cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3mn1t
title: Data from: Global and regional priorities for marine biodiversity protection

description: The ocean holds much of the planet's biodiversity, yet &lt; 4% of
 the ocean is within protected areas. On land, the protecting of areas with
 low biodiversity and under little threat, rather than biodiversity
 hotspots, is a well-known problem. Prudence suggests that we not repeat
 this pattern in the ocean. Here we assessed patterns of global marine
 biodiversity by evaluating the protections of 4352 species for which
 geographic ranges are known, and mapping priority areas using an index
 that considers species vulnerability, coverage by marine protected areas
 (MPAs), and human impacts. Species have, on average, only 3.6% of their
 range protected. Moreover, species of conservation concern (threatened,
 small-ranged, and data deficient) have less protection than species on
 average. Only 5 nations currently protect 10% or more of their exclusive
 economic zone (EEZ) as strict Marine Reserves (IUCN category I–IV) in
 accord with the 2020 Aichi Biodiversity Targets. One nation by itself,
 Australia, accounts for 65% of the global area of Marine Reserves. The
 Coral Triangle is the clear and dominant global priority for biodiversity,
 but we identify additional global and regional priorities in each ocean
 basin. As an example, we show that for the United States, the Marianas and
 Samoan Islands are the top marine conservation priorities. Despite recent
 advances, the world has yet to protect most of the area and species that
 need it. Where to protect those species, however, is increasingly clear.
description: Species list and
 protection attributesThe Excel table lists
 all species included in the analyses, their IUCN Red List status at the
 time of the analyses, the amount of their range overlapping with various
 IUCN categories of protected areas (category 7 indicates no IUCN category
 assigned), and the value of the priority index for the species. PA overlap
 area is in meters square.species_protection_data_dryad.xlsxGeoTIFF rasters of results in figuresRaster files are in TIFF format, LZW compressed, and georeferenced (datum WGS84). Rasters of biodiversity and priorities are in the World Eckert IV projection, which is equal area. Files should be compatible with any standard GIS software.GeoTIFFs_dryad.zip
DOI: 10.5061/dryad.ss035
title: Data from: Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones

description: Evolutionary and ecological consequences of hybridization between native
 and invasive species are notoriously complicated because patterns of
 selection acting on non-native alleles can vary throughout the genome and
 across environments. Rapid advances in genomics now make it feasible to
 assess locus-specific and genome-wide patterns of natural selection acting
 on invasive introgression within and among natural populations occupying
 diverse environments. We quantified genome-wide patterns of admixture
 across multiple independent hybrid zones of native westslope cutthroat
 trout and invasive rainbow trout, the world's most widely introduced
 fish, by genotyping 339 individuals from 21 populations using 9380
 species-diagnostic loci. A significantly greater proportion of the genome
 appeared to be under selection favouring native cutthroat trout (rather
 than rainbow trout), and this pattern was pervasive across the genome
 (detected on most chromosomes). Furthermore, selection against invasive
 alleles was consistent across populations and environments, even in those
 where rainbow trout were predicted to have a selective advantage (warm
 environments). These data corroborate field studies showing that hybrids
 between these species have lower fitness than the native taxa, and show
 that these fitness differences are due to selection favouring many native
 genes distributed widely throughout the genome.
description: RAD_genos_Kovach_etal_2016The attached .xls file contains genotypes for the 9380 putatively diagnostic SNPs used in Kovach et al. 2016. Each row is a different individual. The first column is is population of origin for each individual. The following columns are genotypes for each locus. Locus names designate genomic position within the rainbow trout reference genome (see Hand et al. 2016): chr_chromosome#; chrUn - are loci on unanchored scaffolds; the final number is an identifier. Some RAD contigs have multiple SNPs. NA is missing data. At each locus, a 0 is a homozygote for the westslope cutthroat trout alleles, a 1 is a heterozygote (one rainbow trout allele and one westslope cutthroat trout allele) and a 2 is a rainbow trout homozygote.
DOI: 10.5061/dryad.h3ts8
title: Data from: A new paradigm for biomonitoring: an example building on the Danish Stream Plant Index

