cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5n60v
title: Data from: Fecal cortisol metabolites to assess stress in wildlife: evaluation of a field method in free ranging chamois

description: 1. Non-invasive faecal cortisol metabolite (FCM) analysis is a
 well-established tool to quantify stress in captive and free-ranging
 species. While the method has great potential, its suitability in field
 studies might be limited when faecal samples from unknown individuals are
 used. Possible factors affecting final results and thus jeopardizing
 correct data interpretation are individual and sex-specific variation,
 storage conditions and uneven distribution of metabolites in the faeces.
 2. We tested these factors on a population of free-ranging Alpine chamois
 Rupicapra rupicapra rupicapra in the Austrian Alps. Faecal samples (n =
 183) were analysed with an established enzyme immunoassay (EIA). To
 further validate the assay for FCM in chamois, a high-performance liquid
 chromatography (HPLC) was performed. Sex-specific differences in
 metabolite excretion were evaluated. Effects of storage length and
 temperature on FCM were tested with two experiments. The distribution of
 metabolites in the faeces was determined by the analysis of subsamples of
 single faecal samples. Potential individual effects on FCM levels and
 individually variable reactions to stressful events were evaluated with a
 simulation experiment. 3. Patterns of immunoreactive peaks after HPLC
 separation were similar for different faecal samples, except in one sample
 of a male. In the stability tests, storage time at ambient temperature
 prior to freezing and the individual were the most important variables in
 modulating FCM. Concentrations within single samples varied significantly
 between pellets. Analysis of faecal samples collected from June to October
 showed a highly significant seasonal trend (P &lt; 0·001) and a
 considerable variance of FCM levels within the population. Simulations
 confirmed that individual reactions to stressors in terms of varying
 gradients and FCM levels can explain the observed FCM patterns. 4. Using
 FCM to assess adrenocortical function requires measuring extensively
 metabolized products of glucocorticoids, whose excretion and detection in
 faeces depend on several environmental, endogenous and methodological
 factors. In free-ranging wildlife, these factors and the intrinsic
 individual differences in FCM excretion generate systemic noise and
 substantially distort final results. Therefore, sampling of unknown
 individuals inevitably jeopardizes meaningful interpretation of data, if
 the above named factors are not taken into consideration.
description: Data for
 tab14
 columns (cortisol, study_area, sex, trend), 178 rows, see describtion in
 tab 1Data
 tab1.csvData for
 tab24
 columns (Cortisol, Individual, Sex, diff), 44 rows, see description of tab
 2Data
 tab2.csvData for
 tab33
 columns (Cortisol, male, time), 40 rows, for description see tab
 3Data
 tab3.csvData for
 tab43
 columns (Cortisol, Individual, Sex), 35 rows, for description see tab
 4Data
 tab4.csv
DOI: 10.5281/zenodo.17971735
title: SHM_415569_HST_3D

description: Photogrammetric 3D model of a Middle Neolithic pottery rim fragment in the Pitted Ware Culture/Fagervik II style collected from Fagervik in Östergötland and held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=667

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/733BFDA2-638D-44D4-A0DB-6A5708FD9856
DOI: 10.5061/dryad.82nd6
title: Data from: A potential pitfall in studies of biological shape: does size matter?

