cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.898c4
title: Data from: Occurrence of the isopod Archaeoniscus coreaensis new species from the Lower Cretaceous Jinju Formation, Korea

description: The fossil isopod crustacean genus Archaeoniscus has been known to occur
 in England, France and Germany during the Upper Jurassic, and in Mexico
 and Egypt during the Lower Cretaceous. The morphology of this genus is
 unique in having dorsoventrally compressed body, the cephalon set deeply
 into the first pereionite, pleon as wide as pereion, and a broad
 semicircular pleotelson. These features have resulted in placing the
 classification of the genus in the monotypic family Archaeoniscidae.
 However, due to the lack of detailed morphological data, suprafamilial
 classification of this genus has remained unclear, as well as its ecology
 and lifestyle. Here we report Archaeoniscus coreaensis n. sp. from the
 Jinju Formation, Gyeongsang Basin, Korea. The occurrence of Archaeoniscus
 in the East Asia implies that the genus may have had a worldwide
 distribution. The Gyeongsang Basin was a Cretaceous backarc basin, which
 consists of exclusively non-marine sedimentary sequences. The occurrence
 of this genus, therefore, indicates that Archaeoniscus successfully
 adapted to a freshwater ecosystem as well. Detailed anatomy including
 antennulae, antennae, pereiopods, and uropods was observed from
 well-preserved multiple specimens, which allows better understanding of
 the morphology of Archaeoniscus. The axial structure in the posterior part
 of the body, which was previously interpreted as a unique brood pouch
 characterizing the family, turned out to be a remnant of the hindgut.
 Females of all isopods and most of the members of the superorder
 Peracarida have a thoracic ventral brood pouch, modified from the thoracic
 coxal endites. Based on the morphology of the largely unmodified
 ambulatory pereiopods of A. coreaensis, the possibility of Archaeoniscus
 being ectoparasitic is discounted. Instead, the flattened body and the
 form of limbs of A. coreaensis would have been suitable for a benthic
 lifestyle.
description: SupplementarySelected specimens from the material for this study
DOI: 10.5061/dryad.2637g
title: Data from: The fossil record and phylogeny of the auklets (Pan-Alcidae, Aethiini)

description: The auklets Aethia and Ptychoramphus comprise the smallest known Alcidae
 (Aves, Charadriiformes) and have a fossil record that extends into the
 Miocene. The evolution of auklets is poorly understood because systematic
 hypotheses of relationships among extant auklets are largely incongruent,
 the morphology of auklet fossils has not been evaluated in detail, and
 extinct species of auklets have not been previously included in a
 phylogenetic analysis. Previously described auklet fossil remains are
 reviewed and two new species of auklet, Aethia barnesi and Aethia storeri,
 are described from the Miocene and Pliocene of southern California, USA.
 Previously described auklet fossil remains, the two newly described
 extinct species of auklet, and extant species of auklets and other alcids
 are included in combined phylogenetic analyses of morphological and
 molecular sequence data. Based on the results of the phylogenetic
 analyses, the taxonomy of fossils referred to Aethiini is revised and the
 evolution of the clade is evaluated in a phylogenetic context. The
 osteological morphology of extinct auklets appears to be little-changed
 from their extant relatives, suggesting that the ecological attributes of
 these small wing-propelled divers may also be relatively unchanged since
 the Miocene.
description: auklet
 matrixcombined phylogenetic
 matrix of morphological and molecular sequence dataauklets.nexauklet measurementsmeasurements of extant auklet skeletonsauklets.xlscharacter descriptionsdescriptions and illustrations of morphological characters used in the phylogenetic analysischaracters.docxcomparative materialextant comparative material scored for the phylogenetic analysisCompMat.docgenbank accession datatable of genbank accession numbers and sequence authorshipgenbank#'s.docx
DOI: 10.5061/dryad.36md8
title: Data from: Genetics of gene expression responses to temperature stress in a sea urchin gene network