description: Despite intensive efforts for more than a decade to develop Water
 Framework-compliant assessment systems, shortcomings continue to appear.
 In particular, the lack of reference conditions has hindered the
 development of assessment systems capturing the heart of the Water
 Framework Directive (WFD) – that ecological status should be set as the
 deviation from the natural, undisturbed condition. Recently, the Danish
 Stream Plant Index (DSPI) was developed. This system contrasts existing
 systems in that it builds on an expert interpretation of the normative
 definitions of ecological status classes in the WFD without taking
 pressure–impact relationships into account. Here, we substantiate the
 approach taken in the development of DSPI and examine whether the DSPI
 class decreases with increasing level of anthropogenic stress and,
 additionally, whether the deviation from the natural undisturbed condition
 increases with decreasing DSPI class sensu WFD using trait composition of
 plant assemblages from Danish streams around year 1900 as a reference. We
 furthermore examine the trait composition of the vegetation in sites
 classified into different DSPI status classes to explore whether
 predictable patterns exist that can be used to identify the ultimate
 cause(s) of failure to meet ecological goals and help guide the selection
 of appropriate mitigation measures. We observed that DSPI declined with
 several parameters indicative of environmental stress in Danish streams
 and, furthermore, that the deviation from the natural undisturbed
 condition regarding the trait composition of plant communities declined
 with increasing DSPI, implying that the trait composition of plant
 communities in the high DSPI status class was most similar to those
 occurring in Danish streams around year 1900. We also found that trait
 characteristics capable of disentangling important stressors in Danish
 streams varied consistently among sites classified into different DSPI
 classes. Based on our findings, we call for new thinking. We suggest that
 more effort should be directed at describing reference conditions and
 interpreting the normative definitions of good, moderate, poor and bad
 instead of focusing solely on developing assessment systems using
 pressure–impact frameworks. We find this particularly important with
 respect to streams as these are seldom impacted by only a single stressor.
description: Baattrup-Pedersen et
 al._DVPI_PHYS AND CHEM_MEE2016DVPI and physical and
 chemical dataBaattrup-Pedersen et
 al._DVPI_CWM_MEE2016DVPI and plant trait
 characteristics
DOI: 10.5061/dryad.5934k
title: Data from: Down-regulation of CXCL12/CXCR4 expression alleviates ischemia-reperfusion-induced inflammatory pain via inhibiting glial TLR4 activation in the spinal cord

description: Toll-like receptor 4 (TLR4) is important for the pathogenesis of
 inflammatory reactions and the promotion of pain processing after
 ischemia/reperfusion (IR) in spinal cord. Recently, C-X-C chemokine ligand
 12 (CXCL12) and its receptor, C-X-C chemokine receptor 4 (CXCR4), were
 demonstrated to be simultaneously critical for inflammatory reactions,
 thereby facilitating glial activation. However, whether CXCL12/CXCR4
 expression can contribute to IR-induced inflammatory pain via spinal TLR4
 remained unclear. A rat model was established by 8 min of aortic arch
 occlusion. The effects of CXCL12/CXCR4 expression and TLR4 activation on
 inflammatory hyperalgesia were investigated by pretreatments with
 CXCL12-neutralizing antibody, CXCR4 antagonist (AMD3100) and TLR4
 antagonist (TAK-242) for 5 consecutive days before surgery. The results
 indicated that IR induced significant and sustained inflammatory pain,
 observed as decreases in paw withdrawal threshold (PWT) and paw withdrawal
 latency (PWL), throughout the post-injury period. The increased levels of
 TLR4 and proinflammatory chemokine CXCL12, as well as its receptor, CXCR4,
 were closely correlated with the PWT and PWL trends. Double immunostaining
 further suggested that TLR4, which is mainly expressed on astrocytes and
 microglia, was closely co-localized with CXCL12 and CXCR4 in spinal dorsal
 horn. As expected, intrathecal pretreatment with the TLR4 antagonist,
 TAK-242 markedly ameliorated pain by inhibiting astrocytic and microglial
 activation, as shown by decreases in TLR4 immunoreactivity and the
 percentage of double-labeled cells. These protective effects were likely
 due in part to the reduced production of the downstream cytokines IL-1β
 and TNF-α, as well as for the recruitment of CXCL12 and CXCR4.
 Additionally, intrathecal pretreatment with CXCL12-neutralizing antibody
 and AMD3100 resulted in similar analgesic and anti-inflammatory effects as
 those receiving TAK-242 pretreatment. These results suggest that
 intrathecal blockade of CXCL12/CXCR4 expression may attenuate IR-induced
 pain sensation and the release of inflammatory cytokines by limiting glial
 TLR4 activation in spinal cord.
description: Hemodynamic monitoring
 and Physiologic ParametersSupporting
 Information10.8.docS1 Figfigure
DOI: 10.5061/dryad.h3680
title: Data from: Calcium dynamics regulating the timing of decision-making in C. elegans

