cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2s75n
title: Data from: A year in hypoxia: epibenthic community responses to severe oxygen deficit at a subsea observatory in a coastal inlet

description: Changes in ocean ventilation driven by climate change result in loss of
 oxygen in the open ocean that, in turn, affects coastal areas in upwelling
 zones such as the northeast Pacific. Saanich Inlet, on the west coast of
 Canada, is a natural seasonally hypoxic fjord where certain continental
 shelf species occur in extreme hypoxia. One study site on the VENUS cabled
 subsea network is located in the hypoxic zone at 104 m depth. Photographs
 of the same 5 m2 area were taken with a remotely-controlled still camera
 every 2/3 days between October 6th 2009 and October 18th 2010 and examined
 for community composition, species behaviour and microbial mat features.
 Instruments located on a near-by platform provided high-resolution
 measurements of environmental variables. We applied multivariate
 ordination methods and a principal coordinate analysis of neighbour
 matrices to determine temporal structures in our dataset. Responses to
 seasonal hypoxia (0.1–1.27 ml/l) and its high variability on short
 time-scale (hours) varied among species, and their life stages. During
 extreme hypoxia, microbial mats developed then disappeared as a hippolytid
 shrimp, Spirontocaris sica, appeared in high densities (200 m22) despite
 oxygen below 0.2 ml/l. The slender sole Lyopsetta exilis was abundant in
 severe hypoxia and diminished as oxygen increased in the summer. This
 planktivore may be responding to changes in the depth of the diurnal
 migration of zooplankton. While the squat lobster Munida quadrispina was
 common at all times, juveniles disappeared in fluctuating conditions.
 Despite low oxygen conditions, animal densities were high indicating that
 the risk from hypoxia is balanced by factors such as food availability and
 escape from less tolerant predators. As hypoxia increases on the
 continental shelf, we expect benthic communities to become dominated by
 low diversity, hypoxia-tolerant species of low commercial significance.
description: CHONe_MB08_Matabos_data_year
DOI: 10.5061/dryad.3rn6c
title: Data from: Gene flow between wolf and shepherd dog populations in Georgia (Caucasus)

description: We studied the distribution of the mitochondrial DNA haplotypes and
 microsatellite genotypes at eight loci in 102 grey wolves, 57 livestock
 guarding dogs, and 9 mongrel dogs from Georgia (Caucasus). Most of the
 studied dogs had mitochondrial haplotypes clustered with presumably East
 Asian dog lineages, and most of the studied wolves had the haplotypes
 clustered with European wolves, but 20% of wolves and 37% of dogs shared
 the same mitochondrial haplotypes. Bayesian inference with STRUCTURE
 software suggested that over 13% of the studied wolves had detectable dog
 ancestry and over 10% of the dogs had detectable wolf ancestry. 2-3% of
 the sampled wolves and dogs were identified, with a high probability, as
 first generation hybrids. These results were supported by the relatedness
 analysis which showed that 10% of wolves and 20% of dogs had closest
 relatives from an opposite group. The results of the study suggest that
 wolf-dog hybridization is a common event in the areas where large
 livestock guarding dogs are held in a traditional way, and that gene flow
 between dogs and grey wolves was an important force influencing gene pool
 of dogs for millennia since early domestication events. This process may
 have been terminated (1) in areas outside the natural range of grey wolves
 and (2) since very recent time, when humans started to more tightly
 control contacts of purebred dogs.
description: TabS2microsatellite genotypes
 (number of nucleotides per STR allele) for 167 individual wolves and dogs
 from Georgia (genotypes of wolves from the eastern and from the western
 Georgia shown separately). Microsoft Exel file, single
 spreadsheet.
DOI: 10.15468/dl.s5fnmc
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dielsiodoxa leucantha",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 86 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001274-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n3f4j
title: Data from: Establishment of a refined oral glucose tolerance test in pigs, and assessment of insulin, glucagon and glucagon-like peptide-1 responses

