cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.35j3j
title: Data from: Synthesis of gypsogenin derivatives with capabilities to arrest cell cycle and induce apoptosis in human cancer cells

description: Thirty-two gypsogenin derivatives were synthesized and screened for their
 cytotoxic activities. Their structures were established using IR, 1H NMR,
 13C NMR, and LC-MS spectroscopic data. In MTT assays nearly all the
 compounds displayed good cytotoxicity in the low μM range for several
 human tumour cell lines (A549, LOVO, SKOV3 and HepG2). Low IC50 values
 were obtained especially for the carboxamides 7a–7j, for an oxime
 derivative 3 and a (2,4-dinitrophenyl)hydrazono derivative 4. In
 particular, the IC50 values of compounds 4 (IC50 = 2.97 ± 1.13 µΜ) and 7 g
 (IC50 = 3.59 ± 2.04 µΜ) against LOVO cells were found to be much lower
 than those of the other derivatives and parent compound. These compounds
 were submitted to an extensive biological testing and proved compounds 4
 and 7 g to act mainly by an arrest of the tumour cells in the S phase of
 the cell cycle. In addition, compounds 4 and 7 g triggered the apoptotic
 pathway in cancer cells, showing high apoptosis ratios.
description: Supporting Data for
 "Synthesis of gypsogenin derivatives with capabilities to arrest cell
 cycle and induce apoptosis in human cancer cells"This file includes
 figures, tables, scheme and spectrum of compounds.Supplementary
 Material.docx
DOI: 10.17632/wzs28h35wv
title: Data1

description: data prepared for publication
DOI: 10.5061/dryad.f7b48
title: Data from: Response of Prochilodus nigricans to flood pulse variation in the central Amazon

description: The influence of the flood pulse on fish populations has been posited, but
 infrequently tested or quantified. Here, we tested the effect of habitat
 on population size, using Prochilodus nigricans as a case study species.
 Floodplain habitat was based on the littoral zone area occupied by P.
 nigricans to feed. The magnitude of this habitat in each hydrological
 year, the moving littoral (ML), was expressed as the sum of daily littoral
 areas during the advancing flood pulse, using satellite-based passive
 microwave data. Annual population size was estimated by age-class, using a
 dynamic age-structured model (MULTIFAN-CL) based on catches, effort, and
 fish length frequencies from the Manaus-based fishery over 12.75 years.
 The principal null hypothesis was that ML, using three lag times, had no
 effect on population size of a single age class of P. nigricans. The
 population size at 29 months of age was positively related (P=0.00030) to
 floodplain habitat (ML) earlier in the same year, when the fish were 21-27
 months old. The result implies a density-dependent relationship for the
 population with respect to its feeding habitat. Potential mechanisms
 governed by flood pulse variation and habitat quality for this and other
 species utilizing floodplain habitats are discussed.
description: README for all data
 filesREAD
 ME.txtManaus Fisheries
 datasee
 READMEProchCatchEffortLen.txtLittoralVarssee READMEDrawdown factor Dsee READMED.txt
DOI: 10.17632/wzs28h35wv.2
title: Data1

description: data prepared for publication
DOI: 10.5061/dryad.4hc42
title: Data from: Macroecological patterns of sexual size dimorphism in turtles of the world

