cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.09743
title: Data from: Extreme environments facilitate hybrid superiority - the story of a successful Daphnia galeata × longispina hybrid clone

description: Hybridization within the animal kingdom has long been underestimated.
 Hybrids have often been considered less fit than their parental species.
 In the present study, we observed that the Daphnia community of a small
 lake was dominated by a single D. galeata × D. longispina hybrid clone,
 during two consecutive years. Notably, in artificial community set-ups
 consisting of several clones representing parental species and other
 hybrids, this hybrid clone took over within about ten generations. Neither
 the fitness assay conducted under different temperatures, or under crowded
 and non-crowded environments, nor the carrying capacity test revealed any
 outstanding life history parameters of this hybrid clone. However, under
 simulated winter conditions (i.e. low temperature, food and light), the
 hybrid clone eventually showed a higher survival probability and higher
 fecundity compared to parental species. Hybrid superiority in cold-adapted
 traits leading to an advantage of overwintering as parthenogenetic
 lineages might consequently explain the establishment of successful
 hybrids in natural communities of the D. longispina complex. In extreme
 cases, like the one reported here, a superior hybrid genotype might be the
 only clone alive after cold winters. Overall, superiority traits, such as
 enhanced overwintering here, might explain hybrid dominance in nature,
 especially in extreme and rapidly changing environments. Although any
 favoured gene complex in cyclic parthenogens could be frozen in successful
 clones independent of hybridization, we did not find similarly successful
 clones among parental species. We conclude that the emergence of the
 observed trait is linked to the production of novel recombined hybrid
 genotypes.
description: microsatellite data
 Feldmochinger Lakegenepop file of the
 microsatellite raw data of the Feldmochinger Lake from 2008 till
 2013microsatellitesFELDmicrosatellite data competition experimentgenepop file of the microsatellite data of the competition experiments including the reference MLGs from the experimental clonescompetitionmicrosattelite data for the UPGMA analysisgenepop file of the microsatellite data of the hybrids of Feldmochinger Lake including experimental hybrid clone of other lakesUPGMAFeldmochingerLakeraw data overwintering experimentoverwintering.csvraw data crowding experimentcrowding.csvrawdata temperature experimenttemperature.csvrawdata carryingcapacityrawdatacarryingcapacity.csvcaculated carryingcapacitycarryingcapacity.csv
DOI: 10.5061/dryad.6cc5h8f
title: Data from: Clinical reasoning: a 14-year-old girl with headache, seizures, and confusion

description: In this report, we characterized describe a 14-year-old girl who developed
 progressive cerebral venous sinus thrombosis (CVST) and, with multiple
 organs and systems disfunction in 7 days which are similar to Marfan
 Syndrome in partial clinical characteristics. Through clinical phenotype
 and gene detection information, During our workup we uncovered we found
 two novel compound heterozygous mutations of cystathionine beta-synthase
 (CBS) gene, c.551 T&gt;C and c.949 A&gt;G, leading to
 hyperhomocysteinemia (HHcy). This, which suggested an irreplaceable
 correlation in likely led to her CVST and was a well answer for the
 multiple organs and systems failure in the case multiorgan dysfunction.
 This case highlights that (1) HHcy is of great clinical significance in
 CVST young patients; and (2) for patients with HHcy, excluding all
 exogenous factors of HHcy such as dietary deficiency of vitamins, genetic
 factors. neurologists should recognize the potential genetic component to
 this disorder, especially when there is a strong family history and
 multisystem failure, should be paid much more attention, especially
 accompanied with multiple organs and systems disfunction and/or patient
 family history.
description: Clinical reasoning: A
 14-year-old girl with headache, seizures, and confusion.Comparison of the
 sisters clinical characters. Primers used for mutation screening in CBS
 gene. Sequence results of CBS and MTHFR mutations. Mutations identified in
 this family with homocystinuria.The information of controls. Ethics
 Approval.supplementary
 information.doc
DOI: 10.5061/dryad.3m5c4
title: Data from: Constrained evolution of the sex comb in Drosophila simulans

