cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.th160
title: Data from: Mating status correlates with dorsal brightness in some but not all poison frog populations

description: Sexual signals are important for intraspecific communication and mate
 selection, but their evolution may be driven by both natural and sexual
 selection, and stochastic processes. Strawberry poison frogs (Oophaga
 pumilio) show strong color divergence among populations, but coloration
 also varies among individuals of the same population. The importance of
 coloration for female mate choice has been studied intensely, and sexual
 selection seems to affect color divergence in strawberry poison frogs.
 However, the effect of coloration on mating success under field conditions
 has received very little attention. Furthermore, few studies examined how
 phenotypic variation among individuals of the same color morph affects
 mate selection under natural conditions. We measured the spectral
 reflectance of courting and noncourting individuals and their background
 substrates in three geographically separated populations. In one
 population (Sarapiquí, Costa Rica), we found that naturally occurring
 courting pairs of males and females had significantly brighter dorsal
 coloration than individual males and females not engaged in courtship
 interactions. Our field observations suggest that, in the wild, females
 prefer brighter males while the reason for the higher courtship activity
 of brighter females remains unclear. Overall our results imply that
 brightness differences among individuals of the same color morph may
 actually affect reproductive success in some populations of strawberry
 poison frogs.
description: spectral_meassurementsMeasurements of the dorsal and ventral spectral reflectance variables (ΔL, ΔS, L, S, ΣR(λ))PC_scores.DORSALIndividual scores on the principal components derived from the dorsal spectral measurementsPC_scores.VENTRALIndividual scores on the principal components derived from the ventral spectral measurements
DOI: 10.5061/dryad.dq40b
title: Data from: Molecular evidence for the first records of facultative parthenogenesis in elapid snakes.

description: Parthenogenesis is a form of asexual reproduction by which embryos develop
 from unfertilized eggs. Parthenogenesis occurs in reptiles, however is not
 yet known to occur in the widespread elapid snakes (Elapidae), which
 include well-known taxa such as cobras, mambas, taipans and sea snakes.
 Here, we describe the production of viable parthenogens in two species of
 Australo-Papuan elapids with divergent reproductive modes: the oviparous
 Coastal/Papuan Taipan (Oxyuranus scutellatus) and the viviparous Southern
 Death Adder (Acanthophis antarcticus). Analyses of nuclear SNP data
 excluded paternity for putative fathers and convincingly demonstrated
 asexual reproduction, thus representing the first evidence of facultative
 parthenogenesis in Elapidae. Our finding has broad implications for
 understanding the evolution of reproductive diversity in snakes, as well
 as managing the conservation of genetic diversity in wild and captive
 populations.
description: Data from all
 samplesData from all samples
 used in the study.ddRAD_raw_reads.zip
DOI: 10.5061/dryad.6pn0b
title: Data from: Fear of the human ‘super predator’ reduces feeding time in large carnivores

description: Large carnivores' fear of the human ‘super predator’ has the
 potential to alter their feeding behaviour and result in human-induced
 trophic cascades. However, it has yet to be experimentally tested if large
 carnivores perceive humans as predators and react strongly enough to have
 cascading effects on their prey. We conducted a predator playback
 experiment exposing pumas to predator (human) and non-predator control
 (frog) sounds at puma feeding sites to measure immediate fear responses to
 humans and the subsequent impacts on feeding. We found that pumas fled
 more frequently, took longer to return, and reduced their overall feeding
 time by more than half in response to hearing the human ‘super predator’.
 Combined with our previous work showing higher kill rates of deer in more
 urbanized landscapes, this study reveals that fear is the mechanism
 driving an ecological cascade from humans to increased puma predation on
 deer. By demonstrating that the fear of humans can cause a strong
 reduction in feeding by pumas, our results support that non-consumptive
 forms of human disturbance may alter the ecological role of large
 carnivores.
description: Puma responses to
 playback experiment: sounds of humans and frogsWe report puma
 behavioral responses to a playback experiment that exposed pumas to a
 control sound (frogs) and a treatment sound (conversational human speech)
 at puma kill sites. Behavioral responses reported include fleeing,
 abandonment, latency to return, and feeding over a 24-hour period. Other
 information provided includes puma ID, playback trial ID, and experimental
 treatment.Smith et al. Playback
 Data.xlsx
DOI: 10.5061/dryad.6vn9658
title: Data from: The sea urchin Diadema africanum uses low resolution vision to find shelter and deter enemies