description: Sexual size dimorphism (SSD) is a well-documented phenomenon in both
 plants and animals; however, the ecological and evolutionary mechanisms
 that drive and maintain SSD patterns across geographic space at regional
 and global scales are understudied, especially for reptiles. Our goal was
 to examine geographic variation of turtle SSD and to explore ecological
 and environmental correlates using phylogenetic comparative methods. We
 use published body size data on 135 species from nine turtle families to
 examine how geographic patterns and the evolution of SSD are influenced by
 habitat specialization, climate (annual mean temperature and annual
 precipitation) and climate variability, latitude, or a combination of
 these predictor variables. We also found that geographic variation,
 magnitude, and direction of turtle SSD are best explained by habitat
 association, annual temperature variance, and annual precipitation. Use of
 semi-aquatic and terrestrial habitats was associated with male-biased SSD,
 whereas use of aquatic habitat was associated with female-biased SSD. Our
 results also suggest that greater temperature variability is associated
 with female-biased SSD. In contrast, wetter climates are associated with
 male-biased SSD compared with arid climates that are associated with
 female-biased SSD. We also show support for a global latitudinal trend in
 SSD, with females being larger than males towards the poles, especially in
 the families Emydidae and Geoemydidae. Estimates of phylogenetic signal
 for both SSD and habitat type indicate that closely related species occupy
 similar habitats and exhibit similar direction and magnitude of SSD. These
 global patterns of SSD may arise from sex-specific reproductive behavior,
 fecundity, and sex-specific responses to environmental factors that differ
 among habitats and vary systematically across latitude. Thus, this study
 adds to our current understanding that while SSD can vary dramatically
 across and within turtle species under phylogenetic constraints, it may be
 driven, maintained, and exaggerated by habitat type, climate, and
 geographic location.
description: Body size, sexual size
 dimorphism indices, and habitat classificationExcel file that includes
 mean body size of males and females from 135 turtle species. Also includes
 sexual size dimorphism indices, habitat classification, center of
 geographic range (latitude, longitude), and range associated climate
 data.SSD_10.18.2017.csvTurtle species distribution climate dataExcel file that includes mean climate data collected via (http://www.worldclim.org/bioclim) for 330 turtle species' geographic distributions.Bio_Species_Merge_Total (1).xlsxMean sexual size dimorphism mapArcGIS file including turtle species distribution and mean sexual size dimorphism indices.SSD_Data.gdb.zip
DOI: 10.17632/rzccdmnrvd
title: Open access dataset

description: None.
DOI: 10.17632/rzccdmnrvd.1
title: Open access dataset

description: None.
DOI: 10.5061/dryad.7m48r
title: Data from: Evidence for heterochrony in the cranial evolution of fossil crocodyliforms

description: The southern supercontinent of Gondwana was home to an extraordinary
 diversity of stem-crocodylians (Crocodyliformes) during the Late
 Cretaceous. The remarkable morphological disparity of notosuchian
 crocodyliforms indicates that this group filled a wide range of ecological
 roles more frequently occupied by other vertebrates. Among notosuchians,
 the distinctive cranial morphology and large body sizes of Baurusuchidae
 suggest a role as apex predators in ecosystems in which the otherwise
 dominant predatory theropod dinosaurs were scarce. Large-bodied
 crocodyliforms, modern and extinct, are known to have reached large sizes
 by extending their growth period. In a similar way, peramorphic
 heterochronic processes may have driven the evolution of the similarly
 large baurusuchids. To assess the presence of peramorphic processes in the
 cranial evolution of baurusuchids, we applied a geometric morphometric
 approach to investigate ontogenetic cranial shape variation in a
 comprehensive sample of notosuchians. Our results provide quantitative
 morphological evidence that peramorphic processes influenced the cranial
 evolution of baurusuchids. After applying size and ancestral ontogenetic
 allometry corrections to our data, we found no support for the action of
 either hypermorphosis or acceleration, indicating that these two processes
 alone cannot explain the shape variation observed in Notosuchia.
 Nevertheless, the strong link between cranial shape variation and size
 increase in baurusuchids suggests that peramorphic processes were involved
 in the emergence of hypercarnivory in these animals. Our findings
 illustrate the role of heterochrony as a macroevolutionary driver, and
 stress, once more, the usefulness of geometric morphometric techniques for
 identifying heterochronic processes behind evolutionary trends.
description: TPS
 filesTPS files with digitized
 landmarks (of both lateral and dorsal views).MorphoJ
 scriptMorphoJ script for all
 geometric morphometric analyses performed.Heterochr_Baurusuch.morphojThin plate splineR script for thin plate spline.Supporting Information Godoy et alSupporting Information with supplementary text (with further explanation on the reconstruction of the ancestral ontogenetic trajectory), as well as tables and figures (with supplementary results).
DOI: 10.5061/dryad.q3v30
title: Data from: Stronger social bonds do not always predict greater longevity in a gregarious primate

