cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26008/1912/bco-dmo.986726.1
title: Diel variability in discrete samples of reef seawater temperature, salinity, dissolved inorganic carbon, pH, and stable carbon isotopes from Willemstad, Curaçao from February 2023 to May 2025

description: These data capture bihourly variability in the carbonate chemistry parameters of dissolved inorganic carbon (DIC), pH, and seawater stable carbon isotopes (δ13CDIC) measured from discrete bottle samples of seawater collected from Piscadera (Willemstad), Curaçao during 36-hour field campaigns in February 2023, March 2024, November 2024, and May 2025. In-situ water temperature of each sample was captured via Onset HOBO deployable sensors deployed at the sampling location. DIC concentrations, pH (total scale), and sample salinity were measured via coupled coulometric titration, spectrophotometry, and salinometry, respectively in controlled laboratory conditions at 20 degrees Celsius. δ13CDIC was measured via isotope ratio mass spectrometry (IRMS). Monitoring carbon cycling in shallow water coral reef ecosystems on diel-to-seasonal timescales directly informs our understanding of natural and externally-forced changes to reef metabolism, structure, function, and ultimately stability. These data help establish gradients in modern Southern Caribbean coral reef metabolism and were collected by a team of researchers associated with an NSF P4Climate-supported award on Southern Caribbean climate change studies.
DOI: 10.5061/dryad.cf388r6
title: Data from: Individuals’ expected genetic contributions to future generations, reproductive value, and short-term metrics of fitness in free-living song sparrows (Melospiza melodia)

description: Appropriately defining and enumerating ‘fitness’ is fundamental to
 explaining and predicting evolutionary dynamics. Yet, general theoretical
 concepts of fitness are often hard to translate into quantities that can
 be measured in wild populations experiencing complex environmental,
 demographic, genetic and selective variation. While the ‘fittest’ entities
 might be widely understood to be those that ultimately leave most
 descendants at some future time, such long-term legacies can rarely be
 measured, impeding evaluation of the degree to which tractable short-term
 metrics of individual fitness could potentially serve as useful direct
 proxies. One opportunity for conceptual and empirical convergence stems
 from the principle of individual reproductive value (Vi), defined as the
 number of copies of each of an individual’s alleles that is expected to be
 present in future generations given the individual’s realised pedigree of
 descendants. Since Vi tightly predicts an individual’s longer-term genetic
 contribution, quantifying Vi provides a tractable route to quantifying
 what, to date, has been an abstract theoretical fitness concept. We used
 complete pedigree data from free-living song sparrows (Melospiza melodia)
 to demonstrate that individuals’ expected genetic contributions stabilise
 within an observed 20-year (i.e. ~8 generation) time period, allowing
 estimation of individual Vi. Considerable among-individual variation in Vi
 was evident in both sexes. Standard metrics of individual lifetime
 fitness, comprising lifespan, lifetime reproductive success and projected
 growth rate, typically explained less than half the variation. We thereby
 elucidate the degree to which fitness metrics observed on individuals
 concur with measures of longer-term genetic contributions, and consider
 the degree to which analyses of pedigree structure could provide useful
 complementary insights into evolutionary outcomes.
description: Song sparrow pedigree
 data (restricted)Pedigree data necessary
 to replicate published analyses.Ped_Dryad_Upload.txtSong sparrow adult survival dataSummary of which individual song sparrows from the focal cohorts were alive in which yearsAdSurvival_Dryad_Upload.txtFemale fitness dataSummary data on individual female lifespan, lifetime reproductive success and individual lambdaFemFitness_Dryad_Upload.txtMale fitness dataSummary data on individual male lifespan, lifetime reproductive success and individual lambdaMaleFitness_Dryad_Upload.txt
DOI: 10.5061/dryad.106d4q7
title: Data from: Cognitive ability and fertility amongst Swedish men born 1951-1967. evidence from military conscription registers