description: Diabetes mellitus is increasing worldwide and reliable animal models are
 important for progression of the research field. The pig is a commonly
 used large animal model in diabetes research and the present study aimed
 to refine a model for oral glucose tolerance test (OGTT) in young growing
 pigs, as well as describing intravenous glucose tolerance test (IVGTT) in
 the same age group. The refined porcine OGTT will reflect that used in
 children and adolescents. Eighteen pigs were obtained one week after
 weaning and trained for two weeks to bottle-feed glucose solution,
 mimicking the human OGTT. The pigs subsequently underwent OGTT (1.75 g/kg
 BW) and IVGTT (0.5 g/kg BW). Blood samples were collected from indwelling
 vein catheters for measurements of glucose and the diabetes related
 hormones insulin, glucagon and active glucagon-like peptide-1. The study
 confirmed that pigs can be trained to bottle-feed glucose dissolved in
 water and thereby undergo an OGTT more similar to the human standard OGTT
 than previously described methods in pigs. With the refined method for
 OGTT, oral intake only consists of glucose and water, which is an
 advantage over previously described methods in pigs where glucose is given
 together with feed which will affect glucose absorption. Patterns of
 hormonal secretion in response to oral and intravenous glucose were
 similar to those in humans; however, the pigs were more glucose tolerant
 with lower insulin levels than humans. In translational medicine, this
 refined OGTT and IVGTT methods provide important tools in diabetes
 research when pigs are used as models for children and adolescents in
 diabetes research.
description: glucose tolerance
 datadata_dryad.xlsx
DOI: 10.5061/dryad.j6h56qg
title: Data from: Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: a case study using the sea lamprey Petromyzon marinus L.

description: Many aquatic species of conservation concern exist at low densities and
 are inherently difficult to detect or monitor using conventional methods.
 However, the introduction of environmental (e)DNA has recently transformed
 our ability to detect these species and enables effective deployment of
 limited conservation resources. Identifying areas for breeding, as well as
 the ecological distribution of a species are vital to the survival or
 recovery of a conservation species (i.e. critical habitat). In many
 species, spawning events are associated with a higher relative abundance
 of DNA released within an aquatic system (i.e. gametes, skin cells etc.),
 making this the ideal time to monitor these species using eDNA techniques.
 This study aims to examine whether a ‘snapshot’ eDNA sampling approach
 (i.e. samples taken at fixed points in chronological time) could reveal
 areas of critical habitat including spawning sites for our target species
 Petromyzon marinus. We utilised a species-specific qPCR assay to monitor
 spatial and temporal patterns in eDNA concentration within two river
 catchments in Ireland over three consecutive years. We found that eDNA
 concentration increased at the onset of observed spawning activity and
 patterns of concentration increased from downstream to upstream over time,
 suggesting dispersal into the higher reaches as the spawning season
 progressed. We found P. marinus to be present upstream of several
 potential barriers to migration, sometimes in significant numbers. Out
 results also show that the addition of lamprey-specific fish-pass at an
 ‘impassable’ weir, although assisting in ascent, did not have any
 significant impact on eDNA concentration upstream after pass had been
 installed. eDNA concentration was also found to be significantly
 correlated with both the number of fish and the number of nests
 encountered. The application of snapshot sampling techniques for species
 monitoring therefore has substantial potential for the management of
 low-density species in fast-moving aquatic systems.
description: Mulkear eDNA (pg
 L)Environmental DNA
 'snapshot' concentrations (and sample site locations) for
 Petromyzon Marinus in the Mulkear catchment ( ireland). Shown as
 pg/L.Munster Blackwater eDNA
 (pg L)Environmental DNA
 'snapshot' concentrations (and sample site locations) for
 Petromyzon Marinus in the Munster Blackwater catchment ( Ireland). Shown
 as pg/L.
DOI: 10.5061/dryad.ns5hr
title: Data from: Long fusion correction of degenerative adult spinal deformity and the selection of the upper or lower thoracic region as the site of proximal instrumentation: a systematic review and meta-analysis

