cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.47m18
title: Data from: Molecular evolution of key metabolic genes during transitions to C4 and CAM photosynthesis

description: PREMISE OF THE STUDY: Next-generation sequencing facilitates rapid
 production of well-sampled phylogenies built from very large genetic
 datasets, which can then be subsequently exploited to examine the
 molecular evolution of the genes themselves. We present an evolutionary
 analysis of 83 gene families (19 containing carbon-concentrating mechanism
 (CCM) genes, 64 containing non-CCM genes) in the portullugo clade
 (Caryophyllales), a diverse lineage of mostly arid-adapted plants that
 contains multiple evolutionary origins of all known photosynthesis types
 in land plants (C3, C4, CAM, C4-CAM, and various intermediates). METHODS:
 We inferred a phylogeny of 197 individuals from 167 taxa using
 coalescent-based approaches, and individual gene family trees using
 maximum likelihood. Positive selection analyses were conducted on
 individual gene family trees with a mixed effects model of evolution
 (MEME). We devised new indices to compare levels of convergence and
 prevalence of particular residues between CCM and non-CCM genes, and
 between species with different photosynthetic pathways. KEY RESULTS:
 Contrary to expectation, there were no significant differences in the
 levels of positive selection detected in CCM versus non-CCM genes.
 However, we documented a significantly higher level of convergent amino
 acid substitutions in CCM genes, especially in C4 taxa. CONCLUSIONS: Our
 analyses reveal a new suite of amino acid residues putatively important
 for C4 and CAM function. We discuss both the advantages and challenges of
 using targeted enrichment sequence data for exploratory studies of
 molecular evolution.
description: Goolsby_et_al_AJBThis zip file contains: 1) the ASTRAL species tree with bootstrap support, 2) a folder called gene_family_sequences which contains the alignments for the 83 gene families, and 3) a folder called gene_family_trees which contains RAxML gene family trees generated from the sequences in the gene_family_sequences folder.Goolsby_et_al_trees_and_alignments.zip
DOI: 10.17632/h4bxjk84jb.1
title: Spear-Phishing en español: dataset de correos dirigidos con señales de personalización (SpearPhishMX)

description: El español se utiliza ampliamente en campañas de phishing en el mundo real; sin embargo, los corpus públicos disponibles suelen centrarse en phishing genérico y rara vez permiten estudiar de forma sistemática el carácter dirigido (personalizado) que distingue al spear-phishing, ni ofrecen versiones publicables que reduzcan el riesgo de exponer información sensible. En consecuencia, parte de la investigación en español termina abordando el problema como una detección binaria sin capturar con suficiente fidelidad señales observables de personalización y sin controles de seguridad adecuados para el intercambio de datos.

Spear Phishing en español (SpearPhishMX) aborda esta brecha proporcionando un conjunto de 3,006 correos electrónicos en español etiquetados para clasificación binaria (etiqueta=1 spear-phishing; etiqueta=0 legítimo). Cada registro se identifica mediante una clave hash estable e incluye asunto y una representación del cuerpo preparada para investigación y análisis reproducible. El dataset incorpora una capa de atributos derivados útiles para evaluación comparativa y XAI, incluyendo estadísticas de URLs (p. ej., conteo_urls, urls_desactivadas) y variables para caracterizar personalización dirigida (p. ej., dirigido_a_persona_v2, destinatario_detectado_v2, destinatario_tiene_apellido_v2, destinatario_normalizado).

Un componente definitorio es su enfoque de publicación responsable. La versión pública incluye cuerpo_sanitizado, donde se anonimiza información potencialmente sensible (por ejemplo, correos, teléfonos y patrones fiscales/financieros) mediante marcadores y se desactivan URLs (defanged) para evitar clics accidentales. Adicionalmente, se ofrece un paquete de acceso restringido que conserva una representación más cercana al texto original, pero igualmente protegida mediante redacción de PII y defang de enlaces, con fines de auditoría y trazabilidad.