description: Stress responses play an important role in shaping species distributions
 and robustness to climate change. We investigated how stress responses
 alter the contribution of additive genetic variation to gene expression
 during development of the purple sea urchin, Strongylocentrotus
 purpuratus, under increased temperatures that model realistic climate
 change scenarios. We first measured gene expression responses in the
 embryos by RNA-seq to characterize molecular signatures of mild, chronic
 temperature stress. We found that an increase from 12 °C to 18 °C caused
 widespread alterations in gene expression including in genes involved in
 protein folding, RNA processing, and development. To understand the
 quantitative genetic architecture of this response, we then focused on a
 well-characterized gene network involved in endomesoderm and ectoderm
 specification. Using a breeding design with wild-caught individuals, we
 measured genetic and gene-environment interaction effects on 72 genes
 within this network. We found genetic or maternal effects in 33 of these
 genes, and that the genetic effects were correlated in the network. 14
 network genes also responded to higher temperatures, but we found no
 significant genotype-environment interactions in any of the genes. This
 absence may be due to an effective buffering of the temperature
 perturbations within the network. In support of this hypothesis,
 perturbations to regulatory genes did not affect the expression of the
 genes that they regulate. Together, these results provide novel insights
 into the relationship between environmental change and developmental
 evolution and suggest that climate change may not expose large amounts of
 cryptic genetic variation to selection in this species.
description: Data from: Genetics of
 gene expression responses to temperature stress in a sea urchin gene
 networkThis archive contains
 scripts and data files to duplicate all analyses in the accompanying
 paper. To run, open the file README.R in R, and follow the included
 instructions. Of particular interest is the script labeled
 "Run_uantitative_genetics_models_MCMC.R". This scripts
 implements the hierarchical Bayesian mixed-effect modelwe describe to
 robustly estimate genetic parameters from the gene expression
 data.Runcie_et_al_Dryad.zip
DOI: 10.5061/dryad.v3144
title: Data from: Symbiont community and host genetic structure of the brain coral Platygyra verweyi, at the outlet of a nuclear power plant and adjacent areas

description: In the context of rising seawater temperatures associated with climate
 change, the issue of whether coral holobionts deal with this challenge by
 shuffling their associations with stress- and/or heat-tolerant
 Symbiodinium, by generating heat-resistant host genotypes, or both is
 important for coral survival. In the present study, the composition of
 communities of the endosymbiont Symbiodinium and the population genetics
 of the coral host Platygyra verweyi were examined in a reef impacted by
 hot water discharged from the outlet of a nuclear power plant in operation
 in Kenting, Southern Taiwan since 1984. The water at this site is 2.0-3.0
 ºC warmer than adjacent reefs in summer, which have an average seawater
 temperature of 29.0 ºC. The data were compared with those for the same
 species at other sites within 12 km of the outlet site. Platygyra verwyei
 was associated with one or both of Symbiodinium types C3 (heat sensitive)
 and D1a (heat tolerant) at all sites with the latter being the dominant at
 the nuclear power plant outlet. The proportion of C3 in populations
 increased gradually with increasing distance from the hot-water discharge.
 Genetic analysis of the Platygyra verweyi host using mitochondrial and
 nuclear markers showed no genetic differentiation among sites. Changes in
 the composition of Symbiodinium types associated with P. verweyi among
 closely located sites in Kenting suggested that this coral might have
 acclimatized to the constant thermal stress by selective association with
 heat-tolerant Symbiodinium types, whereas the role of the host in
 adaptation was inconclusive.
description: MainDataThis file contains; 1. Seawater temperature data at different sites for July 2009 and for NPP OL at 3m and 5m depths for the year 2009. 2. qPCR raw data for Symbiodinium clade C and D for all the sites, with C:D ratio and 3. Haplotype network dataIGRfasta file of noncoding intergenic region (IGR) sequencesITSPlatyThe file contains ITS sequences for the host
DOI: 10.5061/dryad.sb432
title: Data from: Reduced drought tolerance during domestication and the evolution of weediness results from tolerance-growth trade-offs

