cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3053g
title: Data from: Extremely high frequency sensitivity in a ‘simple’ ear

description: An evolutionary war is being played out between the bat, which uses
 ultrasonic calls to locate insect prey, and the moth, which uses
 microscale ears to listen for the approaching bat. While the highest known
 frequency of bat echolocation calls is 212 kHz, the upper limit of moth
 hearing is considered much lower. Here, we show that the greater wax moth,
 Galleria mellonella, is capable of hearing ultrasonic frequencies
 approaching 300 kHz; the highest frequency sensitivity of any animal. With
 auditory frequency sensitivity that is unprecedented in the animal
 kingdom, the greater wax moth is ready and armed for any echolocation call
 adaptations made by the bat in the on-going bat-moth evolutionary war.
description: Galleria mellonella
 electrophysiology filesWaxmoth electrophysiology files
 - Biology Letters.zip
DOI: 10.5061/dryad.51256
title: Data from: The interaction of fatigue cracks with a residual stress field using thermoelastic stress analysis and synchrotron x-ray diffraction experiments

description: This article presents an experimental study on the fatigue behaviour of
 cracks emanating from cold-expanded holes utilising thermoelastic stress
 analysis (TSA) and synchrotron x-ray diffraction (SXRD) techniques with
 the aim of resolving the long-standing ambiguity in the literature
 regarding potential relaxation, or modification, of beneficial compressive
 residual stresses as a result of fatigue crack propagation. The crack
 growth rates are found to be substantially lower as the crack tip moved
 through the residual stress zone induced by cold expansion. The TSA
 results demonstrated that the crack tip plastic zones were reduced in size
 by the presence of the residual compressive stresses induced by cold
 expansion. The crack tip plastic zones were found to be insignificant in
 size in comparison to the residual stress zone resulting from cold
 expansion, which implied that they were unlikely to have had a notable
 impact on the surrounding residual stresses induced by cold expansion. The
 residual stress distributions measured along the direction of crack
 growth, using SXRD, showed no signs of any significant stress relaxation
 or redistribution, which validates the conclusions drawn from the TSA
 data. Fractographic analysis qualitatively confirmed the influence on
 crack initiation of the residual stresses induced by the cold expansion.
 It was found that the application of single compressive overload caused a
 relaxation, or reduction in the residual stresses, which has wider
 implications for improving the fatigue life.
description: SXRD
 dataThe file includes the
 data from the SXRD experimentsTSA
 dataThe file includes the
 data from the TSA experimentsCT plastic zone
 codeMatlab code for
 determining crack tip plastic zone
DOI: 10.5061/dryad.qn4br
title: Data from: Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

description: The RADseq technology allows researchers to efficiently develop thousands
 of polymorphic loci across multiple individuals with little or no prior
 information on the genome. However, many questions remain about the biases
 inherent to this technology. Notably, sequence misalignments arising from
 paralogy may affect the development of single nucleotide polymorphism
 (SNP) markers and the estimation of genetic diversity. We evaluated the
 impact of putative paralog loci on genetic diversity estimation during the
 development of SNPs from a RADseq dataset for the nonmodel tree species
 Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the
 frequency of putative paralogous RAD loci as a function of both the depth
 of coverage and the mismatch threshold allowed between loci. Putative
 paralogy was detected in a very variable number of loci, from 1% to more
 than 20%, with the depth of coverage having a major influence on the
 result. Putative paralogy artificially increased the observed degree of
 polymorphism and resulting estimates of diversity. The choice of the depth
 of coverage also affected diversity estimation and SNP validation: A low
 threshold decreased the chances of detecting minor alleles while a high
 threshold increased allelic dropout. SNP validation was better for the low
 threshold (4×) than for the high threshold (18×) we tested. Using the
 strategy developed here, we were able to validate more than 80% of the
 SNPs tested by means of individual genotyping, resulting in a readily
 usable set of 330 SNPs, suitable for use in population genetics
 applications.
description: Fastq_filesRaw sequencing data of the nine sequenced individuals of Robinia pseudoacaciaFastqcReportsreports about the quality of sequencing of each of the nine sequenced individuals of Robinia pseudoacacia
DOI: 10.5281/zenodo.18364822
title: TSSC comet-centered data products from TESS 3I/ATLAS observations

