cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ksn02v785
title: Data from: Palaeobiology and taphonomy of the rangeomorph (Culmofrons plumosa)

description: The deep marine Ediacaran fossil record of Avalonia is dominated by the
 Rangeomorpha, a clade characterized by up to four orders of fractal-like
 branching. Despite their abundance and morphological diversity, little is
 known about their palaeobiology, palaeoecology and phylogenetic position
 in the tree of life. The clade has traditionally been interpreted as
 consisting of organisms that lived erect in the water column and tethered
 to the seafloor, based on the intuitive interpretation of their frondose
 body plan. However, recent work has challenged this view and instead
 proposes a reclining mode of life for several rangeomorph, possibly in
 symbiosis with chemoautotrophic bacteria. In this manuscript, we offer a
 detailed description of exceptionally preserved specimens of Culmofrons
 plumosa from the Discovery Unesco Geopoark in Newfoundland, CA. We suggest
 that Culmofrons plumosa should be reinterpreted as a reclining organism
 based on taphonomic and morphological evidence. Additionally, reproductive
 modes and a growth model of the species are here inferred, and they appear
 to be most consistent with a reclining mode of life, offering a novel
 palaeobiological reconstruction of the species.
DOI: 10.15468/dl.7x6y8x
title: Occurrence Download

description: A dataset containing 15213 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Rovbase - offentlig data",
 "Country is Sweden"
 ]
}

 The dataset includes 15213 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003388-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n02v6wx1g
title: Genetic and phenotypic consequences of local transitions between sexual and parthenogenetic reproduction in the wild

description: Transitions from sexual to asexual reproduction have occurred in numerous
 lineages across the tree of life, but many questions remain about how such
 transitions occur and why asexual populations rarely persist. In
 facultatively parthenogenetic animals, all-female populations can arise
 when males are absent or become extinct and, if such populations can
 persist asexually for many generations, they could ultimately give rise to
 obligately asexual species. However, the initial stages of this process
 remain poorly understood. The facultatively parthenogenetic Australian
 phasmid Megacrania batesii exhibits a spatial mosaic of mixed-sex
 populations that reproduce predominantly sexually and all-female sites
 that reproduce exclusively via parthenogenesis. We used this system to
 compare genetic and phenotypic parameters among multiple natural
 populations that vary in reproductive mode and geographic location.
 Analysis of single nucleotide polymorphisms (SNPs) collected from reduced
 representation whole genome data showed populations grouping by geographic
 location rather than reproductive mode, with little gene-flow between
 them. Mixed-sex populations had drastically higher heterozygosities than
 all-female populations. Phenotypic analysis revealed considerable
 inter-population variation in rates of deformities in (non-functional)
 wings, with higher mean frequency and severity of deformities in
 all-female sites. All-female sites also harbored more parasites, but only
 in swamp habitats. However, reproductive mode did not explain variation in
 mean female fecundity, egg hatching success, or missing appendages. These
 results indicate that local transitions to parthenogenetic reproduction
 can lead to increased rates of developmental abnormalities and increased
 vulnerability to disease but can also occur without substantial fitness
 consequences despite dramatic reductions in genetic diversity and
 heterozygosity.
description: Wild<em> M. batesii </em>individuals were
 photographed on their host plants. We used ImageJ to analyse these photos
 and extract the phenotypic information found in
 "megacrania_morphology.csv". DNA was extracted from <em>M.
 batesii</em> individuals in the field and sent to Diversity Arrays
 for DaRTseq reduced representation whole genome sequencing. We received
 SNPs back found in "Report_DMegac20-5687_SNP_1.csv". These SNPs
 were filtered with the "prep_for_BOTH_analyses.v.0.1.Rmd" script
 and then both the phenotypic data and the genetic data was analysed using
 "BOTH_analyses_clean."
DOI: 10.15468/dl.qtc5yc
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus perryi"
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003390-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8w9ghx3r3
title: Contrasting intra-annual population dynamics of two codominant species are consistent across spatial and temporal scales

