important role in shaping the way lizards adjust
 their signals to challenges in present-day environments. In addition to
 showing how plasticity contributes to interspecific differences in
 communication signals, our findings suggest the vagaries of evolution can
 in itself lead to signal variation between species.
description: READMEOrdTJ-10-0073R2readme.txtOrdTJ-10-0073R2HBspeed.txtOrdTJ-10-0073R2DWspeed.txtOrdTJ-10-0073R2HBduration.txtOrdTJ-10-0073R2DPrepetition.txtOrdTJ-10-0073R2DWduration.txt
DOI: 10.5061/dryad.76gp5
title: Data from: Co-occurrence of related asexual, but not sexual, lineages suggests that reproductive interference limits coexistence

description: We used randomizations to analyse patterns of co-occurrence of sexual and
 apomictic (asexual) members of the North American Crepis agamic complex
 (Asteraceae). We expect strong asymmetry in reproductive interactions in
 Crepis: apomicts produce clonal seeds with no need for pollination and are
 not subject to reproductive interference from co-occurring relatives.
 However, because they still produce some viable pollen, apomicts can
 reduce reproductive success of nearby sexual relatives, potentially
 leading to eventual local exclusion of sexuals. Consistent with this,
 randomizations reveal that sexuals are over-represented in isolated sites,
 while apomicts freely co-occur. Incorporation of taxonomic and
 phylogenetic evidence indicates that this pattern is not driven by local
 origins of asexuals. Our evidence that patterns of local co-occurrence are
 structured by reproductive interference suggests an underappreciated role
 for these interactions in community assembly, and highlights the need for
 explicit tests of the relative contributions of ecological and
 reproductive interactions in generating patterns of limiting similarity.
description: Whitton et al Table
 S1This file includes
 details of the cytotype designations at each site, including genome size
 estimates, inferred ploidy and the details of how we coded each site in
 our randomizations.
DOI: 10.5061/dryad.rv0nv
title: Data from: Bacillus cereus AR156 activates defense responses to Pseudomonas syringae pv. tomato in Arabidopsis thaliana similarly to flg22

description: Bacillus cereus AR156 (AR156) is a plant growth promoting rhizobacterium
 capable of inducing systemic resistance to Pseudomonas syringae pv. tomato
 (Pst) in Arabidopsis thaliana (Arabidopsis). Here we show that when
 applied to Arabidopsis leaves, AR156 acted similarly to flg22, a typical
 pathogen-associated molecular pattern (PAMP), in initiating PAMP-triggered
 immunity (PTI). AR156-elicited PTI responses included phosphorylation of
 MPK3 and MPK6, induction of the expression of defense-related genes PR1,
 FRK1, WRKY22, and WRKY29; production of reactive oxygen species; and
 callose deposition. Pretreatment with AR156 still significantly reduced
 Pst multiplication and disease severity in NahG transgenic plants and
 mutants sid2-2, jar1, etr1, ein2, npr1, and fls2. This suggests that
 AR156-induced PTI responses require neither salicylic acid, jasmonic acid,
 and ethylene signaling; nor flagella receptor kinase FLS2, the receptor of
 flg22. On the other hand, AR156 and flg22 acted in concert to
 differentially regulate a number of AGO1-bound miRNAs that function to
 mediate PTI. A full-genome transcriptional profiling analysis indicated
 that AR156 and flg22 activated similar transcriptional programs,
 co-regulating the expression of 117 genes; their concerted regulation of
 16 genes was confirmed by real-time quantitative PCR analysis. These
 results suggest that AR156 activates basal defense responses to Pst in
 Arabidopsis similarly to flg22.
description: Supplementary Table
 1Transcriptional changes
 that are induced following treatment with AR156 or flg22 in Arabidopsis
 thaliana.Supplementary Table
 2List
 of 1302 differentially expressed genes(DEGs) in AR156 and flg22 treatments
 in Arabidopsis thaliana.Supplementary Table
 3Overview of all 15 KEGG
 pathwaysSupplementary Table
 4List
 of primers used in real-time PCR analysis.
DOI: 10.5061/dryad.bm770
title: Data from: Genetic mapping of molar size relations identifies inhibitory locus for third molars in mice

