cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fxpnvx0sn
title: A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations

description: An optimized, high-throughput and cost-effective genotyping method
 applicable to various crop breeding populations is very important in this
 genomic era. We have developed an optimized Nextera skim-sequencing
 (skim-seq) approach to genotype different populations that can be used for
 genetics studies and genomics-assisted breeding. We performed skim-seq on
 a variety of populations developed through doubled haploid (DH)
 technology, inter-specific recombinants developed through introgression,
 amphidiploid developed through wide crosses, and on known monosomic
 samples. 1. A doubled haploid (DH) population consisting of 48 lines from
 the cross of spring wheat (Triticum aestivum) cultivars CDC Stanley and
 CDC Landmark developed by the Crop Development Centre at the University of
 Saskatchewan. We genotyped these DH with skim-seq and identified the
 genomic segments contributed by each of the two parental lines. 2. A
 population of 335 back cross generation 1 (BC1) skim-seq samples for
 wheat-barley recombinants with group 7 translocations and 839 F1 wheat 5D
 monosomic lines (TA3059) along with 16 standard Chinese Spring lines as
 internal control. 3. A panel of 144 Thinopyrum intermedium x Triticum
 durum (IWG--durum) lines and 141 Thinopyrum intermedium (IWG) lines were
 evaluated to assess skim-seq genome coverage as well as amphiploidy
 levels. The demultiplexed FASTQ files for all samples tested in the
 experiment are available at NCBI SRA public repository with respective
 BioProject accessions; DH lines [PRJNA729723], 5D monosomic line
 [PRJNA742385], wheat-barley recombinants [PRJNA738484], IWG-durum and IWG
 [PRJNA736976]. An example key file for the 5D monosomic line is also
 attached.  This study indicated that skim-seq is an efficient
 approach for genomic evaluation of a range of different populations and
 applications. The scripts have been provided to implement skim-seq data
 for variant calling, identification of genomic segment dosage and alien
 introgression. Each step of the pipeline is described and implemented with
 similar sequencing data from skim-seq libraries.
description: Skim-sequencing data of different populations described in the
 manuscript were generated using Nextera library preparation method. The
 data processing steps were illustrated in the attached pipeline
 script.
description: We have Readme.pdf file which describes about the dataset.
DOI: 10.5061/dryad.f4qrfj6wx
title: Depicting the phenotypic space of the annual plant Diplotaxis acris in hyper-arid deserts

description: The phenotypic space encompasses the assemblage of trait combinations
 yielding well-suited integrated phenotypes. At the population level,
 understanding phenotypic space structure requires the quantification of
 among- and within-population variation in traits and the correlation
 pattern among them. Here, we studied the phenotypic space of the annual
 plant Diplotaxis acris occurring in hyper-arid deserts. Given the advance
 of warming and aridity in vast regions occupied by drylands, D. acris can
 indicate the successful evolutionary trajectory that many other annual
 plant species may follow in expanding drylands. To this end, we conducted
 a greenhouse experiment with 176 D. acris individuals from five Saudi
 populations to quantify the genetic component of variation in
 architectural and life-history traits. We found low among-population
 divergence but high among-individual variation in all traits. In addition,
 all traits showed a high degree of genetic determination in our study
 experimental conditions. We did not find significant effects of
 recruitment and fecundity on fitness. Finally, all architectural traits
 exhibited a strong correlation pattern among them, whereas for
 life-history traits, only higher seed germination implied earlier
 flowering. Seed weight appeared to be an important trait in D. acris, as
 individuals with heavier seeds tended to advance flowering and have a more
 vigorous branching pattern, which led to higher
 fecundity. Population divergence in D. acris might be constrained
 by the severity of the hyper-arid environment, but populations maintain
 high among-individual genetic variation in all traits. Furthermore, D.
 acris showed phenotypic integration for architectural traits and, to a
 lesser extent, for life-history traits. Overall, we hypothesize that D.
 acris may be fine-tuned to its demanding extreme environments.
 Evolutionary speaking, annual plants facing increasing warming, aridity
 and environmental seasonality might modify their phenotypic spaces towards
 new phenotypic configurations strongly dominated by correlated
 architectural traits enhancing fecundity and seed-related traits advancing
 flowering time.
description: See article
description: See ReadMe file.
DOI: 10.5061/dryad.n5tb2rbwr
title: Habitat fragmentation induces rapid phenotypic divergence of migratory and isolated sticklebacks