description: NASA's TESS performed dedicated observations of the comet 3I/ATLAS during January 15 and 22, 2026. This repository contains data products created by the TESS Science Support Center which are background corrected image time series and photometric time series. For more details on these observations visit the TSSC webpage. For details on this data set, how was created, and how to work with this data visit our notebook tutorials here.
DOI: 10.5061/dryad.142q2vb
title: Data from: Zebrafish aggression on the sub-second time-scale: evidence for mutual motor coordination and multi-functional attack maneuvers

description: Most animals fight by repeating complex stereotypic behaviors, yet the
 internal structure of these behaviors has rarely been dissected in detail.
 We characterized the internal structure of fighting behaviors by
 developing a machine learning pipeline that measures and classifies the
 behavior of individual unmarked animals on a sub-second timescale. This
 allowed us to quantify several previously hidden features of zebrafish
 fighting strategies. We found strong correlations between the velocity of
 the attacker and the defender indicating a dynamic matching of approach
 and avoidance efforts. While velocity matching was ubiquitous, the spatial
 dynamics of attacks showed phase-specific differences. Contest phase
 attacks were characterized by a paradoxical sideways attraction of the
 retreating animal towards the attacker suggesting that the defender
 combines avoidance maneuvers with display-like maneuvers. Post-resolution
 attacks lacked display-like features and the the defender was
 avoidance-focused. From the perspective of the winner, game theory
 modeling further suggested that highly energetically costly post
 resolution attacks occurred because the winner was trying to increase its
 relative dominance over the loser. Overall, the rich structure of
 zebrafish motor coordination during fighting indicates a greater
 complexity and layering of strategies than has previously been recognized.
description: code_and_dataA zipped folder containing both code and data in separate folders. Each code file is explained in the comments inside the code files. The data files are grouped into fights. Each fight is labelled according to the day each fight was filmed and the order in which this was done. Inside a fight folder, the tracked trajectories can be found in the data2_x.mat files. Colorx.mat files give animal color for some videos.
DOI: 10.15468/dl.b8ykvd
title: Occurrence Download

description: A dataset containing 3014 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "StateProvince is one of (La Jagua de Ibirico, Cesar)",
 "Year 2020-2026",
 "Country is one of (Colombia)",
 "GadmGid is one of (COL.12.14_2)",
 "PublishingOrg is one of (1a2bfe99-b7ca-4e3c-a5a2-18c85789e7d1, 188fd36a-2d61-4f35-8b67-d5529efb0005, e2e717bf-551a-4917-bdc9-4fa0f342c530, 8ee4c3d9-b194-4f81-b41a-402e5c077e05, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, 67c63221-0c74-4c18-97f9-e2b2acb739ce, 2a7e3080-28a9-11dd-97cd-b8a03c50a862, 112087f6-a6c0-4cee-8441-387f900d34f9, 69ad50d2-2560-42a4-b522-171f6eca4fa3, b8b274e0-3216-48b8-afea-5616ec326ce1)",
 "IucnRedListCategory is one of (EN, CR, VU, NT, LC)",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Material sample)",
 "OccurrenceStatus is one of (Present)",
 "TaxonKey is one of (Malvales [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 3014 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000382-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7j3rq
title: Data from: Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