description: We examine the relationship between cognitive ability and childbearing
 patterns in contemporary Sweden using administrative register data. The
 topic has a long history in the social sciences and has been the topic of
 a large number of studies, many reporting a negative gradient between
 intelligence and fertility. We link fertility histories to military
 conscription tests with intelligence scores for all Swedish men born 1951
 to 1967. We find a positive relationship between intelligence scores and
 fertility, and this pattern is consistent across the cohorts we study. The
 relationship is most pronounced for the transition to a first child, and
 men with the lowest categories of IQ-scores have the fewest children.
 Using fixed effects models we additionally control for all factors that
 are shared by siblings, and after such adjustments we find a stronger
 positive relationship between IQ and fertility. Furthermore, we find a
 positive gradient within groups at different levels of education.
 Compositional differences of this kind are therefore not responsible for
 the positive gradient we observe - instead the relationship is even
 stronger after controlling for both educational careers and parental
 background factors. In our models where we compare brothers to one another
 we find that, relative to men with IQ 100, the group with the lowest
 category of cognitive ability have 0.58 fewer children, and men with the
 highest category have 0.14 more children.
description: Collection of source
 code and aggregated data for the publicationCode in Stata 15 used in
 our analyses, as well as aggregated output, and R-files to create graphs.
 See readme file in zip folder and comments in the code for further
 information.Supplemental material S1 -
 Analysis code and aggregated data.zip
DOI: 10.5061/dryad.kk6cn22
title: Data from: Incorporating the disease triangle framework for testing the effect of soil-borne pathogens on tree species diversity

description: 1. The enemies-induced Janzen-Connell (JC) effect, a classic model
 invoking conspecific negative density dependence (CNDD) and distance
 dependence, is a primary biodiversity maintenance hypothesis. Yet,
 conflicting evidence for the JC effect leads to disagreement about its
 role in maintaining forest diversity. 2. We focus this review on
 soil-borne pathogens, which are the primary agent inducing the JC effect
 in many forest ecosystems. Although the test of the pathogen-induced JC
 effect in ecology critically rests on the seedling mortality caused by
 soil pathogens, what has not been explicitly explored in the early
 literature but has increasingly received attention is the long-recognized
 fact that the environment can alter virulence of pathogens and host
 susceptibility (and thus pathogen-host interactions), as predicted by the
 classic disease triangle framework enlightened by pathology research in
 agricultural systems. 3. Here, following the disease triangle framework we
 review evidence on how the pathogen-induced JC effect may be contingent on
 context (e.g., environmental conditions, pathogen inoculum load, and
 genetic divergence in host and pathogen populations). The reviewed
 evidence reveals and clarifies the conditions where pathogens may or may
 not cause disease to hosts, thus contributing to reconciling the
 inconsistent results about the pathogen-induced JC effect in the
 literature. The context-dependence of the disease triangle predicts that
 the pathogen-induced JC effect would change under global change. 4.
 Gaining insights from evidence that the pathogen-induced JC effect is
 context-dependent, we suggest that future tests on the JC hypothesis be
 conducted under the framework of disease triangle, and we stress the
 necessity by controlling the effect of context factors on plant-pathogen
 interactions when testing for the JC effect. We conclude the review by
 proposing three lines of future research for testing the importance of the
 JC effect in maintaining global forest tree species diversity, with a
 particular emphasis on testing the effect of global warming on the
 strength of pathogen-host interactions for better predicting changes of
 forest biodiversity under climate change.
description: Liu & He_Table
 3_Raw_DataRaw data for testing for
 effects of ambient conditions on seedling mortality of Ormosia
 glaberrima.
DOI: 10.5287/ora-xo5mbmxo1
title: Predicting progression in MS (NMR data)

description: This dataset contains serum 1H NMR metabolomics profiles generated to support the study “Serum GFAP and NfL Augment a Metabolomics-Driven Strategy for Long-Term Prediction of Multiple Sclerosis Progression.” Serum samples were acquired from individuals with multiple sclerosis and analysed using standardised NMR spectroscopy protocols. The data include processed spectral features and quantified metabolites used for multivariate modelling and longitudinal prediction of disease progression.
DOI: 10.5061/dryad.m3s165k
title: Data from: Components of cowpea resistance to the seed beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae: Bruchinae)

