cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.21k5t
title: Data from: Regional environmental pressure influences population differentiation in turbot (Scophthalmus maximus)

description: Unravelling the factors shaping the genetic structure of mobile marine
 species is challenging due to the high potential for gene flow. However,
 genetic inference can be greatly enhanced by increasing the genomic,
 geographic or environmental resolution of population genetic studies. Here
 we investigated the population structure of turbot (Scophthalmus maximus)
 by screening 17 random and gene-linked markers in 999 individuals at 290
 geographical locations throughout the Northeast Atlantic Ocean. A seascape
 genetics approach with the inclusion of high resolution oceanographic data
 was used to quantify the association of genetic variation with spatial,
 temporal and environmental parameters. Neutral loci identified three
 subgroups: an Atlantic group, a Baltic Sea group and one on the Irish
 Shelf. The inclusion of loci putatively under selection suggested an
 additional break in the North Sea, subdividing southern from northern
 Atlantic individuals. Environmental and spatial seascape variables
 correlated marginally with neutral genetic variation, but explained
 significant proportions (respectively 8.7 % and 10.3 %) of adaptive
 genetic variation. Environmental variables associated with outlier allele
 frequencies included salinity, temperature, bottom shear stress, dissolved
 oxygen concentration and depth of the pycnocline. Furthermore, levels of
 explained adaptive genetic variation differed markedly among basins (3% vs
 12% in the North and Baltic Sea, respectively). We suggest that stable
 environmental selection pressure contributes to relatively strong local
 adaptation in the Baltic Sea. Our seascape genetic approach using a large
 number of sampling locations and associated oceanographic data proved
 useful for the identification of population units as the basis of
 management decisions.
description: Dryad
 entry.zipthis zip file contains
 all data required to perfom both the population genetic analysis, outlier
 tests and seascape genetics on turbot as discribed in the
 article.
DOI: 10.5061/dryad.qc2qq
title: Data from: Population genomics reveals seahorses (Hippocampus erectus) of the western mid-Atlantic coast to be residents rather than vagrants

description: Understanding population structure and areas of demographic persistence
 and transients is critical for effective species management. However,
 direct observational evidence to address the geographic scale and
 delineation of ephemeral or persistent populations for many marine fishes
 is limited. The Lined seahorse (Hippocampus erectus) can be commonly found
 in three western Atlantic zoogeographic provinces, though inhabitants of
 the temperate northern Virginia Province are often considered tropical
 vagrants that only arrive during warm seasons from the southern provinces
 and perish as temperatures decline. Although genetics can locate regions
 of historical population persistence and isolation, previous evidence of
 Virginia Province persistence is only provisional due to limited genetic
 sampling (i.e., mitochondrial DNA and five nuclear loci). To test
 alternative hypotheses of historical persistence versus the ephemerality
 of a northern Virginia Province population we used a RADseq generated
 dataset consisting of 11,708 single nucleotide polymorphisms (SNP) sampled
 from individuals collected from the eastern Gulf of Mexico to Long Island,
 NY. Concordant results from genomic analyses all infer three genetically
 divergent subpopulations, and strongly support Virginia Province
 inhabitants as a genetically diverged and a historically persistent
 ancestral gene pool. These results suggest that individuals that emerge in
 coastal areas during the warm season can be considered “local” and
 supports offshore migration during the colder months. This research
 demonstrates how a large number of genes sampled across a geographical
 range can capture the diversity of coalescent histories (across loci)
 while inferring population history. Moreover, these results clearly
 demonstrate the utility of population genomic data to infer peripheral
 subpopulation persistence in difficult-to-observe species.
description: RAD "unitag"
 FASTA files for H. erectusThis FASTA file contains
 the RADseq "unitag" (unique RAD single end sequences) sequences
 for H. erectus.Boehm_H_erectus_RAD_unitags.fasta.zip
DOI: 10.5061/dryad.s70m4
title: Data from: Specialization and accuracy of host-searching butterflies in complex and simple environments