description: In group-living species, individuals often have preferred affiliative
 social partners, with whom ties or bonds can confer advantages that
 correspond with greater fitness. For example, in adult female baboons and
 juvenile horses, individuals with stronger or more social ties experience
 greater survival. We used detailed behavioral and life history records to
 explore the relationship between tie quality and survival in a gregarious
 monkey (Cercopithecus mitis stuhlmanni), while controlling for dominance
 rank, group size, and life history strategy. We used Cox proportional
 hazards regressions to model the cumulative (multi-year) and current
 (single-year) relationships of social ties and the hazard of mortality in
 83 wild adult females of known age, observed 2–8 years each (437
 subject-years) in eight social groups. The strength of bonds with close
 partners was associated with increased mortality risk under certain
 conditions: Females that had strong bonds with close partners that were
 inconsistent over multiple years had a higher risk of mortality than
 females adopting any other social strategy. Within a given year, females
 had a higher risk of death if they were strongly bonded with partners that
 changed from the previous year versus with partners that remained
 consistent. Dominance rank, number of adult female groupmates, and age at
 first reproduction did not predict the risk of death. This study
 demonstrates that costs and benefits of strong social bonds can be
 context-dependent, relating to the consistency of social partners over
 time.
description: tdc.dataAnnual predictors of survival for time dependent covariate survival analysis.fixedeffects.dataMulti-year predictors for fixed effects survival analysispermuted strength-consistency class coefficientsCoefficients of fixed-effects survival models with strength consistency classes based on values of bond strength and partner consistency from permuted DSI matrices.1000 permuted values of strength and consistency (for top 3 and 6)Strength consistency classes (of top 3 and top 6 partners) based on values of bond strength and partner consistency from permuted DSI matrices.observed coefficientsObserved coefficients of strength consistency classes from fixed effect survival models.Code NAT MCR Code for all survival analyses and permutation tests.
DOI: 10.5061/dryad.f7f57
title: Data from: Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms

description: After decades of molecular phylogenetic studies, the deep phylogeny of
 gymnosperms has not been resolved, and the phylogenetic placement of
 Gnetales remains one of the most controversial issues in seed plant
 evolution. To resolve the deep phylogeny of seed plants and to address the
 sources of phylogenetic conflict, we conducted a phylotranscriptomic study
 with a sampling of all 13 families of gymnosperms and main lineages of
 angiosperms. Multiple datasets containing up to 1 296 042 sites across
 1308 loci were analysed, using concatenation and coalescence approaches.
 Our study generated a consistent and well-resolved phylogeny of seed
 plants, which places Gnetales as sister to Pinaceae and thus supports the
 Gnepine hypothesis. Cycads plus Ginkgo is sister to the remaining
 gymnosperms. We also found that Gnetales and angiosperms have similar
 molecular evolutionary rates, which are much higher than those of other
 gymnosperms. This implies that Gnetales and angiosperms might have
 experienced similar selective pressures in evolutionary histories.
 Convergent molecular evolution or homoplasy is partially responsible for
 the phylogenetic conflicts in seed plants. Our study provides a robustly
 reconstructed backbone phylogeny that is important for future molecular
 and morphological studies of seed plants, in particular gymnosperms, in
 the light of evolution.
description: concatenation datasets
 and ML treesconcatenation.rar1308 aligned CDS sequencesCDS_fine.rarML_tree_RAxMLRAxML_bipartitions.CDS_FcC_supermatrix_partition1308Divergence times of gymnospermsDivergence times of gymnosperms estimated by MCMCTree with Bayesian relaxed molecular clock based on the combined CDS (1st + 2nd) sequencesFigTree.tre
DOI: 10.5061/dryad.2139f
title: Data from: Seascape genetics and biophysical connectivity modelling support conservation of the seagrass Zostera marina in the Skagerrak-Kattegat region of the eastern North Sea