description: Cowpea serves as a major source of dietary protein in many tropical and
 subtropical regions around the world. To identify loci associated with
 agronomically desirable traits, eight elite cowpea cultivars were
 systematically inter-crossed for eight generations to yield 305
 recombinant inbred lines. Here, we investigated whether these founder
 parents also possess resistance to the seed beetle Callosobruchus
 maculatus (F.) (Coleoptera: Chrysomelidae), a highly destructive
 post-harvest pest. We estimated larval survival in seeds, egg-to-adult
 development time, adult mass at emergence, and seed acceptance for
 oviposition. Survival varied significantly among cowpea cultivars, but the
 pattern was complicated by an unexpected source of mortality; on three
 cultivars, mature larvae in a substantial fraction of seeds (20-36%)
 exited seeds prematurely, and consequently failed to molt into viable
 adults. Even if such seeds were eliminated from the analysis, survival in
 the remaining seeds varied from 49% to 92% across the eight parents.
 Development time and body mass also differed among hosts, with
 particularly slow larval development on three closely related cultivars.
 Egg-laying females readily accepted all cultivars except one with a
 moderately rugose seed coat. Overall, suitability ranks of the eight
 cultivars depended on beetle trait; a cultivar that received the most eggs
 (IT82E-18) also conferred low survival. However, one cultivar
 (IT93K-503-1) was a relatively poor host for all traits. Given the
 magnitude of variation among parental cultivars, future assays of
 genotyped recombinant progeny can identify genomic regions and candidate
 genes associated with resistance to seed beetles.
description: C. mac-cowpea host
 acceptance dataThis csv file contains
 the host acceptance data, that is the number of replicates where eggs were
 (Y) versus were not (N) laid on a given cowpea line.CowpeaParents_egg-laying.csvC. mac-cowpea survival dataThis csv file contains the survival data. For each cowpea line, the number of hatched larvae that survived to adult (Y), died inside the seed (NINSIDE) and prematurely exited the seed (NOUTSIDE) is given.CowpeaParents_survival.csvC. mac-cowpea weight and development time dataThis csv file contains the adult weight and development time data. Each row provides data for one seed beetle, which includes the cowpea line (HOST), weight (WEIGHT) and development time in days (DEVT).CowpeaParents_wt-devt.csvHost acceptance R scriptThis R script contains the commands to fit the Bayesian model for host acceptance with the rjags interface with JAGS.commandsAccept.RR script for survival dataThis R script contains the commands to fit the Bayesian model for survival with the rjags interface with JAGS.commandsSurvival.RR script for weight and development timeThis R script contains the commands to fit the Bayesian models for weight and development time with the rjags interface with JAGS.commandsWtDev.R
DOI: 10.5061/dryad.ct40nm7
title: Data from: MHC structuring and divergent allele advantage in a urodele amphibian: a hierarchical multi-scale approach

description: The proteins encoded by extraordinarily polymorphic major
 histocompatibility complex (MHC) genes are involved in the adaptive immune
 response. Balancing selection is believed to maintain MHC polymorphism in
 the long-term, although neutral processes also play a role in shaping MHC
 diversity. However, the relative contribution of these processes is poorly
 understood. Here we characterized MHC class II variation of a
 low-dispersal, pond-breeding newt (Triturus carnifex) over a restricted,
 geographically structured area. We aimed to: (1) evaluate the contribution
 of selection and neutral processes to shaping MHC diversity at two
 geographic scales; and (2) test for signatures of divergent allele
 advantage (DAA), a potentially important mechanism of balancing selection.
 The dominant role of selection in shaping MHC variation was suggested by
 the lack of correlation between MHC and neutral (microsatellite)
 variation. Although most variation occurred within populations for both
 types of markers, they differed in the extent of structuring at the two
 spatial scales. MHC structuring was more pronounced at local scales,
 suggesting the role of local selection, while structuring was not
 detectable at a larger scale, possibly an effect of balancing selection.
 Microsatellites showed the opposite pattern. As expected under DAA, the
 observed genotypes combined more sequence diversity than expected under
 random association of alleles. Thus, DAA may contribute to maintaining MHC
 polymorphism, which is ancient, as supported by signatures of historical
 positive selection and trans-species polymorphism. Our results point to
 the importance of a multi-scale approach in studying MHC variation,
 especially in low-dispersal taxa, genetically structured at fine spatial
 scales.
description: Archived data for:
 "MHC structuring and divergent allele advantage in a urodele
 amphibian: A hierarchical multi-scale approach"Talarico_etal_HDY.zip
DOI: 10.5061/dryad.cf604dn
title: Data from: Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset

description: Engineering allosteric transcriptional repressors containing an
 environmental sensing module (ESM) and a DNA recognition module (DRM) has
 the potential to unlock a combinatorial set of rationally designed
 biological responses. We demonstrated that constructing hybrid repressors
 by fusing distinct ESMs and DRMs provides a means to flexibly rewire
 genetic networks for complex signal processing. We have used
 coevolutionary traits among LacI homologs to develop a model for
 predicting compatibility between ESMs and DRMs. Our predictions accurately
 agree with the performance of 40 engineered repressors. We have harnessed
 this framework to develop a system of multiple toggle switches with a
 master OFF signal that produces a unique behavior: each engineered
 biological activity is switched to a stable ON state by different
 chemicals and returned to OFF states in response to a common signal. One
 promising application of this design is to develop living diagnostics for
 monitoring multiple parameters in complex physiological environments and
 it represents one of many circuit topologies that can be explored with
 modular repressors designed with coevolutionary information.
description: MSA LacI
 homologsMultiple sequence
 alignments for 74,287 LacI homologs. All the sequences are obtained from
 Uniprot database by using the hmm profile of LacI with the command
 hmmsearch.MSA_LacI_homologs.fastaLacI eij hi parametersPairwise coupling and local fields parameters computed from about 70,000 LacI homologs by DCA method (DCAparameters.m). Therefore, the data type of it is MAT file, which can be read by MATLAB.LacI_eij_hi_parameters.mat8 LacI homolgs shuffled at 47Multiple sequence alignment of CelR, GalR, LacI, MalR, RbsR, ScrR, XltR, and PurR native sequences, and their hybrids shuffled at the homologous position of LacI 47.8_LacI_homolgs_shuffled_at_47.txtLacI family residue pairs with top 1500 DI valuesCoevolving residue pairs between DNA recognition module and environmental sensing module, with top 1500 direct information values computed by DCA method (dca.m). The original dca.m code can be found in dca.rice.edu.LacI_family_residue_pairs_with_top_1500_DI_values.txtREADME
DOI: 10.60964/rnd-k7dq-bw93
title: Human brain LFP recordings

description: The description of this dataset is being prepared.
DOI: 10.5061/dryad.6f462d4
title: Data from: Quantifying habitat use of migratory fish across riverscapes using space-time isotope models