description: Brains regulate behavioral responses with distinct timings. Here we
 investigate the cellular and molecular mechanisms underlying the timing of
 decision-making during olfactory navigation in Caenorhabditis elegans. We
 find that, based on subtle changes in odor concentrations, the animals
 appear to choose the appropriate migratory direction from multiple trials
 as a form of behavioral decision-making. Through optophysiological,
 mathematical and genetic analyses of neural activity under virtual odor
 gradients, we further find that odor concentration information is
 temporally integrated for a decision by a gradual increase in
 intracellular calcium concentration ([Ca2+]i), which occurs via L-type
 voltage-gated calcium channels in a pair of olfactory neurons. In
 contrast, for a reflex-like behavioral response, [Ca2+]i rapidly increases
 via multiple types of calcium channels in a pair of nociceptive neurons.
 Thus, the timing of neuronal responses is determined by cell
 type-dependent involvement of calcium channels, which may serve as a
 cellular basis for decision-making.
description: The data of 100 worms
 during odor avoidance behavior.The Excel sheets
 contains x and y positions (mm), the odor concentration at the position
 (micro-M) and the behavioral states (Run or Pirouette) of 100 animals
 during 121-720 s of the odor avoidance assay. This dataset was used in
 Figures 1 and 2.Tanimoto_100worms_v2.xlsx
DOI: 10.5061/dryad.631kf
title: Data from: Little white lies: pericarp color provides insights into the origins and evolution of Southeast Asian weedy rice

description: Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that
 infests rice fields and results in severe crop losses. Weed strains in
 different world regions appear to have originated multiple times from
 different domesticated and/or wild rice progenitors. In the case of
 Malaysian weedy rice, a multiple-origin model has been proposed based on
 neutral markers and analyses of domestication genes for hull color and
 seed shattering. Here we examined variation in pericarp (bran) color and
 its molecular basis to address how this trait evolved in Malaysian weeds
 and its possible role in weed adaptation. Functional alleles of the Rc
 gene confer proanthocyanidin pigmentation of the pericarp, a trait found
 in most wild and weedy Oryzas and associated with seed dormancy;
 nonfunctional rc alleles were strongly favored during rice domestication,
 and most cultivated varieties have non-pigmented pericarps. Phenotypic
 characterizations of 52 Malaysian weeds revealed that most strains are
 characterized by the pigmented pericarp; however, some weeds have white
 pericarps, suggesting close relationships to cultivated rice. Phylogenetic
 analyses indicate that the Rc haplotypes present in Malaysian weeds likely
 have at least three distinct origins: wild Oryza rufipogon, white-pericarp
 cultivated rice, and red-pericarp cultivated rice. These diverse origins
 contribute to high Rc nucleotide diversity in the Malaysian weeds.
 Comparison of Rc allelic distributions with other rice domestication genes
 suggests that functional Rc alleles may confer particular fitness benefits
 in weedy rice populations, for example, by conferring seed dormancy. This
 may promote functional Rc introgression from local wild Oryza populations.
description: Rc NEW filter data
 aligment used in contruct ML tree and TCS analysis but no subsitute Het by
 question mark FOR DYR submittionThe full alignment of Rc
 gene for constructing ML tree
DOI: 10.13120/fl5bmm
title: Gelatinous zooplankton validated sightings reported by avvistAPP users

description: Validated sightings reported by avvistAPP users. avvistAPP is a free citizen science tool that allows everyone to actively contribute to the monitoring of marine animals. Available both in Google and Apple app stores. App description: https://doi.org/10.13120/h127-9v54
DOI: 10.5061/dryad.j333r
title: Data from: Rodents: food or pests in Neolithic Orkney