El conjunto de datos se distribuye en CSV (UTF-8, separador “;”) y se acompaña de documentación (README) y un esquema JSON de columnas para facilitar reutilización. SpearPhishMX se publica exclusivamente para investigación defensiva en ciberseguridad, ML/NLP y explicabilidad; no debe emplearse para campañas ofensivas ni para reactivar/operacionalizar enlaces.
DOI: 10.5061/dryad.c4r81
title: Data from: Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age

description: We investigated how population changes and fluctuations in the pink-footed
 goose might have been affected by climatic and anthropogenic factors.
 First, genomic data confirmed the existence of two separate populations:
 western (Iceland) and eastern (Svalbard/Denmark). Second, emographic
 inference suggests that the species survived the last glacial period as a
 single ancestral population with a low population size (100-1,000
 individuals) that split into the current populations at the end of the
 Last Glacial Maximum with Iceland being the most plausible glacial refuge.
 While population changes during the last glaciation were clearly
 environmental, we hypothesize that more recent demographic changes are
 human-related: (1) the inferred population increase in the Neolithic is
 due to deforestation to establish new lands for agriculture, increasing
 available habitat for pink-footed geese (2) the decline inferred during
 the Middle Ages is due to human persecution and (3) improved protection
 explains the increasing demographic trends during the 20th century. Our
 results suggest both environmental (during glacial cycles) and
 anthropogenic effects (more recent) can be a threat to species survival.
description: Haplotype_Dataset_Genotyped_All_IndividualsHaplotype data obtained using loci genotyped in all individualsHaplotype_Dataset_Genotyped_66%IndividualsHaplotype data obtained using loci genotyped in &gt;66.67% of the individuals
DOI: 10.17632/gd8cj57std
title: Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates

description: This repository contains the data for the paper "Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates"

Buddhabhushan Girish Salve, Sonal H, Nagarjun Vijay

Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India

*Author for Correspondence: Nagarjun Vijay, nagarjun@iiserb.ac.in
DOI: 10.5061/dryad.gb682
title: Data from: The effects of sub-curative praziquantel treatment on life-history traits and trade-offs in drug-resistant Schistosoma mansoni

description: Natural selection acts on all organisms, including parasites, to maximise
 reproductive fitness. Drug resistance traits are often associated with
 life-history costs in the absence of treatment. Schistosomiasis control
 programmes rely on mass drug administration to reduce human morbidity and
 mortality. Although hotspots of reduced drug efficacy have been reported,
 resistance is not widespread. Using Bayesian State-Space Models (SSMs)
 fitted to data from an in vivo laboratory system, we tested the hypothesis
 that the spread of resistant Schistosoma may be limited by life-history
 costs not present in susceptible counterparts. Schistosoma mansoni
 parasites from a praziquantel–susceptible (S), a praziquantel–resistant
 (R) or a mixed line of originally resistant and susceptible parasites (RS)
 were exposed to a range of praziquantel doses. Parasite numbers at each
 life stage were quantified in their molluscan intermediate and murine
 definitive hosts across four generations, and SSMs were used to estimate
 key life-history parameters for each experimental group over time. Model
 outputs illustrated that parasite adult survival and fecundity in the
 murine host decreased across all lines, including R, with increasing drug
 pressure. Trade-offs between adult survival and fecundity were observed in
 all untreated lines, and these remained strong in S with praziquantel
 pressure. In contrast, trade-offs between adult survival and fecundity
 were lost under praziquantel pressure in R. As expected, parasite
 life-history traits within the molluscan host were complex, but trade-offs
 were demonstrated between parasite establishment and cercarial output. The
 observed trade-offs between generations within hosts, which were modified
 by praziquantel treatment in the R line, could limit the spread of R
 parasites under praziquantel pressure. Whilst such complex life-history
 costs may be difficult to detect using standard empirical methods, we
 demonstrate that SSMs provide robust estimates of life history parameters,
 aiding our understanding of costs and trade-offs of resistant parasites
 within this system and beyond.
description: Mouse_dataCounts of adults worms and miracidea of 3 different lines (susceptible, resistant and mixed resistant-susceptible) inside the mouse host exposed to three different treatments: control, low praziquantel dose and high praziquantel dose; across 4 generations. Mouse health parameters such as body, spleen and liver weight also available.Snail_dataCounts of cercariae of 3 different lines (susceptible, resistant and mixed resistant-susceptible) inside 2 different species of snail host, across 4 generations. The cercariae are from worms that had been exposed to three different treatments: control, low praziquantel dose and high praziquantel dose during passage in the mouse host. Snail health parameters such as egg masses and offspring production also available.
DOI: 10.17632/gd8cj57std.1
title: Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates

description: This repository contains the data for the paper "Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates"

Buddhabhushan Girish Salve, Sonal H, Nagarjun Vijay

Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India

*Author for Correspondence: Nagarjun Vijay, nagarjun@iiserb.ac.in
DOI: 10.5061/dryad.p781p
title: Data from: Intracontinental plant invader shows matching genetic and chemical profiles and might benefit from high defence variation within populations

description: 1. Whereas many studies have revealed mechanisms driving plant invasions
 between continents, research on intracontinental range-expanders is
 scarce. Therefore, we studied genetic, chemical and ecological traits of a
 range-expanding Brassicaceae, assuming that high genetic diversity should
 maintain chemical variation, which potentially benefits the invasion
 success. Moreover, we expected that within-individual defence diversity
 plays an essential role in biotic interactions. 2. We compared Bunias
 orientalis plants from 16 populations of native, invasive or exotic
 non-invasive origin. The genetic structure was investigated by analysing
 the plastid DNA and AFLPs. For characterisation of the leaf chemistry,
 metabolic fingerprinting and profiling of glucosinolates as defence
 compounds were performed. The plant defence potential was tested using the
 generalist herbivore Mamestra brassicae. 3. We found two major genetic
 lineages, which were mirrored in distinct chemical fingerprints of the
 plants. Genetic differentiation patterns point to a multiple introduction
 history of B. orientalis underlying the range expansion. Moreover, the
 genetic distance between individuals was correlated with the distance in
 chemical features. Genetic diversity tended to be reduced in potential
 leading edge (exotic) populations and was positively associated with
 quantitative metabolic diversity. Concentrations of indole glucosinolates
 were elevated in non-native populations and high glucosinolate diversity
 was associated with low herbivore survival. 4. Synthesis. This study
 suggests that the invasion success of this species may be facilitated by
 high chemical variation within populations. Moreover, high defence
 diversity within individuals of a population might be the main factor
 reducing herbivory and can be more important than the total concentration
 of defences. The combination of genetic and chemical analyses combined
 with bioassays revealed to be a powerful tool to study the differentiation
 between native and non-native populations and should be applied more often
 to explore intraspecific divergence.
description: raw_data_Tewes_et_al_2017raw data for AFLP loci, mass traces, glucosinolate concentrations, herbivore survival and population-based measures
DOI: 10.5061/dryad.jf7np
title: Data from: Disparity, diversity, and duplications in the Caryophyllales

