cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cq275
title: Data from: Physiological status drives metabolic rate in Mediterranean geckos infected with pentastomes

description: Negative effects of parasites on their hosts are well documented, but the
 proximate mechanisms by which parasites reduce their host’s fitness are
 poorly understood. For example, it has been suggested that parasites might
 be energetically demanding. However, a recent meta-analysis suggests that
 they have statistically insignificant effects on host resting metabolic
 rate (RMR). It is possible, though, that energetic costs associated with
 parasites are only manifested during and/or following periods of activity.
 Here, we measured CO2 production (a surrogate for metabolism) in
 Mediterranean geckos (Hemidactylus turcicus) infected with a lung
 parasite, the pentastome Raillietiella indica, under two physiological
 conditions: rested and recently active. In rested geckos, there was a
 negative, but non-significant association between the number of
 pentastomes (i.e., infection intensity) and CO2 production. In recently
 active geckos (chased for 3 minutes), we recorded CO2 production from its
 maximum value until it declined to a stationary phase. We analyzed this
 decline as a 3 phase function (initial decline, secondary decline,
 stationary). Geckos that were recently active showed, in the secondary
 phase, a significant decrease in CO2 production as pentastome intensity
 increased. Moreover, duration of the secondary phase showed a significant
 positive association with the number of pentastomes. These results suggest
 that the intensity of pentastome load exerts a weak effect on the
 metabolism of resting geckos, but a strong physiological effect on geckos
 that have recently been active; we speculate this occurs via mechanical
 constraints on breathing. Our results provide a potential mechanism by
 which pentastomes can reduce gecko fitness.
description: Raillietella indica
 parasites in Mediterranean gecko hostsWithin the
 RAIN-Gecko.zip package accompanying the above publication there are 3
 files. For any further queries please contact icabal@tamu.edu The
 following files are included: 1) README.txt - This file includes a
 description of the variables and a listing of the files used for
 statistical analyses. 2) "RecentlyActiveGeckos.csv" This is the
 dataset used for the analysis of recently active geckos. 3)
 "RestedGeckos.csv" This is the dataset used for the analysis of
 rested geckos.RAIN-Gecko.zip
DOI: 10.5281/zenodo.18364430
title: Spin 1/2 without QM

description: Open for discussion
DOI: 10.5061/dryad.j6j09
title: Data from: Antipredator escape distances of common and threatened birds

description: Most animals keep a safe distance from humans and other potential
 predators, forcing animals to trade foraging and other critical behaviors
 against flight with potentially negative consequences for population
 trends if energy budgets are consistently negative. Animals can adapt to
 human proximity through habituation or microevolution, and island,
 domesticated and urbanized animals have all reduced their threshold of
 fear compared to controls. We tested whether a common cause of threat
 status is susceptibility to human proximity. We did so by estimating
 whether 48 pairs of closely related bird species differing in their threat
 status consistently had longer flight initiation distances (FID, the
 distance at which the individual takes flight from an approaching human)
 in the more threatened species. We estimated threat status by relying on
 existing categorization of threat status by the European Union. Threatened
 species had consistently longer FID than their closely related species in
 both parametric and nonparametric tests. Common species were indeed more
 often recorded during field work while recording FID than were threatened
 species, the difference being almost 2-fold. This result provides a link
 between antipredator behavior, human proximity, threat status, and
 abundance.
description: FID and threat status
 information of pairs of bird speciesFlight initiation
 distance (FID) information of pairs of bird species, sample size (n), the
 identity of these pairs of species, their threat status and the difference
 in their FID.dryad
 file.csv
DOI: 10.5061/dryad.tk718
title: Data from: Landscape-scale eco-evolutionary dynamics: selection by seed predators and fire determine a major reproductive strategy