description: Male fitness is dependent on sexual traits that influence mate acquisition
 (pre-copulatory sexual selection) and paternity (post-copulatory sexual
 selection), and while many studies have documented the form of selection
 in one or the other of these arenas, fewer have done it for both.
 Nonetheless, it appears that the dominant form of sexual selection is
 directional, although theoretically, populations should converge on peaks
 in the fitness surface, where selection is stabilizing. Many factors,
 however, can prevent populations from reaching adaptive peaks. Genetic
 constraints can be important if they prevent the development of highest
 fitness phenotypes, as can the direction of selection if it reverses
 across episodes of selection. In this study, we examine the evidence that
 these processes influence the evolution of the multivariate sex comb
 morphology of male Drosophila simulans. To do this, we conduct a
 quantitative genetic study together with a multivariate selection analysis
 to infer how the genetic architecture and selection interact. We find
 abundant genetic variance and covariance in elements of the sex comb.
 However, there was little evidence for directional selection in either
 arena. Significant nonlinear selection was detected prior to copulation
 when males were mated to non-virgin females, and post-copulation during
 sperm offence (again with males mated to non-virgins). Thus contrary to
 our predictions, the evolution of the D. simulans sex comb is limited
 neither by genetic constraints nor by antagonistic selection between pre-
 and post-copulatory arenas, but nonlinear selection on the multivariate
 phenotype may prevent sex combs from evolving to reach some fitness
 maximising optima.
description: RawQGSexCombDataHalf sib breeding design to estimate the genetic variances and covariance for sex comb traits.RawSexCombFitnessDataSelection on sex combs across several episodes of selection.
DOI: 10.5061/dryad.cn1c3
title: Data from: Temporal population genetic structure in the pollen pool for flowering time: a field experiment with Brassica rapa (Brassicaceae)

description: Premise of the study: Assortative mating by flowering time can cause
 temporal genetic structure in species with heritable flowering times. A
 strong temporal structure, when coupled with a seasonal shift in
 selection, may lead to adaptive temporal clines. We implemented a
 prospective and retrospective method to estimate the temporal genetic
 structure in the pollen pool of Brassica rapa. Methods: The prospective
 method uses flowering schedules to estimate the seasonal shift in the
 pollen donors’ phenotype. By examining the offspring generation, we can
 get a direct estimate of temporal genetic structure, i.e., a retrospective
 estimate. However, this estimate is problematic because of the phenotypic
 correlation of the trait of interest, flowering time, between dam and
 sire. We developed a novel retrospective method that isolates flowering
 time by holding the maternal contribution constant and sampled the pollen
 pool in eight open-pollinated field plots throughout the flowering season.
 Key results: We found temporal genetic structure for flowering time in
 seven of the eight field plots. Interestingly, the direct (retrospective)
 temporal structure estimate was 35% larger than the prospective estimate
 based on flowering schedules. Spatial clumping of pollen donors did not
 affect temporal structure, but structure intensified when heritability was
 experimentally enhanced. Conclusions: Temporal genetic structure,
 especially for flowering time, likely occurs in many plant populations and
 may be underestimated using a prospective method. We discuss the
 genome-wide consequences of temporal genetic structure and the potential
 for adaptive temporal clines in plant populations.
description: Ison&WeisDataFilesThis folder includes 6 data files, 3 metadata files, and 1 R script.
DOI: 10.5061/dryad.9n815
title: Data from: Molecular and pollen-based vegetation analysis in lake sediments from central Scandinavia

description: Plant and animal biodiversity can be studied by obtaining DNA directly
 from the environment. This new approach in combination with the use of
 generic barcoding primers (metabarcoding) has been suggested as
 complementary or alternative to traditional biodiversity monitoring in
 ancient soil sediments. However, the extent to which metabarcoding truly
 reflects plant composition remains unclear, as does its power to identify
 species with no pollen or macrofossil evidence. Here, we compared
 pollen-based and metabarcoding approaches to explore the Holocene plant
 composition around two lakes in central Scandinavia. At one site, we also
 compared barcoding results with those obtained in earlier studies with
 species-specific primers. The pollen analyses revealed a larger number of
 taxa (46), of which the majority (78%) was not identified by
 metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed
 identification to a lower taxonomical level. The combined analyses
 identified 52 taxa. The barcoding primers may favour amplification of
 certain taxa, as they did not detect taxa previously identified with
 species-specific primers. Taphonomy and selectiveness of the primers are
 likely the major factors influencing these results. We conclude that
 metabarcoding from lake sediments provides a complementary, but not an
 alternative, tool to pollen analysis for investigating past flora. In the
 absence of other fossil evidence, metabarcoding gives a local and
 important signal from the vegetation, but the resulting assemblages show
 limited capacity to detect all taxa, regardless of their abundance around
 the lake. We suggest that metabarcoding is followed by pollen analysis and
 the use of species-specific primers to provide the most comprehensive
 signal from the environment.
description: The core pollen and age
 data filetrnL sequences and
 taxonomic assignments NGStrnL sequences and
 taxonomic assignments Sanger
DOI: 10.5061/dryad.1rr88
title: Data from: The 5S rDNA gene family in mollusks: characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels

description: Several reports on the characterization of 5S ribosomal DNA (5S rDNA) in
 various animal groups have been published to date, but there is a lack of
 studies analyzing this gene family in a much broader context. Here, we
 have studied 5S rDNA variation in several molluskan species, including
 bivalves, gastropods, and cephalopods. The degree of conservation of
 transcriptional regulatory regions was analyzed in these lineages,
 revealing a conserved TATA-like box in the upstream region. The evolution
 of the 120 bp coding region (5S) was also studied, suggesting the
 occurrence of paralogue groups in razor clams, clams, and cockles. In
 addition, 5S rDNA sequences from 11 species and seven genus of Mytilidae
 Rafinesque, 1815 mussels were sampled and studied in detail. Four
 different 5S rDNA types, based on the nontranscribed spacer region were
 identified. The phylogenetic analyses performed within each type showed a
 between-species gene clustering pattern, suggesting ancestral
 polymorphism. Moreover, some putative pseudogenized 5S copies were also
 identified. Our report, together with previous studies that found high
 degree of intragenomic divergence in bivalve species, suggests that
 birth-and-death evolution may be the main force driving the evolution of
 5S rDNA in these animals, even at the genus level.
description: Supplementary
 filesSupplementary files
 (Tables and Figures)Sequence alignments,
 clones analyzed and constraints applied
DOI: 10.5061/dryad.6dn80
title: Data from: Does hybridization with a widespread congener threaten the long-term persistence of the Eastern Alpine rare local endemic Knautia carinthiaca?

description: Interspecific hybridization, especially when regularly followed by
 backcrossing (i.e., introgressive hybridization), conveys a substantial
 risk for many endangered organisms. This is particularly true for narrow
 endemics occurring within distributional ranges of widespread congeners.
 An excellent example is provided by the plant genus Knautia
 (Caprifoliaceae): Locally endemic K. carinthiaca is reported from two
 isolated populations in southern Austria situated within an area
 predominantly occupied by widespread K. arvensis. While K. carinthiaca
 usually inhabits low-competition communities on rocky outcrops, K.
 arvensis occurs mainly in dry to mesic managed grasslands, yet both
 species can coexist in marginal environments and were suspected to
 hybridize. Flow cytometry revealed that diploid K. carinthiaca only occurs
 at its locus classicus, whereas the second locality is inhabited by the
 morphologically similar but tetraploid K. norica. In the, therefore,
 single population of K. carinthiaca, flow cytometry and AFLP
 fingerprinting showed signs of introgressive hybridization with diploid K.
 arvensis. Hybridization patterns were also reflected in intermediate
 habitat preferences and morphology of the hybrids. Environmental barriers
 to gene flow seem to prevent genetic erosion of K. carinthiaca individuals
 from the core ecological niches, restricting most introgressed individuals
 to peripheral habitats. Efficient conservation of K. carinthiaca will
 require strict protection of its habitat and ban on forest clear cuts in a
 buffer zone to prevent invasion of K. arvensis. We demonstrate the large
 potential of multidisciplinary approaches combining molecular, cytometric,
 and ecological tools for a reliable inventory and threat assessment of
 rare species.
description: Certner_2015_EcolEvolThis MS Excel file contains all the primary data and some partial results.
DOI: 10.5061/dryad.5vv33
title: Data from: Contrasting diversity and demographic signals in sympatric narrow range endemic shrubs of the southwest Western Australian semi-arid zone

