cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7k22p
title: Data from: Variation in two phases of post-winter development of a butterfly

description: The temporal aspects of life cycle characteristics, such as diapause
 development, are under strong selection in seasonal environments.
 Fine-tuning of the life cycle may be particularly important to match the
 phenology of potential mates and resources as well as for optimizing
 abiotic conditions at eclosion. Here, we experimentally study the spring
 phenology of the orange tip butterfly, Anthocharis cardamines, by
 analysing post-winter pupal development in three populations along a
 latitudinal cline in each of Sweden and the United Kingdom. These
 countries differ substantially in their seasonal temperature profile. By
 repeatedly recording pupal weights, we established that post-winter
 development has two separate phases, with a more rapid weight loss in the
 second phase than in the first, likely corresponding to a ramping up of
 the rate of development. Variation in the duration of the first phase
 contributed more strongly than the second phase to the differences in
 phenology between the localities and sexes. We found that insects from
 Sweden had a faster overall rate of development than those from the United
 Kingdom, which is consistent with countergradient variation, as Sweden is
 colder during the spring than the United Kingdom. Similar trends were not
 observed at the within-country scale, however. A cogradient pattern was
 found within Sweden, with populations from the north developing more
 slowly, and there was no clear latitudinal trend within the United
 Kingdom. In all localities, males developed faster than females. Our
 results point to the importance of variation in the progression of
 post-winter development for spring phenology.
description: postdia_datapostdia_dev_r1_r2analysis_postdiamale_female_compStan
DOI: 10.5061/dryad.b0vt6
title: Data from: Evolutionary history of a complex adaptation: tetrodotoxin resistance in salamanders

description: Understanding the processes that generate novel adaptive phenotypes is
 central to evolutionary biology. We used comparative analyses to reveal
 the history of tetrodotoxin (TTX) resistance in TTX-bearing salamanders.
 Resistance to TTX is a critical component of the ability to use TTX
 defensively but the origin of the TTX-bearing phenotype is unclear.
 Skeletal muscle of TTX-bearing salamanders (modern newts, family:
 Salamandridae) is unaffected by TTX at doses far in excess of those that
 block action potentials in muscle and nerve of other vertebrates. Skeletal
 muscle of non TTX-bearing salamandrids is also resistant to TTX but at
 lower levels. Skeletal muscle TTX-resistance in the Salamandridae results
 from the expression of TTX-resistant variants of the voltage-gated sodium
 channel NaV 1.4 (SCN4a). We identified four substitutions in the coding
 region of salSCN4a that are likely responsible for the TTX-resistance
 measured in TTX-bearing salamanders and variation at one of these sites
 likely explains variation in TTX-resistance among other lineages. Our
 results suggest that exaptation has played a role in the evolution of the
 TTX-bearing phenotype and provide empirical evidence that complex
 physiological adaptations can arise through the accumulation of beneficial
 mutations in the coding region of conserved proteins.
description: Key for
 electrophysiology data filesThis provides guidance
 for individual recording filesPhysiology
 Data.pdfData for
 SalNAVCompressed folder of
 recordings
DOI: 10.5061/dryad.km38g
title: Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