description: Objective: The aim of this study was to compare outcomes when the upper
 and lower thoracic regions were used as the site of proximal
 instrumentation to treat adult spinal deformity. Methods: Medline, Embase
 and Cochrane library searches were performed to identify studies that
 compared outcome measures when the upper and lower thoracic vertebrae (UTV
 and LTV, respectively) were used as the site of proximal instrumentation.
 The weighted mean difference (WMD) was calculated for continuous outcomes,
 and the relative risk (RR) was calculated for dichotomous outcomes.
 Results: Seven articles (n=554patients) met the final inclusion criteria,
 and we compared the outcome measures of a long fusion extending to the
 upper and lower thoracic regions. The pooled analysis revealed that
 extending fixation into the upper thoracic region decreased the risk of
 proximal junctional kyphosis (PJK) revision surgery (RR: 0.36, 95% CI:
 0.14 to 0.90; P&lt;0.05).The operation time (WMD: 0.93;95% CI: 0.48,
 1.39; P&lt;0.05) and estimated blood loss (WMD: 0.59;95% CI: 0.33,
 0.85; P&lt;0.05) were significantly greater in the UTV group than in
 the LTV group. No significant differences were found in the Scoliosis
 Research Society (SRS) pain, self-image, function, mental health,
 subtotal, satisfaction, or total scores; the total number of
 complications; or the total number of revision surgeries. Conclusion: Long
 posterior fixation extending into the upper thoracic region reduces the
 incidence of revision surgery related to PJK; however, it increased the
 operative level resulting in a longer operative time and greater estimated
 blood loss. This initial analysis indicates that extending fixation to the
 upper thoracic region is appropriate for patients who are likely to
 develop PJK following initial scoliosis correction.
description: The raw
 dataThe data from included
 studies
DOI: 10.5061/dryad.gc735
title: Data from: N/P imbalance as a key driver for the invasion of oligothrophic dune systems by a woody legume

description: Oligotrophic ecosystems, previously considered to be more resilient to
 invasive plants, are now recognised to be highly vulnerable to invasions.
 In these systems, woody legumes show belowground ecosystem engineering
 characteristics that enable invasion, however, the underlying processes
 are not well understood. Using a Portuguese primary dune ecosystem as an
 oligotrophic model system, belowground biomass pools, turnover rates and
 stoichiometry of a native (Stauracanthus spectabilis) and an invasive
 legume (Acacia longifolia) were compared and related to changes in the
 foliage of the surrounding native (Corema album) vegetation. We
 hypothesized that the invasive legume requires less phosphorus per unit of
 biomass produced and exhibits an enhanced nutrient turnover compared to
 the native vegetation, which could drive invasion by inducing a systemic
 N/P imbalance. Compared with the native legumes, A. longifolia plants had
 larger canopies, higher SOM levels and lower tissue P concentrations.
 These attributes were strongly related to legume influence as measured by
 increased foliar N content and less depleted δ15N signatures in the
 surrounding C. album vegetation. Furthermore, higher root N concentration
 and increased nutrient turnover in the rhizosphere of the invader were
 associated with depleted foliar P in C. album. Our results emphasize that
 while A. longifolia itself maintains an efficient phosphorus use in
 biomass production, at the same time it exerts a strong impact on the N/P
 balance of the native system. Moreover, this study highlights the
 engineering of a belowground structure of roots and rhizosphere as a
 crucial driver for invasion, due to its central role in nutrient turnover.
 These findings provide new evidence that, under nutrient-limited
 conditions, considering co-limitation and nutrient cycling in oligotrophic
 systems is essential to understand the engineering character of invasive
 woody legumes.
description: OIK-03810 Dryad
 FilesAll data used in the
 Manuscript as pure csv files, all with description and associated
 figure/table number.
DOI: 10.5061/dryad.c2v35
title: Data from: How predation shaped fish: the impact of fin spines on body form evolution across teleosts

description: It is well known that predators can induce morphological changes in some
 fish: individuals exposed to predation cues increase body depth and the
 length of spines. We hypothesize that these structures may evolve
 synergistically, as together, these traits will further enlarge the body
 dimensions of the fish that gape-limited predators must overcome. We
 therefore expect that the orientation of the spines will predict which
 body dimension increases in the presence of predators. Using phylogenetic
 comparative methods, we tested this prediction on the macroevolutionary
 scale across 347 teleost families, which display considerable variation in
 fin spines, body depth and width. Consistent with our predictions, we
 demonstrate that fin spines on the vertical plane (dorsal and anal fins)
 are associated with a deeper-bodied optimum. Lineages with spines on the
 horizontal plane (pectoral fins) are associated with a wider-bodied
 optimum. Optimal body dimensions across lineages without spines
 paralleling the body dimension match the allometric expectation.
 Additionally, lineages with longer spines have deeper and wider body
 dimensions. This evolutionary relationship between fin spines and body
 dimensions across teleosts reveals functional synergy between these two
 traits and a potential macroevolutionary signature of predation on the
 evolutionary dynamics of body shape.
description: Morphological data -
 species averagesMorphological data: body
 depth, body width, standard length, dorsal fin spine length, anal fin
 spine length and pectoral fin spine lengths. Measured on a single exemplar
 species for 347 teleost fish families at the California Academy of
 SciencesESM_Dataset.txt
DOI: 10.5061/dryad.6v5hq
title: Data from: Comparative evolution of an archetypal adaptive radiation: innovation and opportunity in Anolis lizards