description: Rodents have important effects on contemporary human societies, sometimes
 providing a source of food but more often as agricultural pests, or as
 vectors and reservoirs of disease. Skeletal remains of rodents are
 commonly found in archaeological assemblages from around the world,
 highlighting their potential importance to ancient human populations.
 However, there are few studies of the interactions between people and
 rodents at such sites and most of these are confined to locations where
 rodents have formed a part of the recent diet. Here we compare the
 accumulation pattern of rodent remains from four locations within and
 adjacent to the renowned Neolithic site of Skara Brae, Orkney, showing
 that those within the settlement itself were the result of deliberate
 human activity. The accumulation and nature of burnt bones, incorporated
 over an extended period within deposits of household waste, indicate that
 rodents were used as a nutritional resource and may have been the subject
 of early pest control. We, therefore, provide the first evidence for the
 exploitation or control of rodents by the Neolithic inhabitants of Europe.
description: MeasurementsMeasurements of rodent skeletal remainsMNE - Minimum number of skeletal elementsMinimum number of skeletal elements among rodent remains from each trench and contextMNE.xlsNISP - Number of individual specimensNumber of individual rodent specimens from each trench and contextNISP.xlsTable_S1For each trench and context: obtained minimum number of elements (MNE), minimum number of individuals (MNI) per species, expected MNE based on MNI, relative frequencies (abundance) based on obtained and expected MNE, mean frequencies and radiocarbon datingTable_S2-4Table S2 - Summary measurements of Orkney vole skeletal elements. Table S3 - Rodent skeletal element relative frequencies and long bone fragmentation. Table S4 - Skeletal fragmentation in contexts from each trench.
DOI: 10.5061/dryad.r4d09
title: Data from: Incomplete control and concessions explain mating skew in male chimpanzees

description: Sexual selection theory predicts that because male reproductive success in
 mammals is limited by access to females, males will attempt to defend
 access to mates and exclude rivals from mating. In mammals, dominance rank
 is correlated with male reproductive success; however, the highest-ranking
 (alpha) male rarely monopolizes reproduction completely. To explain why,
 incomplete control models propose that alpha males simply cannot control
 other males' access to mates. If true, then dominance rank should be
 a key factor influencing subordinate (non-alpha) male mating success.
 Alternatively, the concession model states that alpha males can prevent
 other males from gaining access to mates but posits that they concede
 matings to subordinates in exchange for social favours. This predicts that
 a male's grooming interactions with the alpha should mediate his
 access to females. We test these predictions using 36 years of data,
 encompassing the tenures of eight alpha male chimpanzees at Gombe National
 Park, Tanzania. Incomplete control models were most strongly supported. At
 a given copulation event, the probability that the alpha was the male that
 mated was negatively associated with the number of males and sexually
 receptive females in the party. Additionally, as the number of males
 increased, high dominance rank was associated with an increased likelihood
 that a particular non-alpha male mated. The concession model, however, was
 also supported. The amount of time a male spent grooming with the alpha
 was positively associated with his likelihood of mating when the alpha was
 present in the party. As grooming is a major affiliative component of male
 social relationships, our results suggest that social bonds with dominant
 individuals are leveraged for mating access, particularly in species in
 which males form coalitions.
description: R
 ScriptThe R script with all
 code and instructions for running the analyses. Requires the .RData
 image.Bray_Proceedings
 B_Analysis.RData Tables and Model
 OutputsThis is an .RData image
 with the data tables used in the statistical models. It also includes the
 model output objects. This is to be used alongside the R
 script.Bray_Proceedings
 B_Data.RData
DOI: 10.5061/dryad.t63mn
title: Data from: A geographical distribution database of the genus Dysdera in the Canary Islands (Araneae, Dysderidae)