description: 1. Despite asymmetric competition and a wide array of functional
 similarities, two ecologically important C4 perennial grasses, Andropogon
 gerardii and Sorghastrum nutans, frequently codominate areas of the mesic
 tallgrass prairie of the US Great Plains. A subtle difference in their
 vegetative reproduction strategies may play a role in preventing exclusion
 of S. nutans, the presumed weaker competitor in this region. 2. While A.
 gerardii vegetative tiller densities peak in the early growing season and
 decline thereafter (determinate recruitment), those of S. nutans may
 continue to increase throughout the growing season (indeterminate
 recruitment), providing a potential avenue for recovery from more
 intensive early season competition. However, until now these patterns have
 only been informally observed in the field. 3. We examined the
 year-to-year consistency of growing season vegetative tiller dynamics
 (measured as seasonal change in tiller densities) of each grass species
 from at an intact tallgrass prairie in Kansas - a site within the core of
 both species’ distributions - over a period of 8 years. Then, to
 investigate environmental effects on these dynamics, we examined whether
 they differ across a Kansas landscape varying in topography, fire
 management regimes and the abundances of the study species. Finally, we
 expanded the investigation of environmental effects on growing season
 tiller dynamics by observing them at the periphery of the species’
 distributions in central Colorado, where climatic conditions are dryer and
 the study species’ abundances are reduced. 4. Synthesis: We found that the
 tiller densities of A. gerardii decline within seasons with striking
 consistency regardless of spatio-temporal scale or environmental factors
 (topography and fire regimes). In contrast, we found the seasonal dynamics
 of S. nutans tiller densities were dependent on environmental factors,
 with seasonal tiller density increases occurring only within the Kansas
 populations but not consistently between years. These observations lay the
 groundwork for establishing differences in tiller recruitment determinacy
 as a potentially important yet underappreciated mechanism for promoting
 coexistence and codominance among perennial plant species.
DOI: 10.5281/zenodo.18399938
title: Microscopy Data for "FLNB and TTC26 regulate ciliary Hedgehog signaling to maintain intervertebral disc matrix homeostasis in adolescent idiopathic scoliosis"
DOI: 10.5281/zenodo.18399939
title: Microscopy Data for "FLNB and TTC26 regulate ciliary Hedgehog signaling to maintain intervertebral disc matrix homeostasis in adolescent idiopathic scoliosis"
DOI: 10.5061/dryad.x3ffbg7p9
title: Anticipating fluctuations of bigeye tuna in the Pacific Ocean from three-dimensional ocean biogeochemistry