description: Recent work in model systems has demonstrated significant effects of rapid
 evolutionary change on ecological processes (eco-evolutionary dynamics).
 Fewer studies have addressed whether eco-evolutionary dynamics structure
 natural ecosystems. We investigated variation in the frequency of serotiny
 in lodgepole pine (Pinus contorta), a widespread species in which postfire
 seedling density and ecosystem structure are largely determined by
 serotiny. Serotiny, the retention of mature seeds in cones in a canopy
 seed bank, is thought to be an adaptation for stand-replacing fire, but
 less attention has been paid to the potential selective effects of seed
 predation on serotiny. We hypothesized that spatial variation in
 percentage serotiny in lodgepole pine forests results from an
 eco-evolutionary dynamic where the local level of serotiny depends on the
 relative strengths of conflicting directional selection from fire
 (favoring serotiny) and seed predation (favoring cones that open at
 maturity). We measured percentage serotiny, the abundance of American red
 squirrels (Tamiasciurus hudsonicus; the primary pre-dispersal seed
 predator of lodgepole pine), and several measures of forest structure in
 Yellowstone National Park, USA. Fire frequency strongly predicted the
 frequency of serotiny, a pattern that is well-supported in the literature.
 At sites with high fire frequency (return intervals of 135–185 years)
 where fire favors increased serotiny, squirrel abundance was negatively
 associated with serotiny, suggesting that selection from predation can
 overwhelm selection from fire when squirrels are abundant. At sites with
 low fire frequency (return intervals of 280–310 years), serotiny was
 nearly universally uncommon (&lt;10%). Finally, forest structure
 strongly predicted squirrel density independently of serotiny, and
 serotiny provided no additional explanatory power, suggesting that the
 correlation is caused by selection against serotiny exerted by squirrels,
 rather than squirrels responding to variation in percentage serotiny.
description: serotinyDataField data collected in Yellowstone National Park, USA
DOI: 10.5061/dryad.442r8
title: Data from: Altitudinal migration and the future of an iconic Hawaiian honeycreeper in response to climate change and management

description: Altitudinal movement by tropical birds to track seasonally variable
 resources can move them from protected areas to areas of increased
 vulnerability. In Hawaiʻi, historical reports suggest that many Hawaiian
 honeycreepers such as the ‘I'iwi (Drepanis coccinea) once undertook
 seasonal migrations, but the existence of such movements today is unclear.
 Because Hawaiian honeycreepers are highly susceptible to avian malaria,
 currently minimal in high-elevation forests, understanding the degree to
 which honeycreepers visit lower elevation forests may be critical to
 predict the current impact of malaria on population dynamics and how
 susceptible bird populations may respond to climate change and mitigation
 scenarios. Using radio telemetry data, we demonstrate for the first time
 that a large fraction of breeding adult and juvenile ‘I'iwi
 originating from an upper-elevation (1920 m) population at Hakalau Forest
 NWR exhibit post-breeding movements well below the upper elevational limit
 for mosquitoes. Bloom data suggest seasonal variation in floral resources
 is the primary driver of seasonal movement for ‘I'iwi. To understand
 the demographic implications of such movement, we developed a spatial
 individual-based model calibrated using previously published and original
 data. ʻI'iwi dynamics were simulated backwards in time, to estimate
 population levels in the absence of avian malaria, and forwards in time,
 to assess the impact of climate warming as well as two potential
 mitigation actions. Even in disease-free ‘refuge’ populations, we found
 that breeding densities failed to reach the estimated carrying capacity,
 suggesting the existence of a seasonal ‘migration load’ as a result of
 travel to disease-prevalent areas. We predict that ‘I'iwi may be on
 the verge of extinction in 2100, with the total number of pairs reaching
 only ~ 0.2 to 12.3% of the estimated pre-malaria density, based on an
 optimistic climate change scenario. The probability of extinction of
 ‘I'iwi populations, as measured by population estimates for 2100, is
 strongly related to their estimated migration propensity. Long-term
 conservation strategies likely will require a multi-pronged response
 including a reduction of malaria threats, habitat restoration and
 continued landscape-level access to seasonally variable nectar resources.
description: I‘iwi movement
 locationsDate, bird band number,
 age, sex, location (UTM X,Y), elevation, and distance moved from banding
 location for radio telemetry tracked I‘iwi1km_IIWI_move_Dryad.csv
DOI: 10.6084/m9.figshare.31157107
title: 2026_StellatoEtAL_Spheroids

description: The "Spheroids" folder contains 3 8-bit, no LUT, z-stack composed of 262 slices, referring to 3 multicellular A549 lung cancer spheroid acquired with an LSFM (MA1_F05_ang1_8bitnoLUT); The manually segmented 3D mask of the z-stack (MA1_F05_ang1_Masks_GT, MA2_G09_ang1_8bitNoLUT, MA3_G04_ang1_8bitNoLUT); The automatic segmentation 3D mask obtained using MatRad-OIDS (MA1_F05_ang1_Masks_MatRad-OIDS, MA2_G09_ang1_Masks_MatRad-OIDS, MA3_G04_ang1_Masks_MatRad-OIDS).
DOI: 10.6084/m9.figshare.31157107.v1
title: 2026_StellatoEtAL_Spheroids