description: The ground-dweller spider genus Dysdera shows very high species richness
 on the oceanic archipelago of the Canary Islands, providing one of the
 most outstanding examples of island radiation among spiders, only
 paralleled by Tetragnatha spiders on the Hawaiian archipelago. A
 georeferenced database of the 48 Dysdera species occurring in the Canary
 Islands was assembled to facilitate ongoing and future research on this
 remarkable lineage. All species are endemic to the archipelago except for
 the cosmopolitan Dysdera crocata. The dataset consists of 794
 distributional records documented from 1971 to 2015, each locality being
 represented only once per species. Distribution maps are provided for each
 species, along with basic diversity and distribution information. The
 database and geographical maps included in this article stand for the most
 updated, accurate and complete information on the distribution of the
 spider genus Dysdera in the Canary Islands.
description: Macías-Hernandez et al
 (2016), Zookeys, Species Distribution TableDistribution of each
 Dysdera species, indicating species name, locality, district, island, type
 of habitat, geographic coordinates, and altitude (m).Macías-Hernandez et al (2016),
 Zookeys, Species Distribution
 Table.xlsxMacías-Hernandez et al
 (2016), Zookeys, Species Distribution MapsDistributional map of
 each species of Dysdera (alphabetically ordered)Macías-Hernandez et al (2016),
 Zookeys, Species Distribution Maps.pdf
DOI: 10.5061/dryad.7t3t3
title: Data from: Fast-slow life history is correlated with individual differences in movements and prey selection in an aquatic predator in the wild

description: Fast and slow life histories are proposed to covary with consistent
 individual differences in behaviour, but little is known whether it holds
 in the wild, where individuals experience natural fluctuations of the
 environment. We investigated whether individual differences in behaviour,
 such as movement traits and prey selection, are linked to variation in
 life-history traits in Eurasian perch (Perca fluviatilis) in the wild.
 Using high-resolution acoustic telemetry, we collected the positional data
 of fish in a whole natural lake and estimated individual movement traits
 by fitting a two-state correlated random walk model. Prey selection was
 inferred from stable isotope analysis using scale samples. Life-history
 traits were estimated by fitting a biphasic growth model to an individual
 growth trajectory back-calculated from scale samples. Life-history traits
 were correlated with behavioural traits such as movements and prey
 selection. Individuals with higher reproductive effort were found to
 switch more frequently between active and inactive modes and show greater
 reliance on prey from pelagic pathways (indicated by lower δ13C). Further,
 individuals with faster juvenile growth were found to stay active for a
 longer time during the adult stage. Our results demonstrate the link
 between individual behavioural differences and fast–slow life-history
 traits under ecologically relevant conditions.
description: Movement of individual
 perch in November 2010Coordinates of
 individual perch recorded at every 3 minutes (15 - 28 November 2010). The
 columns are (1) unique individual ID, (2) x coordinate, (3) y coordinate,
 (4) day or night (0 or 1), (5) location-specific standard deviation of the
 measurement.november2010.txtMovement of individual perch in January 2011Coordinates of individual perch recorded at every 3 minutes (15 - 28 January 2011). The columns are (1) unique individual ID, (2) x coordinate, (3) y coordinate, (4) day or night (0 or 1), (5) location-specific standard deviation of the measurement.january2011.txt
DOI: 10.5061/dryad.3b426
title: Data from: Disintegrating the fly: a mutational perspective on phenotypic integration and covariation

description: The structure of environmentally induced phenotypic covariation can
 influence the effective strength and magnitude of natural selection. Yet
 our understanding of the factors that contribute to and influence the
 evolutionary lability of such covariation is poor. Most studies have
 either examined environmental variation without accounting for
 covariation, or examined phenotypic and genetic covariation without
 distinguishing the environmental component. In this study we examined the
 effect of mutational perturbations on different properties of
 environmental covariation, as well as mean shape. We use strains of
 Drosophila melanogaster bearing well-characterized mutations known to
 influence wing shape, as well as naturally-derived strains, all reared
 under carefully-controlled conditions and with the same genetic
 background. We find that mean shape changes more freely than the
 covariance structure, and that different properties of the covariance
 matrix change independently from each other. The perturbations affect
 matrix orientation more than they affect matrix eccentricity or total
 variance. Yet, mutational effects on matrix orientation do not cluster
 according to the developmental pathway that they target. These results
 suggest that it might be useful to consider a more general concept of
 ‘decanalization’, involving all aspects of variation and covariation.
description: Data and R
 codeRaw data, R code, and
 other information required to reproduce the analyses, figures, and tables
 in Haber and Dworkin 2016: "Dis-integrating the fly: A mutational
 perspective on phenotypic integration and
 covariation."intMutant_FruitFly_Evolution2016.zip