description: 1. Subseasonal to decadal ocean forecasting can make significant
 contributions to achieving effective management of living marine resources
 in a changing ocean. Most applications rely on indirect proxies, however,
 often measured at the ocean surface and lacking a direct mechanistic link
 to the dynamics of marine populations. 2. Here we take advantage of
 three-dimensional, dynamical reconstructions and forecasts of ocean
 biogeochemistry based on a global Earth System Model to hindcast and
 assess the capacity to anticipate fluctuations in the dynamics of bigeye
 tuna (Thunnus obesus Lowe) in the Pacific Ocean during the last six
 decades. We reconstructed spatial patterns in catch per unit effort (CPUE)
 through the combination of physiological indices capturing both habitat
 preferences and physiological tolerance limits in bigeye tuna. 3. Our
 analyses revealed a sequence of four distinct regimes characterized by
 changes in the zonal distribution and average CPUE of bigeye tuna in the
 Pacific Ocean. Habitat models accounting for basin-wide fluctuations in
 the thermal structure and oxygen concentration throughout the water column
 captured interannual fluctuations in CPUE and regime switches that models
 based solely on surface information were unable to reproduce. Decade-long
 forecast experiments further suggested that forecasts of three-dimensional
 biogeochemical information might enable anticipation of fluctuations in
 bigeye tuna several years ahead. 4. Synthesis and applications. Together,
 our results reveal the impact of variability of biogeochemical conditions
 in the ocean interior on the dynamics of bigeye tuna in the Pacific Ocean,
 raising concerns about the future impact of ocean warming and
 deoxygenation. The results also lend support to incorporating subsurface
 biogeochemical information into ecological forecasts to implement
 efficient dynamic management strategies and promote the sustainable use of
 marine living resources.
description: Reconstructions and forecasts of bigeye tuna CPUE in the Pacific
 Ocean. The data set  also includes environmental covariates and habitat
 quality indices described in the text and derived from BGC fields. Ocean
 reanalysis and decade-long forecast experiments provided by the Ensemble
 Coupled Data Assimilation system integrating the Carbon, Ocean
 Biogeochemistry and Lower Trophics biogeochemical model [ECDA-COBALT; see
 Park et al
 2018 and Park et al
 2019]. Please check the file `readme.qmd` for
 further details.
description: Dataset includes both R rds files that
 can be explored using R function readRDS, and NetCDF files that, among many other alternatives (see e.g. the software list at Unidata), can be explored using software packages like Panoply or ncview.
DOI: 10.5061/dryad.4qrfj6qdv
title: Data from: 2-D sex images elicit mate copying in fruit flies

description: Although the environment is three-dimensional (3-D), humans are able to
 extract subtle information from two-dimensional (2-D) images, particularly
 in the domain of sex. However, whether animals with simpler nervous
 systems are capable of such information extraction remains to be
 demonstrated, as this ability would suggest a functional generalisation
 capacity. Here, we performed mate-copying experiments
 in Drosophila melanogaster using 2-D artificial stimuli.
 Mate copying occurs when naïve females observe the mating success of
 potential mates and use that social information to build their own mating
 preference. By replacing live demonstrations with (i) photos or (ii)
 simplified images of copulating pairs, we found that even crudely
 simplified images of sexual intercourse still elicit mate copying,
 suggesting that Drosophila is able to extract
 sex-related information even from a degraded image. This new
 method constitutes a powerful tool to further investigate mate
 copying in that species and sexual preferences in general.
description: We did behavioral observations of fruit fly mate choice
 decisions.
DOI: 10.15468/dl.4qnvub
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gilletiodendron kisantuense",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 42 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003391-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k3j9kd5br
title: Data from: Reliable and fast genotyping protocol for galactosylceramidase (GALC) in the Twitcher (Twi) mouse

description: The Twitcher (Twi) mouse is a neurological Krabbe disease (KD, or globoid
 cell leukodystrophy) spontaneous mutant line. The genome of the Twi mouse
 presents a single nucleotide polymorphism (SNP), leading to an
 enzymatically inactive galactosylceramidase (GALC) protein and causing KD.
 In this context, mouse Twi genotyping is an essential step in KD research.
 To date, the genotyping method used is labor-intensive and often
 drives ambiguous results. Here, we evaluate a novel protocol for
 the genotype determination of GALC mutation status in Twi mice based on
 the allele-discrimination real-time polymerase chain reaction (PCR).DNA is
 extracted from Twi mice (n = 20, pilot study; n = 120, verification study)
 and control group (n = 10, pilot study; n = 30 verification study) and
 assessed by allele-discrimination real-time PCR to detect SNP
 c.355G&gt;A.Using the allele-discrimination PCR, all the samples are
 identified correctly with the genotype GG (wild-type, WT), GA
 (heterozygote, HET), or AA (homozygote, HOM) by the first analysis and no
 animals were not genotyped.We demonstrated that this novel method can be
 used to distinguish timely, accurately and without ambiguity
 among HOM, WT, and HET animals. This protocol represents a great
 opportunity to increase accuracy and speed in KD research.
description: DNA samples were obtained from
 tail biopsies using Euroclone spinNAker Universal Genomic DNA mini kit.
 Pilot study and validation study data were acquired with Applied
 Biosystems Real-Time PCR System. GALC activity data was acquired with the
 microplate GloMax fluorescence reader. Body weight data were collected
 with a scale. Latency to fall data was acquired with the rotarod apparatus
 (Ugo Basile). 
description: Data files are uploaded as an
 OpenDocument Spreadsheet (. ods) format. The .ods files can be opened with
 some spreadsheet applications, such as OpenOffice.org Calc and Google
 Docs.
DOI: 10.5061/dryad.69p8cz95g
title: Mandibular characteristics of early Glires (Mammalia) reveal mixed rodent and lagomorph morphotypes