description: A major goal of speciation research is to reveal the genomic signatures
 that accompany the speciation process. Genome scans are routinely used to
 explore genome-wide variation and identify highly differentiated loci that
 may contribute to ecological divergence, but they do not incorporate
 spatial, phenotypic or environmental data that might enhance outlier
 detection. Geographic cline analysis provides a potential framework for
 integrating diverse forms of data in a spatially explicit framework, but
 has not been used to study genome-wide patterns of divergence. Aided by a
 first-draft genome assembly, we combined an FCT scan and geographic cline
 analysis to characterize patterns of genome-wide divergence between
 divergent pollination ecotypes of Mimulus aurantiacus. FCT analysis of 58
 872 SNPs generated via RAD-seq revealed little ecotypic differentiation
 (mean FCT = 0.041), although a small number of loci were
 moderately-to-highly diverged. Consistent with our previous results from
 the gene MaMyb2, which contributes to differences in flower colour, 130
 loci have cline shapes that recapitulate the spatial pattern of trait
 divergence, suggesting that they may reside in or near the genomic regions
 that contribute to pollinator isolation. In the narrow hybrid zone between
 the ecotypes, extensive admixture among individuals and low linkage
 disequilibrium between markers indicate that most outlier loci are
 scattered throughout the genome, rather than being restricted to one or a
 few divergent regions. In addition to revealing the genomic consequences
 of ecological divergence in this system, we discuss how geographic cline
 analysis is a powerful but under-utilized framework for studying
 genome-wide patterns of divergence.
description: contigsA draft assembly generated form 100 bp non-overlapping paired-end reads (~500 bp insert) (SRA bioproject PRJNA317499) using the program Velvet
DOI: 10.5061/dryad.gd8gp17
title: Data from: Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species

description: Speciation is a complex process that is fundamental to the origins of
 biological diversity. While there has been considerable progress in our
 understanding of speciation, there are still many unanswered questions,
 especially regarding barriers to gene flow in diverging populations.
 Eucalyptus is an appropriate system for investigating speciation
 mechanisms since it comprises species that are rapidly evolving across
 heterogeneous environments. We examined patterns of genetic variation
 within and among six closely related Eucalyptus species in subgenus
 Eucalyptus section Eucalyptus in south-eastern Australia (commonly known
 as the ‘green ashes’). We used reduced representation genome sequencing to
 genotype samples from populations across altitudinal and latitudinal
 gradients. We found one species, Eucalyptus cunninghamii, to be highly
 genetically differentiated from the others, and a population of mallees
 from Mount Banks to be genetically distinct and therefore likely to be a
 new undescribed species. Only modest levels of differentiation were found
 between all other species in the study. There was population structure
 within some species (e.g. E. obstans) corresponding to geographical
 factors, indicating that vicariance may have played a role in the
 evolution of the group. Overall, we found that lineages within the green
 ashes are differentiated to varying extents, from strongly diverged to
 much earlier stages of the speciation continuum. Furthermore, our results
 suggest the green ashes represent a group where a range of mechanisms
 (e.g. reticulate evolution and vicariance) have been operating in concert.
 These findings not only offer insights into recent speciation mechanisms
 in Eucalyptus, but also other species complexes.
description: Speciation in the
 presence of gene flow_DArTseq_Report-DE15-1659DArTseq analysis of six
 Eucalyptus species from south-eastern Australia. The file comprises two
 datasets: Silico DArTs (presence/absence markers) and SNPs. The SNPs are
 presented in both single line format and two line
 format.Speciation in the presence of
 gene flow data_Report-DE15-1659.xlsx
DOI: 10.5061/dryad.nj5h5
title: Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)

description: As molecular phylogenetic analyses incorporate ever-greater numbers of
 loci, cases of cytonuclear discordance – the phenomenon in which nuclear
 gene trees deviate significantly from organellar gene trees – are being
 reported more frequently. Plant examples of topological discordance,
 caused by recent hybridization between extant species, are well known.
 However, examples of branch-length discordance are less reported in plants
 relative to animals. We use a combination of de novo assembly and
 reference-based mapping using short-read shotgun sequences to construct a
 robust phylogeny of the plastome for multiple individuals of all the
 common Populus species in North America. We demonstrate a case of
 strikingly high plastome divergence, in contrast to little nuclear genome
 divergence, in two closely related balsam poplars, Populus balsamifera and
 Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous
 studies with nuclear loci indicate that the two species (or subspecies)
 diverged since the late Pleistocene, whereas their plastomes indicate deep
 divergence, dating to at least the Pliocene (6–7 Myr ago). Our finding is
 in marked contrast to the estimated Pleistocene divergence of the nuclear
 genomes, previously calculated at 75 000 yr ago, suggesting plastid
 capture from a ‘ghost lineage’ of a now-extinct North American poplar.
description: Populus-aligned plastome
 sequence alignmentsWGS short reads were
 aligned to the Nisqually-1 chloroplast reference genome (GenBank:
 EF489041.1) using BWA version 0.6.2. For each position in the reference
 plastome, bases were called only if the coverage was greater than 1000
 reads, as the average read depth for each base pair was 7000 or greater.
 To improve accuracy, bases were only called if the 1000+ calls agreed for
 either the reference or alternate base for at least 80% of the reads. Any
 position not meeting these criteria was called as missing data. Indels
 were excluded for all analyses.populus_sal.phyManihot-aligned plastome sequence alignmentsUsing the same protocol as the Populus-aligned dataset, but aligned to the Manihot esculenta reference plastome (NCBI Reference Sequence: NC_010433.1).manihot.phypop_to_manihot_beauti.xmlXML file generated by BEAUTi for use by BEAST for dating analyses.pop_to_manihot_gtr.xmlpop_to_manihot.logBEAST log filepop_to_manihot_4.logpop_to_manihot.treesNEXUS tree file containing trees generated by BEAST.pop_to_manihot_4.treesns_vs_sDivergence statistics for the four species that were de novo assembled (P. trichocarpa, P. balsamifera, P. fremontii, Salix interior). These were calculated using scripts "parse_fasta_to_genes.pl" and "diffs.pl" from https://github.com/daisieh/phylogenomics/releases/tag/v1.01-nph
DOI: 10.5061/dryad.kt540
title: Data from: Range-wide ecological niche comparisons of parasite, hosts and dispersers in a vector-borne plant parasite system