description: The "Spheroids" folder contains 3 8-bit, no LUT, z-stack composed of 262 slices, referring to 3 multicellular A549 lung cancer spheroid acquired with an LSFM (MA1_F05_ang1_8bitnoLUT); The manually segmented 3D mask of the z-stack (MA1_F05_ang1_Masks_GT, MA2_G09_ang1_8bitNoLUT, MA3_G04_ang1_8bitNoLUT); The automatic segmentation 3D mask obtained using MatRad-OIDS (MA1_F05_ang1_Masks_MatRad-OIDS, MA2_G09_ang1_Masks_MatRad-OIDS, MA3_G04_ang1_Masks_MatRad-OIDS).
DOI: 10.5061/dryad.44770
title: Data from: Holocene variability of an Amazonian hyperdominant

description: Little is known regarding the long-term stability or instability of
 Amazonian plant communities. We assessed whether the most abundant
 species, hyperdominants, may have risen to prominence at the
 Pleistocene–Holocene transition, following subsequent changes in moisture
 regimes, or as a result of human activity later in the Holocene. The
 fossil pollen history of the commonest western Amazonian tree, Iriartea
 deltoidea (hereafter Iriartea), is investigated using fossil pollen data
 from 13 lakes. Iriartea is a monospecific genus with diagnostic pollen. It
 is also considered a ‘useful’ plant, and its abundance could have been
 enriched by human action. Iriartea pollen was found to have increased in
 abundance in the last 3000 years, but did not show a consistent
 relationship with human activity. The suggestion that the hyperdominants
 in modern Amazonian forests are a legacy of pre-Columbian people is
 unsupported. The abundance of Iriartea pollen is related to increasing
 precipitation, not human activity over the last 3000 years. This member of
 the hyperdominant category of Amazonian trees has only recently acquired
 this status. Synthesis. Our findings are consistent with the observation
 that communities in complex systems are ephemeral. The populations of even
 the most abundant species can change over a few tens of generations. The
 relative abundance of tree species, even in relatively stable systems such
 as those of Amazonian floodplains, changes on ecological not evolutionary
 timescales.
description: Holocene Iriartea
 percentages for thirteen lakes in AmazoniaThe csv file contains
 the data for 13 lakes in Amazonia. Columns include site name, depth, age,
 Iriartea percentage, and maize percentage (when
 available).Iriartea_for_R_age_depth.csv
DOI: 10.5061/dryad.fg6kt38
title: Data from: Immunotherapy-related adverse events (irAEs): extraction from FDA drug labels and comparative analysis

description: Objectives: Immune checkpoint inhibitors (ICIs) have dramatically improved
 outcomes in cancer patients. However, ICIs are associated with significant
 immune-related adverse events (irAEs) and the underlying biological
 mechanisms are not well-understood. To ensure safe cancer treatment,
 research efforts are needed to comprehensively detect and understand
 irAEs. Materials and Methods: We manually extracted and standardized irAEs
 from FDA drug labels for six FDA-approved ICIs. We compared irAE profile
 similarities among ICIs and 1,507 FDA-approved non-ICI drugs. We
 investigated how irAEs have differential effects on human organs by
 classifying irAEs based on their targeted organ systems. Finally, we
 identified broad-spectrum (non-target specific) and narrow-spectrum
 (target-specific) irAEs. Results: A total of 893 irAEs were extracted.
 31.4% irAEs were shared among ICIs as compared to the 8.0% between ICIs
 and non-ICI drugs. irAEs were resulted from both on- and off-target
 effects: irAE profiles were more similar for ICIs with same target than
 different targets, demonstrating the on-target effects; irAE profile
 similarity for ICIs with the same target is less than 50%, demonstrating
 unknown off-target effects. ICIs significantly target many organ systems,
 including endocrine system (3.4-fold enrichment), metabolism (3.7-fold
 enrichment), immune system (3.6-fold enrichment) and autoimmune system
 (4.8-fold enrichment). We identified 21 broad-spectrum irAEs shared among
 all ICIs, 20 irAEs specific for PD-L1/PD-1 inhibition, and 28 irAEs
 specific for CTLA-4 inhibition. Discussion and Conclusion: Our study
 presents the first effort toward building a standardized database of
 irAEs. The extracted irAEs can serve as a goldstandard for automatic irAE
 extractions from other data resources and set a foundation to understand
 biological mechanisms of irAEs.
description: pembrolizumab_SE
DOI: 10.5061/dryad.k3v35
title: Data from: Phylogeography of willow grouse (Lagopus lagopus) in the Arctic: taxonomic discordance as inferred from molecular data