description: Background: Some clover species, particularly Trifolium subterraneum, have
 previously been reported to have highly unusual plastomes, relative to
 closely related legumes, enlarged with many duplications, gene losses and
 the presence of DNA unique to Trifolium, which may represent horizontal
 transfer. In order to pinpoint the evolutionary origin of this phenomenon
 within the genus Trifolium, we sequenced and assembled the plastomes of
 eight additional Trifolium species widely sampled from across the genus.
 Results: The Trifolium plastomes fell into two groups: those of Trifolium
 boissieri, T. strictum and T. glanduliferum (representing subgenus
 Chronosemium and subg. Trifolium section Paramesus) were tractable,
 assembled readily and were not unusual in the general context of Fabeae
 plastomes. The other Trifolium species (“core Trifolium”) proved
 refractory to assembly mainly because of numerous short duplications.
 These species form a single clade, which we call the “refractory clade”
 (comprising subg, Trifolium sections Lupinaster, Trifolium,
 Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the
 refractory clade are the presence of numerous short duplications and 7-15%
 longer genomes than the tractable species. Molecular dating estimates that
 the origin of the most recent common ancestor (MRCA) of the refractory
 clade is approximately 13.1 million years ago (MYA). This is considerably
 younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA)
 andTrifolium subg. Trifolium (16.1 MYA). Conclusions: We conclude that the
 unusual repetitive plastome type previously characterized in Trifolium
 subterraneum had a single origin within Trifolium and is characteristic of
 most (but not all) species of subgenus Trifolium. It appears that an
 ancestral plastome within Trifolium underwent an evolutionary change
 resulting in plastomes that either actively promoted, were permissive to,
 or were unable to control, duplications within the genome. The precise
 mechanism of this important change in the mode and tempo of plastome
 evolution deserves further investigation.
description: Trifolium_plastid_codingA concatenated matrix of 59 protein coding plastid genes. Only coding regions were used, introns and intergenic regions were excluded in the alignment, due to plastome rearrangements (see manuscript of further description). The alignment was generated using Mafft v7.053b using -auto flag and trimmed using TrimAl with the -automated1 flag. This process was pipelined using Plast2Phy (https://github.com/saemi/plast2phy).Trifolium_plastid_coding_MLML tree generated using GARLI (the config file is the ReadMe file). The model used GTR+G, based on a jModelTest search and an AIC test. 10 starts were prefromed and a 100 bootstrap replicates. Medicago truncatula is the outrgroup.
DOI: 10.5061/dryad.74gp6
title: Data from: Combined effects of turbulence and different predation regimes on zooplankton in highly colored water – implications for environmental change in lakes

description: In aquatic ecosystems, predation is affected both by turbulence and
 visibility, but the combined effects are poorly known. Both factors are
 changing in lakes in the Northern Hemisphere; the average levels of
 turbulence are predicted to increase due to increasing wind activities,
 while water transparency is decreasing, e.g., due to variations in
 precipitation, and sediment resuspension. We explored experimentally how
 turbulence influenced the effects of planktivorous fish and invertebrate
 predators on zooplankton when it was combined with low visibility caused
 by high levels of water color. The study was conducted as a factorial
 design in 24 outdoor ponds, using the natural zooplankton community as a
 prey population. Perch and roach were used as vertebrate predators and
 Chaoborus flavicans larvae as invertebrate predators. In addition to calm
 conditions, the turbulent dissipation rate used in the experiments was
 10−6 m2 s−3, and the water color was 140 mg Pt L−1. The results
 demonstrated that in a system dominated by invertebrates, predation
 pressure on cladocerans increased considerably under intermediate
 turbulence. Under calm conditions, chaoborids caused only a minor
 reduction in the crustacean biomass. The effect of fish predation on
 cladocerans was slightly reduced by turbulence, while predation on
 cyclopoids was strongly enhanced. Surprisingly, under turbulent conditions
 fish reduced cyclopoid biomass, whereas in calm water it increased in the
 presence of fish. We thus concluded that turbulence affects fish
 selectivity. The results suggested that in dystrophic
 invertebrate-dominated lakes, turbulence may severely affect the abundance
 of cladocerans. In fish-dominated dystrophic lakes, on the other hand,
 turbulence-induced changes in planktivory may considerably affect copepods
 instead of cladocerans. In lakes inhabited by both invertebrates and fish,
 the response of top-down regulation to turbulence resembles that in
 fish-dominated systems, due to intraguild predation. The changes in
 planktivorous predation induced by abiotic factors may possibly cascade to
 primary producers.
description: Mesocosm data for
 crustacean zooplankton under turbulenceMesocosm data, collected
 in the field. Data includes the raw crustacean zooplankton data collected
 during a six week study period per each sampling day and mesocosm
 (indicated by sample number); the biomass of crustacean zooplankton in
 each size class per sampling day and mesocosm (indicated by sample
 number); physico-chemical data measured in the mesocosms during each
 sampling day; and average RMS velocities measured for each mesocosm
 (indicated by pond). The treatments indicated by numbers in the file
 correspond to: 11=CALM-CNTRL; 12=CALM-I; 13=CALM-F; 14=CALM-IF;
 21=TURB-CNTRL; 22=TURB-I; 23=TURB-F; 24=TURB-IF.Harkonen_etal_PLOSONE_Zooplankton_mesocosmdata.xlsx
DOI: 10.5061/dryad.06bb5
title: Data from: Dispersal dynamics in food webs

