cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.736t01r
title: Data from: Decreased brain connectivity in smoking contrasts with increased connectivity in drinking

description: In a group of 831 participants from the general population in the Human
 Connectome Project, smokers exhibited low overall functional connectivity,
 and more specifically of the lateral orbitofrontal cortex which is
 associated with non-reward mechanisms, the adjacent inferior frontal
 gyrus, and the precuneus. Participants who drank a high amount had overall
 increases in resting state functional connectivity, and specific increases
 in reward-related systems including the medial orbitofrontal cortex and
 the cingulate cortex. Increased impulsivity was found in smokers,
 associated with decreased functional connectivity of the
 non-reward-related lateral orbitofrontal cortex; and increased impulsivity
 was found in high amount drinkers, associated with increased functional
 connectivity of the reward-related medial orbitofrontal cortex. The main
 findings were cross-validated in an independent longitudinal dataset with
 1176 participants, IMAGEN. Further, the functional connectivities in
 14-year-old non-smokers (and also in female low-drinkers) were related to
 who would smoke or drink at age 19. An implication is that these
 differences in brain functional connectivities play a role in smoking and
 drinking, together with other factors.
description: Data_for_eLifeData_for_eLife
DOI: 10.5061/dryad.pk8qv
title: Data from: Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean Patagonia

description: The current study describes the taxonomic and functional composition of
 metagenomic sequences obtained from a filamentous microbial mat isolated
 from the Comau fjord, located in the northernmost part of the Chilean
 Patagonia. The taxonomic composition of the microbial community showed a
 high proportion of members of the Gammaproteobacteria, including a high
 number of sequences that were recruited to the genomes of Moritella marina
 MP-1 and Colwellia psycherythraea 34H, suggesting the presence of
 populations related to these two psychrophilic bacterial species.
 Functional analysis of the community indicated a high proportion of genes
 coding for the transport and metabolism of amino acids, as well as in
 energy production. Among the energy production functions, we found
 protein-coding genes for sulfate and nitrate reduction, both processes
 associated with Gammaproteobacteria-related sequences. This report
 provides the first examination of the taxonomic composition and genetic
 diversity associated with these conspicuous microbial mat communities and
 provides a framework for future microbial studies in the Comau fjord.
description: Comau metagenomic reads,
 taxonomy annotationTaxonomic annotation of
 the sequence reads obtained from a microbial mat in the Comau Fjord,
 Chile. The reads were classified using MG-TAXA.MGTAXA_Comau_Reads.txt.zipComau metagenomic reads, functional annotationFunctional annotation of the metagenomic sequences of a microbial mat from the Comau Fjord, Chile. The annotation was done using CAMERA, with the RAMMCAP pipelineCamera_Comau_Reads_Annotated.txt.zip
DOI: 10.5061/dryad.q0b78b5
title: Data from: Extending phylogeography to account for lineage fusion

description: Secondary contact between long isolated populations has several possible
 outcomes. These include the strengthening of preexisting reproductive
 isolating mechanisms via reinforcement, the emergence of a hybrid lineage
 that is distinct from its extant parental lineages and which occupies a
 spatially restricted zone between them, or complete merging of two
 populations such that parental lineages are no longer extant
 ("lineage fusion" herein). The latter scenario has rarely been
 explicitly considered in single-species and comparative phylogeographic
 studies, yet it has the potential to impact inferences about population
 history and levels of congruence. In this paper, we explore the idea that
 insights into past lineage fusion may now be possible, owing to the advent
 of next-generation sequencing. Using simulated DNA sequence haplotype
 datasets (i.e., loci with alleles comprised of a set of linked nucleotide
 polymorphisms), we examined basic requirements (number of loci and
 individuals sampled) for identifying cases when a present-day panmictic
 population is the product of lineage fusion, using an exemplar statistical
 framework—approximate Bayesian computation. We found that with
 approximately 100 phased haplotype loci (400 bp) and modest sample sizes
 of individuals (10 per population), lineage fusion can be detected under
 rather challenging scenarios. This included some scenarios where
 reticulation was fully contained within a Last Glacial Maximum timeframe,
 provided that mixing was symmetrical, ancestral gene pools were moderately
 to deeply diverged, and the lag time between the fusion event and gene
 pool sampling was relatively short. However, the more realistic case of
 asymmetrical mixing is not prohibitive if additional genetic data (e.g.,
 400 loci) are available. Notwithstanding some simplifying assumptions of
 our simulations and the knowledge gaps that remain about the circumstances
 under which lineage fusion is potentially detectable, we suggest that the
 recent release from data limitation allows phylogeographers to expand the
 scope of inferences about long-term population history.
description: Garrick_etal_2018b_Simulated_Data.zipSimulated DNA sequence haplotype data sets associated with Garrick et al. Extending phylogeography to account for lineage fusion. J. Biogeography.
DOI: 10.5061/dryad.kd58f
title: Data from: Detection of human adaptation during the past 2000 years