description: Adaptive radiation is a widely recognized pattern of evolution wherein
 substantial phenotypic change accompanies rapid speciation. Adaptive
 radiation may be triggered by environmental opportunities resulting from
 dispersal to new areas or via the evolution of traits, called key
 innovations, that allow invasion of new niches. Species sampling is a
 known source of bias in many comparative analyses, yet classic adaptive
 radiations have not been studied comparatively with comprehensively
 sampled phylogenies. In this study we use unprecedented comprehensive
 phylogenetic sampling of Anolis lizard species to examine comparative
 evolution in this well-studied adaptive radiation. We compare adaptive
 radiation models within Anolis and in the Anolis clade and a potential
 sister lineage, the Corytophanidae. We find evidence for island (i.e.,
 opportunity) effects and no evidence for trait (i.e., key innovation)
 effects causing accelerated phenotypic evolution within Anolis. However,
 island effects are scale dependent: when Anolis and Corytophanidae are
 analyzed together, no island effect is evident. We find no evidence for an
 island effect on speciation rate, and tenuous evidence for greater
 speciation rate due to trait effects. These results suggest the need for
 precision in treatments of classic adaptive radiations such as Anolis, and
 further refinement of the concept of adaptive radiation.
description: DryadDataAmNatNovember2017ThreeTraitsTable of morphological data: maximum body length, mean relative hindlimb length, and mean number of scales across the snout.
DOI: 10.5061/dryad.d3v78
title: Data from: Locomotor mode and the evolution of the hindlimb in Western Mediterranean Anurans

description: The evolutionary association between morphology, locomotor performance and
 habitat use is a central element of the ecomorphological paradigm, and it
 is known to underlie the evolution of phenotypic diversity in numerous
 animal taxa. In anuran amphibians the hindlimb acts as the propulsive
 agent, and as such, it is directly associated with jumping performance. In
 this study we combine individual- and species-level analyses to examine
 the effects of locomotor mode on body size and hindlimb morphology of
 Western Mediterranean anurans. In addition to the commonly studied
 hindlimb traits, we also examine the ratio between tibiofibula and femur
 length. Body size shows no signs of an evolutionary association to
 locomotor mode. Instead, hindlimb traits are significantly differentiated
 between locomotor groups, both at the individual and species levels.
 Specifically, we observe a gradient of tibiofibula to femur ratio values
 that matches biomechanical predictions. The analysis of adult static
 allometries indicates that these differences arise early in ontogeny. By
 comparing the fit of distinct evolutionary models we provide evidence that
 the locomotor mode adopted by each species to match the requirements of
 the habitat it frequents has shaped the evolution of the hindlimb, but not
 body size.
description: WM_anurans_phylogenyThe file “WM_anurans.nex” contains the phylogeny hypothesis employed in Nexus format. We used the tree of Roelants et al. 2007 as a time-scaled reference to calibrate the phylogeny of all amphibians (Pyron and Wiens 2011) using the function congruify.phylo (Eastman et al. 2013) of geiger R-package (Harmon et al. 2008). We then trimmed the ultrametric phylogeny obtained to match the list of taxa studied.WM_anurans.nexWM_anurans_traitsThe file “WM_anurans_traits.csv” is a comma-delimited file that contains the trait values analysed in Enriquez-Urzelai et al. 2015. These consist of raw measurements for each individual included in the study. ‘SPECIES’ column corresponds to the species scientific name, ‘SP’ column contains the species abbreviated name, ‘SVL’ snout-vent length, ‘TFL’ tibiofibula length, ‘FL’ femur length, ’T.F’ tibiofibula to femur ratio, ‘LOC’ the mode of displacement. We also provide the collection number, the entrance number, and the collection name. Here is the key for modes of displacement (LOC): JT = Jumper terrestrial JA = Jumper arboreal WH = Walker/hopper BWH = Burrower/walker/hopperREAD_MEInformation about the provided data files
DOI: 10.5061/dryad.ms700
title: Data from: Short- and long-term effects of litter size manipulation in a small wild-derived rodent