description: Studies of food webs suggest that limited nonrandom dispersal can play an
 important role in structuring food webs. It is not clear, however, whether
 density-dependent dispersal fits empirical patterns of food webs better
 than density-independent dispersal. Here, we study a spatially distributed
 food web, using a series of population-dispersal models that contrast
 density-independent and density-dependent dispersal in landscapes where
 sampled sites are either homogeneously or heterogeneously distributed.
 These models are fitted to empirical data, allowing us to infer mechanisms
 that are consistent with the data. Our results show that models with
 density-dependent dispersal fit the α, β, and γ tritrophic richness
 observed in empirical data best. Our results also show that
 density-dependent dispersal leads to a critical distance threshold beyond
 which site similarity (i.e., β tritrophic richness) starts to decrease
 much faster. Such a threshold can also be detected in the empirical data.
 In contrast, models with density-independent dispersal do not predict such
 a threshold. Moreover, preferential dispersal from more centrally located
 sites to peripheral sites does not provide a better fit to empirical data
 when compared with symmetric dispersal between sites. Our results suggest
 that nonrandom dispersal in heterogeneous landscapes is an important
 driver that shapes local and regional richness (i.e., α and γ tritrophic
 richness, respectively) as well as the distance-decay relationship (i.e.,
 β tritrophic richness) in food webs.
description: Scientific names and
 numerical id of the plant, aphid and parasitoids species
 studiedInclude the scientific
 name of all the plant, aphid and parasitoids species as well as the id for
 each species and the site id where the data was
 collectedScientificNamesANDCodesPlantAphidParasitoids.csvid for each site and plant, aphid and parasitoid speciesInclude the id for each site and plant, aphid and parasitoid speciesSiteCodePlantAphidParasitoids.csvTotal number of tritrophic chains and the species composition of each chainInclude total number of tritrophic chains and the species composition of each chainNumberTritrophicChains.csvGeographic pairwise Euclidean distance for the 302 sampled sitesInclude the geographic pairwise Euclidean distance for the 302 sampled sitesGeographicEuclideanDistance.csv
DOI: 10.5061/dryad.7qs06
title: Data from: Developmental stress predicts social network position

description: The quantity and quality of social relationships, as captured by social
 network analysis, can have major fitness consequences. Various studies
 have shown that individual differences in social behaviour can be due to
 variation in exposure to developmental stress. However, whether these
 developmental differences translate to consistent differences in social
 network position is not known. We experimentally increased levels of the
 avian stress hormone corticosterone (CORT) in nestling zebra finches in a
 fully balanced design. Upon reaching nutritional independence, we released
 chicks and their families into two free-flying rooms, where we measured
 daily social networks over five weeks using passive integrated transponder
 tags. Developmental stress had a significant effect on social behaviour:
 despite having similar foraging patterns, CORT chicks had weaker
 associations to their parents than control chicks. Instead, CORT chicks
 foraged with a greater number of flock mates and were less choosy with
 whom they foraged, resulting in more central network positions. These
 findings highlight the importance of taking developmental history into
 account to understand the drivers of social organization in gregarious
 species.
description: Boogert et al. Raw
 DataThis datafile contains
 three worksheets. The first worksheet displays all the PIT-tag data as
 automatically recorded by the PIT-tag readers integrated in the bird
 feeder entrances (or 'antennae'; column E). The second worksheet
 contains information on the relatedness of birds, their life history
 traits, sex (1=male, 0=female) and CORT-treatment (1 = fed with CORT, 0 =
 control, NA=adult). The third worksheet contains info on the leg band
 numbers worn by the birds (referred to in the first worksheet) and their
 indices as reported in the second worksheet. Note that ID 100 refers to
 the experimenter (NJB).
DOI: 10.5061/dryad.83452
title: Data from: Dynamic visual cues induce jaw opening and closing by tiger beetles during pursuit of prey