description: Many sea urchins can detect light on their body surface and some species
 are reported to possess image-resolving vision. Here we measure the
 spatial resolution of vision in the long-spined sea urchin Diadema
 africanum, using two different visual responses: a taxis towards dark
 objects and an alarm response of spine-pointing towards looming stimuli.
 For the taxis response we used isoluminant visual stimuli to discriminate
 spatial vision from phototaxis. Individual animals were placed in the
 centre of a cylindrical arena under bright down-welling light, with
 stimuli of varying angular dimensions placed on the arena wall at
 pseudorandom directions from the centre. We tracked the direction of
 movement of individual animals in relation to the stimuli to determine
 whether the animals oriented towards the stimulus. We found that D.
 africanum responds by taxis towards isoluminant stimuli with a spatial
 resolution of 38° - 89°, assuming a contrast threshold of 10%. The visual
 acuity of the alarm response of D. africanum was tested by exposing
 animals to different sized dark looming and appearing stimuli on a
 monitor. We found that D. africanum displays a spine-pointing response to
 appearing black circles with a spatial resolution of 60° - 116°, assuming
 the same contrast threshold as above.
description: Produce difference of
 Gaussians stimulus imageCode to generate an
 image containing an isoluminant visual stimulus derived from a difference
 of Gaussians.Create
 patterns.zipSpatial resolution
 MATLAB filesMATLAB scripts which can
 be used to model the spatial resolution required to detect a visual signal
 of a particular type and arc width.Spatial
 resolution.zipUrchin model
 imagesMicro-tomographic images
 of the skeleton of Diadema africanum. These images were used to produce 3D
 reconstructions of the entire skeleton and of a section including tube
 foot pores.Urchin
 model.zip
DOI: 10.5061/dryad.q90j2
title: Data from: The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii)

description: We conducted comparative phylogeographic and population genetic analyses
 of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic
 to islands in the southern Ryukyus, to explore different factors that have
 influenced population structure. Previous phylogenetic studies using
 partial mitochondrial DNA (mtDNA) indicate similar divergence times from
 their respective closest relatives, suggesting that differences in
 population structure are driven by intrinsic attributes of either species
 rather than the common set of extrinsic factors that both presumably have
 been exposed to throughout their history. In this study, analysis of mtDNA
 sequences and microsatellite polymorphism demonstrate contrasting patterns
 of phylogeography and population structure: P. kishinouyei exhibits a
 lower genetic variability and lower genetic differentiation among islands
 than P. stimpsonii, consistent with recent population expansion. However,
 historical demographic analyses indicate that the relatively high genetic
 uniformity in P. kishinouyei is not attributable to recent expansion. We
 detected significant isolation-by-distance patterns among P. kishinouyei
 populations on the land bridge islands, but not among P. stimpsonii
 populations occurring on those same islands. Our results suggest that P.
 kishinouyei populations have maintained gene flows across islands until
 recently, probably via ephemeral Quaternary land bridges. The lower
 genetic variability in P. kishinouyei may also indicate smaller effective
 population sizes on average than that of P. stimpsonii. We interpret these
 differences as a consequence of ecological divergence between the two
 species, primarily in trophic level and habitat preference.
description: Microsatellite genotype
 of Plestiodon kishinouyeiThis file includes
 genotypes of 108 individuals of Plestiodon kishinouyei for seven
 microsatellite loci in GenAlEx format. The locality names correspond to
 those of Table 2 in the text.Microsatellite genotype
 of Plestiodon stimpsoniiThis file includes
 genotypes of 71 individuals of Plestiodon stimpsonii for five
 microsatellite loci in GenAlEx format. The locality names correspond to
 those of Table 2 in the text.
DOI: 10.5061/dryad.7266m
title: Data from: Prognostic and clinical significance of miRNA-205 in endometrioid endometrial cancer

