cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bnzs7h481
title: Diatom sedimentary ancient DNA metabarcoding from western Fram Strait and Kronotsky Peninsula

description: In this study we use sedimentary ancient DNA metabarcoding from two marine
 sediment cores. The first Kastenlot core MSM05/5-712-2 was taken at
 western Fram Strait (subarctic North Atlantic) from which we collected 12
 samples including one biological replicate. The second Kastenlot core
 SO201-2-12KL was retrieved from Kamchatka Strait (subarctic North Pacific)
 from which we collected 9 samples and 2 samples were collected from a
 pilot core taken next to the Kastenlot core. Total DNA was extracted from
 approximately 2ml sediment per sample in 3 batches with up to 9 samples
 and one extraction blank. Total DNA was concentrated and if necessary
 diluted to 2.5 ng/µl. For each batch we performed PCRs in triplicates
 including a PCR no template control (NTC). We amplified a diatom-specific,
 76 bp long part of the rbcL gene with tagged primers Diat_rbcL_705F
 (AACAGGTGAAGTTAAAGGTTCATAYTT) and Diat_rbcL_808R
 (TGTAACCCATAACTAAATCGATCAT). The PCR-products were purified and pooled in
 equal concentrations. The sequencing library was prepared with the Mid
 Output kit v. 2 according to the Fasteris Metafast protocol for low
 complexity amplicon sequencing and checked by qPCR. The library was
 sequenced (2 x 150 bp, paired-end) on the Illumina NextSeq 500 at the
 Fasteris SA sequencing service (Switzerland). For two samples we sequenced
 4 PCR-products and for two samples we could only get 2 PCR-products with
 sufficient DNA content for sequencing.
description: Here, we provide the raw paired-end sequencing data received from
 Fasteris as gz-compressed fastq files (frorward reads:
 190128_NB501850_A_L1-4_AGAK-6_R1.fastq.gz; reverse reads:
 190128_NB501850_A_L1-4_AGAK-6_R2.fastq.gz). Data processing, which
 includes assignment of the sequencing reads to the different samples with
 a tagfile (tagfile_AGAK-6.txt), denoising and taxonomic assignment of
 reads, was performed with the OBITools pipeline
 (https://pythonhosted.org/OBITools/welcome.html). The script containing
 the commands used to process the data is provided (AGAK-6.log). Taxonomic
 assignment based on (diat_embl138_final.fasta). Finally, we provide the
 resulting table which was annotated with the age and depth information per
 sample (AGAK-6_rbcL_embl138.txt).
DOI: 10.15468/dl.sbtwy4
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cadia pedicellata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 53 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002487-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.z8w9ghx92
title: Altruistic bet-hedging and the evolution of cooperation in a Kalahari bird

description: Analyses of the global biogeography of altruism suggest that unpredictable
 environments have favoured the evolution of altruistic helping behaviour
 (helping to rear the offspring of others). It has therefore been
 hypothesised that selection for altruism may frequently arise because
 helping reduces variance in the reproductive success of relatives in
 unpredictable environments (a scenario termed ‘altruistic bet-hedging’).
 Here we show that helping behaviour does reduce environmentally-induced
 variance in the reproductive success of relatives in a wild cooperative
 bird, the white-browed sparrow-weaver (Plocepasser mahali). Our
 decade-long study in the Kalahari desert reveals that non-breeding helpers
 have no overall effect on the mean reproductive success of related
 breeders, but instead reduce variance in the
 reproductive success of related breeders. Moreover, this variance
 reduction arises in part because helpers specifically reduce unpredictable
 rainfall-induced variance in reproductive success, just as hypothesised by
 global comparative analyses. Our novel analytical approach implicates
 effects of helping per se rather than correlated effects
 of group size and isolates within-mother effects of helping from
 potentially confounding among-mother variation in performance. Our
 findings lend new strength to the leading explanation for the global
 biogeography of altruism and highlight the wider importance of considering
 the impacts of altruism on both the mean and variance in performance of
 recipients.
description: "1 - Provisioning
 analysis - RAW DATA.csv": provisioning data, analysis presented in
 Fig. 1D, 1E "2a - Experimental removal
 all female helpers - RAW DATA.csv": helper removal experiment data,
 analysis presented in Fig. 1F and Table S8 "2b - Experimental removal
 all male helpers - RAW DATA.csv": helper removal experiment data,
 analysis presented in Fig. 1F and Table S8 "3 - Bivariate models - RAW
 DATA.csv": data for the analysis of variance of reproductive success,
 analysis presented in Fig. 2 "4 - Nestling survival
 analysis - RAW DATA.csv": data for the analysis of nestling survival,
 analysis presented in Fig. 3
DOI: 10.5281/zenodo.18332141
title: Bathymetry grids compiled from multibeam sonar on the TAN2412 voyage of the R/V Tangaroa