description: Comparative studies of sympatric species that integrate both
 phylogeographical and population genetic approaches provide insight into
 how demographic events and life history traits shape adaptive potential
 and drive species persistence. Such studies are rare for species-rich and
 strongly structured environments, especially those of the southern
 hemisphere. For two sympatric, perennial shrubs of the south-west Western
 Australian semi-arid zone, Grevillea globosa and Mirbelia sp.
 Bursarioides, we assessed historical and contemporary genetic diversity
 and structure, demographic processes and ratios of pollen to seed
 dispersal. Phylogeographical structure was not detected and haplotype
 networks were star-like. Number of haplotypes, nucleotide diversity,
 haplotype diversity, and allelic diversity were statistically
 significantly lower for G. globosa than for M. sp. Bursarioides. Levels of
 haplotype divergence and more contemporary genetic divergence and expected
 heterozygosity were lower for G. globosa than for M. sp. Bursarioides, but
 differences were not statistically significant. Both species exhibited
 signals of isolation by distance and low pollen to seed dispersal ratios
 (5.26:1 and 6.88:1). Grevillea globosa displayed signals of historical and
 contemporary demographic expansion. Results imply an important role for
 aspects of seed ecology that impact population demography, as well as
 direct dispersal and a significant contribution of seed dispersal to
 genetic connectivity in a semi-arid landscape.
description: Genotype data for 12
 nuclear microsatellite loci for Grevillea globosa in GenAlEx
 formatGenotype data for 12
 nuclear microsatellite loci for Grevillea globosa in GenAlEx
 format.Gg
 ms data for dryad.xlsxGenotype data for 12
 nuclear microsatellite loci for Mirbelia sp. Bursarioides in GenAlEx
 format.Genotype data for 12
 nuclear microsatellite loci for Mirbelia sp. Bursarioides in GenAlEx
 format.Mb
 ms data for dryad.xlsxHaplotype data for
 Grevillea globosa in nexus format.Haplotype data for
 Grevillea globosa in nexus format.Gg haps data for
 dryad.nexHaplotype data for
 Mirbelia sp. Bursarioides in nexus format.Haplotype data for
 Mirbelia sp. Bursarioides in nexus format.Mb haps data for
 dryad.nex
DOI: 10.5061/dryad.677v3
title: Data from: Recent ecological selection on regulatory divergence is shaping clinal variation in Senecio on Mount Etna

description: The hybrid zone on Mount Etna (Sicily) between Senecio aethnensis and
 Senecio chrysanthemifolius (two morphologically and physiologically
 distinct species) is a classic example of an altitudinal cline.
 Hybridization at intermediate altitudes and gradients in phenotypic and
 life-history traits occur along altitudinal transects of the volcano. The
 cline is considered to be a good example of ecological selection with
 species differences arising by divergent selection opposing gene flow.
 However, the possibility that the cline formed from recent secondary
 contact following an allopatric phase is difficult to exclude. We
 demonstrate a recent split between S. aethnensis and S. chrysanthemifolius
 (as recent as ∼32,000 years ago) and sufficient gene flow (2Nm &gt; 1)
 to have prevented divergence (implicating a role for diversifying
 selection in the maintenance of the cline). Differentially expressed genes
 between S. aethnensis and S. chrysanthemifolius exhibit significantly
 higher genetic divergence relative to “expression invariant” controls,
 suggesting that species differences may in part be mediated by divergent
 selection on differentially expressed genes involved with altitude-related
 adaptation. The recent split time and the absence of fixed differences
 between these two ecologically distinct species suggest the rapid
 evolution to an altitudinal cline involving selection on both sequence and
 expression variation.
description: 1 Arlequin input file
 for DNA sequences Table S4These haplotypes should
 accompany file 1 in the same folder2 Arlequin input file
 for microsatellites Table S4
DOI: 10.5281/zenodo.18323560
title: DArch: LLM-Assisted Logical Architecture Modeling Tool for Safety-Critical Software (Experience Results)

description: The dataset consists of two components.

The first is a compressed archive named “FSE 2026 Tool Demo”, which contains our experimental data, as well as publicly available tool links and tutorials.