description: Endometrial cancer is one of the most common malignancies of the
 reproductive female tract, with endometrioid endometrial cancer being the
 most frequent type. Despite the relatively favourable prognosis in cases
 of endometrial cancer, there is a necessity to evaluate clinical and
 prognostic utility of new molecular markers. MiRNAs are small, non-coding
 RNA molecules that take part in RNA silencing and post-transcriptional
 regulation of gene expression. Altered expression of miRNAs may be
 associated with cancer initiation, progression and metastatic
 capabilities. MiRNA-205 seems to be one of the key regulators of gene
 expression in endometrial cancer. In this study, we investigated clinical
 and prognostic role of miRNA-205 in endometrioid endometrial cancer. After
 total RNA extraction from 100 archival formalin-fixed paraffin-embedded
 tissues, real-time quantitative RT-PCR was used to define miRNA-205
 expression levels. The aim of the study was to evaluate miRNA-205
 expression levels in regard to patients’ clinical and histopathological
 features, such as: survival rate, recurrence rate, staging, myometrial
 invasion, grading and lymph nodes involvement. Higher levels of miRNA-205
 expression were observed in tumours with less than half of myometrial
 invasion and non-advanced cancers. Kaplan-Maier analysis revealed that
 higher levels of miRNA-205 were associated with better overall survival (p
 = 0,034). These results indicate potential clinical utility of miRNA-205
 as a prognostic marker.
description: RQ miR205
 dryadFiles include RAW data
 on qRT-PCR (Ct values and RQ values) and, additionally, basic clinical
 data are provided (the summary of clinical data is presented in the
 article).
DOI: 10.5061/dryad.184s0
title: Data from: A unique feeding strategy of the extinct marine mammal Kolponomos: convergence on sabretooths and sea otters

description: Mammalian molluscivores feed mainly by shell-crushing or suction-feeding.
 The extinct marine arctoid, Kolponomos, has been interpreted as an
 otter-like shell-crusher based on similar dentitions. However, neither the
 masticatory biomechanics of the shell-crushing adaptation, nor the way
 Kolponomos may have captured hard-shelled prey, have been tested. Based on
 mandibular symphyseal morphology shared by Kolponomos and sabretoothed
 carnivores, we hypothesize a sabretooth-like mechanism for Kolponomos
 prey-capture, whereby the mandible functioned as an anchor. Torque
 generated from jaw closure and head flexion was used to dislodge prey by
 prying, with prey then crushed using cheek teeth. We test this
 hypothesized feeding sequence using phylogenetically-informed
 biomechanical simulations and shape analyses, and find a strongly
 supported, shared high mandibular stiffness in simulated prey-capture
 bites and mandibular shape in Kolponomos and the sabretoothed cat
 Smilodon. These two distantly related taxa converged on using mandibles to
 anchor cranial torquing forces when prying substrate-bound prey in the
 former and sabre-driving forces during prey-killing in the latter.
 Simulated prey-crushing bites indicate that Kolponomos and sea otters
 exhibit alternative structural stiffness-bite efficiency combinations in
 mandibular biomechanical adaptation for shell-crushing. This unique
 feeding system of Kolponomos exemplifies a mosaic of form-function
 convergence relative to other Carnivora.
description: Tsengetal_PRSB_STL_filesSTL files of 3D mandible models analyzed in the study.Tsengetal_PRSB_FE_modelsFinite element models of all species analyzed in the study, with forces loaded. In Strand7 file format.
DOI: 10.5281/zenodo.17909620
title: Data set for "Handling Transitions Across Singularities For UR-like Serial Robots"

description: See the attached read me file
DOI: 10.5281/zenodo.16607907
title: Data set for "Handling Transitions Across Singularities For UR-like Serial Robots"

description: See the attached read me file
DOI: 10.5061/dryad.17r39p2
title: Data from: Urban colonization through multiple genetic lenses: the city-fox phenomenon revisited