description: Populations that have access to a variety of resources are often composed
 of individuals that specialize on different subsets of resources.
 Understanding the behavioral mechanisms that drive such individual
 specialization will help us predict the strength of this specialization
 across different environments. Here, we explore the idea that individual
 specialization may be a consequence of constraints on an individual’s
 ability to process information. Because many environments contain an
 overwhelming number of resources and associated stimuli, individuals that
 specialize by focusing on only a subset of these resources may make more
 accurate decisions than individuals that generalize. Furthermore, we
 expect individuals in complex environments, where there are more resources
 and associated stimuli to process, to specialize during their search for
 resources compared to individuals in simple environments. We tested these
 predictions by measuring the accuracy and degree of specialization of
 naïve cabbage white butterflies (Pieris rapae) searching for two target
 host species (radish and cabbage) in simple (one distractor species) and
 more complex (four distractor species) environments. Only butterflies that
 specialized on cabbage were more accurate than butterflies that visited a
 mixture of both radish and cabbage. Furthermore, naïve butterflies
 searching for hosts in complex environments did not adopt more specialized
 foraging strategies than naive butterflies searching for hosts in simple
 environments. Taken together, these results suggest that the foraging
 benefits associated with specialization might only apply to certain
 resources (perhaps those that have readily recognizable cues) and that
 such specializations can be related to accuracy across multiple
 environments.
description: Behavioral data,
 caterpillar rearing data, and reflectance dataThis excel sheet
 contains: 1) raw behavioral data for individual butterflies as they
 searched for and landed on host plants in three different environments, 2)
 individual-level summaries of performance in behavioral trials (calculated
 from the raw behavioral data), 3) rearing data for caterpillars raised on
 different types of host plants, and 4) reflectance spectra for host and
 non-host plant species used in trials.IndivHostSearchComplexity.xlsx
DOI: 10.5061/dryad.h8gh3
title: Data from: Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef

description: Connectivity underpins the persistence and recovery of marine ecosystems.
 The Great Barrier Reef (GBR) is the world's largest coral reef
 ecosystem and managed by an extensive network of no-take zones; however,
 information about connectivity was not available to optimize the
 network's configuration. We use multivariate analyses, Bayesian
 clustering algorithms and assignment tests of the largest population
 genetic data set for any organism on the GBR to date (Acropora tenuis,
 &gt;2500 colonies; &gt;50 reefs, genotyped for ten microsatellite
 loci) to demonstrate highly congruent patterns of connectivity between
 this common broadcast spawning reef-building coral and its congener
 Acropora millepora (~950 colonies; 20 reefs, genotyped for 12
 microsatellite loci). For both species, there is a genetic divide at
 around 19°S latitude, most probably reflecting allopatric differentiation
 during the Pleistocene. GBR reefs north of 19°S are essentially panmictic
 whereas southern reefs are genetically distinct with higher levels of
 genetic diversity and population structure, most notably genetic
 subdivision between inshore and offshore reefs south of 19°S. These
 broadly congruent patterns of higher genetic diversities found on southern
 GBR reefs most likely represent the accumulation of alleles via the
 southward flowing East Australia Current. In addition, signatures of
 genetic admixture between the Coral Sea and outer-shelf reefs in the
 northern, central and southern GBR provide evidence of recent gene flow.
 Our connectivity results are consistent with predictions from recently
 published larval dispersal models for broadcast spawning corals on the
 GBR, thereby providing robust connectivity information about the dominant
 reef-building genus Acropora for coral reef managers.
description: AtenuisGBR_Dryad_DataThe file contains one ReadMe and two data sheets. The first data sheet is the microsatellite dataset comprising ten loci for 2014 colonies of Acropora tenuis from 54 sites sampled throughout the Great Barrier Reef. Each colony has a unique multi-locus genotype. The second data sheet is a microsatellite dataset of the same 10 loci for 708 individuals of A. tenuis sampled from six sites in the Palm Islands. Each data set also includes the latitude and longitude of each sampled colony used in the TESS analyses. Each line in each dataset represents an individual colony and some colonies are present in both datasets and these have the same colonyID. The columns in each dataset are ordered as follows; colonyID, siteID, alleles 1 and 2 of each of the 10 microsatellite loci, longitude and latitude. The sampling data are summarised Table 1 of the supplementary online material associated with the publication in Molecular Ecology.
DOI: 10.5061/dryad.c115v23
title: Data from: Molecular mechanisms of polybrominated diphenyl ethers (BDE-47, -100 and -153) in human breast cancer cells and patient-derived xenografts