description: Detection of recent natural selection is a challenging problem in
 population genetics. Here we introduce the Singleton Density Score (SDS),
 a method to infer very recent changes in allele frequencies from
 contemporary genome sequences. Applied to data from the UK10K Project, SDS
 reflects allele frequency changes in the ancestors of modern Britons
 during the past ~2,000-3,000 years. We see strong signals of selection at
 lactase and the MHC, and in favor of blond hair and blue eyes. For
 polygenic adaptation we find that recent selection for increased height
 has driven allele frequency shifts across most of the genome. Moreover, we
 identify shifts associated with other complex traits, suggesting that
 polygenic adaptation has played a pervasive role in shaping genotypic and
 phenotypic variation in modern humans.
description: SDS_UK10K_n3195_release_Sep_19_2016.tabSingleton Density Score (SDS) computed for autosomal SNPs with let least 5% minor allele frequency over a set of 3,195 individuals from the UK10K project. This is a gzipped tab-delimited file and the first row is a column header. Columns correspond to: (1) chromosome; (2) genomic position (hg19); (3) SNP id (rsid); (4) ancestral allele; (5) derived allele; (6) derived allele frequency; (7) SDS. See our manuscript for further description of the SDS method as well as the data quality control and SNP filtering.
DOI: 10.5061/dryad.5v2t8
title: Data from: A within-animal comparison of skilled forelimb assessments in rats

description: A variety of skilled reaching tasks have been developed to evaluate
 forelimb function in rodent models. The single pellet skilled reaching
 task and pasta matrix task have provided valuable insight into recovery of
 forelimb function in models of neurological injury and disease. Recently,
 several automated measures have been developed to reduce the cost and time
 burden of forelimb assessment in rodents. Here, we provide a
 within-subject comparison of three common forelimb assessments to allow
 direct evaluation of sensitivity and efficiency across tasks. Rats were
 trained to perform the single pellet skilled reaching task, the pasta
 matrix task, and the isometric pull task. Once proficient on all three
 tasks, rats received an ischemic lesion of motor cortex and striatum to
 impair use of the trained limb. On the second week post-lesion, all three
 tasks measured a significant deficit in forelimb function. Performance was
 well-correlated across tasks. By the sixth week post-lesion, only the
 isometric pull task measured a significant deficit in forelimb function,
 suggesting that this task is more sensitive to chronic impairments. The
 number of training days required to reach asymptotic performance was
 longer for the isometric pull task, but the total experimenter time
 required to collect and analyze data was substantially lower. These
 findings suggest that the isometric pull task represents an efficient,
 sensitive measure of forelimb function to facilitate preclinical
 evaluation in models of neurological injury and disease.
description: Isometric Pull Session
 RecordsSession records,
 including individual trial results and force signal snippets, for all
 isometric pull task training and testing sessions. Data files can be read
 into MATLAB using the provided *.m file.isometric_pull.zipPasta Matrix Session RecordsGrid records for every training and testing pasta matrix session. Each pixel of the *.png image files represents the location of one pasta strand. Pasta strands broken during each session are indicated with a white pixel, unbroken strands are indicated with a black pixel. The reaching slot location is relative to the top left corner of each image. Subject identifier and timestamp are contained in each filename.pasta_matrix.zipSkilled Reaching Session RecordsSpreadsheet showing session records, including total trial counts, hit counts, miss counts, and attempts counts, as scored by a trained rater, for every skilled reaching testing session.skilled_reaching.csvLesions DatesSpreadsheet showing lesion dates for all subjects, for aligning pre- and post-lesion timepoints in provided data files.lesion_dates.csv
DOI: 10.15468/2e4nuu
title: Evolution of nuptial-gift-related male prosomal structures: taxonomic revision and cladistic analysis of the genus Oedothorax (Araneae: Linyphiidae: Erigoninae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Lin, Shou-Wang, Lopardo, Lara, Uhl, Gabriele (2022): Evolution of nuptial-gift-related male prosomal structures: taxonomic revision and cladistic analysis of the genus Oedothorax (Araneae: Linyphiidae: Erigoninae). Zoological Journal of the Linnean Society 195: 417-584, DOI: 10.1093/zoolinnean/zlab033
DOI: 10.15468/x8ss24
title: 1989 Onwards, Previously Occupied Swift Nests, UK

description: This dataset is intended to be a comprehensive inventory of previously occupied common swift (Apus apus) nests (where swifts were known to nest previously, but no longer do so). 