description: 1. The number of published studies using geometric morphometrics (GM) for
 analysing biological shape has increased steadily since the beginning of
 the 1990’s, covering multiple research areas such as ecology, evolution,
 development, taxonomy and palaeontology. Unfortunately, we have observed
 that many published studies using GM do not evaluate the potential
 allometric effects of size on shape, which normally require consideration
 or assessment This might lead to misinterpretations and flawed conclusions
 in certain cases, especially when size effects explain a large part of the
 shape variation. 2. We assessed, for the first time and in a systematic
 manner, how often published studies that have applied GM consider the
 potential effects of allometry on shape. 3. We reviewed the 300 most
 recent published papers that used GM for studying biological shape. We
 also estimated how much of the shape variation was explained by allometric
 effects in the reviewed papers. 4. More than one third (38%) of the
 reviewed studies did not consider the allometric component of shape
 variation. In studies where the allometric component was taken into
 account, it was significant in 88% of the cases, explaining up to 87.3% of
 total shape variation. We believe that one reason that may cause the
 observed results is a misunderstanding of the process that superimposes
 landmark configurations, i.e. the Generalized Procrustes Analysis, which
 removes isometric effects of size on shape, but not allometric effects. 5.
 Allometry can be a crucial component of shape variation. We urge authors
 to address, and report, size effects in studies of biological shape.
 However, we do not propose to always remove size effects, but rather to
 evaluate the research question with and without the allometric component
 of shape variation. This approach can certainly provide a thorough
 understanding of on how much size contributes to observed shaped
 variation.
description: Dataset for
 size-evaluation in studies of shapeThis dataset contains
 for each revised paper: whether the paper evaluated the allometric effects
 of size on shape, the impact factor of the journal, the dimensionality of
 the landmarks used in the paper, the type of allometry (if known with
 certainty) and the mean percentage of shape variation explained by size
 (if available).Dataset_Outomuro&Johansson.txt
DOI: 10.5061/dryad.r6b0q05
title: Data from: Testing the effects of heterozygosity on growth rate plasticity in the seaweed Gracilaria chilensis (Rhodophyta)

description: Heterozygosity has been positively associated with fitness and population
 survival. However, the relationship between heterozygosity and adaptive
 phenotypic plasticity (i.e., plasticity which results in fitness
 homeostasis or improvement in changing environments), is unclear and has
 been poorly explored in seaweeds. In this study, we explored this
 relationship in the clonal red seaweed, Gracilaria chilensis by conducting
 three growth rate plasticity experiments under contrasting salinity
 conditions and by measuring heterozygosity with five microsatellite DNA
 markers. Firstly, we compared growth rate plasticity between the haploid
 and diploid phases. Secondly, we compared growth rate plasticity between
 diploids with different numbers of heterozygous loci. Finally, we compared
 growth rate plasticity between diploid plants from two populations that
 are expected to exhibit significant differences in heterozygosity. We
 found that, (i) diploids displayed a higher growth rate and lower growth
 rate plasticity than haploids, (ii) diploids with a higher number of
 heterozygous loci displayed lower growth rate plasticity than those
 exhibiting less heterozygosity, and (iii) diploid sporophytes from the
 population with higher heterozygosity displayed lower growth rate
 plasticity than those with lower heterozygosity. Accordingly, this study
 suggests that heterozygosity is inversely related to growth rate
 plasticity in G. chilensis. However, better genetic tools in seaweeds are
 required for a more definitive conclusion on the relationship between
 heterozygosity and phenotypic plasticity.
description: Heterozygosity and
 growth rate plasticity_RawDataRaw genetic
 (microsatellites) and growth (biomass) data gathered and used in
 "Testing the effects of heterozygosity on growth rate plasticity in
 the seaweed Gracilaria chilensis (Gallegos et al.
 2018)".Testing the effects of
 heterozygosity on growth rate plasticity in the seaweed Gracilaria
 chilensis (Gallegos et al.
 2018)_RawData.rar
DOI: 10.5061/dryad.pb8s4
title: Data from: Fixation of mutators in asexual populations: the role of genetic drift and epistasis

description: We study the evolutionary dynamics of an asexual population of nonmutators
 and mutators on a class of epistatic fitness landscapes. We consider the
 situation in which all mutations are deleterious and mutators are produced
 from nonmutators continually at a constant rate. We find that in an
 infinitely large population, a minimum nonmutator-to-mutator conversion
 rate is required to fix the mutators but an arbitrarily small conversion
 rate results in the fixation of mutators in a finite population. We
 calculate analytical expressions for the mutator fraction at
 mutation-selection balance and fixation time for mutators in a finite
 population when the difference between the mutation rate for mutator and
 nonmutator is smaller (regime I) and larger (regime II) than the selection
 coefficient. Our main result is that in regime I, the mutator fraction and
 the fixation time are independent of epistasis but in regime II, mutators
 are rarer and take longer to fix when the decrease in fitness with the
 number of deleterious mutations occurs at an accelerating rate
 (synergistic epistasis) than at a diminishing rate (antagonistic
 epistasis). Our analytical results are compared with numerics and their
 implications are discussed.
description: Program to find fixation
 timeProgram to find fixation
 time for mutators without and with beneficial mutationsdryad.tar.gz
DOI: 10.5061/dryad.6vf1s
title: Data from: Restricting access to invasion hubs enables sustained control of an invasive vertebrate