description: Aim: To test whether the distribution of the mistletoe Phoradendron
 californicum is mediated by host distributions (host niche hypothesis,
 HNH), or by factors such as the mistletoe’s autecology (parasite niche
 hypothesis, PNH) or that of its vectors (vector niche hypothesis, VNH).
 Our null hypothesis is that the ecological niche of the mistletoe will not
 be distinct from that of its hosts or vectors; alternatively, mistletoe
 infections might appear in hosts only in regions where host distributions
 overlap suitable conditions for the parasite. Location: Sonoran and Mojave
 deserts, western North America. Methods: We used ecological niche
 modelling approaches to summarize suitable environmental conditions for
 hosts infected and uninfected with mistletoes, as well as for avian
 dispersers during winter and throughout the year. We compared ecological
 niches among pairs of species using background similarity tests in
 relation to the climatic conditions available and accessible to each
 species. Result:s Niche comparisons supported all PNH expectations, but
 none of the predictions of HNH or VNH. Main conclusions: Hosts and
 dispersers of mistletoes generally have distinct ecological niches;
 mistletoe infections occur in non-random environmental subsets of host and
 disperser ecological niches; mistletoe infections in different hosts,
 however, occur under similar climatic conditions. Hence, in this system,
 the parasite has a rather strictly circumscribed ecological niche, and
 host species become infected with mistletoe only where they overlap its
 suitable areas.
description: Mistletoe-infected and
 non-infected hosts and dispersers niche models and environmental
 dataASCII files of niche
 models and environmental data of mistletoe-infected and non-infected hosts
 and dispersers (year-round and winter).Lira-Noriega&Peterson_distributions_environments_ascii.zip
DOI: 10.5061/dryad.gm354
title: Data from: Resource partitioning by insectivorous bats in Jamaica

description: In this investigation, we use variation in wing morphology, echolocation
 behaviour, patterns of habitat use and molecular diet analysis to
 demonstrate that six species of sympatric insectivorous bats in Jamaica
 show significant differences that could explain resource partitioning
 among the species. High-intensity echolocating species that used shorter,
 broadband signals and had shorter, broader wings (Pteronotus macleayii,
 Pteronotus quadridens, Mormoops blainvillii) foraged most in edge
 habitats, but differed in timing of peak activity. P. macleayii and M.
 blainvillii differed in diet, but low sample size precluded diet analysis
 for P. quadridens. High-intensity echolocating species that used longer,
 more narrowband signals and had longer, narrower wings (Molossus molossus,
 Tadarida brasiliensis) foraged most in open areas and differed in diet
 from the other species. Two disparate species were most active in clutter
 (dense vegetation). Pteronotus parnellii used high-duty-cycle echolocation
 apparently specialized for detecting fluttering targets in clutter.
 Macrotus waterhousii used low-intensity, broadband echolocation calls and
 presumably uses prey-generated sounds when foraging. These two species
 also differed in diet. Our data show that differences in morphology and
 echolocation behaviour coincide with differences in habitat use and diet,
 resulting in minimal overlap in resource use among species.
description: File 1 Dryad
 EntryFile 2 Dryad Group
 IDFile 3 Dryad M
 blainvillii reps BLASTFile 4 Dryad M molossus
 reps BLASTFile 5 Dryad M
 waterhousii reps BLASTFile 6 Dryad P macleayi
 reps BLASTFile 7 Dryad P parnellii
 reps BLASTFile 8 Dryad T
 brasiliensis reps BLASTFile 9 Dryad Adult
 Insectivore MorphologyFile 10 Dryad
 AIFile 11 Dryad Flight
 speedsFile 12 Call
 ParametersDryad Read Me
 File
DOI: 10.5061/dryad.25f7g
title: Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics

description: Noncoding markers have a particular appeal as tools for phylogenomic
 analysis because, at least in vertebrates, they appear less subject to
 strong variation in GC content among lineages. Thus far, ultraconserved
 elements (UCEs) and introns have been the most widely used noncoding
 markers. Here we analyze and study the evolutionary properties of a new
 type of noncoding marker, conserved non-exonic elements (CNEEs), which
 consists of noncoding elements that are estimated to evolve slower than
 the neutral rate across a set of species. Although they often include
 UCEs, CNEEs are distinct from UCEs because they are not ultraconserved,
 and, most importantly, the core region alone is analyzed, rather than both
 the core and its flanking regions. Using a data set of 16 birds plus an
 alligator outgroup, and ∼3600 - ∼3800 loci per marker type, we found that
 although CNEEs were less variable than bioinformatically-derived UCEs or
 introns and in some cases exhibited a slower approach to branch resolution
 as determined by phylogenomic subsampling, the quality of CNEE alignments
 was superior to those of the other markers, with fewer gaps and missing
 species. Phylogenetic resolution using coalescent approaches was
 comparable among the three marker types, with most nodes being fully and
 congruently resolved. Comparison of phylogenetic results across the three
 marker types indicated that one branch, the sister group to the
 passerine+falcon clade, was resolved differently and with moderate
 (&gt; 70%) bootstrap support between CNEEs and UCEs or introns.
 Overall, CNEEs appear to be promising as phylogenomic markers, yielding
 phylogenetic resolution as high as for UCEs and introns but with fewer
 gaps, less ambiguity in alignments and with patterns of nucleotide
 substitution more consistent with the assumptions of commonly used methods
 of phylogenetic analysis.
description: Supplementary_Files_Edwards_CNEEs_2017Supplementary Files S1, S3, S4, S5, and S6.Supplementary File S2Alignment summary measures for all loci.Supplementary_FileS2.xlsxSupplementary File S7Summary of jModelTest output for all loci.Supplementary_FileS7.xlsxSupplementary_Figures_CNEEs_Edwards_2017Supplementary Figures S1-7.Raw_data_alignments_trees_CNEEs_Syst_Biol
DOI: 10.5061/dryad.11j304c
title: Data from: Hedonic processing in humans is mediated by an opioidergic mechanism in a mesocorticolimbic system

description: It has been hypothesized that the pleasure of a reward in humans is
 mediated by an opioidergic system involving the hypothalamus, nucleus
 accumbens and the amygdala. Importantly, enjoying the pleasure of a reward
 is distinct from incentive salience induced by cues predicting the reward.
 We investigated this issue using a within subject, pharmacological
 challenge design with the opioid receptor antagonist naloxone and fMRI.
 Our data show that blocking opioid receptors reduced pleasure associated
 with viewing erotic pictures more than viewing symbols of reward such as
 money. This was paralleled by a reduction of activation in the ventral
 striatum, lateral orbitofrontal cortex, amygdala, hypothalamus and medial
 prefrontal cortex. Crucially, the naloxone induced activation decrease was
 observed at reward delivery, but not during reward anticipation,
 indicating that blocking opioid receptors decreases the pleasure of
 rewards in humans.
description: Data for
 paperreadme.txt files within
 ZIP archivedata_upload.zip