description: Molar size in Mammals shows considerable disparity and exhibits variation
 similar to that predicted by the Inhibitory Cascade model. The importance
 of such developmental systems in favoring evolutionary trajectories is
 also underlined by the fact that this model can predict macroevolutionary
 patterns. Using backcross mice, we mapped QTL for molar sizes controlling
 for their sequential development. Genetic controls for upper and lower
 molars appear somewhat similar, and regions containing genes implied in
 dental defects drive this variation. We mapped three relationship QTLs
 (rQTL) modifying the control of the mesial molars on the focal third
 molar. These regions overlap Shh, Sostdc1 and Fst genes, which have
 pervasive roles in development and should be buffered against new
 variation. It has theoretically been shown that rQTL produces new
 variation channeled in the direction of adaptive changes. Our results
 provide evidence that evolutionary/disease patterns of tooth size
 variation could result from such a non-random generating process.
description: cross_toothSizeR/qtl cross object with molar size and genetic data
DOI: 10.5061/dryad.kp36q
title: Data from: Male mate choice via cuticular hydrocarbon pheromones drives reproductive isolation between Drosophila species

description: Mate discrimination is a key mechanism restricting gene flow between
 species. While studied extensively with respect to female mate choice,
 mechanisms of male mate choice between species are far less studied. Thus,
 we have little knowledge of the relative frequency, importance, or overall
 contribution of male mate discrimination to reproductive isolation. In the
 present study, we estimated the relative contributions of male and female
 choice to reproductive isolation between Drosophila simulans and D.
 sechellia, and show that male mate discrimination accounts for the
 majority of the current isolation between these species. We further
 demonstrate that males discriminate based on female cuticular hydrocarbon
 pheromones, and collect evidence supporting the hypothesis that male mate
 discrimination may alleviate the costs associated with heterospecific
 courtship and mating. Our findings highlight the potentially significant
 contribution of male mate choice to the formation of reproductive
 isolating barriers, and thus the speciation process.
description: simsech_courtmateCourtship frequency, effort, and mating frequency data for heterospecific and conspecific pairings of D. simulans and D. sechellia males.Longevity_assayData for cost of male courtship assay for individual males, conspecific pairings, and heterospecific pairings. Data includes the % of vials displaying offspring each week.RItables_tarsiless-100000bootstraps100,000 bootstraps of the RI table calculations for pooled (table1), simulans males (Table S1), sechellia males (Table S2), and tarsi-less males (Figure 2).
DOI: 10.5061/dryad.8h05p
title: Data from: Lateralized feeding behavior is associated with asymmetrical neuroanatomy and lateralized gene expressions in the brain in scale-eating cichlid fish

description: Lateralized behavior (‘handedness’) is unusual, but consistently found
 across diverse animal lineages, including humans. It is thought to reflect
 brain anatomical and/or functional asymmetries, but its neuro-molecular
 mechanisms remain largely unknown. Lake Tanganyika scale-eating cichlid
 fish, Perissodus microlepis show pronounced asymmetry in their jaw
 morphology as well as handedness in feeding behavior – feeding scales
 preferentially only from one or the other side of their victims. This
 makes them an ideal model in which to investigate potential laterality in
 neuroanatomy and transcription in the brain in relation to behavioral
 handedness. After determining behavioral handedness in P. microlepis
 (preferred attack side), we estimated the volume of the hemispheres of
 brain regions and captured their gene expression profiles. Our analyses
 revealed that the degree of behavioral handedness is mirrored at the level
 of neuroanatomical asymmetry, particularly in the tectum opticum.
 Transcriptome analyses showed that different brain regions (tectum
 opticum, telencephalon, hypothalamus and cerebellum) display distinct
 expression patterns, potentially reflecting their developmental
 interrelationships. For numerous genes in each brain region, their extent
 of expression differences between hemispheres was found to be correlated
 with the degree of behavioral lateralization. Interestingly, the tectum
 opticum and telencephalon showed divergent biases on the direction of up-
 or down-regulation of the laterality candidate genes (e.g., grm2) in the
 hemispheres, highlighting the connection of handedness with gene
 expression profiles and the different roles of these brain regions. Hence,
 handedness in predation behavior may be caused by asymmetric size of brain
 hemispheres and also by lateralized gene expressions in the brain.
description: Lee_et_al_Perissodus_Expression_dataGene expression values of the data set used.
DOI: 10.5061/dryad.c3610
title: Data from: Demonstrating multiple benefits from periodically harvested fisheries closures