description: Not to be used for navigational purposes.

This dataset contains bathymetry grids from the TAN2412 survey of the R/V Tangaroa in 2024 around the southwest Pacific Ocean,

This overall research project aims to resolve the long-standing mystery of New Zealand longfin (Anguilla dieffenbachii) and shortfin (A. australis schmidtii) eel life cycles using cutting-edge approaches. Our primary objectives with this voyage were to: (1) generate an isotopic map of the western South Pacific Ocean (WSP) to improve understanding of eel migration and spawning environments, (2) investigate the region’s biogeochemistry and primary productivity drivers, and (3) analyse the broader structure and functioning of WSP ecosystems. As such, the TAN2412 research voyage aboard the RV Tangaroa (17 October – 21 November 2024) collect seawater, plankton, and micronekton specimen samples, alongside hydrographic, acoustic, and multi-beam mapping data, to achieve these goals. Samples were collected at specific stations while acoustic and multi-beam data was collected while underway and at each station."

Bathymetric data was collected using a Kongsberg EM302 multibeam system using a Applanix POS MV Oceanmaster GPS Inertial Navigation System.

Multibeam data was collected mainly along transits. Sound velocity profiles were generated using the Sound Speed Manager v.2018.1.50 application and the World Ocean Database 2013.

The raw multibeam data has been uploaded into the International Hydrographic Organization’s Data Centre for Digital Bathymetry (IHO DCDB) available at https://www.ncei.noaa.gov/iho-data-centre-digital-bathymetry.
DOI: 10.5281/zenodo.18332140
title: Bathymetry grids compiled from multibeam sonar on the TAN2412 voyage of the R/V Tangaroa

description: Not to be used for navigational purposes.

This dataset contains bathymetry grids from the TAN2412 survey of the R/V Tangaroa in 2024 around the southwest Pacific Ocean,

This overall research project aims to resolve the long-standing mystery of New Zealand longfin (Anguilla dieffenbachii) and shortfin (A. australis schmidtii) eel life cycles using cutting-edge approaches. Our primary objectives with this voyage were to: (1) generate an isotopic map of the western South Pacific Ocean (WSP) to improve understanding of eel migration and spawning environments, (2) investigate the region’s biogeochemistry and primary productivity drivers, and (3) analyse the broader structure and functioning of WSP ecosystems. As such, the TAN2412 research voyage aboard the RV Tangaroa (17 October – 21 November 2024) collect seawater, plankton, and micronekton specimen samples, alongside hydrographic, acoustic, and multi-beam mapping data, to achieve these goals. Samples were collected at specific stations while acoustic and multi-beam data was collected while underway and at each station."

Bathymetric data was collected using a Kongsberg EM302 multibeam system using a Applanix POS MV Oceanmaster GPS Inertial Navigation System.

Multibeam data was collected mainly along transits. Sound velocity profiles were generated using the Sound Speed Manager v.2018.1.50 application and the World Ocean Database 2013.