description: The role played by whole genome duplication (WGD) in plant evolution is
 actively debated. WGDs have been associated with advantages such as
 superior colonization, various adaptations, and increased effective
 population size. However, the lack of a comprehensive mapping of WGDs
 within a major plant clade has led to uncertainty regarding the potential
 association of WGDs and higher diversification rates. Using seven
 chloroplast and nuclear ribosomal genes, we constructed a phylogeny of
 5036 species of Caryophyllales, representing nearly half of the extant
 species. We phylogenetically mapped putative WGDs as identified from
 analyses on transcriptomic and genomic data and analyzed these in
 conjunction with shifts in climatic occupancy and lineage diversification
 rate. Thirteen putative WGDs and 27 diversification shifts could be mapped
 onto the phylogeny. Of these, four WGDs were concurrent with
 diversification shifts, with other diversification shifts occurring at
 more recent nodes than WGDs. Five WGDs were associated with shifts to
 colder climatic occupancy. While we find that many diversification shifts
 occur after WGDs, it is difficult to consider diversification and
 duplication to be tightly correlated. Our findings suggest that
 duplications may often occur along with shifts in either diversification
 rate, climatic occupancy, or rate of evolution.
description: phylogenetic
 information- align.fasta =
 alignment - align.models = gene regions - align_w_shtest.tre = maximum
 likelihood tree with SH-like test listed - align_w_shtest_treepl_3samp.tre
 = maximum likelihood tree with divergence time estimation and 3 minimum
 samples - raxml_fasttree_sh_boot_all.tre = bootstrap tree set with SH-like
 test with divergence time estimationphylo.zipdiversification information- BS_summ_div.tre = bootstrap results for medusa diversification - ML_summ_div.tre = ML results for medusa diversificationdivers.zipclimate informationbioclimatic climate data for each speciesclimate_3samp.txt
DOI: 10.17632/btkw3phr5t.1
title: data for: Early diagenetic dolomitization in methane seep carbonates constrained by coupled Mo and Mg isotopes

description: Raw data for all figures in the manuscript to be published by Geochimica et Cosmochimica Acta as "Early diagenetic dolomitization in methane seep carbonates constrained by coupled Mo and Mg isotopes".
DOI: 10.5061/dryad.9202s
title: Data from: Phylogenomic analyses reveal extensive gene flow within the magic flowers (Achimenes)

description: Premise of the study: The Neotropical Gesneriaceae is a lineage known for
 its colorful and diverse flowers, as well as an extensive history of
 intra- and intergeneric hybridization, particularly among Achimenes (the
 magic flowers) and other members of the subtribe Gloxiniinae. Despite
 numerous studies seeking to elucidate the evolutionary relationships of
 these lineages, relatively few have sought to infer specific patterns of
 gene flow despite evidence of widespread hybridization. Methods: To
 explore the utility of phylogenomic data for reassessing phylogenetic
 relationships and inferring patterns of gene flow among species of
 Achimenes, we sequenced 12 transcriptomes. We used a variety of methods to
 infer the species tree, examine gene tree discordance, and infer patterns
 of gene flow. Key results: Phylogenomic analyses resolve clade
 relationships at the crown of the lineage with high support. In contrast
 to previous analyses, we recovered strong support for several new
 relationships despite a significant amount of gene tree discordance. We
 present evidence for at least two introgression events between two species
 pairs that share pollinators and suggest that the species status of A.
 admirabilis be reexamined. Conclusions: Our study demonstrates the utility
 of transcriptome data for phylogenomic analyses and inferring patterns of
 gene flow despite gene tree discordance. Moreover, these data provide
 another example of prevalent interspecific gene flow among Neotropical
 plants that share pollinators.
description: Ortholog
 treesAll ortholog trees in
 newick format (n=1306) used in the current study.trees.zipOrtholog alignmentsAll ortholog alignments in fasta format (n=1306) used in the current study.seqs.zipOrtholog bootstrap replicatesAll ortholog bootstrap replicates in newick format (n=1306) used in the current study.bs_trees.zipSpecies trees and input filesInferred species trees from RAxML, ASTRAL, and ASTRID. Additional files include the concatenated sequence alignment (in phylip format) used for RAxML analysis and the two files (newick trees and bootstrap replicates) used in ASTRAL and ASTRID analyses.Species-Trees.zip
DOI: 10.5061/dryad.60n2m
title: Data from: The effect of ethylene glycol on pore arrangement of anodic aluminum oxide prepared by hard anodization