description: Polybrominated Diphenyl Ethers (PBDEs) have been used as flame retardants
 in household materials. Their environmental persistence has led to
 continuous human exposure and significant tissue levels. Three PBDE
 congeners (BDE-47, -100, and -153) have been frequently detected in human
 serum. While these compounds appear to possess endocrine disrupting
 activity, studies are largely missing to determine the biological
 mechanisms of PBDEs in breast cancer cells. Here, we assessed PBDE
 bio-activities with three complementary strategies: receptor
 binding/activity assays; non-biased RNA-sequencing analysis using an
 estrogen-dependent breast cancer cell line MCF-7aroERE; and in vivo
 assessments using patient-derived xenograft (PDX) models of human breast
 cancer. According to the results from in vitro experiments, the PBDE
 congeners regulate distinct nuclear receptor signaling pathways. BDE-47
 acts as a weak agonist of both estrogen receptor α (ERα) and
 estrogen-related receptor α (ERRα); it could stimulate proliferation of
 MCF-7aroERE and induced expression of ER-regulated genes (including cell
 cycle genes). BDE-153 was found to act as a weak antagonist of ERα.
 BDE-100 could act as 1) an agonist of aryl hydrocarbon receptor (AhR),
 inducing expression of CYP1A1 and CYP1B1 and 2) as a very weak
 agonist/antagonist of ERα. In vivo, a mixture of the three congeners with
 ratios detected in human serum was tested in an ER+ PDX model. The mixture
 exhibited estrogenic activity through apoptosis/cell cycle regulation and
 increased the expression of a proliferation marker, Ki-67. These results
 advance our understanding of the mechanisms of PBDE exposure in breast
 cancer cells.
description: Supplemental Figures and
 TablesFinal
 Tox Sci-Supplemental Figures and Tables
 Kanaya-Chen.pdf
DOI: 10.5061/dryad.6nv688k
title: Data from: Sperm morphology, sperm motility and paternity success in the bluethroat (Luscinia svecica)

description: Postcopulatory sexual selection may select for male primary sexual
 characteristics like sperm morphology and sperm motility, through sperm
 competition or cryptic female choice. However, how such characteristics
 influence male fertilization success remains poorly understood. In this
 study, we investigate possible correlations between sperm characteristics
 and paternity success in the socially monogamous bluethroat (Luscinia
 svecica svecica), predicting that sperm length and sperm swimming speed is
 positively correlated with paternity success. In total, 25 % (15/61) of
 broods contained extra-pair offspring and 10 % (33/315) of the offspring
 were sired by extra-pair males. Paternity success did not correlate
 significantly with sperm morphology or any aspects of sperm motility.
 Furthermore, sperm morphology and sperm motility did not correlate
 significantly with male morphological characters that previously have been
 shown to be associated with paternity success. Thus, the sperm
 characteristics investigated here do not appear to be strong predictors of
 paternity success in bluethroats.
description: Genotypes
 Genotypes.xlsx.
 Excel file with three sheets, one for each of the three years of this
 study (2013, 2014 and 2015), containing the genotypes of all individuals.
 The columns of each sheet are explained in
 README_Genotypes.docx  
 
 Nest
 info Nest_info.xlsx. Excel
 file with an overview of the social parents of each nest in all three
 years, where they were known. It contains both the individual ID (sample
 number) and the band number for the social male and female.
  