description: Biological invasions often occur through expansion of satellite
 populations that become established at ‘invasion hubs’. Invasion hubs can
 result from random dispersal events, but frequently arise when invading
 individuals actively choose habitats using cues that signify high-quality
 environments where the fitness consequences are positive. Theoretical
 studies suggest that targeted control at invasion hubs can effectively
 suppress the populations and impacts of invaders. In arid Australia, small
 dams that provide water for livestock function as invasion hubs by
 providing an invasive vertebrate, the cane toad Rhinella marina, with
 refuge from extreme aridity during the annual dry season. Toads are
 attracted to dams and use them as stepping stone habitats from which they
 disperse during rainy periods. Here, we ask whether sustained control of
 this invasive vertebrate can be achieved by converting invasion hubs into
 ecological traps. We did this by manipulating invasion hub habitats to
 induce a mismatch between toads' habitat preference and the fitness
 consequences of their habitat choice to cause high mortality. We
 constructed fences to exclude toads from dams and maintained these fences
 for 1 year. This period encompassed periods of dry and wet seasonal
 climatic conditions. Our manipulation did not alter the attractive cues
 for invading toads which died en masse while attempting to settle at
 fenced dams that prevented toads from reaching water. Toad populations at
 the fenced dams were suppressed by 1–2 orders of magnitude compared to
 unfenced controls and procedural controls. Toad populations remained
 suppressed for a year after exclusion. By excluding toads from dams, we
 converted invasion hubs into ecological traps and effectively thwarted the
 reinvasion of cane toads. Our research suggests that water exclusion
 devices could be used to prevent toad invasion or to control cane toad
 populations in arid landscapes colonized by toads. Synthesis and
 applications. Our study demonstrates that sustained control of invader
 populations can be achieved by restricting their access to invasion hubs.
 Control of invasive species via elimination of invasion hubs could be
 conducted reactively, to control established populations of invaders, or
 conducted strategically, by rendering invasion hubs unsuitable for
 colonization ahead of the invasion front to prevent further population
 spread.
description: Letnic et al.
 Restricting access to invasion hubs enables sustained control of an
 invasive vertebrateData for rainfall,
 counts of dead toads and live toads
DOI: 10.5061/dryad.5m8f6
title: Data from: Effects of mountaintop removal mining and valley filling on the occupancy and abundance of stream salamanders

description: Human-induced land-use changes are among the primary causes of ecosystem
 degradation and biodiversity loss. Across central Appalachia (USA),
 mountaintop removal mining and valley filling (MTR/VF) is the prevailing
 form of land-use change and represents a stressor to stream ecosystems.
 Salamanders are the dominant vertebrate in Appalachian headwater streams.
 Thus, we addressed the question: Is salamander occupancy and conditional
 abundance reduced in streams impacted by MTR/VF? We conducted repeated
 counts of adult and larval salamanders within 10-m reaches in 11
 valley-filled streams and 12 reference streams in south-eastern Kentucky.
 Relationships between occupancy, conditional abundance, and site type
 (MTR/VF vs. reference) were modelled using the hurdle model (Ecology, 94,
 2013 and 1472), where occupancy is modelled separately from abundance
 while accounting for differences in per-individual detection probabilities
 among groups. We found mean occupancy probabilities were &gt;0·85 for
 all groups in reference reaches, whereas mean occupancy probabilities were
 relatively lower in MTR/VF reaches (ranging from 0·23 to 0·66). Posterior
 means of the difference in occupancy between site types were negative
 across all groups, although MTR/VF stream reaches were at least 95% less
 likely to be occupied by spring salamander Gyrinophilus porphyriticus,
 adult southern two-lined salamander Eurycea cirrigera and larval dusky
 salamanders Desmognathus compared to reference reaches. Posterior means of
 the difference in conditional abundance between MTR/VF and reference
 stream reaches were negative across all groups; 95% credible interval for
 difference in conditional abundance covered zero for only one species (red
 salamander Pseudotriton ruber). After adjusting for goodness-of-fit, point
 estimates of differences in occupancy and conditional abundance still
 remained below zero for most species. Additionally, MTR/VF reaches had
 higher ion concentrations, total organic carbon and specific conductance
 compared to reference reaches. Synthesis and applications. Our study
 concludes that mountaintop removal mining and valley filling (MTR/VF)
 reduces salamander occupancy and conditional abundance. Although the
 potential mechanisms responsible for reduction are numerous, our findings
 suggest a change in the current regulatory framework is needed to offset
 the impacts of MTR/VF on stream ecosystems and biota. Reclamation
 techniques that enhance conditions for vegetative succession within
 catchments may improve habitat on reclaimed surface mines.
description: Price et al.
 JAPPL-2015-count-datasalamander counts, site
 covariates and sampling covariates
DOI: 10.5061/dryad.rh27t
title: Data from: Warming has a greater effect than elevated CO2 on predator–prey interactions in coral reef fish