description: Maintaining and enabling evolutionary processes within meta-populations is
 critical to resistance, resilience and adaptive potential. Knowledge about
 which populations act as sources or sinks, and the direction of gene flow,
 can help to focus conservation efforts more effectively and forecast how
 populations might respond to future anthropogenic and environmental
 pressures. As a foundation species and habitat provider, Zostera marina
 (eelgrass) is of critical importance to ecosystem functions including
 fisheries. Here we estimate connectivity of Z. marina in the
 Skagerrak-Kattegat region of the North Sea based on genetic and
 biophysical modelling. Genetic diversity, population structure and
 migration were analysed at 23 locations using 20 microsatellite loci and a
 suite of analytical approaches. Oceanographic connectivity was analysed
 using Lagrangian dispersal simulations based on contemporary and
 historical distribution data dating back to the late 19th century.
 Population clusters, barriers and networks of connectivity were found to
 be very similar based on either genetic or oceanographic analyses. A
 single-generation model of dispersal was not realistic, whereas
 multi-generation models that integrate stepping-stone dispersal and extant
 and historic distribution data were able to capture and model genetic
 connectivity patterns well. Passive rafting of flowering shoots along
 oceanographic currents is the main driver of gene flow at this
 spatial-temporal scale and extant genetic connectivity strongly reflects
 the “ghost of dispersal past” sensu Benzie 1999. The identification of
 distinct clusters, connectivity hotspots and areas where connectivity has
 become limited over the last century is critical information for spatial
 management, conservation and restoration of eelgrass.
description: matrix_microsatellite_genotypesMicrosatellite genotypesConnectivity Matricesoceanographic connectivity matrices
DOI: 10.5061/dryad.5kg33
title: Data from: Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae)

description: Background: Habronattus is a diverse clade of jumping spiders with complex
 courtship displays and repeated evolution of Y chromosomes. A
 well-resolved species phylogeny would provide an important framework to
 study these traits, but has not yet been achieved, in part because the few
 genes available in past studies gave conflicting signals. Such discordant
 gene trees could be the result of incomplete lineage sorting (ILS) in
 recently diverged parts of the phylogeny, but there are indications that
 introgression could be a source of conflict. Results: To infer Habronattus
 phylogeny and investigate the cause of gene tree discordance, we assembled
 transcriptomes for 34 Habronattus species and 2 outgroups. The
 concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by
 Maximum Likelihood (ML) with high bootstrap support (95-100%) at most
 nodes, with some uncertainty surrounding the relationships of H.
 icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species
 tree analyses by ASTRAL and SVDQuartets gave almost completely congruent
 results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial
 data are incongruent with the nuclear phylogeny and indicate possible
 mitochondrial introgression: the internal relationships of the americanus
 and the coecatus groups, the relationship between the altanus, decorus,
 banksi, and americanus group, and between H. clypeatus and the coecatus
 group. To determine the relative contributions of ILS and introgression,
 we analyzed gene tree discordance for nuclear loci longer than 1 kb using
 Bayesian Concordance Analysis (BCA) for the americanus group (679 loci)
 and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517
 loci) and found signals of introgression in both. Finally, we tested
 specifically for introgression in the concatenated nuclear matrix with
 Patterson’s D statistics and DFOIL. We found nuclear introgression
 resulting in substantial admixture between americanus group species,
 between H. roberti and the clypeatus group, and between the clypeatus and
 coecatus groups. Conclusions: Our results indicate that the phylogenetic
 history of Habronattus is predominantly a diverging tree, but that
 hybridization may have been common between phylogenetically distant
 species, especially in subgroups with complex courtship displays.
description: Matrices of concatenated
 aligned sequences5 files. Three are
 partitions of nuclear transcriptomes (primary matrix of 1877 genes;
 secondary matrices of (MS) loci with species missing and (NL) noncoding
 loci. The fourth matrix is of the mitochondrial transcriptomes; the fifth
 is the mix of 16s and ND1 from the transcriptomes, and previous data from
 Sanger sequencing.Leduc-Robert&Maddison_Habronattus-AlignedMatrices.tgzNEXUS file of inferred phylogenetic treesInferred trees from the various analyses and partitions of the transcriptome data.Leduc-Robert&Maddison_Habronattus-Trees.nex
DOI: 10.5061/dryad.7t7ff
title: Data from: Genome-wide expression reveals multiple systemic effects associated with detection of anticoagulant poisons in bobcats (Lynx rufus)