description: The adaptive capacity of many organisms is seriously challenged by
 human-imposed environmental change, which currently happens at
 unprecedented rates and magnitudes. For migratory fish, habitat
 fragmentation is a major challenge that can compromise their survival and
 reproduction. Therefore, it is important to study if fish populations can
 adapt to such modifications of their habitat. Here, we study whether
 originally anadromous three-spined stickleback populations (Gasterosteus
 aculeatus; ‘migrants’) changed in behavior and morphology in response to
 human-induced isolation. We made use of a natural field-experiment, where
 the construction of pumping stations and sluices in the 1970s unintendedly
 created replicates of land-locked stickleback populations (‘resident’) in
 the Netherlands. For two years, we systematically tested populations of
 residents and migrants for differences in morphology and behavioral traits
 (activity, aggressiveness, exploration, boldness and shoaling) in
 lab-based assays. We detected differences between migrant and resident
 populations in virtually all phenotypic traits studied: compared to the
 ancestral migrants, residents were smaller in size, had fewer and smaller
 plates and were significantly more active, aggressive, exploratory and
 bolder and shoaled less. Despite large ecological differences between 2018
 and 2019, results were largely consistent across the two years. Our study
 shows that human-induced environmental change has led to the rapid and
 consistent morphological and behavioral divergence of stickleback
 populations in about 50 generations. Such changes may be adaptive but this
 remains to be tested.
DOI: 10.5061/dryad.xsj3tx9gd
title: Dying to cooperate: the role of environmental harshness in human collaboration

description: It has been proposed that environmental stress acted as a selection
 pressure on the evolution of human cooperation. Through agent-based
 evolutionary modelling, mathematical analysis and human experimental data
 we illuminate the mechanisms by which the environment influences
 cooperative success and decision making in a Stag Hunt game. The modelling
 and mathematical results show that only cooperative foraging phenotypes
 survive the harshest of environments but pay a penalty for
 mis-coordination in favourable environments. When agents are allowed to
 coordinate their hunting intentions by communicating, cooperative
 phenotypes outcompete those who pursue individual strategies in almost all
 environmental and payoff scenarios examined. Data from human participants
 show flexible decision-making in face of cooperative uncertainty,
 favouring high-risk, high-reward strategy when environments are harsher
 and starvation is imminent. Converging lines of evidence from the three
 approaches indicate a significant role for environmental variability in
 human cooperative dynamics and the species-unique cognition designed to
 support it.
description: Detailed methods avaiable in the paper.
DOI: 10.5061/dryad.ksn02v751
title: Integrating venom peptide libraries into a phylogenetic and broader biological framework