description: Using independently segregating nuclear single nucleotide polymorphisms
 (SNPs) and mitochondrial control region sequences, we found an east–west
 division among sampled willow grouse Lagopus lagopus subspecies. This
 division cut across the range of the subspecies with the largest
 distribution (lagopus) and thus contradicted existing taxonomic
 classifications. Russian Lagopus lagopus lagopus tended to cluster with
 North American willow grouse partly classified as other subspecies.
 Scandinavian willow grouse (L. l. lagopus) clustered with red grouse from
 Britain and Ireland (Lagopus lagopus scoticus and Lagopus lagopus
 hibernicus) but substructuring confirmed the monophyly of the latter. In
 North America, we could not detect any major genetic divisions apart from
 two birds described as alexandrae from the Heceta Island (Alaska) when
 using mitochondrial sequences. Other samples from North America were
 intermingled regardless of whether they were described as muriei,
 alexandrae or lagopus. A specimen described as alexandrae was to some
 extent distinct when analysing the SNP data. The genetic analyses
 indicated some concordance between genetics and taxonomy but not complete
 congruence. This is particularly evident for mitochondrial DNA network
 analyses. We suggest that the taxonomy of this species would benefit by a
 careful re-examination of the available evidence for subspecies. It
 appears as if subspecies status is a poor proxy for assigning evolutionary
 significant units and management units in this species.
description: WillowGrouse_SNP_data
DOI: 10.5061/dryad.gg3f1
title: Data from: Notes on the acoustic repertoire of Melanophryniscus klappenbachi Prigioni & Langone, 2000

description: The genus Melanophryniscus Gallardo, 1961 currently comprises 25
 recognized species (Frost 2012) arranged in three (Cruz &
 Caramaschi 2003) to four species groups (Cespedez & Motte 2001,
 quoted by Maneyro et al. 2008) on the basis of morphological characters.
 The Melanophryniscus stelzneri species group currently contains nine
 species, i.e. M. atroluteus (Miranda-Ribeiro, 1920), M. cupreuscapularis
 Céspedez & Alvarez, 2000, M. dorsalis (Mertens, 1933), M.
 fulvoguttatus (Mertens, 1937), M. klappenbachi Prigioni & Langone,
 2000, M. krauczuki Baldo & Basso, 2004, M. montevidensis
 (Philippi, 1902), M. rubriventris (Vellard, 1947), and M. stelzneri
 (Weyenbergh, 1875). So far, advertisement calls of only four of these
 species have been described, i.e. those of M. atroluteus, M. dorsalis, M.
 krauczuki, and M. montevidensis (Kwet et al. 2005, Baldo & Basso
 2004). Herein, we describe the courtship call and distress call of M.
 klappenbachi and compare it with the calls of other members of the group.
description: Kurth_et_al._call_Melanophryniscus_script_Appendix_S1R script for semiautomatic processing of sound files (*.wav)
DOI: 10.5061/dryad.cb7ns
title: Data from: Microbe-mediated host defence drives the evolution of reduced pathogen virulence

description: Microbes that protect their hosts from pathogens are widespread in nature
 and are attractive disease control agents. Given that pathogen adaptation
 to barriers against infection can drive changes in pathogen virulence,
 ‘defensive microbes’ may shape disease severity. Here we show that
 co-evolving a microbe with host-protective properties (Enterococcus
 faecalis) and a pathogen (Staphylococcus aureus) within Caenorhabditis
 elegans hosts drives the evolution of reduced pathogen virulence as a
 by-product of adaptation to the defensive microbe. Using both genomic and
 phenotypic analyses, we discover that the production of fewer
 iron-scavenging siderophores by the pathogen reduces the fitness of the
 defensive microbe and underpins the decline in pathogen virulence. These
 data show that defensive microbes can shape the evolution of pathogen
 virulence and that the mechanism of pathogen resistance can determine the
 direction of virulence evolution.
description: CSV
 filesCompressed zip file of
 all the CSV files containing the data for all figures for the
 paper.
DOI: 10.5061/dryad.269pp30
title: Data from: Rapid divergence of wing volatile profiles between subspecies of the butterfly Pieris rapae (Lepidoptera: Pieridae)