description: Ocean acidification and warming, driven by anthropogenic CO2 emissions,
 are considered to be among the greatest threats facing marine organisms.
 While each stressor in isolation has been studied extensively, there has
 been less focus on their combined effects, which could impact key
 ecological processes. We tested the independent and combined effects of
 short-term exposure to elevated CO2 and temperature on the predator–prey
 interactions of a common pair of coral reef fishes (Pomacentrus wardi and
 its predator, Pseudochromis fuscus). We found that predator success
 increased following independent exposure to high temperature and elevated
 CO2. Overall, high temperature had an overwhelming effect on the escape
 behaviour of the prey compared with the combined exposure to elevated CO2
 and high temperature or the independent effect of elevated CO2. Exposure
 to high temperatures led to an increase in attack and predation rates. By
 contrast, we observed little influence of elevated CO2 on the behaviour of
 the predator, suggesting that the attack behaviour of P. fuscus was robust
 to this environmental change. This is the first study to address how the
 kinematics and swimming performance at the basis of predator–prey
 interactions may change in response to concurrent exposure to elevated CO2
 and high temperatures and represents an important step to forecasting the
 responses of interacting species to climate change.
description: Allan et al. 2017 PROC B
 DRYAD DATA
DOI: 10.5061/dryad.db827
title: Data from: Coevolution between flight morphology, vertical stratification and sexual dimorphism: what can we learn from tropical butterflies?

description: Occurrence patterns are partly shaped by the affinity of species with
 habitat conditions. For winged organisms, flight-related attributes are
 vital for ecological performance. However, due to the different
 reproductive roles of each sex, we expect divergence in flight energy
 budget, and consequently different selection responses between sexes. We
 used tropical frugivorous butterflies as models to investigate coevolution
 between flight morphology, sex dimorphism and vertical stratification. We
 studied 94 species of Amazonian fruit-feeing butterflies sampled in seven
 sites across 3341 ha. We used wing-thorax ratio as a proxy for flight
 capacity and hierarchical Bayesian modeling to estimate stratum
 preference. We detected a strong phylogenetic signal in wing-thorax ratio
 in both sexes. Stouter fast-flying species preferred the canopy, while
 more slender slow-flying species preferred the understorey. However, this
 relationship was stronger in females than in males, suggesting that female
 phenotype associates more intimately with habitat conditions. Within
 species, males were stouter than females and sexual dimorphism was sharper
 in understorey species. Because trait-habitat relationships were
 independent from phylogeny, the matching between flight morphology and
 stratum preference is more likely to reflect adaptive radiation than
 shared ancestry. This study sheds light on the impact of flight and sexual
 dimorphism on the evolution and ecological adaptation of flying organisms.
description: JEB-2017-00293_dataData matrix on morphological and ecological traits of 94 species of tropical fruit-feeding butterflies. WTR refers to wing-thorax ratio, calculated as wtr = forewing length²/thorax volume; cf refers to canopy fidelity, estimated from hierarchical Bayesian modeling on butterfly occurrence in canopy or understorey; tv refers to thoracic volume, calculated as tv = thorax length x thorax width²; war refers to wing aspect ratio, calculated as war = 4 x forewing length²/wing area. Traits are separated for males and females.
DOI: 10.5061/dryad.c7v943t
title: Data from: Added value of autoregulation and multi-step kinetics of transcription initiation