description: The increased reproductive potential, size, shoot allocation, and growth
 rate of weedy plants may result from reduced resource allocation to other
 aspects of plant growth and defense. To investigate whether changes in
 resource allocation occurred during domestication or the evolution of
 weediness, we compared the mycorrhizal responsiveness, growth, and drought
 tolerance of nine native ruderal, nine agriculturally weedy (four US weedy
 and five Australian weedy), and fourteen domesticated populations (eight
 ancient landraces and six improved cultivars) of the common sunflower
 (Helianthus annuus). Domesticated sunflower cultivars were less drought
 tolerant, but had higher plant growth and fecundity and coarser roots than
 wild populations. There were no changes in level of drought tolerance
 between improved cultivars and ancient landraces plants, but there was an
 increase in allocation to flowers with recent selection. Weedy populations
 were intermediate between domesticated cultivars and native ruderal
 populations for plant growth rate, root architecture and drought
 tolerance. Weedy populations benefited most from mycorrhizal inoculation
 by having fewer wilted leaves and wetter soil. Overall, we found that
 trade-offs between drought tolerance and several aspects of plant growth,
 including growth rate, allocation to flowering and root architecture,
 govern evolution during sunflower domestication and the invasion of
 disturbed habitat.
description: blub pop resids for
 avdiamSAS code to perform the
 analysis of BLUPs for root architecture measurements.blub pop resids for
 final measuresSAS code to analyze the
 BLUPs for plant growth characters of size and
 flowering.Drought Data dec 10th
 2009-1Full experiment data
 sheet the includes all ther measurements for the drought and mhycorrhizal
 response treatments of the experiment.Drought Data
 infectionData of how
 mycorrhizally infected each non-drought stressed plant
 was.drought
 infectionCode to analyze
 mycorrhizal infectionend of experiment final
 measures Weedy3 Oct 2011Code to analyze the full
 experiment drought responsehelianthus root
 architecturedata sheet of root
 architecture measurementsMay 2011 full experiment
 blupsData sheet of BLUP
 outputs
DOI: 10.5061/dryad.j35fc
title: Data from: Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

description: The cyprinid tribe Labeonini (sensu Rainboth, 1991) is a large group of
 freshwater fishes containing around 40 genera and 400 species. They are
 characterized by an amazing diversity of modifications to their lips and
 associated structures. In this study, a total of 34 genera and 142 species
 of putative members of this tribe, which represent most of the generic
 diversity and more than one third of the species diversity of the group,
 were sampled and sequenced for four nuclear genes and five mitochondrial
 genes (totalling 9,465 bp). Phylogenetic relationships and subdivision of
 this tribe were investigated and the placement and status of most genera
 are discussed. Partitioned maximum likelihood analyses were performed
 based on the nuclear dataset, mitochondrial dataset, combined dataset, and
 the dataset for each nuclear gene. Inclusion of the genera
 Paracrossochilus, Barbichthys, Thynnichthys, and Linichthys in the
 Labeonini was either confirmed or proposed for the first time. None of the
 genera Labeo, Garra, Bangana, Cirrhinus, and Crossocheilus are
 monophyletic. Taxonomic revisions of some genera were made: the generic
 names Gymnostomus Heckel, 1843, Ageneiogarra Garman, 1912 and Gonorhynchus
 McClelland, 1839 were revalidated; Akrokolioplax Zhang and Kottelat, 2006
 becomes a junior synonym of Gonorhynchus; the species Osteochilus nashii
 was found to be a member of the barbin genus Osteochilichthys. Five
 historical hypotheses on the classification of the Labeonini were tested
 and rejected. We proposed to subdivide the tribe, which is strongly
 supported as monophyletic, into four subtribes: Labeoina, Garraina,
 Osteochilina, and Semilabeoina. The taxa included in each subtribe were
 listed and those taxa that need taxonomic revision were discussed.
description: LabeoninicombinedExpandedDatasetLabeoniniCombinedExpandedDataset (for Fig. 1)GenePartitionsGenePartitions
DOI: 10.5061/dryad.c03c2
title: Data from: Patterns of paternity skew among polyandrous social insects: What can they tell us about the potential for sexual selection?