description: The influence of ethylene glycol (EG) addition on pore self-ordering
 process in anodic aluminum oxide (AAO) membranes prepared by hard
 anodization (HA) was investigated. It was illustrated that EG has a
 substantial effect on the pore arrangement of AAO, which revealed that a
 smaller pore size can be obtained as EG concentration reaching 20 wt% in
 aqueous electrolyte. The number of estimated defects of AAO increase
 significantly with additive EG concentration at 50 wt%. Excellent ordering
 pore was realized when the samples were anodized in the 30
 wt%-EG-containing aqueous electrolyte.electrolyte. The number of estimated
 defects of AAO increases significantly upon the added EG concentration
 reaching 50wt%. Excellent ordering pore was achieved when the samples were
 anodized in a 30wt%-EG-containing aqueous electrolyte.
description: the data for preparation
 process of AAO1.the data for
 preparation process of AAO;2.the examples for figuring the estimated of
 defect numbers;3.the original data for current vs time;4.the regularity
 parameters.
DOI: 10.17632/f8s34zd23t
title: Data for "Ultrasensitive detection of macromolecules in water via flowing particles on a chip"

description: Raw data for the manuscript "Ultrasensitive detection of macromolecules in water via flowing particles on a chip"
DOI: 10.17632/f8s34zd23t.1
title: Data for "Ultrasensitive detection of macromolecules in water via flowing particles on a chip"

description: Raw data for the manuscript "Ultrasensitive detection of macromolecules in water via flowing particles on a chip"
DOI: 10.5061/dryad.77646
title: Data from: Rapid response to changing environments during biological invasions: DNA methylation perspectives

description: Dissecting complex interactions between species and their environments has
 long been a research hot spot in the fields of ecology and evolutionary
 biology. The well-recognized Darwinian evolution has well-explained
 long-term adaptation scenarios; however, “rapid” processes of biological
 responses to environmental changes remain largely unexplored, particularly
 molecular mechanisms such as DNA methylation that have recently been
 proposed to play crucial roles in rapid environmental adaptation. Invasive
 species, which have capacities to successfully survive rapidly changing
 environments during biological invasions, provide great opportunities to
 study molecular mechanisms of rapid environmental adaptation. Here, we
 used the methylation-sensitive amplified polymorphism (MSAP) technique in
 an invasive model ascidian, Ciona savignyi, to investigate how species
 interact with rapidly changing environments at the whole-genome level. We
 detected quite rapid DNA methylation response: significant changes of DNA
 methylation frequency and epigenetic differentiation between treatment and
 control groups occurred only after 1 hr of high-temperature exposure or
 after 3 hr of low-salinity challenge. In addition, we detected
 time-dependent hemimethylation changes and increased intragroup epigenetic
 divergence induced by environmental stresses. Interestingly, we found
 evidence of DNA methylation resilience, as most stress-induced DNA
 methylation variation maintained shortly (~48 hr) and quickly returned
 back to the control levels. Our findings clearly showed that invasive
 species could rapidly respond to acute environmental changes through DNA
 methylation modifications, and rapid environmental changes left
 significant epigenetic signatures at the whole-genome level. All these
 results provide fundamental background to deeply investigate the
 contribution of DNA methylation mechanisms to rapid contemporary
 environmental adaptation.
description: MSAP raw
 dataThis file contains the
 raw MSAP matrix of 667 MSAP bands scored across 192 Ciona savignyi
 individuals assigned to five treatments and differet time
 points.MSAP-RAWdata.xlsxMSAP-transformed dataThis file contains 628 U-, 651 M- and 639 H-sub-epiloci respectively by transforming 667 MSAP raw data according to "Mix scoring 2" method.Pairwise AMOVAThis file contains three matrixs with pairwise AMOVA results of U-, M- and H-sub-epiloci among the 32 study groups.