description: The venomous marine snails are conventionally divided into three groups,
 the cone snails (family Conidae), the auger snails (family Terebridae) and
 the turrids (formerly all assigned to a single family, Turridae). In this
 study, a library of venom peptides from species conventionally assigned to
 the genus Turris was correlated to a phylogenetic analysis. Nucleotide
 sequences of multiple genes from transcriptomes were used to assess the
 phylogenic relationships across a diverse set of species. The resulting
 tree shows that as conventionally defined, the Conoidean genus Turris, is
 polyphyletic. We describe a new genus, Purpuraturris gen. nov., that
 comprises the outlier species. In addition to morphological distinctions,
 molecular data reveal that this group are more closely related to
 Unedogemmula and Turridrupa than to Turris sensu stricto. The correlation
 between phylogenetic information and multiple peptide sequences from the
 library of venom peptides was used to highlight those peptides mostly
 likely to be unique and intimately associated with biological diversity.
 The plethora of peptide sequences available requires two prioritization
 decisions: which subset of peptides to initially characterize, and after
 these are characterized, which to comprehensively investigate for
 potential biomedical applications such as drug developments.
description: Adapter clipping and quality trimming of raw reads were performed
 using fqtrim software (Version 0.9.4, ) and PRINSEQ (Version 0.20.4).
 After processing, sequences shorter than 70 bps and those containing more
 than 5% ambiguous bases (Ns) were discarded. De novo transcriptome
 assembly was performed using Trinity Version 2.0.5 with a kmer size for
 building De Bruijn Graphs of 31, a minimum kmer coverage of 10, and a
 minimum glue of 10. Assembled transcripts were annotated using Blastx
 (NCBI-Blast-2.2.28+) against conotoxin sequences extracted from the
 ConoServer and UniProt databases.  Common genes that were shared between
 all datasets were identified using the blast identities of assembled
 contigs (e &lt; 10-4).<br> Fasta contig sequences were aligned
 using mafft v7.222 (with the “auto” flag).  For each alignment file we
 used the RAxML (Stamatakis 2006) program with a GTRGAMMA model
 (unpartitioned) to determine the “best” tree. Each zip
 file is a compressed folder.<br> fasta.zip has the contiq sequences
 from each sample grouped by blast identity gene name.  Each file is named
 according to the Swiss-Prot identifier.<br> aligned.zip has mafft
 aligned sequences from all samples in fasta format.<br> bestTree.zip
 has has the “best” RaxML trees for all genes.
DOI: 10.5061/dryad.pvmcvdnmw
title: Data from: Sex differences in costly signalling in rural Western China

description: Numerous empirical studies suggest that individuals convey their
 commitment to communities and impart the qualities of being a reliable
 partner through costly behaviours. We collected religious practices data
 ranging from daily trivial practices to infrequent grand distant
 pilgrimages in an agricultural Tibetan village. We predict that
 1) villagers who invest more in religious practices are more
 likely to be nominated as having various prosocial qualities.
 2) Investment in grand distant pilgrimages has more efficacy than
 daily trivial religious acts on recognition of prosocial qualities.
 3) The males are more likely to receive nominations than females
 across all prosocial traits. Using Hurdle Models and Exponential Random
 Graph Models, we found that religious practice is mediated by demographic
 factors like wealth rank, age, and the gender. Daily religious investment
 positively associates with nominations of devoutness, but not with other
 prosocial traits. Distant pilgrimage positively associates with
 nominations of devoutness, as well as other prosocial traits. Females are
 inclined to prefer investing in daily religious acts, but males are
 inclined to invest in distant pilgrimages. Generally, females receive
 fewer nominations than males across all prosocial traits.
description: The demographic census contained the basic individual information
 such as name, gender, age, ethnic group, ever being a monk, educational
 level, marital status, birthplace, number of siblings and children (in or
 out of the household) and occupation; kinship information, as well as the
 religious weights questions for measuring the religiosity; financial
 position (month income, source of revenue) and the religious investment
 conditions. The reputational nomination and religious
 practices questionnaire were collected after the demographic data.
 Individuals were asked to nominate those who have the following prosocial
 traits: Devout, Generous, Good character, Hardworking. They were also
 asked about the specific frequencies and locations of religious practices.
 We then divided these practices into two categories, grand distant
 pilgrimage, and daily trivial practices (local pilgrimage, accounting
 beads, prostrating, burning, and fasting).
DOI: 10.5061/dryad.7h44j0zv7
title: Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives

description: Despite the economic, ecological, and scientific importance of the genera
 Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens)
 Salicaceae, we know little about the sources of differences in species
 diversity between the genera and of the phylogenetic conflict that often
 confounds estimating phylogenetic trees. Salix subgenera and sections, in
 particular, have been difficult to classify, with one recent attempt
 termed a ‘spectacular failure’ due to a speculated radiation of the
 subgenera Vetrix and Chamaetia. Here we use targeted sequence capture to
 understand the evolutionary history of this portion of the Salicaceae
 plant family. Our phylogenetic hypothesis was based on 787 gene regions
 and identified extensive phylogenetic conflict among genes. Our analysis
 supported some previously described subgeneric relationships and confirmed
 polyphyly of others. Using an fbranch analysis we identified several cases
 of hybridization in deep branches of the phylogeny, which likely
 contributed to discordance among gene trees. In addition, we identified a
 rapid increase in diversification rate near the origination of the
 Vetrix-Chamaetia clade in Salix. This region of the tree coincided with
 several nodes that lacked strong statistical support, indicating a
 possible increase in incomplete lineage sorting due to rapid
 diversification. The extraordinary level of both recent and ancient
 hybridization in both Salix and Populus have played important roles in the
 diversification and diversity in these two genera.
description: Sequence alignments, gene trees, VCFs, and supplementary files
 are found here. Details of data collection and sequencing are provided in
 the manuscript and in the Supplemental Methods described herein.
DOI: 10.5061/dryad.dv41ns204
title: Fine-scale spatial patterns of wildlife disease are common and understudied