description: Monogamy results in high genetic relatedness among offspring and thus it
 is generally assumed to be favoured by kin selection. Female multiple
 mating (polyandry) has nevertheless evolved several times in the social
 Hymenoptera (ants, bees and wasps), and a substantial amount of work has
 been conducted to understand its costs and benefits. Relatedness and
 inclusive fitness benefits are, however, not only influenced by queen
 mating frequency but also by paternity skew, which is a quantitative
 measure of paternity biases among the offspring of polyandrous females. We
 performed a large scale phylogenetic analysis of paternity skew across
 polyandrous social Hymenoptera. We found a general and significant
 negative association between paternity frequency and paternity skew. High
 paternity skew, which increases relatedness amongst colony members and
 thus maximizes inclusive fitness gains, characterized species with low
 paternity frequency. However, species with highly polyandrous queens had
 low paternity skew, with paternity equalized amongst potential sires.
 Equal paternity shares among fathers are expected to maximize fitness
 benefits derived from genetic diversity among offspring. We discuss the
 potential for post-copulatory sexual selection to influence patterns of
 paternity in social insects, and suggest that sexual selection may have
 played a key, yet overlooked role in social evolution.
description: Jaffe et
 al-Interspecific sims Sall by superfamilySampling protocol and
 simulations used to construct the null hypothesis under random paternity
 allocation. Interspecific simulations based on the entire data set (Sall,
 n = 72 species), performed within ants, bees and wasps.Jaffe et
 al-Interspecific sims SallSampling protocol and
 simulations used to construct the null hypothesis under random paternity
 allocation. Interspecific simulations based on the entire data set (Sall,
 n = 72 species), performed accross all species.Jaffe et
 al-Interspecific sims Ssig by superfamilySampling protocol and
 simulations used to construct the null hypothesis under random paternity
 allocation. Interspecific simulations based on the species with skew
 values differing from the random skew expectation (Ssig, n = 56 species),
 performed within ants, bees and wasps.Jaffe et
 al-Interspecific sims SsigSampling protocol and
 simulations used to construct the null hypothesis under random paternity
 allocation. Interspecific simulations based on the species with skew
 values differing from the random skew expectation (Ssig, n = 56 species),
 performed across all species.Jaffe et
 al-Intraspecific simulationsSampling protocol and
 simulations used to construct the null hypothesis under random paternity
 allocation. Intraspecific simulations.Jaffe et al-null
 hypothesis filesReadMe
 file
DOI: 10.25387/g3.31043098
title: Supplementary Material for Aközbek et al., 2026

description: Supplementary Material for A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana
DOI: 10.25387/g3.31043098.v1
title: Supplementary Material for Aközbek et al., 2026

description: Supplementary Material for A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana
DOI: 10.5061/dryad.731f5
title: Data from: SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites

description: We used a high density SNP array to genotype 75 P. falciparum isolates
 recently collected from Senegal and The Gambia in order to search for
 signals of selection in this malaria endemic region. We found little
 geographic or temporal stratification of the genetic diversity among the
 sampled parasites. Through application of the iHS and REHH haplotype-based
 tests for positive selection, we found evidence of recent selective sweeps
 at a known drug resistance locus, at several known antigenic loci, and at
 several genomic regions not previously identified as sites of recent
 selection. We discuss the value of deep population-specific genomic
 analyses for identifying selection signals within sampled endemic
 populations of parasites, which may correspond to local selection
 pressures such as distinctive therapeutic regimes or mosquito vectors.
description: senegambia_genotype_dataPlasmodium falciparum isolates from Senegal and The Gambia, some DNA directly drawn and some from culture-adapted parasites; only single infections included. SNP calling was as described in (Van Tyne, et al. 2011): Parasite DNA was hybridized to a P. falciparum Affymetrix array containing 74,656 SNP markers and genotypes called using the BRLMM-P algorithm. SNPs were validated by comparing array genotypes with Sanger sequencing genotypes for 17 reference strains (Van Tyne, et al. 2011); perfect concordance was required, as was a minimum 80% call rate. Genomic positions and translations are based on the PlasmoDB v5.0 assembly and annotation.
DOI: 10.5061/dryad.g6r70
title: Data from: Testing for ecological limitation of diversification: a case study using parasitic plants

