cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.48s4f93
title: Data from: Newly recognized Famennian lungfishes from East Greenland reveal tooth plate diversity and blur the Devonian–Carboniferous boundary

description: Three specimens of lungfishes from the late Famennian of East Greenland
 are described. One forms the holotype of a new genus and species,
 Celsiodon ahlberg gen. et sp. nov., which, in cladistic analyses, is
 placed close to the Carboniferous genus Ctenodus. The analyses reveal some
 Late Devonian lungfishes clustering with Early Carboniferous taxa,
 suggesting that Late Devonian lungfishes included more crownward taxa than
 previously appreciated, and that the Devonian-Carboniferous boundary was
 more fluid for lungfish taxa than supposed. Further study of other
 specimens shows a range of tooth plate morphologies and tooth crown
 morphologies, suggesting that the Late Devonian lungfishes were even more
 diverse and occupied a wider range of feeding strategies than previously
 suspected.
description: NHMD-141985 Oervigia
 nordica - Raw Scan DataDryad scan
 data.zipSupplementary
 InformationAdditional Data and
 Cladograms, Character List, and Character MatrixCelsiodon Tooth
 PlatesCelsiodon_tooth_plates.movnhmd-141985 Tooth Platesnhmd-141985_Tooth_plates.movnhmd154310 Tooth Platesnhmd154310_tooth_plates.mov
DOI: 10.5518/1508
title: Data associated with 'Phase coexistence and transitions between antiferromagnetic and ferromagnetic states in a synthetic antiferromagnet'

description: This dataset is associated with a paper on phase coexistence and transitions of a synthetic antiferromagnetic multilayer, and contains imaging using a number of different complimentary microscopies to study the transition mechanisms of the synthetic antiferromagnet. Samples were measured in the bulk using SQUID-VSM, imaged on the surface using magnetic force microscopy around the transition point and XMCD-PEEM at fields near zero, and imaged in transmission using both Fresnel and DPC Lorentz transmission electron microscopy at the transition point. This data was used to build up a picture of the transition mechanism of the synthetic antiferromagnet and image chiral textures therein.
DOI: 10.5061/dryad.kn206
title: Data from: Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA

description: Population genetics is essential for understanding and managing marine
 ecosystems, but sampling remains challenging. We demonstrate that
 high-throughput sequencing of seawater environmental DNA can provide
 useful estimates of genetic diversity in a whale shark (Rhincodon typus)
 aggregation. We recover similar mitochondrial haplotype frequencies in
 seawater compared to tissue samples, reliably placing the studied
 aggregation in a global genetic context and expanding the applications of
 environmental DNA to encompass population genetics of aquatic organisms.
description: DL1Illumina MiSeq data for
 control region fragment DL1DL2_run1Illumina MiSeq data for control region fragment DL2, first sequencing runDL2_run_1.zipDL2_run2Illumina MiSeq data for control region fragment DL2, second sequencing runDL2_run_2.zipControlsIllumina MiSeq data for extraction and PCR blanks, as well as for old and new mock sample
DOI: 10.5061/dryad.bb3h52t
title: Data from: Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling

description: Nyssa sylvatica complex consists of several woody taxa occurring in
 eastern North America. These taxa were recognized as two or three species
 including three or four varieties by different authors. Due to high
 morphological similarities and complexity of morphological variation,
 classification and delineation of taxa in the group have been difficult
 and controversial. Here we employ data from RAD-seq to elucidate the
 genetic structure and phylogenetic relationships within the group. Using
 the genetic evidence, we evaluate previous classifications and delineate
 species. We also employ Species Distribution Modeling (SDM) to evaluate
 impacts of climatic changes on the ranges of the taxa and to gain insights
 into the relevant refugia in eastern North America. Results from Molecular
 Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum
 likelihood, Bayesian Inference, and Splittree methods of RAD-seq data
 strongly support a two-clade pattern, largely separating samples of N.
 sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis
 with BEAST suggests the two clades diverged in the mid Miocene. The
 ancestor of the present trees of N. sylvatica was suggested to be in the
 Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene.
 Results from SDM predicted a smaller range in the southern part of the
 species present range of each clade during the Last Glacial Maximum (LGM).
 A northward expansion of the ranges during interglacial period and a
 northward shift of the ranges in the future under a model of global
 warming were also predicted. Our results support the recognition of two
 species in the complex, N. sylvatica and N. biflora, following the
 phylogenetic species concept. We found no genetic evidence supporting
 recognitions of intraspecific taxa. However, we propose subsp. ursina and
 subsp. biflora within N. biflora due to their distinction in habits,
 distributions, and habitats. Our results further support movements of
 trees in eastern North America in response to climatic changes. Finally,
 our study demonstrates that RAD-seq data and a combination of population
 genomics and SDM are valuable in resolving relationship and biogeographic
 history of closely related species that are taxonomically difficult.
description: READMEThis file should be
 replaced by the files uploaded via FTP. They should include two raw fastq
 files: "Nyssa_GBS_R1.fq.gz" and "Nyssa_GBS_R2.fq.gz";
 One barcode file: "barcode2.key"; 9 parameter files for
 extracting different matrix via pyRAD software.ML_treeM50 matrix for ML tree.parameter_settingAll the parameter files during RAD-seq analysis.Forward raw dataNyssa_GBS_R1.fq.gzReverse raw dataNyssa_GBS_R2.fq.gz
DOI: 10.5281/zenodo.7802443
title: Aquafarm Segmentation for Climate Smart Shrimp

description: Mapping aquaculture ponds, which is critical for restoration and climate adaptation efforts, is labor and time-intensive. Most existing automated techniques are focused only on spatial location and do not classify these areas based on production intensification (extensive vs intensive). 

We trained deep-learning computer vision models to predict pond locations and classifications in the Philippines and Indonesia using openly available PlanetScope multispectral satellite data. Our best-performing model achieves an F1 score of 71.8% and sufficiently identifies intensive ponds from other classes despite the inherent class imbalance in the training data. 

To support model development, we also present our process of creating a human-annotated, expert-validated dataset of pond classifications over the Philippines and Indonesia, which is made readily available and usable for other researchers doing similar work on aquaculture mapping.

We've uploaded the model, the training data, and the rollout data.



model.zip contains the Pytorch Lightning model checkpoint of the trained model

training_data.zip contains TIFF files of the training images and raster masks. It also contains a geopackage of the training polygons that were rasterized into masks

rollout_data.zip contains TIFF files of images across Indonesia and the Philippines for aquaculture segmentation. It also contains a geopackage of the predicted aquaculture polygons.


We've also uploaded the underlying data behind the site suitability criteria for Climate Smart Shrimp



idn_site_scoring_datasets for Indonesian criteria

phl_site_scoring_datasets for Philippine criteria


Link to Github repo: https://github.com/thinkingmachines/aquafarm-segmentation

Link to the project web app: https://ci-aquafarm-mapping.web.app/
DOI: 10.5281/zenodo.7802444
title: Aquafarm Segmentation for Climate Smart Shrimp

description: Mapping aquaculture ponds, which is critical for restoration and climate adaptation efforts, is labor and time-intensive. Most existing automated techniques are focused only on spatial location and do not classify these areas based on production intensification (extensive vs intensive). 

We trained deep-learning computer vision models to predict pond locations and classifications in the Philippines and Indonesia using openly available PlanetScope multispectral satellite data. Our best-performing model achieves an F1 score of 71.8% and sufficiently identifies intensive ponds from other classes despite the inherent class imbalance in the training data. 

To support model development, we also present our process of creating a human-annotated, expert-validated dataset of pond classifications over the Philippines and Indonesia, which is made readily available and usable for other researchers doing similar work on aquaculture mapping.

We've uploaded the model, the training data, and the rollout data.



model.zip contains the Pytorch Lightning model checkpoint of the trained model

training_data.zip contains TIFF files of the training images and raster masks. It also contains a geopackage of the training polygons that were rasterized into masks

rollout_data.zip contains TIFF files of images across Indonesia and the Philippines for aquaculture segmentation. It also contains a geopackage of the predicted aquaculture polygons.