description: 1.Periodically harvested closures (PHCs) are one of the most common forms
 of fisheries management in Melanesia, demonstrating multiple objectives,
 including sustaining fish stocks and increasing catch efficiency to
 support small-scale fisheries. No studies have comprehensively assessed
 their ability to provide short-term fisheries benefits across the entire
 harvest regime. 2.We present a novel analytical framework to guide a
 meta-analysis and assist future research in conceptualizing and assessing
 the potential of PHCs to deliver benefits for multiple fisheries-related
 objectives. 3.Ten PHCs met our selection criteria and on average, they
 provided a 48% greater abundance and 92% greater biomass of targeted
 fishes compared with areas open to fishing prior to being harvested.
 4.This translated into tangible harvest benefits, with fishers removing
 21% of the abundance and 49% of the biomass within PHCs, resulting in few
 post-harvest protection benefits. 5.When PHCs are larger, closed for
 longer periods or well enforced, short-term fisheries benefits are
 improved. However, an increased availability of fish within PHCs leads to
 greater removal during harvests. 6.Synthesis and applications.
 Periodically harvested closures (PHCs) can provide short-term fisheries
 benefits. Use of the analytical framework presented here will assist in
 determining long term fisheries and conservation benefits. We recommend
 PHCs be closed to fishing for as long as possible, be as large as
 possible, that compliance be encouraged via community engagement and
 enforcement, and strict deadlines/goals for harvesting set to prevent
 overfishing.
description: Stereo Diver Operated
 Video DataStereo Diver Operated
 Video Data for the four villages, Natokalau, Nauouo, Ovalau and
 Kiobo.2013-10_Natokalau.PHC_stereoDOVs_ImagePtPair.zip
DOI: 10.5061/dryad.hc4bj
title: Data from: Control of proline accumulation under drought via a novel pathway comprising the histone methylase CAU1 and the transcription factor ANAC055

description: Proline plays a crucial role in the drought stress response in plants.
 However, there are still gaps in our knowledge about the molecular
 mechanisms that regulate proline metabolism under drought stress. Here, we
 report that the histone methylase encoded by CAU1, which is genetically
 upstream of P5CS1 (encoding the proline biosynthetic enzyme
 Δ1-pyrroline-5-carboxylate synthetase 1), plays a crucial role in
 proline-mediated drought tolerance. We determined that the transcript
 level of CAU1 decreased while that of ANAC055 (encoding a transcription
 factor) increased in wild-type Arabidopsis under drought stress. Further
 analyses showed that CAU1 bound to the promoter of ANAC055 and suppressed
 its expression via H4R3sme2-type histone methylation in the promoter
 region. Thus, under drought stress, a decreased level of CAU1 led to an
 increased transcript level of ANAC055, which induced the expression of
 P5CS1 and increased proline level independently of CAS. Drought tolerance
 and the level of proline were found to be decreased in the cau1 anac055
 double-mutant, while proline supplementation restored drought sensitivity
 in the anac055 mutant. Our results reveal the details of a novel pathway
 leading to drought tolerance mediated by CAU1.
description: Fig.
 S1Fig
 s1.tifFig.
 S2Fig
 s2.tifFig.
 S3Fig
 s3.tifSupplementary Table
 1Supplementary
 Table1.doc
DOI: 10.5061/dryad.gp78p
title: Data from: Influence of range position on locally adaptive gene-environment associations in Populus flowering time genes