description: 1. All parasites are heterogeneous in space, yet little is known about the
 prevalence and scale of this spatial variation, particularly in wild
 animal systems. To address this question, we sought to identify and
 examine spatial dependence of wildlife disease across a wide range of
 systems. 2. Conducting a broad literature search, we collated 31 such
 datasets featuring 89 replicates and 71 unique host-parasite combinations,
 only 51% of which had previously been used to test spatial hypotheses. We
 analysed these datasets for spatial dependence within a standardised
 modelling framework using Bayesian linear models, and we then
 meta-analysed the results to identify generalised determinants of the
 scale and magnitude of spatial autocorrelation. 3. We detected spatial
 autocorrelation in 48/89 model replicates (54%) across 21/31 datasets
 (68%), spread across parasites of all groups. Even some very small study
 areas (under 0.01km2) exhibited substantial spatial variation. 4. Despite
 the common manifestation of spatial variation, our meta-analysis was
 unable to identify host-, parasite-, or sampling-level determinants of
 this heterogeneity across systems. Parasites of all transmission modes had
 easily detectable spatial patterns, implying that structured contact
 networks and susceptibility effects are potentially as important in
 spatially structuring disease as are environmental drivers of transmission
 efficiency. 5. Our findings demonstrate that fine-scale spatial patterns
 of infection manifest frequently and across a range of wild animal
 systems, and many studies are able to investigate them – whether or not
 the original aim of the study was to examine spatially varying processes.
 Given the widespread nature of these findings, studies should more
 frequently record and analyse spatial data, facilitating development and
 testing of spatial hypotheses in disease ecology. Ultimately, this may
 pave the way for an a priori predictive framework for spatial variation in
 novel host-parasite systems.
DOI: 10.5061/dryad.9w0vt4bgw
title: Allosteric modulation of the adenosine A2A receptor by cholesterol

description: Cholesterol is a major component of the cell membrane and commonly
 regulates membrane protein function. Here, we investigate how cholesterol
 modulates the conformational equilibria and signaling of the adenosine A2A
 receptor (A2AR) in reconstituted phospholipid nanodiscs. This model system
 conveniently excludes possible effects arising from cholesterol-induced
 phase separation or receptor oligomerization and focuses on the question
 of allostery. GTP hydrolysis assays show that cholesterol weakly enhances
 the basal signaling of A2AR while decreasing the agonist EC50. Fluorine
 nuclear magnetic resonance (19F NMR) spectroscopy shows that this
 enhancement arises from an increase in the receptor’s active state
 population and a G-protein-bound precoupled state. 19F NMR of fluorinated
 cholesterol analogs reveals transient interactions with A2AR, indicating a
 lack of high-affinity binding or direct allosteric modulation. The
 combined results suggest that the observed allosteric effects are largely
 indirect and originate from cholesterol-mediated changes in membrane
 properties, as shown by membrane fluidity measurements and high-pressure
 NMR.
description: This dataset contains source data files for the article
 "Allosteric modulation of the adenosine A2A receptor by
 cholesterol", published in <em>eLife</em>. Included here
 are Excel and Prism files for Figure 2 (GTPase assays, cholesterol-NECA
 titration), Figure 5 (rigidity transmission allostery), Figure 7b and c
 (Laurdan fluorescence), Figure
 2—figure supplement 1 (DLS), and Figure
 6—figure supplement 1 (GTPase assays, effects of
 19F-cholesterol and ligands on A2AR activity). Methods details are given
 in the article.
description: GraphPad Prism and Microsoft Excel
DOI: 10.5061/dryad.zcrjdfncx
title: Spatial probability maps of the superior parietal sulcus in the human brain