It includes records collected as part of various swift mapping projects including The Swift Inventory, The Swift Survey and The Swift Mapper. The aim of these projects was to better understand the reasons for the decline in swifts in the UK, and to help target conservation of swift nest sites. They collated data from a variety of sources, primarily a public request for information and local surveys. 
 
Between 2009-2015, records were collected as part of the ‘Swift Inventory’. This was a cooperative project involving the support of Concern for Swifts - Scotland, London's Swifts, Northern Ireland Swifts, the RSPB, Swift Conservation and UK Swifts. 

The ‘Swift Survey’ then ran from 2016 -2019. This was a national survey, including a website developed by Environmental Resource Management (ERM) to collect data from the public on nesting swifts. 

From 2020 onwards the ‘Swift Mapper’ tool has been used to collect records. The Swift Mapper is a mapping tool involving RSPB, Natural Apptitude, Swift Conservation, Action for Swifts and Swifts Local Network. 

Records prior to 2009 were provided by swift conservation groups and RSPB surveys. 
 
Accompanying datasets of occupied nests, nest boxes and low-level screaming swifts (probable breeders) are also available on the NBN. 
 
This dataset will be updated annually.
DOI: 10.5061/dryad.ds6gc
title: Data from: Estimation of a killer whale (Orcinus orca) population’s diet using sequencing analysis of DNA from feces

description: Estimating diet composition is important for understanding interactions
 between predators and prey and thus illuminating ecosystem function. The
 diet of many species, however, is difficult to observe directly. Genetic
 analysis of fecal material collected in the field is therefore a useful
 tool for gaining insight into wild animal diets. In this study, we used
 high-throughput DNA sequencing to quantitatively estimate the diet
 composition of an endangered population of wild killer whales (Orcinus
 orca) in their summer range in the Salish Sea. We combined 175 fecal
 samples collected between May and September from five years between 2006
 and 2011 into 13 sample groups. Two known DNA composition control groups
 were also created. Each group was sequenced at a ~330bp segment of the 16s
 gene in the mitochondrial genome using an Illumina MiSeq sequencing
 system. After several quality controls steps, 4,987,107 individual
 sequences were aligned to a custom sequence database containing 19
 potential fish prey species and the most likely species of each
 fecal-derived sequence was determined. Based on these alignments,
 salmonids made up &gt;98.6% of the total sequences and thus of the
 inferred diet. Of the six salmonid species, Chinook salmon made up 79.5%
 of the sequences, followed by coho salmon (15%). Over all years, a clear
 pattern emerged with Chinook salmon dominating the estimated diet early in
 the summer, and coho salmon contributing an average of &gt;40% of the
 diet in late summer. Sockeye salmon appeared to be occasionally important,
 at &gt;18% in some sample groups. Non-salmonids were rarely observed.
 Our results are consistent with earlier results based on surface prey
 remains, and confirm the importance of Chinook salmon in this population’s
 summer diet.
description: Mitochondrial 16s
 ribosomal gene fragment sequences from killer whale
 fecesThere are 15 fasta files
 containing DNA sequences from a ~330bp fragment of the mitochondrial 16s
 ribosomal RNA gene. These sequences were amplified from 175 killer whale
 feces collected from the wild. The samples are pooled into 13 experimental
 groups; the numbers in the file names correspond to the sample pools
 described in Table S1 of the associated publication which contains
 sampling information (time, location, whale ID if known). Samples 23 and
 24 are controls, as described in the publication. Methodological details
 including primers and sequencing methods are described in the associated
 publication.16s fecal summer prey sequences
 for dryad.zip
DOI: 10.5061/dryad.nb028
title: Data from: Transcriptome profile analysis from different sex types of Ginkgo biloba L.

description: In plants, sex determination is a comprehensive process of correlated
 events, which involves genes that are differentially and/or specifically
 expressed in distinct developmental phases. Exploring gene expression
 profiles from different sex types will contribute to fully understanding
 sex determination in plants. In this study, we conducted RNA-sequencing of
 female and male buds (FB and MB) as well as ovulate strobilus and
 staminate strobilus (OS and SS) of Ginkgo biloba to gain insights into the
 genes potentially related to sex determination in this species.
 Approximately 60 Gb of clean reads were obtained from eight cDNA
 libraries. De novo assembly of the clean reads generated 108,307 unigenes
 with an average length of 796 bp. Among these unigenes, 51,953 (47.97%)
 had at least one significant match with a gene sequence in the public
 databases searched. A total of 4,709 and 9,802 differentially expressed
 genes (DEGs) were identified in MB vs. FB and SS vs. OS, respectively.
 Genes involved in plant hormone signal and transduction as well as those
 encoding DNA methyltransferase were found to be differentially expressed
 between different sex types. Their potential roles in sex determination of
 G. biloba were discussed. Pistil-related genes were expressed in male buds
 while anther-specific genes were identified in female buds, suggesting
 that dioecism in G. biloba was resulted from the selective arrest of
 reproductive primordia. High correlation of expression level was found
 between the RNA-Seq and quantitative real-time PCR results. The
 transcriptome resources that we generated allowed us to characterize gene
 expression profiles and examine differential expression profiles, which
 provided foundations for identifying functional genes associated with sex
 determination in G. biloba.
description: UnigeneAssembly unigene set from Ginkgo biloba transcriptomeunigene.fasta
DOI: 10.5061/dryad.1hf24
title: Data from: The effect of collective dispersal on the genetic structure of a subdivided population