description: Local adaptation is pervasive in forest trees, which are characterized by
 large effective population sizes spanning broad climatic gradients. In
 addition to having relatively contiguous populations, many species also
 form isolated populations along the rear edge of their range. These
 rear-edge populations may contain unique adaptive diversity reflecting a
 history of selection in marginal environments. Thus, discovering genomic
 regions conferring local adaptation in rear edge populations is a key
 priority for landscape genomics to ensure conservation of genetic
 resources under climate change. Here, we report on adaptive
 gene-environment associations in SNPs from 27 genes in the Populus
 flowering time gene network, analyzed on a range-wide collection of
 &gt;1000 balsam poplar trees, including dense sampling of the southern
 range edge. We use a combined approach of local adaptation scans to
 identify candidate SNPs, followed by modeling the compositional turnover
 of adaptive SNPs along multivariate climate gradients using Gradient
 Forests (GF). Flowering time candidate genes contained extensive evidence
 of climate adaptation, namely outlier population structure and
 gene-environment associations, along with allele frequency divergence
 between the core and edge of the range. GF showed strong allele frequency
 turnover along gradients of elevation and diurnal temperature variability,
 as well as threshold responses to summer temperature and precipitation,
 with turnover especially strong in edge populations that occur at high
 elevation but southerly latitudes. We discuss these results in light of
 how climate may disrupt locally adaptivegene-environment relationships,
 and suggest that rear edge populations hold climate-adaptive variants that
 should be targeted for conservation.
description: Keller_etal_2017_JoH_SNPdata_DRYADDiploid genotypes for 291 SNP loci identified from 27 flowering time genes. SNPs were genotyped using the Sequenom i-Plex assay on 1021 Populus balsamifera individuals, along with 12 individuals from other
DOI: 10.5061/dryad.90kp2
title: Data from: Accommodating temporary emigration in spatial distance sampling models

description: 1.Model-based distance sampling is commonly used to understand spatial
 variation in the density of wildlife species. The standard approach
 assumes that individuals are distributed uniformly and models spatial
 variation in density using plot-level effects. Thinned point process (TPP)
 models for surveys of unmarked populations (spatial distance sampling)
 better leverage the spatial information underlying individual encounters,
 and in the presence of within-plot variation in density, may explain a
 larger proportion of the spatial variation in density. However, existing
 spatial distance sampling approaches are conditioned on the assumption
 that all individuals are present and available for sampling. Temporary
 emigration of individuals can therefore result in biased estimates of
 abundance. 2.We extended spatial distance sampling models to accommodate
 temporary emigration (TPP model). Using simulations of a thinned
 inhomogeneous point process, we assessed the performance of the TPP model
 relative to the temporary emigration distance sampling (TEDS) model, which
 implies a uniform distribution of individuals. In addition, we compared
 inferences between TPP and TEDS models using data for two passerine
 species in Alaska. 3.Parameter estimates from the TPP model exhibited
 improved coverage probability and precision relative to the TEDS model
 including a 26% reduction in the coefficient of variation (CV) of the
 population size estimate. 4.In the applied example, the TEDS model
 indicated weak relationships between abundance and habitat covariates,
 whereas the TPP model indicated strong relationships for those same
 effects, suggesting that spatial distance sampling models can provide
 considerably stronger inference in the presence of within-plot variation
 in density. In addition, the CV of the population size estimates for the
 two passerine species were 32% and 4% smaller under the TPP model.
 5.Synthesis and applications. We expect our extension accommodating
 temporary emigration will be a critical specification for spatial distance
 sampling models, particularly for studies assessing changes in the
 distribution and abundance of highly mobile species including passerines.
description: ATSPCounts2spNDVI_200NDVI_250pcovariatesSAVSAppendix_S3
DOI: 10.5061/dryad.kr8t0
title: Data from: Accelerated degradation of polyetheretherketone and its composites in the deep sea

description: The performance of polymer composites in seawater under high hydrostatic
 pressure (typically few tens of MPa), for simulating exposures at great
 depths in seas and oceans, has been little studied. In this paper, PEEK
 and its composites reinforced by carbon fibers and glass fibers were
 prepared, respectively. And the seawater environments with different
 seawater hydrostatic pressure ranging from normal pressure to 40 MPa was
 simulated with special equipment, in which the seawater absorption and
 wear behaviors of PEEK and PEEK-based composites were examined in situ.
 The effects of seawater hydrostatic pressure on the mechanical properties,
 wear resistance and microstructure of PEEK and its composites were focused
 on. The results showed that seawater absorption of PEEK and its composites
 were greatly accelerated by increased hydrostatic pressure in the deep
 sea. And affected by seawater absorption, both for neat PEEK and
 composites, the degradation on mechanical properties, wear resistance and
 crystallinity were induced, the degree of which were increasingly serious
 with the hydrostatic pressure of seawater environment increasing. And
 there existed a good correlation in an identical form of exponential
 function between the wear rate and the seawater hydrostatic pressure.
 Moreover, the corresponding mechanisms of the effects of deep-sea
 hydrostatic pressure were also discussed.
description: Seawater uptake,
 mechanical strength, wear rate of PEEK composites in seawater under
 hydrostatic pressuredata.rar