description: Urbanization is driving environmental change on a global scale, creating
 novel environments for wildlife to colonize. Through a combination of
 stochastic and selective processes, urbanization is also driving
 evolutionary change. For instance, difficulty traversing human-modified
 landscapes may isolate newly established populations from rural sources,
 while novel selective pressures, such as altered disease risk, toxicant
 exposure, and light pollution, may further diverge populations through
 local adaptation. Assessing the evolutionary consequences of urban
 colonization and the processes underlying them is a principle aim of urban
 evolutionary ecology. In the present study, we revisited the genetic
 effects of urbanization on red foxes (Vulpes vulpes) that colonized
 Zurich, Switzerland. Through use of genome-wide single nucleotide
 polymorphisms and microsatellite markers linked to the major
 histocompatibility complex (MHC), we expanded upon a previous neutral
 microsatellite study to assess population structure, characterize patterns
 of genetic diversity, and detect outliers associated with urbanization.
 Our results indicated the presence of one large evolutionary cluster, with
 substructure evident between geographic sampling areas. In urban foxes, we
 observed patterns of neutral and functional diversity consistent with
 founder events, and reported increased differentiation between populations
 separated by natural and anthropogenic barriers. We additionally reported
 evidence of selection acting on MHC-linked markers, and identified outlier
 loci with putative gene functions related to energy metabolism, behavior,
 and immunity. We concluded that demographic processes primarily drove
 patterns of diversity, with outlier tests providing preliminary evidence
 of possible urban adaptation. This study contributes to our overall
 understanding of urban colonization ecology and emphasizes the value of
 combining datasets when examining evolutionary change in an increasingly
 urban world.
description: Swiss fox MHC-linked
 microsatellite genotypesThis data file contains
 genotypes for nine microsatellite markers linked to major
 histocompatibility complex (MHC) genes that were genotyped in 100 red
 foxes (Vulpes vulpes) sampled in Zurich, Switzerland. Metadata includes
 sample identification number, sampling location, habitat type, and sex.
 The five sampling locations span urban (Ueast and Uwest) and rural (Reast,
 Rwest, and Rnorth) habitats in and around Zurich. Please see the map
 provided in the inset of Figure 2 to better visualize sampling locations.
 Missing genotype data is indicated with zeros.swiss_fox_MHC_msat_genotypes_2018.12.14.xlsx
DOI: 10.5061/dryad.5d4mb06
title: Data from: Multiple forms of selection shape reproductive isolation in a primate hybrid zone

description: Speciation occurs when populations diverge and become reproductively
 isolated from each other. Natural selection is commonly accepted to play a
 large role in this process and it has been widely assumed that
 reproductive isolation often results as a byproduct of divergence driven
 by adaptation in allopatry. When such populations come into secondary
 contact, reinforcement can act to strengthen reproductive isolation, but
 the frequency and importance of this process is still unknown. Here, we
 explored genomic signatures of selection in allopatry and sympatry for
 loci associated with reproductive isolation using a natural primate hybrid
 zone. By analyzing reduced-representation sequencing data, we quantified
 admixture and population structure across a howler monkey hybrid zone and
 examined the relationship between locus-specific differentiation and
 introgression. We detected extensive admixture that was mostly limited to
 the narrow contact zone. Loci with reduced introgression into the
 heterospecific genomic background (the pattern expected for loci
 associated with reproductive isolation due to selection against hybrids)
 were significantly more differentiated between allopatric parental
 populations than loci with neutral and increased introgression, supporting
 the hypothesis that reproductive isolation is a by-product of divergence
 in allopatry. Further, loci with reduced introgression showed greater
 differentiation in sympatry than in allopatry, suggesting a role for
 reinforcement. Thus, our results reflect multiple forms of selection that
 have shaped reproductive isolation in this system. We conclude that
 reproductive isolation may have initially been driven by divergence in
 allopatry, but later reinforced by divergent selection in sympatry.
description: Alouatta
 genotypesThis file contains
 ddRADseq genotype data at 6,415,368 sites for individuals sampled in the
 wild from the Alouatta palliata x Alouatta pigra hybrid zone and
 surrounding allopatric parental populations. We merged overlapping read
 pairs, aligned merged and unmerged reads to the Alouatta palliata genome
 assembly (PVK00000000) using BWA-MEM. We called variants using samtools
 mpileup and bcftools call, removed SNPs within 5bp of an indel and
 retained variants with a minimum quality score of 20.filtered_final_4.vcf.gz
DOI: 10.5061/dryad.j95t2
title: Data from: What triggers colour change? Effects of background colour and temperature on the development of an alpine grasshopper