description: Correlated dispersal paths between two or more individuals are widespread
 across many taxa. The population genetic implications of this collective
 dispersal have received relatively little attention. Here we develop
 two-sample coalescent theory that incorporates collective dispersal in a
 finite island model to predict expected coalescence times, genetic
 diversities and F-statistics. We show that collective dispersal reduces
 mixing in the system, which decreases expected coalescence times and
 increases FST. The effects are strongest in systems with high migration
 rates. Collective dispersal breaks the invariance of within-deme
 coalescence times to migration rate, whatever the deme size. It can also
 cause FST to increase with migration rate because the ratio of within- to
 between-deme coalescence times can decrease as migration rate approaches
 unity. This effect is most biologically relevant when deme size is small.
 We find qualitatively similar results for diploid and gametic dispersal.
 We also demonstrate with simulations and analytical theory the strong
 similarity between the effects of collective dispersal and anisotropic
 dispersal. These findings have implications for our understanding of the
 balance between drift-migration-mutation in models of neutral evolution.
 This has applied consequences for the interpretation of genetic structure
 (e.g. chaotic genetic patchiness) and estimation of migration rates from
 genetic data.
description: Matlab
 scriptsThis zip file contains
 two matlab scripts used to simulate equilibrium Fst values in an Island
 Model with anisotropic migration rates.matlabScripts.zipMathematica NotebookMathematica notebook for the calculations in the main paper.CollectiveDispersal_EvolutionPaper.nbMatlab Simulations (Random anisotropic migration)Simulation data summarized in Table 1 of the paper. These simulations are for anisotropic migration rates that randomly vary every generation.RandomSims.zipMatlab Simulations (Constant anisotropic migration)Simulation data summarized in Table 1 of the paper. These simulations are for anisotropic migration rates that are constant. This case is described by Lehmann & Perrin (2006) Ecology, Vol. 87, p1844-1855ConstantSims.zip
DOI: 10.5061/dryad.50j03
title: Data from: Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): comparative analysis of global accessions and Senegalese landraces

description: Background: Pearl millet is a staple food for people in arid and semi-arid
 regions of Africa and South Asia due to its high drought tolerance and
 nutritional qualities. A better understanding of the genomic diversity and
 population structure of pearl millet germplasm is needed to support
 germplasm conservation and genetic improvement of this crop. Here we
 characterized two pearl millet diversity panels, (i) a set of global
 accessions from Africa, Asia, and the America, and (ii) a collection of
 landraces from multiple agro-ecological zones in Senegal. Results: We
 identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl
 millet accessions, comprised of 252 global accessions and 248 Senegalese
 landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced
 representation libraries. We used these SNPs to characterize genomic
 diversity and population structure among the accessions. The Senegalese
 landraces had the highest levels of genetic diversity (π), while
 accessions from southern Africa and Asia showed lower diversity levels.
 Principal component analyses and ancestry estimation indicated clear
 population structure between the Senegalese landraces and the global
 accessions, and among countries in the global accessions. In contrast,
 little population structure was observed across in the Senegalese
 landraces collections. We ordered SNPs on the pearl millet genetic map and
 observed much faster linkage disequilibrium (LD) decay in Senegalese
 landraces compared to global accessions. A comparison of pearl millet GBS
 linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum
 bicolor) genomes indicated extensive regions of synteny, as well as some
 large-scale rearrangements in the pearl millet lineage. Conclusions: We
 identified 83,875 SNPs as a genomic resource for pearl millet improvement.
 The high genetic diversity in Senegal relative to other regions of Africa
 and Asia supports a West African origin of this crop, followed by wide
 diffusion. The rapid LD decay and lack of confounding population structure
 along agro-ecological zones in Senegalese pearl millet will facilitate
 future association mapping studies. Comparative population genomics will
 provide insights into panicoid crop evolution and support improvement of
 these climate-resilient crops.
description: SNP data by genotyping
 by sequnecing in pearl millet germplasmThe upload SNP data,
 including 83,875 SNPs, was generated by genotyping by sequencing in 500
 pearl millet germplasm collected from several different
 countries.SNP_PEARL_MILLET_GERMPLASM.txt