The second is a PDF file titled “LusGen_ Leveraging LLMs for Safety-Critical Lustre Design and Requirements Traceability.pdf”, which presents the paper on intelligent detailed design generation and intelligent generation of requirements traceability links.
DOI: 10.5281/zenodo.18382301
title: DArch: LLM-Assisted Logical Architecture Modeling Tool for Safety-Critical Software (Experience Results)

description: The dataset consists of two components.

The first is a compressed archive named “FSE 2026 Tool Demo”, which contains our experimental data, as well as publicly available tool links and tutorials.

The second is a PDF file titled “LusGen_ Leveraging LLMs for Safety-Critical Lustre Design and Requirements Traceability.pdf”, which presents the paper on intelligent detailed design generation and intelligent generation of requirements traceability links.
DOI: 10.5061/dryad.8994
title: Data from: Hybridization, species collapse, and species reemergence after disturbance to premating mechanisms of reproductive isolation

description: There are now a number of well-studied cases in which hybridization
 between closely related sympatric species has increased, sometimes
 resulting in the replacement of species pairs by hybrid swarms. Many of
 these cases have been linked to anthropogenic environmental change, but
 the mechanisms leading from environmental change to species collapse, and
 the long-term effects of hybridization on species pairs, remain poorly
 understood. We used an individual-based stochastic simulation model to
 explore the conditions under which disturbances that weaken premating
 barriers to reproduction between sympatric species might lead to increased
 hybridization and to species collapse. Disturbances often resulted in
 bouts of hybridization, but in many cases strong reproductive isolation
 spontaneously reemerged. This was sometimes true even after hybrid swarms
 had replaced parental species. The reemergence of species pairs was most
 likely when disturbances were of short duration. Counterintuitively,
 incipient species pairs were more likely to reemerge after strong but
 temporary disturbances than after weaker disturbances of the same
 duration. Even temporary bouts of hybridization often led to substantial
 homogenization of species pairs. This suggests that ecosystem managers may
 be able to refill ecological niches, but in general will not be able to
 resurrect lost species after species collapse.
description: Dryad
 files"collapse_trails.m" is MatLab code used to test the resistance and resilience of simulated incipient species pairs to disturbance. "select6t_sc.m", "mateD6kt_sc.m", and "checkspec.m" are functions called by "collapse_trials.m". Files beginning in "rs" are the simulated incipient species pairs used in the published study. Alternatively, new simulated incipient species can be generated by modifying "collapse_trials.m".
DOI: 10.5061/dryad.rn6gg
title: Data from: High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement

description: Although adaptive change is usually associated with complex changes in
 phenotype, few genetic investigations have been conducted of adaptations
 that involve sets of high dimensional traits. Microarrays have supplied
 high-dimensional descriptions of gene expression, and phenotypic change
 resulting from adaptation often results in large-scale changes in gene
 expression. We demonstrate how genetic analysis of large-scale changes in
 gene expression generated during adaptation can be accomplished by
 determining by high-dimensional variance partitioning within classical
 genetic experimental designs. A microarray experiment conducted on a panel
 of recombinant inbred lines (RILs) generated from two populations of
 Drosophila serrata that have diverged in response to natural selection,
 revealed genetic divergence in 10.6% of 3762 gene products examined. Over
 97% of the genetic divergence in transcript abundance was explained by
 only 12 genetic modules. The two most important modules, explaining 50% of
 the genetic variance in transcript abundance, were genetically correlated
 with the morphological traits that are known to be under selection. The
 expression of three candidate genes from these two important genetic
 modules was assessed in an independent experiment using qRT-PCR on 430
 individuals from the panel of RILs, and confirmed the genetic association
 between transcript abundance and morphological traits under selection.
description: RIL RTPCR and CHC
 dataqRT-PCR data for three
 genes (AmyPres CL481res NinaDres) and cuticular hydrocarbons (lc1 lc2 lc3
 lc5 lc6 lc7 lc8 lc9) for 430 individuals from 41 RILs and 2 parental lines
 (EUNGC and FORS4). Canonical variates for genes (V1, V2, V3) and CHCs (W1,
 W2, W3) are also given.15 RIL CHC and gene
 factor meansRIL line means for 12
 genetic factors and 9 cuticular hydrocarbons for the line-mean analysis
 presented in Table 2.