description: 1.Migratory animals pose difficult challenges to conservation and
 management because identifying critical habitats used throughout their
 lives is rarely possible. Endogenous tracers (e.g., isotope ratios)
 recorded in sequentially growing biogenic tissues, however, represent a
 potential source of unique insights at the more elusive temporal and
 spatial scales central to understanding the ecology of mobile species. To
 this end, a general probabilistic framework has emerged that
 quantitatively compares predictive models of isotopic variation across
 landscapes (called isoscapes) to the isotopic composition recorded in a
 biological tissue to determine the provenance and movements of animals
 throughout their lives. 2.Although this spatially continuous approach to
 isotope‐based geographic assignment is becoming more common across taxa
 and ecosystems, adopting this framework to take advantage of serial
 isotope records stored within sequentially growing biogenic tissues (e.g.,
 teeth or otoliths) is less common. 3.Here, we construct a novel space‐time
 isotope model of provenance (STIMP) that determines the habitat use
 through time of migratory fish across river basins. To do so, this model
 integrates: strontium isotope (87Sr/86Sr) ratios across a riverscape, the
 serial records of 87Sr/86Sr within otoliths, habitat geomorphology, and
 the directional movement patterns of fish through river networks. 4.To
 illustrate an application of the model, we applied it to a published
 dataset from Chinook salmon (Oncorhynchus tshawytscha) harvested in 2011
 during a coastal fishery in Bristol Bay, Alaska, U.S.A. Using this model,
 we show how individuals exploit an array of habitat types to achieve their
 juvenile growth prior to ocean migration, and that the intensity of
 habitat use among habitat types across the basin shifts spatially over the
 course of freshwater residence (e.g., from headwaters to migration
 corridors). The STIMP presented here integrates diverse information
 sources to reveal the cryptic juvenile movement patterns of a highly
 migratory species, providing new insights critical to their conservation.
 This general framework is applicable to any migratory taxa that use
 isotopically heterogeneous landscapes during their lives and record such
 variation in sequentially growing biogenic tissues.
description: TableS5_edg_dist_sqTable S5: Square distance matrix for directional movement prior; needed to run STIMP model
DOI: 10.18167/dvn1/8lyuwo
title: Genotyping and phenotyping data of 250 individuals of the Fleur11 x IpaCor AB-QTL population phenotyped during three consecutive years (2020, 2021 and 2022) at Nioro research Station, Senegal

description: This dataset relates to the paper "Mapping QTLs for early leafspot resistance and yield component traits using an interspecific AB-QTL population in peanut" published in 2024 in Frontiers in Plant Science. It gathers three years of phenotyping data collected during the rainy season (July-October) 2020, 2021, and 2022, including traits such as leafspot and yield components-related traits, as well as genotyping data for 2329 SNPs. The data is in a .csv file, with a format that fits the r/qtl package
DOI: 10.5061/dryad.33jn722
title: Data from: New Zealand tree and giant wētā (Orthoptera) transcriptomics reveal divergent selection patterns in metabolic loci

description: Exposure to low temperatures requires an organism to overcome
 physiological challenges. New Zealand wētā belonging to the genera
 Hemideina and Deinacrida are found across a wide range of thermal
 environments and therefore subject to varying selective pressures. Here we
 assess the selection pressures across the wētā phylogeny, with a
 particular emphasis on identifying genes under positive or diversifying
 selection. We used RNA-seq to generate transcriptomes for all 18
 Deinacrida and Hemideina species. A total of 755 orthologous genes were
 identified using a bidirectional best hit approach, with the resulting
 gene set encompassing a diverse range of functional classes. Analysis of
 orthologue ratios of synonymous to non-synonymous amino acid changes found
 83 genes that are under positive selection for at least one codon. A wide
 variety of Gene Ontology terms, enzymes and KEGG pathways are represented
 among these genes. In particular, enzymes involved in oxidative
 phosphorylation, melanin synthesis and free-radical scavenging are
 represented, consistent with physiological and metabolic changes that are
 associated with adaptation to alpine environments. Structural alignment of
 the transcripts with the most codons under positive selection revealed
 that the majority of sites are surface residues, and therefore have the
 potential to influence the thermostability of the enzyme, with the
 exception of prophenoloxidase where two residues near the active site are
 under selection. These proteins provide interesting candidates for further
 analysis of protein evolution
description: Gene
 AnnotationGene annotations,
 including GO terms, EC codes for each transcriptGene_set_annotations.xlsxPaml Branch Tests ResultsSummary of likelihoods, LRT, omega values for all paml branch testsBranch_tests_final.xlsxPaml Site Test ResultsPaml_site_final.xlsxAlignments755 final gene alignments in .phy formatTranscriptomesFinal Cleaned de novo assembled transcriptomes for each species