description: In dynamic locomotory contexts, visual cues often trigger adaptive
 behaviour by the viewer, yet studies investigating how animals determine
 impending collisions typically employ either stationary viewers or
 objects. Here, we describe a dynamic situation of visually guided prey
 pursuit in which both impending prey contact and escape elicit observable
 adaptive behaviours in the pursuer, a predatory beetle. We investigated
 which visual cues may independently control opening and closing of the
 beetle's jaws during chases of prey dummies. Jaw opening and closing
 typically occur when prey is within the 60° binocular field, but not at
 specific distances, angular sizes or time-to-collision. We show that a
 sign change in the expansion rate of the target image precedes jaw opening
 (16 ms) and closing (35 ms), signalling to the beetle that it is gaining
 on the target or that the target is getting away. We discuss the
 ‘sloppiness' of such variation in the lag of the behavioural
 response, especially jaw closing, as an adaptation to uncertainty about
 target position due to degradation of the target image by motion blur from
 the fast-running beetle.
description: visual parameters during
 tiger beetle prey pursuitContains frame-by-frame
 data of visual parameters experienced by a tiger beetle when chasing a
 prey dummy. Variables were calculated from coordinates determined in each
 video frame, and smoothed using a 3-frame moving average. "Open"
 and "close" columns indicate frames where jaw opening/closing
 begins, with a lag of 0 to 20 frames before that event.tiger beetle jaw
 data.dat
DOI: 10.5061/dryad.cb58n
title: Data from: Inbreeding depression and purging in a haplodiploid: gender-related effects

description: Compared with diploid species, haplodiploids suffer less inbreeding
 depression because male haploidy imposes purifying selection on recessive
 deleterious alleles. However, alleles of genes only expressed in the
 diploid females are protected in heterozygous individuals. This leads to
 the prediction that haplodiploids suffer more from inbreeding effects on
 life-history traits controlled by genes with female-limited expression. To
 test this, we used a wild population of the haplodiploid mite Tetranychus
 urticae. First, negative effects of inbreeding were investigated by
 comparing maturation rate, juvenile survival, oviposition rate and
 longevity between lines created by three generations of either outbreeding
 or mother–son inbreeding. Second, purging through inbreeding was
 investigated by comparing the intensity of inbreeding depression between
 outbred families with known inbreeding/outbreeding mating histories.
 Negative effects of inbreeding and evidence for purging were found for the
 female trait oviposition rate, but not for juvenile survival and
 longevity. Both male and female maturation rate were negatively affected
 by inbreeding, most likely due to maternal effects because inbred
 offspring of outbred mothers was not affected. These results support the
 hypothesis that, in haplodiploids inbreeding effects and genetic variation
 due to deleterious recessive alleles may depend on gender.
description: data inbreeding paper
 Tetranychus urticaeThis Excel file contains
 the data of the two-part experiment on inbreeding depression and purging
 in Tetranychus urticae. The data of the two parts are presented in
 separate worksheets, labels are provided above the columns with comments
 explaining the labels.
DOI: 10.17866/rd.salford.30086731
title: Base Semantics - Rule Set