The raw multibeam data has been uploaded into the International Hydrographic Organization’s Data Centre for Digital Bathymetry (IHO DCDB) available at https://www.ncei.noaa.gov/iho-data-centre-digital-bathymetry.
DOI: 10.5061/dryad.qjq2bvqdd
title: Linking behavioural thermoregulation, boldness and individual state in male Carpetan rock lizards

description: Mechanisms affecting consistent inter-individual behavioural variation
 (i.e. animal personality) are of wide scientific interest. In
 poikilotherms, ambient temperature is one of the most important
 environmental factors with a direct link to a variety of fitness-related
 traits. Recent empirical evidence suggests that individual differences in
 boldness are linked to behavioural thermoregulation strategy in
 heliothermic species, as individuals are regularly exposed to predators
 during basking. Here, we tested for links between behavioural
 thermoregulation strategy, boldness and individual state in adult males of
 the high mountain Carpetan rock lizard (Iberolacerta cyreni). Principal
 Component Analysis revealed the following latent links in our data: (i) a
 positive relationship of activity with relative limb length and colour
 brightness (PC1, 23% variation explained), (ii) a negative relationship of
 thermoregulatory precision with parasite load and risk-taking (PC2, 20.98%
 variation explained) and (iii) a negative relationship between preferred
 body temperature and relative limb length (PC3, 19.23% variation
 explained). We conclude that differences in boldness and behavioural
 thermoregulatory strategy could be explained by both stable and labile
 state variables. The moderate link between behavioural thermoregulatory
 strategy and risk-taking personality in our system is plausibly the result
 of differences in reproductive state of individuals or variation in
 ecological conditions during the breeding season.
DOI: 10.5061/dryad.0cfxpnw01
title: Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding

description: Although the presence of archaic hominin legacies in humans is taken for
 granted, little attention has been given as to how the data fit with how
 humans colonised the world.  Here I show that Neanderthal and
 Denisovan legacies are strongly correlated and that, like heterozygosity,
 distance from Africa predicts legacy size.  Simulations confirm
 that, once created, legacy size is extremely stable: it may reduce through
 admixture with lower legacy populations but cannot increase detectably
 through neutral drift.  Consequently, populations carrying the
 highest legacies must also be those whose ancestors inter-bred most with
 archaics.  However, the populations with the highest legacies are
 globally scattered and are unified, not by having origins within the known
 Neanderthal range, but instead by living in locations that lie furthest
 from Africa.  Furthermore, the Simons Genome Diversity Project
 data reveal two very distinct correlations between Neanderthal and
 Denisovan legacies, one that starts in North Africa and increases west to
 east across Eurasia and into some parts of Oceania, and a second, much
 steeper trend that starts in Africa, peaking with the San and Ju/’hoansi
 and which, if extrapolated, predicts the large inferred legacies of both
 archaics found in Oceania / Australia.  These trends are
 difficult to reconcile with classical models of how introgression occurred
 but may fit a speculative model in which the loss of diversity that
 occurred when humans moved further from Africa created a gradient in
 heterozygosity that in turn progressively reduced mutation rate such that
 populations furthest from Africa have diverged less from our common
 ancestor and hence from the archaics.  The two distinct trends
 could be interpreted in terms of two ‘out of Africa’ events, an early one
 ending in Oceania and Australia and a later one that colonised Eurasia and
 the Americas.
description: These data files contain the processed outputs from individual
 chromosome vcf files for the Denisovan genome, downloaded from http://cdna.eva.mpg.de/denisova/VCF/human/.  For analyses presented in this paper I focused only on homozygote archaic bases, accepting only those with 10 or more reads, fewer than 250 reads and where &gt;80% of reads were of one particular base.  Each file contains, in order, the following fields: location in basepairs, human reference base, followed by counts for each read of bases A, C, G and T. 
description: Once unzipped, these files are in the correct format for use by
 the C++
 script used to calculate nd10 values for the 1000 genomes
 populations.  For companion files for chimpanzee aligments and equivalent
 files for the Neanderthal genomes, please go to the Dryad entry for
 "Signals
 interpreted as archaic introgression are driven primarily by accelerated
 evolution in Africa".
DOI: 10.5061/dryad.98sf7m0gj
title: Contemporary genetic structure affects genetic stock identification of steelhead trout in the Snake River basin