 
 Sperm
 measurements Sperm_measurements.xlsx.
 Excel file with four sheets, explained in
 README_Sperm_measurements.docx
DOI: 10.15482/usda.adc/28790756
title: Data from: Assessing agroecosystem resilience in annual cropping systems with ecometabolomics

description: Plant ecometabolomics is a growing field of study which allows broader understanding of the metabolomic dynamics within and between plants and their ecosystem. Plants constantly respond to environmental cues, producing plant secondary metabolites (PSMs) to communicate with and adapt to their everchanging ecosystems. Plant secondary metabolites allow plants to withstand biotic and abiotic stressors and are mediators of interactions between their above and belowground ecosystem. However, the way PSMs are affected by and respond to agricultural management is poorly understood. As part of the Long-Term Agroecosystem Research (LTAR) Network, we assessed ecometabolomic profiles of corn (<i>Zea mays</i> L.) leaves and roots between contrasting prevailing (prevailing practice, PP) and alternative (alternative practice, AP) cropping practices which utilized cover crops and cover crop interseeding. The ecometabolomic profiles of corn leaves and roots were 90% and 71%, respectively, richer in PSMs in the AP than PP treatments. Our untargeted metabolomic analyses resulted in 124 annotated features, with 68 features significantly different between AP and PP treatments. We detected 43 features annotated as PSMs, 39 of which were greater (p ≤ 0.10) in the AP than PP treatments. This research shows that our agricultural management practices influence the way plants respond within their agroecosystem. Increased production of PSMs allows plants to better adapt to various abiotic and biotic stresses, enhancing the resilience of plants within their ecosystem.
DOI: 10.15482/usda.adc/28790756.v1
title: Data from: Assessing agroecosystem resilience in annual cropping systems with ecometabolomics

description: Plant ecometabolomics is a growing field of study which allows broader understanding of the metabolomic dynamics within and between plants and their ecosystem. Plants constantly respond to environmental cues, producing plant secondary metabolites (PSMs) to communicate with and adapt to their everchanging ecosystems. Plant secondary metabolites allow plants to withstand biotic and abiotic stressors and are mediators of interactions between their above and belowground ecosystem. However, the way PSMs are affected by and respond to agricultural management is poorly understood. As part of the Long-Term Agroecosystem Research (LTAR) Network, we assessed ecometabolomic profiles of corn (<i>Zea mays</i> L.) leaves and roots between contrasting prevailing (prevailing practice, PP) and alternative (alternative practice, AP) cropping practices which utilized cover crops and cover crop interseeding. The ecometabolomic profiles of corn leaves and roots were 90% and 71%, respectively, richer in PSMs in the AP than PP treatments. Our untargeted metabolomic analyses resulted in 124 annotated features, with 68 features significantly different between AP and PP treatments. We detected 43 features annotated as PSMs, 39 of which were greater (p ≤ 0.10) in the AP than PP treatments. This research shows that our agricultural management practices influence the way plants respond within their agroecosystem. Increased production of PSMs allows plants to better adapt to various abiotic and biotic stresses, enhancing the resilience of plants within their ecosystem.
DOI: 10.5061/dryad.c1657
title: Data from: Interactive effects of exogenous and endogenous factors on demographic rates of an African rodent

description: Exogenous and endogenous environmental factors can have simultaneous
 additive as well as interacting effects on life-history traits. Ignoring
 such interactions can lead to a biased understanding of variability in
 demographic rates and consequently population dynamics. These interactions
 have been the focus of decades-long debates on the mechanisms underlying
 small mammal population fluctuations. They have often been studied
 indirectly through seasonal effects, but studies considering them directly
 and more mechanistically are rare. We investigated the joint effects of
 exogenous (temperature, food availability) and endogenous (population
 density) factors on the demographic rates of a group-living diurnal
 rodent, the African striped mouse Rhabdomys pumilio using nine-year
 mark–recapture data from a population in the Succulent Karoo, South
 Africa. In general, higher temperatures and lower food availability were
 associated with higher survival, whereas high population densities were
 either beneficial or detrimental to survival depending on interacting food
 availability. High reproductive rates were related to lower temperatures,
 higher food availability and lower population density, and interactions
 among environmental factors mediated the strength of these relationships.
 Our study highlights the complex ways in which different environmental
 factors can interact to shape demographic rates and emphasizes the
 importance of explicitly including interactions among exogenous and
 endogenous factors into studies of population dynamics.
description: RhabdomysPumilio_Mark-RecapturePartial data from 9 years of a monthly mark-recapture study of African striped mice (Rhabdomys pumilio) from the Succulent Karoo in South Africa (females with estimable age only). Monthly mean values of three environmental factors: temperature, plant cover and mouse population density. More detailed information can be found in the ReadMe file.RhabdomysPumilio_CMR_Ver2.csv
DOI: 10.5061/dryad.51q03
title: Data from: Performance and agreement of risk stratification instruments for postoperative delirium in persons aged 50 years or older