description: Iteroparous organisms maximise their overall fitness by optimising their
 reproductive effort over multiple reproductive events. Hence, changes in
 reproductive effort are expected to have both short- and long-term
 consequences on parents and their offspring. In laboratory rodents,
 manipulation of reproductive efforts during lactation have however
 revealed little short-term reproductive adjustments, suggesting that
 female laboratory rodents might express maximal rather than optimal levels
 of reproductive investments as observed in semelparous organisms. Using a
 litter size manipulation (LSM) experiment in a small wild-derived rodent
 (the common vole; Microtus arvalis), we show that females altered their
 reproductive efforts in response to LSM, with females having higher
 metabolic rates and showing alternative body mass dynamics when rearing an
 enlarged rather than reduced litter. Those differences in female
 reproductive effort were nonetheless insufficient to fully match their
 pups’ energy demand, pups being lighter at weaning in enlarged litters.
 Interestingly, female reproductive effort changes had long-term
 consequences, with females that had previously reared an enlarged litter
 being lighter at birth of their subsequent litter and producing lower
 quality pups. We discuss the significance of using wild-derived animals in
 studies of reproductive effort optimisation.
description: Reproductive parameters
 for short- and long term effects of litter size manipulation in the common
 vole"Short term
 data"-sheet includes data collected during litter size manipulation.
 "Long term data" -sheet includes data collected from subsequent
 reproductive event without manipulation. RMR is resting metabolic rate of
 the mother measured at day 15-17 of lactation. "Mass_change_ "
 indicates body mass change of the mother during given period. Days in
 variable names indicate days after birth.
 "Mass_change_weaning_pairing%" indicates body mass change of the
 mother, in percentage, from the weaning of previous litter until the
 beginning of the next pairing. Data was collected in the laboratory using
 wild-derived F2 generation (parents) common voles.Short long
 costs.xlsx
DOI: 10.5061/dryad.8n2f4
title: Data from: Do arbuscular mycorrhizal fungi stabilize litter-derived carbon in soil?

description: 1. Fine roots and mycorrhiza often represent the largest input of carbon
 (C) into soils, and are therefore of primary relevance to the soil C
 balance. Arbuscular mycorrhizal (AM) fungi have previously been found to
 increase litter decomposition which may lead to reduced soil C stocks, but
 these studies have focused on immediate decomposition of relatively high
 amounts of high-quality litter and may therefore not hold in many
 ecological settings over longer terms. 2. Here we assessed the effect of
 mycorrhizal fungi on the fate of C and nitrogen (N) contained within a
 realistic amount of highly 13C/15N labelled root-litter in soil. This
 litter was either added fresh or after a 3-month incubation period under
 field conditions to a hyphal in-growth core where mycorrhizal abundance
 was either reduced or not through rotation. After three months of
 incubation with a plant under greenhouse conditions, the effect of turning
 cores on residual 13C and 15N inside the cores was measured, as well as
 13C incorporation in microbial signature fatty acids and 15N incorporation
 of plants. 3. Turning of cores increased abundance of fungal decomposers
 and 13C loss from cores, while 15N content of cores and plants was
 unaffected. Despite the difference in disturbance that turning the cores
 could have caused, the results suggest that mycorrhizal fungi and field
 incubation of litter acted to additively increase proportion of 13C left
 in cores. 4. Synthesis. Apart from stimulating litter decomposition as
 previously shown, mycorrhizas can also stabilize C during litter
 decomposition and this effect is persistent through time.
description: Data of soil core
 experimentFirst three headers
 contain sample and treatment descriptors (ID, and the two factors; litter
 age, old_litter=y means old litter, n=new litter, and turning, turned=y
 means turned cores, n=static cores). All other headers describe various
 measured response variables that are self-explanatory in combination with
 the paper.DataforDryad.xlsx