description: Glires (rodents, lagomorphs and their fossil kin) is the most speciose and
 arguably most diversified clade of living placentals. Different lineages
 within the Glires evolved basically opposite chewing movements: a mostly
 transversal power stroke in lagomorphs, and a mostly proal power stroke in
 rodents, but the ancestral condition for Glires is as yet unclear. To
 address on this knowledge gap, we studied the mandibles of Paleocene
 Glires from China representing the duplicidentate (lagomorph-like;
 Mimotona) and simplicidentate (rodent-like; Eomylus and Heomys) lineages.
 To assess the mechanical resistance of mandibles to bending and torsion,
 we calculated the section modulus. The dentaries differ in depth,
 curvature of the ventral margin, the bending of the dental row and the
 region where the maximum grinding force was likely applied. In general,
 the early Paleocene Mimotona lii and the middle Paleocene Mimotona robusta
 and Heomys orientalis all show a pattern of increasing strength moving
 distally along the mandible, similar to sciurids and the mountain beaver.
 In contrast, the late Paleocene Eomylus sp. had a mandible that was
 strongest in the region of m1, a pattern seen in lagomorphs and also the
 stem placental Zofialestes. Our results indicate the early diversification
 of mandible structure of Glires, demonstrate a mixture of duplicidentate
 and simplicidentate characters among the basal Glires and suggest an early
 occurrence of a lagomorph-like morphotype.
description: The Paleocene Glires specimens from the collection of Institute
 of Vertebrate Paleontology and Paleoanthropology CAS (IVPP), China were
 scanned using the 225 kV micro-CT scanner developed by the Institute of
 High Energy Physics, Chinese Academy of Sciences (CAS) at the Key
 Laboratory of Vertebrate Evolution and Human Origins, CAS. The specimens
 of Paleocene Glires were scanned with a beam energy of 120 kV and current
 of 120 mA at the resolution of 12.55µm per voxel using a 360° rotation
 with a step size of 0.5°. A total of 720 projections were reconstructed in
 a 2,048 x 2,048 matrix of 1,536 slices using a two-dimensional
 reconstruction software developed by the Institute of High Energy Physics,
 CAS. 
description: The file formats are STL and PLY.
DOI: 10.5061/dryad.1c59zw3zz
title: The maternal effects of dietary restriction on Dnmt expression and reproduction in two clones of Daphnia pulex

description: The inheritance of epigenetic marks induced by environmental variation in
 a previous generation is broadly accepted as a mediator of phenotypic
 plasticity. Transgenerational effects linking maternal experiences to
 changes in morphology, gene expression, and life history of successive
 generations are known across many taxa. While the number of studies
 linking epigenetic variation to ecological maternal effects is increasing
 rapidly, few if any attempts have been made to investigate molecular
 mechanisms governing epigenetic functions in the context of ecologically
 relevant maternal effects. Daphnia make an ideal model for investigating
 molecular epigenetic mechanisms and ecological maternal effects because
 they will reproduce asexually in the lab. Daphnia are also known
 to have strong maternal effects, involving a variety of traits and
 environmental variables. Using two clones of Daphnia pulex, we
 investigated the plasticity of life history and DNA methyltransferase
 (Dnmt) gene expression with respect to food limitation within- and
 across-generations. We found strong evidence of genotypic variation of
 responses of life history and Dnmt expression to low food diets, both
 within- and across-generations. In general, effects of offspring diet were
 larger than either the direct maternal effect or offspring-maternal
 environment interactions, but the direction of the maternal effect was
 usually in the opposite direction of the within-generation
 effect.  For both life history and Dnmt expression, we
 also found that when offspring had low food, effects of the maternal
 environment were stronger than when offspring had high food.
DOI: 10.5061/dryad.v15dv4209
title: Hourly detections of echolocation clicks in Hawaiian Island HARP data from Hawai`i, Kaua`i, and Manawai with species labels