description: Several risk stratification instruments for postoperative delirium in
 older people have been developed because early interventions may prevent
 delirium. We investigated the performance and agreement of nine commonly
 used risk stratification instruments in an independent validation cohort
 of consecutive elective and emergency surgical patients aged ≥50 years
 with ≥1 risk factor for postoperative delirium. Data was collected
 prospectively. Delirium was diagnosed according to DSM-IV-TR criteria. The
 observed incidence of postoperative delirium was calculated per risk score
 per risk stratification instrument. In addition, the risk stratification
 instruments were compared in terms of area under the receiver operating
 characteristic (ROC) curve (AUC), and positive and negative predictive
 value. Finally, the positive agreement between the risk stratification
 instruments was calculated. When data required for an exact implementation
 of the original risk stratification instruments was not available, we used
 alternative data that was comparable. The study population included 292
 patients: 60% men; mean age (SD), 66 (8) years; 90% elective surgery. The
 incidence of postoperative delirium was 9%. The maximum observed incidence
 per risk score was 50% (95%CI, 15–85%); for eight risk stratification
 instruments, the maximum observed incidence per risk score was ≤25%. The
 AUC (95%CI) for the risk stratification instruments varied between 0.50
 (0.36–0.64) and 0.66 (0.48–0.83). No AUC was statistically significant
 from 0.50 (p≥0.11). Positive predictive values of the risk stratification
 instruments varied between 0–25%, negative predictive values between
 89–95%. Positive agreement varied between 0–66%. No risk stratification
 instrument showed clearly superior performance. In conclusion, in this
 independent validation cohort, the performance and agreement of commonly
 used risk stratification instruments for postoperative delirium was poor.
 Although some caution is needed because the risk stratification
 instruments were not implemented exactly as described in the original
 studies, we think that their usefulness in clinical practice can be
 questioned.
description: Risk stratification
 delirium dataFile in IBM SPSS
 Statistics version 22 format format including the data on the performance
 and agreement of nine commonly used risk stratification instruments for
 postoperative delirium in an independent validation cohort of 292
 consecutive elective and emergency surgical patients aged ≥50 years with
 ≥1 risk factor for postoperative delirium.Risk stratification
 delirium dataFile in CSV format
 including the data on the performance and agreement of nine commonly used
 risk stratification instruments for postoperative delirium in an
 independent validation cohort of 292 consecutive elective and emergency
 surgical patients aged ≥50 years with ≥1 risk factor for postoperative
 delirium.
DOI: 10.5061/dryad.470ft
title: Data from: Hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (Oryza sativa L.)

description: Viability and fertility in organisms depend on epistatic interactions
 between loci maintained in lineages. Here, we describe reduced fitness of
 segregants (hybrid breakdown, HB) that emerged in an F2 population derived
 from a cross between 2 rice (Oryza sativa L.) cultivars, “Tachisugata”
 (TS) and “Hokuriku 193” (H193), despite both parents and F1s showing
 normal fitness. Quantitative trait locus (QTL) analyses detected 13 QTLs
 for 4 morphological traits associated with the HB and 6 associated with
 principal component scores calculated from values of the morphological
 traits in the F2 population. Two-way analysis of variance of the putative
 QTLs identified 4 QTL pairs showing significant epistasis; among them, a
 pair on chromosomes 1 and 12 made the greatest contribution to HB. The
 finding was supported by genetic experiments using F3 progeny. HB emerged
 only when a plant was homozygous for the TS allele at the QTL on
 chromosome 1 and homozygous for the H193 allele at the QTL on chromosome
 12, indicating that each allele behaves as recessive to the other. Our
 results support the idea that epistasis is an essential part of hybrid
 fitness.
description: Matsubara et al._the
 primary data