description: Bacterial gene expression regulation occurs mostly during transcription,
 which has two main rate-limiting steps: the close complex formation, when
 the RNA polymerase binds to an active promoter, and the subsequent open
 complex formation, after which it follows elongation. Tuning these steps
 kinetics by the action of, e.g., transcription factors, allows for a wide
 diversity of dynamics. For example, adding autoregulation generates
 single-gene circuits able to perform more complex tasks. Using stochastic
 models of transcription kinetics with empirically validated parameter
 values, we investigate how autoregulation and the multi-step transcription
 initiation kinetics of single-gene autoregulated circuits can be combined
 to fine tune steady state mean and cell-to-cell variability in protein
 expression levels, as well as response times. Next, we investigate how
 they can be jointly tuned to control complex behaviors, namely, time
 counting, switching dynamics, and memory storage. Overall, our finding
 suggests that, in bacteria, jointly regulating a single-gene circuit’s
 topology and the transcription initiation multi-step dynamics allows
 enhancing complex task performance.
description: Matlab_codesFile contains a folder with matlab code files, along with *.g files of the models that are simulated using Matlab and SGNSim (http://www.cs.tut.fi/%7Esanchesr/tool_SGNSim/SGNSim.html)
DOI: 10.5061/dryad.s022h
title: Data from: Shrub encroachment does not reduce the activity of some soil enzymes in Mediterranean semiarid grasslands

description: Shrub encroachment is a worldwide phenomenon with implications for
 desertification and global change. We evaluated its effects on the
 activities of urease, phosphatase and b-glucosidase in Mediterranean
 semiarid grasslands dominated by Stipa tenacissima by sampling 12 sites
 with and without resprouting shrubs along a climatic gradient. The
 presence of shrubs affected the evaluated enzymes at different spatial
 scales. Soils under S. tenacissima tussocks and in bare ground areas
 devoid of vascular plants had higher values of phosphatase and urease when
 the shrubs were present. For the b-glucosidase, this effect was
 site-specific. At the scale of whole plots (30 m 30 m), shrubs increased
 soil enzyme activities between 2% (b-glucosidase) and 22% (urease), albeit
 these differences were significant only in the later case. Our results
 indicate that shrub encroachment does not reduce the activity of
 extracellular soil enzymes in S. tenacissima grasslands.
description: Soil enzyme
 (phosphatase, b-glucosidase and urease) data from encroached/unencroached
 Stipa tenacissima steppes from SpainMaestre_SBB43.zip
DOI: 10.5061/dryad.j5s12
title: Data from: Drug delivery in a tumour cord model: a computational simulation

description: The tumour vasculature and microenvironment is complex and heterogeneous,
 contributing to reduced delivery of cancer drugs to the tumour. We have
 developed an in silico model of drug transport in a tumour cord to explore
 the effect of different drug regimes over a 72 h period and how changes in
 pharmacokinetic parameters affect tumour exposure to the cytotoxic drug
 doxorubicin. We used the model to describe the radial and axial
 distribution of drug in the tumour cord as a function of changes in the
 transport rate across the cell membrane, blood vessel and intercellular
 permeability, flow rate, and the binding and unbinding ratio of drug
 within the cancer cells. We explored how changes in these parameters may
 affect cellular exposure to drug. The model demonstrates the extent to
 which distance from the supplying vessel influences drug levels and the
 effect of dosing schedule in relation to saturation of drug-binding sites.
 It also shows the likely impact on drug distribution of the aberrant
 vasculature seen within tumours. The model can be adapted for other drugs
 and extended to include other parameters. The analysis confirms that
 computational models can play a role in understanding novel cancer
 therapies to optimize drug administration and delivery.
description: RSOS_CodeMatlab code used to produce model results for paper.