description: Anticoagulant rodenticides (ARs) are indiscriminate toxicants that
 threaten non-target predatory and scavenger species through secondary
 poisoning. Accumulating evidence suggests that AR exposure may have
 disruptive sublethal consequences on individuals that can affect fitness.
 We evaluated AR-related effects on genome wide expression patterns in a
 population of bobcats in southern California. We identify differential
 expression of genes involved in xenobiotic metabolism, endoplasmic
 reticulum stress response, epithelial integrity, and both adaptive and
 innate immune function. Further, we find that differential expression of
 immune related genes may be attributable to AR-related effects on
 leukocyte differentiation. Collectively, our results provide an
 unprecedented understanding of the sublethal effects of AR exposure on a
 wild carnivore. These findings highlight potential detrimental effects of
 ARs on a wide variety of species worldwide that may consume poisoned
 rodents and indicate the need to investigate gene expression effects of
 other toxicants added to natural environments by humans.
description: Raw read counts, GC
 content, and Mean Gene LengthThis file contains the
 raw HT-seq read counts generated from raw fastq sequence reads after
 alignment to the domestic cat genome. The first two columns include the
 mean GC content and mean gene length for all genes, which were used for
 filtering and normalization.RawCount_genelenght_Gccontent.xlsxSupplementaryTable_S1File includes summaries of data processing (sequence counts data), and metadata (technical and biological traits) for each bobcat.SupplementaryTable_S3File contains Gene Symbol, linear model coefficients and q-values, and WGCNA module assignments
DOI: 10.5061/dryad.s02p0
title: Data from: Rapid phenotypic evolution following shifts in life cycle complexity

description: Life cycle strategies have evolved extensively throughout the history of
 metazoans. The expression of disparate life stages within a single
 ontogeny can present conflicts to trait evolution, and therefore may have
 played a major role in shaping metazoan forms. However, few studies have
 examined the consequences of adding or subtracting life stages on patterns
 of trait evolution. By analyzing trait evolution in a clade of closely
 related salamander lineages we show that shifts in number of life cycle
 stages are associated with rapid phenotypic evolution. Specifically,
 salamanders with an aquatic-only (paedomorphic) life cycle have frequently
 added vertebrae to their trunk skeleton compared to closely related
 lineages with a complex aquatic-to-terrestrial (biphasic) life cycle. The
 rate of vertebral column evolution is also substantially lower in biphasic
 lineages, which may reflect the functional compromise of a complex cycle.
 This study demonstrates that the consequences of life cycle evolution can
 be detected at very fine-scales of divergence due to rapid evolutionary
 responses to shifts in selective regimes following changes in life cycle
 complexity.
description: E_tynerensis_190_genomic_regionsThis nexus file contains a concatenated alignment of 190 nuclear gene regions from 121 loci collected from 28 populations of the Oklahoma Salamanders (Eurycea tynerensis) using anchored-hybrid enrichment (AHE).
DOI: 10.17632/z3mckkj5fj
title: Tackling Impacts of Ship Waste

description: I used the references from different data sources
DOI: 10.5061/dryad.ps22r
title: Data from: Improving accuracies of genomic predictions for drought tolerance in maize by joint modeling of additive and dominance effects in multi-environment trials

description: Breeding for drought tolerance is a challenging task that requires costly,
 extensive and precise phenotyping. Genomic selection (GS) can be used to
 maximize selection efficiency and the genetic gains in maize (Zea mays L.)
 breeding programs for drought tolerance. Here we evaluated the accuracy of
 genomic selection of additive (A) against additive+dominance (AD) models
 to predict the performance of untested maize single-cross hybrids for
 drought tolerance in multi-environment trials. Phenotypic data of five
 drought-tolerance traits were measured in 308 hybrids in eight trials
 under water-stressed (WS) and well-watered (WW) conditions over two years
 and two locations in Brazil. Hybrids’ genotypes were inferred based on
 their parents’ genotypes (inbred lines) using single nucleotide
 polymorphism data obtained via genotyping-by-sequencing. GS analyses were
 performed using genomic best linear unbiased prediction by fitting a
 factor analytic (FA) multiplicative mixed model. Results showed
 differences in the predictive accuracy between A and AD models for the
 five traits under consideration in both water conditions. For grain yield
 (GY), the AD model doubled the predictive accuracy in comparison to the A
 model. FA framework allowed for investigating the stability of additive
 and dominance effects across environments, as well as the additive- and
 dominance-by-environment interactions, with interesting applications for
 parental and hybrid selection. Prediction performance of untested hybrids
 using GS that benefit from borrowing information from correlated trials
 increased 40% and 9% for A and AD models, respectively. These results
 highlighted the importance of multi-environment trial analysis with GS
 that incorporate dominance effects into genomic predictions of GY in maize
 single-cross hybrids.
description: Pheno_DataField data of 312 single-cross maize hybrids evaluated in 8 trials.Geno_DataAdditive and dominance genomic relationship matrices.