description: Genetic stock identification is a widely applied tool for the mixed-stock
 management of salmonid species throughout the North Pacific Rim. The
 effectiveness of genetic stock identification is dependent on the level of
 differentiation among stocks which is often high due to the life history
 of these species that involves high homing fidelity to their natal
 streams. However, the utility of this tool can be reduced when natural
 genetic structuring has been altered by hatchery translocation and/or
 supplementation. We examined the genetic population structure of
 ESA-listed steelhead in the Snake River basin of the United States. We
 analyzed 9,613 natural-origin adult steelhead returning to Passive
 Integrated Transponder detection sites throughout the basin from 2010
 through 2017. Individuals were genotyped at 180 single nucleotide
 polymorphic genetic markers and grouped into 20 populations based on their
 return location. While we expected to observe a common pattern of
 hierarchical genetic structuring due to isolation by distance, we observed
 low genetic differentiation between populations in the upper Salmon River
 basin compared to geographically distant populations in the lower Snake
 River basin. These results were consistent with lower genetic stock
 assignment probabilities observed for populations in this upper basin. We
 attribute these patterns of reduced genetic structure to the translocation
 of lower basin steelhead stocks and ongoing hatchery programs in the upper
 Salmon River basin. We discuss the implications of these findings on the
 utility of genetic stock identification in the basin and discuss
 opportunities for increasing assignment probabilities in the face of low
 genetic structure.
DOI: 10.5061/dryad.08kprr50j
title: Diversification or collapse of self-incompatibility haplotypes as a rescue process

description: In angiosperm self-incompatibility systems, pollen with an allele matching
 the pollen recipient at the self-incompatibility locus is rejected.
 Extreme allelic polymorphism is maintained by frequency-dependent
 selection favoring rare alleles. However, two challenges result in a
 "chicken-egg"problem for the spread of a new allele (a tightly
 linked haplotype in this case) under the widespread "collaborative
 non-self recognition" mechanism. A novel pollen-function mutation
 alone would merely grant compatibility with a nonexistent style-function
 allele: a neutral change at best. A novel pistil-function mutation alone
 could only be fertilized by pollen with a nonexistent pollen-function
 allele: a deleterious change that would eliminate all seed set. However, a
 pistil-function mutation complementary to a previously neutral pollen
 mutation may spread if it restores self-incompatibility to a
 self-compatible intermediate. We show that novel haplotypes can also drive
 elimination of existing ones with fewer siring opportunities. We calculate
 relative probabilities of increase and collapse in haplotype number given
 the initial collection of incompatibility haplotypes and the population
 gene conversion rate. Expansion in haplotype number is possible when
 population gene conversion rate is large, but large contractions are
 likely otherwise. A Markov chain model derived from these expansion and
 collapse probabilities generates a stable haplotype number distribution in
 the realistic range of 10--40 under plausible parameters. However, smaller
 populations might lose many haplotypes beyond those lost by chance during
 bottlenecks.
description: The file equilibria.txt, which contains the equilibrium
 frequencies of self-compatible intermediates, was created by numerically
 solving genotype frequency recursions in Mathematica using the uploaded
 notebook sc-balance.nb. All other data were generated by simulation or
 deterministic iteration using custom R scripts. Data were used either to
 calculate derived values or as starting points for further simulations, as
 described in the readme.
description: The transition matrices contain NA values, which are the result
 of a reflecting lower boundary: the state at the lower boundary is never
 reached, so transitions out from it were never calculated. See the
 README.txt for the workflow for generating the data.
DOI: 10.5061/dryad.0k6djh9xm
title: Social network position experiences more variable selection than weaponry in wild subpopulations of forked fungus beetles