description: Background: Colour polymorphisms are a fascinating facet of many natural
 populations of plants and animals, and the selective processes that
 maintain such variation are as relevant as the processes which promote
 their development. Orthoptera, the insect group that encompasses
 grasshoppers and bush crickets, includes a particularly large number of
 species that are colour polymorphic with a marked green-brown polymorphism
 being particularly widespread. Colour polymorphism has been associated
 with the need for crypsis and background matching and background-dependent
 homochromy has been described in a few species. However, when and how
 different environmental conditions influence variation in colour remains
 poorly understood. Here we test for effects of background colour and
 ambient temperature on the occurrence of colour morph switches (green to
 brown or brown to green) and developmental darkening in the alpine
 dwelling club-legged grasshopper Gomphocerus sibiricus. Results: We
 monitored individually housed nymphae across three of their four
 developmental stages and into the first week after final ecdysis. Our data
 show an absence of colour morph switches in G. sibiricus, without a single
 switch observed in our sample. Furthermore, we test for an effect of
 temperature on colouration by manipulating radiant heat, a limiting factor
 in alpine habitats. Radiant heat had a significant effect on developmental
 darkening: individuals under low radiant heat tended to darken, while
 individuals under high radiant heat tended to lighten within nymphal
 stages. Young imagoes darkened under either condition. Conclusions: Our
 results indicate a plastic response to a variable temperature and indicate
 that melanin, a multipurpose pigment responsible for dark colouration and
 presumed to be costly, seems to be strategically allocated according to
 the current environmental conditions. Unlike other orthopterans, the
 species is apparently unable to switch colour morphs (green/brown) during
 development, suggesting that colour morphs are determined genetically (or
 very early during development) and that other processes have to contribute
 to crypsis and homochromy in this species.
description: ColourDataTableThe data set includes the colour scorings for all observations from both rounds included in all analyses.
DOI: 10.5061/dryad.5t0g4
title: Data from: Limitations of rotational manoeuvrability in insects and hummingbirds: evaluating the effects of neuro-biomechanical delays and muscle mechanical power

description: Flying animals ranging in size from fruit flies to hummingbirds are nimble
 fliers with remarkable rotational manoeuvrability. The degrees of
 manoeuvrability among these animals, however, are noticeably diverse and
 do not simply follow scaling rules of flight dynamics or muscle power
 capacity. As all manoeuvres emerge from the complex interactions of
 neural, physiological and biomechanical processes of an animal's
 flight control system, these processes give rise to multiple limiting
 factors that dictate the maximal manoeuvrability attainable by an animal.
 Here using functional models of an animal's flight control system, we
 investigate the effects of three such limiting factors, including neural
 and biomechanical (from limited flapping frequency) delays and muscle
 mechanical power, for two insect species and two hummingbird species,
 undergoing roll, pitch and yaw rotations. The results show that for
 animals with similar degree of manoeuvrability, for example, fruit flies
 and hummingbirds, the underlying limiting factors are different, as the
 manoeuvrability of fruit flies is only limited by neural delays and that
 of hummingbirds could be limited by all three factors. In addition, the
 manoeuvrability also appears to be the highest about the roll axis as it
 requires the least muscle mechanical power and can tolerate the largest
 neural delays.
description: Data sets and analysis
 codeThe files here contain
 the datasets and analysis code that support this article. They are 1.
 Modeling - contain data and code used to analyze the effects of neural and
 biomechanical delays 2. Aerodynamics - contains code used to estimate
 damping coefficient 3. Power - contains code used to estimate power 4.
 Stability Margin - contains code used to calculate stability
 matgin
DOI: 10.15468/dl.app64w
title: Occurrence Download

description: A dataset containing 16305 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, 28eb1a3f-1c15-4a95-931a-4af90ecb574d)",
 "TaxonKey is Cornu aspersum"
 ]
}

 The dataset includes 16305 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001435-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.