description: Complex signaling traits such as pheromone profiles can play an important
 role in the early stages of reproductive isolation between populations.
 These signals can diverge along multiple trait axes, and signal receivers
 are often sensitive to subtle differences in signal properties. In the
 Lepidoptera, prior research has highlighted that natural selection can
 drive rapid chemical signal divergence, for instance via mate recognition
 to maintain species boundaries. Much less is known about the occurrence of
 such changes for predominantly sexually-selected chemical signals, such as
 those released by many male lepidopterans. We evaluated the divergence in
 male and female wing volatile profiles between two recently-isolated
 subspecies of the pierid butterfly Pieris rapae: Pieris rapae rapae and
 Pieris rapae crucivora. In laboratory settings, these subspecies exhibit
 strong pre-mating isolation, with females rejecting males of the opposite
 subspecies despite the fact that males direct equivalent courtship effort
 toward females of either subspecies. Using gas chromatography-mass
 spectrometry, we analyzed the volatile chemical profiles of individual
 males and females of each subspecies. We find that males of each
 subspecies differ in their wing volatile profiles, including quantitative
 differences in a male sex pheromone, ferrulactone. In contrast, female
 wing volatiles profiles have diverged significantly less. These
 sex-specific patterns suggest that male chemical profiles may play a role
 in the observed pre-mating isolation between these two subspecies,
 providing support for future investigations of sexually-selected chemical
 traits in population divergence.
description: Peak data for volatile
 wing chemicalsData included are raw
 peak integrations from spectra of each individual. Only the components of
 chemical extracts discussed in the work are included. Also included are
 the size metrics and lab stock family identifiers for each individual. In
 the spreadsheet "P" indicates Pieris rapae rapae, and
 "J" indicates Pieris rapae crucivora.RawData_11_06_2017.csv
DOI: 10.5061/dryad.8s574
title: Data from: A non-parametric maximum test for the Behrens–Fisher problem

description: Non-normality and heteroscedasticity are common in applications. For the
 comparison of two samples in the non-parametric Behrens–Fisher problem,
 different tests have been proposed, but no single test can be recommended
 for all situations. Here, we propose combining two tests, the Welch t test
 based on ranks and the Brunner–Munzel test, within a maximum test.
 Simulation studies indicate that this maximum test, performed as a
 permutation test, controls the type I error rate and stabilizes the power.
 That is, it has good power characteristics for a variety of distributions,
 and also for unbalanced sample sizes. Compared to the single tests, the
 maximum test shows acceptable type I error control.
description: MaximumTestExactR code to analyze the example data set with the proposed maximum test.
DOI: 10.5061/dryad.b2038
title: Data from: Interpreting the FLOCK algorithm from a statistical perspective

description: We show that the algorithm in the program FLOCK (Duchesne &
 Turgeon 2009) can be interpreted as an estimation procedure based on a
 model essentially identical to the STRUCTURE (Pritchard et al. 2000) model
 with no admixture and non-correlated allele frequency priors. Rather than
 using MCMC, the FLOCK algorithm searches for the maximum-a-posteriori
 estimate of this STRUCTURE model via a simulated annealing algorithm with
 a rapid cooling schedule (namely, the exponent on the objective function
 --&gt; ∞). We demonstrate the similarities between the two programs in
 a two step approach. First, to enable rapid batch processing of many
 simulated data sets, we modified the source code of STRUCTURE to use the
 FLOCK algorithm, producing the program FLOCKTURE. With simulated data we
 confirmed that results obtained with FLOCK and FLOCKTURE are very similar
 (though ockture is some 200 times faster). Second, we simulated multiple
 large data sets under varying levels of population differentiation for
 both microsatellite and SNP genotypes. We analyzed them with FLOCKTURE and
 STRUCTURE and assessed each program on its ability to cluster individuals
 to their correct subpopulation. We show that FLOCKTURE yields results
 similar to STRUCTURE albeit with greater variability from run to run.
 FLOCKTURE did perform better than STRUCTURE when genotypes were composed
 of SNPs and differentiation was moderate (FST = 0.022 - 0.032). When
 differentiation was low, STRUCTURE outperformed FLOCKTURE for both marker
 types. On large data sets like those we simulated, it appears that
 FLOCK's reliance on inference rules regarding its “plateau record”
 are not helpful. Interpreting FLOCK's algorithm as a special case of
 the model in STRUCTURE should aid in understanding the program's
 output and behavior.
description: flock-compareA collection of scripts and data to reproduce simulations and analyses.flocktureSource code repository for program flockture. Code modified from structure to do what FLOCK does.