description: The rapid evolution of malware variants has increasingly undermined traditional signature-based detection techniques, which are easily evaded through obfuscation and polymorphism that preserve malicious functionality. This challenge is particularly acute in Internet of Things (IoT) environments, where device heterogeneity, resource constraints, and large-scale deployment limit the adoption of heavyweight security mechanisms. As a result, IoT systems have become prime targets for sophisticated malware campaigns, including botnets, ransomware, and spyware, highlighting the need for adaptive, lightweight, and behaviourally robust detection approaches. This paper addresses a fundamental limitation of existing malware detection systems by exploiting persistent semantic characteristics that remain invariant across evolving variants within malware families. A comprehensive methodology combining static, dynamic, and memory analysis is employed to extract core semantic features that capture essential malicious behaviours. These features are used to construct compact semantic signatures capable of detecting previously unseen and zero-day variants within the same family. Extensive experimental evaluation demonstrates that the proposed approach significantly improves detection accuracy while reducing the size of the signature database. Comparative analysis against three state-of-the-art anti-malware tools shows superior accuracy, lower memory overhead, and faster scanning performance. Overall, this work provides a robust and scalable semantic-based detection framework for both host-based and IoT security systems in an evolving malware landscape.
DOI: 10.17866/rd.salford.30086731.v1
title: Base Semantics - Rule Set

description: The rapid evolution of malware variants has increasingly undermined traditional signature-based detection techniques, which are easily evaded through obfuscation and polymorphism that preserve malicious functionality. This challenge is particularly acute in Internet of Things (IoT) environments, where device heterogeneity, resource constraints, and large-scale deployment limit the adoption of heavyweight security mechanisms. As a result, IoT systems have become prime targets for sophisticated malware campaigns, including botnets, ransomware, and spyware, highlighting the need for adaptive, lightweight, and behaviourally robust detection approaches. This paper addresses a fundamental limitation of existing malware detection systems by exploiting persistent semantic characteristics that remain invariant across evolving variants within malware families. A comprehensive methodology combining static, dynamic, and memory analysis is employed to extract core semantic features that capture essential malicious behaviours. These features are used to construct compact semantic signatures capable of detecting previously unseen and zero-day variants within the same family. Extensive experimental evaluation demonstrates that the proposed approach significantly improves detection accuracy while reducing the size of the signature database. Comparative analysis against three state-of-the-art anti-malware tools shows superior accuracy, lower memory overhead, and faster scanning performance. Overall, this work provides a robust and scalable semantic-based detection framework for both host-based and IoT security systems in an evolving malware landscape.
DOI: 10.5061/dryad.4k5st
title: Data from: Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria

description: Background: Microsatellite loci have high mutation rates and thus are
 indicative of mutational processes within the genome. By concentrating on
 the symbiotic and aposymbiotic cnidarians, we investigated if
 microsatellite abundances follow a phylogenetic or ecological pattern.
 Individuals from eight species were shotgun sequenced using 454 GS-FLX
 Titanium technology. Sequences from the three available cnidarian genomes
 (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera)
 were added to the analysis for a total of eleven species representing two
 classes, three subclasses and eight orders within the phylum Cnidaria.
 Results: Trinucleotide and tetranucleotide repeats were the most abundant
 motifs, followed by hexa- and dinucleotides. Pentanucleotides were the
 least abundant motif in the data set. Hierarchical clustering and log
 likelihood ratio tests revealed a weak relationship between phylogeny and
 microsatellite content. Further, comparisons between cnidaria harboring
 intracellular dinoflagellates and those that do not, show microsatellite
 coverage is higher in the latter group. Conclusions: Our results support
 previous studies that found tri- and tetranucleotides to be the most
 abundant motifs in invertebrates. Differences in microsatellite coverage
 and composition between symbiotic and non-symbiotic cnidaria suggest the
 presence/absence of dinoflagellates might place restrictions on the host
 genome.
description: Figure5_CnidarianTreeNetwickBayesian genealogy of ten cnidarian species studied, based on partial COI sequences (approx. 700 bp) in Newick format.Figure5_CnidarianTreeNewick.txtCnidarianProteinProtein alignment in Nexus format for the COI phylogeny. Includes Mr. Bayes block.ScirokoResultsAllforDryadScirokoResultsAll.xlsx