description: 1. The phenotypic expression and fitness consequences of behaviors that
 are exhibited during social interactions are especially sensitive to their
 local social context. This context-dependence is expected to generate more
 variation in the sign and magnitude of selection on social behavior than
 that experienced by static characters like morphology. Relatively few
 studies, however, have examined selection on behavioral traits in multiple
 populations. 2. We estimated sexual selection in the wild to determine if
 the strength and form of selection on social phenotypes is more variable
 than that on morphology. 3. We compared selection gradients on social
 network position, body size, and weaponry of male forked fungus beetles
 (Bolitotherus cornutus) as they influenced mating success across nine
 natural subpopulations. 4. Male horn length consistently experienced
 positive sexual selection. However, the sign and magnitude of selection on
 individual measures of network centrality (strength and betweenness)
 differed significantly among subpopulations. Moreover, selection on social
 behaviors occurred at local scale (“soft selection”), whereas selection on
 horn length occurred at the metapopulation scale (“hard selection”). 5.
 These results indicate that an individual with a given social phenotype
 could experience different fitness consequences depending on the network
 it occupies. While individuals seem to be unable to escape the fitness
 effects of their morphology, they may have the potential to mediate the
 pressures of selection on behavioral phenotypes by moving among
 subpopulations or altering social connections within a network.
description: The data were collected as described in the methods of the paper.
  In summary, behavioral interactions were recorded if individuals were
 within 5 cm of each other, those data were then turned into an association
 matrix, the simple ratio index was then calcualted based on the
 observations.  Using the SRI data, social networks were created for each
 subpopulation.  The uploaded data set is the attribute file with
 calculated social network metrics (strength, betweeness, and clustering
 coefficent), fitness measures (number of succesful inseminations, and
 morphological traits (honrs and elytra size).
DOI: 10.5061/dryad.612jm641k
title: Raw in vitro screening data and R scripts for: A Bayesian method for population-wide cardiotoxicity hazard and risk characterization using an in vitro human model

description: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an
 established model for testing potential chemical hazards. Inter-individual
 variability in toxicodynamic sensitivity has also been demonstrated in
 vitro; however, quantitative characterization of the population-wide
 variability has not been fully explored. We sought to develop a method to
 address this gap by combining a population-based iPSC-derived
 cardiomyocyte model with Bayesian concentration-response modeling. A total
 of 136 compounds, including 44 pharmaceuticals and 82 environmental
 chemicals, were tested in iPSC-derived cardiomyocytes from 43 non-diseased
 humans. Hierarchical Bayesian population concentration-response modeling
 was conducted for five phenotypes reflecting cardiomyocyte function or
 viability. Toxicodynamic variability was quantified through the derivation
 of chemical- and phenotype-specific variability factors (TDVF).
 Toxicokinetic modeling was used for probabilistic in vitro-to-in vivo
 extrapolation in order to derive population-wide margins of safety (MOS)
 for pharmaceuticals and margins of exposure (MOE) for environmental
 chemicals. Pharmaceuticals were found to be active across all phenotypes.
 Over half of tested environmental chemicals showed activity in at least
 one phenotype, most commonly positive chronotropy. TDVF estimates for the
 functional phenotypes were greater than those for cell viability, usually
 exceeding the generally-assumed default of ~3. Population
 variability-based MOS for pharmaceuticals were correctly predicted to be
 relatively narrow, between 10-100; however, MOE for environmental
 chemicals, based on population exposure estimates, generally exceeded
 1000, suggesting they pose little risk at general population exposures
 even to sensitive sub populations. This study represents a first of its
 kind human in vitro model that can be used to characterize toxicodynamic
 population variability in cardiotoxic risk.
description: See the attached README in the Blanchette2020_ToxSci_RScripts
 folder.