description: The superior parietal sulcus (SPS) is the defining sulcus within the
 superior parietal lobule. The morphological variability of the SPS was
 examined in individual magnetic resonance imaging (MRI) scans of the human
 brain that were registered to the Montreal Neurological Institute (MNI)
 standard stereotaxic space. Two primary morphological patterns were
 consistently identified across hemispheres: 1) the SPS was identified as a
 single sulcus, separating the anterior from the posterior part of the
 superior parietal lobule and 2) the SPS was found as a complex of multiple
 sulcal segments. These morphological patterns were subdivided based on
 whether the SPS or SPS complex remained distinct or merged with
 surrounding parietal sulci. The morphological variability and spatial
 extent of the SPS were quantified using volumetric and surface spatial
 probabilistic mapping. The current investigation established consistent
 morphological patterns in a common anatomical space, the MNI stereotaxic
 space, to facilitate structural and functional analyses within the
 superior parietal lobule.
DOI: 10.21979/n9/kub3xv
title: Replication Data for: "Steganographic Passport: An Owner and User Verifiable Credential for Deep Model IP Protection Without Retraining"

description: Implementation of CVPR 2024 paper "Steganographic Passport: An Owner and User Verifiable Credential for Deep Model IP Protection Without Retraining"
DOI: 10.5061/dryad.7d7wm37w5
title: Data from: Convergent mosaic brain evolution is associated with the evolution of novel electrosensory systems in teleost fishes

description: Brain region size generally scales allometrically with total brain size,
 but mosaic shifts in brain region size independent of brain size have been
 found in several lineages and may be related to the evolution of
 behavioral novelty. African weakly electric fishes (Mormyroidea) evolved a
 mosaically enlarged cerebellum and hindbrain, yet the relationship to
 their behaviorally novel electrosensory system remains unclear. We
 addressed this by studying South American weakly electric fishes
 (Gymnotiformes) and weakly electric catfishes (Synodontis spp.),
 which evolved varying aspects of electrosensory systems, independent of
 mormyroids. If the mormyroid mosaic increases are related to evolving an
 electrosensory system, we should find similar mosaic shifts in
 gymnotiforms and Synodontis. Using micro-computed tomography
 scans, we quantified brain region scaling for multiple electrogenic,
 electroreceptive, and non-electrosensing species. We found mosaic
 increases in cerebellum in all three electrogenic lineages relative to
 non-electric lineages and mosaic increases in torus semicircularis and
 hindbrain associated with the evolution of electrogenesis and
 electroreceptor type. These results show that evolving novel
 electrosensory systems is repeatedly and independently associated with
 changes in the sizes of individual brain regions independent of brain
 size, which suggests that selection can impact structural brain
 composition to favor specific regions involved in novel behaviors.
DOI: 10.5061/dryad.tb2rbp01q
title: Data from: Post-fledging behavioral ecology of migratory songbirds: How do fledgling activity rates vary across species?

description: This datsaset contains data for a comparison of fledgling activity rates
 from 9 songbird species in east-central Illinois, USA, described in the
 paper: "Jones, TM, and MP Ward. 2021. Post-fledging behavioral
 ecology of migratory songbirds: how do fledgling activity rates vary
 across species?"; published in Behavioral Ecology. The dataset
 contains estimates of fledgling activity rates during the daytime,
 nighttime, and across the post-fledging period, which were compared to
 estimates of fledgling morphologies (e.g. mass, tarsus, wing development)
 and post-fledging survival. Analyses, which can be reproduced with this
 data, showed that overall rates of post-fledging
 activity differed by species, but species showed similarities in
 the development of activity rates across the period. All species exhibited
 a stead increase in activity rates with age and general patterns mirrored
 rates of post-fledging mortality, including the presence and absence of
 post-fledging bottlenecks within each species. Additionally, our findings
 suggest that fledgling wing development and brood size at fledging
 contribute to variatio in activity rates within and across species.