description: This dataset consists of counts of detections of echolocation clicks at
 three sites in the Hawaiian Islands Archipelago. These sites are Hawaii,
 Kauai, and Manawai (also known as Pearl and Hermes Reef).
 Echolocation clicks have been labeled using a neural network classifier
 that was trained and tested on data from the Hawaiian Islands and can
 successfully identify many species of regionally present odontocetes.
 During the labeling process, clicks were grouped into one-minute bins and
 each bin was given a species' label. The data provided here is
 further binned at an hourly level, where counts of a given species
 represent the number of one-minute bins within a given hour that were
 labeled as that species (up to a maximum of 60). One file is provided per
 site, and files are in .csv format that can be read using any desired
 coding language. 
description: A ReadMe file is included in the data as 'README.txt'
 and provides information about the provided data.
DOI: 10.5061/dryad.4b8gthtgs
title: Supplementary files for: Why should we compare morphological and molecular disparity?

description: 1. Indices of morphological disparity seek to summarise the highly
 multivariate morphological variation across groups of species within
 clades, time bins or other groups. Morphological variation can be
 quantified using geometric morphometric, outline or surface-based methods.
 These are most effective when morphological differences are relatively
 modest and there are numerous ubiquitous landmarks and phase-aligned
 features of shape variation. The most disparate samples, such as those
 across classes and phyla, typically necessitate the use of discrete
 characters. Unfortunately, such characters are often compiled subjectively
 in a manner reflecting the level of morphological and taxonomic focus and
 the intensity of taxon sampling. 2. Sampling intensity is often highly
 variable within a single data set, especially in repurposed and
 amalgamated cladistic matrices. Here we propose indices of molecular
 disparity analogous to those of morphological disparity. Molecular
 sequence data can be obtained in a more objective, automated and scaleable
 manner than morphological data. 3. Comparisons of the morphological and
 molecular disparity of subclades in sixteen large data sets suggest that
 molecular disparity is less susceptible to sampling biases than
 morphological disparity. Moreover, distance matrices inferred from
 individual genes tend to correlate strongly with each other and with
 distances from all concatenated genes. By contrast, morphological and
 molecular disparity are typically not significantly correlated across
 subclades, such that comparisons for groups can help to give a fuller
 picture of their evolution. Within mammals, Afrotheria have conspicuously
 high morphological disparity but modest molecular disparity, suggesting
 unusually high morphological plasticity. Even more strikingly, the
 molecular disparity of rodents is over five times that for Artiodactyla,
 despite having only half of their morphological disparity. These contrasts
 suggest the differential operation of geometric, biomechanical,
 ontogenetic and environmental constraints on form. 4. Given the increasing
 abundance of total evidence data sets in the literature and the widespread
 and sometimes uncritical repurposing of discrete morphological characters,
 we propose the comparison of morphological and molecular disparity as a
 useful tool to understand subclade evolution more fully.  
description: This dataset was collated from 16 published total evidence
 datasets. Hereby we supply the molecular and morphological character data
 for each dataset as well as the associated phylogeny and GTR distance file
 in CSV format.
description: Discrete character and DNA alignment files can be opened with
 Mesquite (nexus format) or with the R packages Claddis and Ape.