description: Imbalances in phylogenetic diversity could be the result of variable
 unbounded diversification rates, differing limits on diversity, or a
 combination of the two. We propose an approach to distinguish between
 rates and limits as the primary cause of phylogenetic imbalance, using
 parasitic plants as a model. With sister-taxon comparisons, we show that
 parasitic plant lineages are typically much less diverse than their
 autotrophic sisters. We then use age estimates for taxa used in the
 sister-taxon comparisons to test for correlations between clade age and
 diversity. We find that parasitic plant diversity is not significantly
 correlated with the age of the lineage, whereas there is a strong positive
 correlation between the age and diversity of autotrophic sister lineages.
 The Ericaceae sister-pair Monotropoideae (parasitic) and Arbutoideae
 (autotrophic) are sufficiently well samples at the species level to allow
 more parametric comparisons of diversification patterns. Model-fitting for
 this group supports ecological limitation in Monotropoideae and
 unconstrained diversification in Arbutoideae. Thus, differences in
 diversity between parasitic plants and their autotrophic sisters might be
 caused by a mixture of ecological limitation and unbounded
 diversification. A combination of sister-taxon comparisons of diversity
 and age, coupled with model-fitting of well-sampled phylogenies of focal
 taxa, provides a powerful test of likely causes of asymmetry in the
 diversity of lineages.
description: GammaSpotR function. Has one argument, a phylogenetic tree of class phylo. Returns a vector with 2 elements. The first is the subtree with the lowest Gamma statistic. The second is an ordered vector of subtree Gamma statistics.Monotropoideae_Arbutoideae_chronoBEAST estimate of relationships and divergence times among species of parasitic Monotropoideae species and autotrophic Arbutoideae species.Monotropoideae_Arbutoideae_BEASTXML file for BEAST. This was used to get tree in Monotropoideae_Arbutoideae_chrono.tre.BoraginaceaeML_SHBoraginaceae phylogeny in newick format with local SH nodal supports. Tree estimated with RAxML from multilocus DNA sequence dataset.EricalesML_SHEricales phylogeny in newick format with local SH support values on nodes. Tree estimated with RAxML from multi-locus DNA dataset.EricalesEricales DNA sequence data in relaxed phylip format used by RAxML.Ericales_partitionFile to specify data partitions for RAxML. The DNA sequence data was partitioned by genome and codon position.BoraginaceaeBoraginaceae DNA data in relaxed phylip format.Boraginaceae_partitionFile to specify DNA partitions to RAxML. Data were partitioned by genome and codon position.
DOI: 10.5281/zenodo.18377522
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - JAEN - (June 24 - May 25)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2024, to May 31, 2025, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Jaén:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5281/zenodo.18377523
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - JAEN - (June 24 - May 25)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2024, to May 31, 2025, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Jaén:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.15468/q3a54h
title: Michigan State University Herbarium non-lichenized fungi

description: The MSU Herbarium was founded in 1863 with the donation of a large collection of plants from Michigan and the eastern U.S. Today, we remain focused on plant and fungal diversity from Michigan, but the collection is also rich in plants from Mexico and southeast Asia, and lichens from the Caribbean and the subantarctic region. With over half a million specimens, the MSU Herbarium is among the 50 largest herbaria in the United States.