We've also uploaded the underlying data behind the site suitability criteria for Climate Smart Shrimp



idn_site_scoring_datasets for Indonesian criteria

phl_site_scoring_datasets for Philippine criteria


Link to Github repo: https://github.com/thinkingmachines/aquafarm-segmentation

Link to the project web app: https://ci-aquafarm-mapping.web.app/
DOI: 10.5061/dryad.fb41s
title: Data from: Multi-modal ultra-high resolution structural 7-Tesla MRI data repository

description: Structural brain data is key for the understanding of brain function and
 networks, i.e., connectomics. Here we present data sets available from the
 ‘atlasing of the basal ganglia (ATAG)’ project, which provides ultra-high
 resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young,
 middle-aged, and elderly participants. The ATAG data set includes
 whole-brain and reduced field-of-view MP2RAGE and T2*-weighted scans of
 the subcortex and brainstem with ultra-high resolution at a sub-millimeter
 scale. The data can be used to develop new algorithms that help building
 high-resolution atlases both relevant for the basic and clinical
 neurosciences. Importantly, the present data repository may also be used
 to inform the exact positioning of electrodes used for
 deep-brain-stimulation in patients with Parkinson’s disease and
 neuropsychiatric diseases.
description: Demographics_participantsMRI_Exam_card_flashExam_card_flash.xlsxMRI_Exam_card_mp2rage_slabExam_card_mp2rage_slab.xlsxMRI_Exam_card_mp2rage_whole_brainExam_card_mp2rage_whole_brain.xlsxflash_youngThe flash scans of the young participants.mp2rage_slab_youngThe mp2rage slab scans for the young participants.mp2rage_whole_brain_youngThe mp2rage whole brain scans for the young participants.flash_middleThe flash scans of the middle aged participantsmp2rage_slab_middleThe mp2rage slab scans of the middle aged participants.mp2rage_whole_brain_middleThe mp2rage whole brain scans of the middle aged participants.flash_elderlyThe flash scans of the elderly participants.mp2rage_slab_elderlyThe mp2rage slab scans of the elderly participants.mp2rage_whole_brain_elderlyThe mp2rage whole brain scans of the elderly participants.readme
DOI: 10.5061/dryad.r217r
title: Data from: Climatic thresholds shape northern high-latitude fire regimes and imply vulnerability to future climate change

description: Boreal forests and arctic tundra cover 33% of global land area and store
 an estimated 50% of total soil carbon. Because wildfire is a key driver of
 terrestrial carbon cycling, increasing fire activity in these ecosystems
 would likely have global implications. To anticipate potential
 spatiotemporal variability in fire-regime shifts, we modeled the spatially
 explicit 30-yr probability of fire occurrence as a function of climate and
 landscape features (i.e. vegetation and topography) across Alaska. Boosted
 regression tree (BRT) models captured the spatial distribution of fire
 across boreal forest and tundra ecoregions (AUC from 0.63–0.78 and Pearson
 correlations between predicted and observed data from 0.54–0.71),
 highlighting summer temperature and annual moisture availability as the
 most influential controls of historical fire regimes. Modeled fire–climate
 relationships revealed distinct thresholds to fire occurrence, with a
 nonlinear increase in the probability of fire above an average July
 temperature of 13.4°C and below an annual moisture availability (i.e.
 P-PET) of approximately 150 mm. To anticipate potential fire-regime
 responses to 21st-century climate change, we informed our BRTs with
 Coupled Model Intercomparison Project Phase 5 climate projections under
 the RCP 6.0 scenario. Based on these projected climatic changes alone
 (i.e. not accounting for potential changes in vegetation), our results
 suggest an increasing probability of wildfire in Alaskan boreal forest and
 tundra ecosystems, but of varying magnitude across space and throughout
 the 21st century. Regions with historically low flammability, including
 tundra and the forest–tundra boundary, are particularly vulnerable to
 climatically induced changes in fire activity, with up to a fourfold
 increase in the 30-yr probability of fire occurrence by 2100. Our results
 underscore the climatic potential for novel fire regimes to develop in
 these ecosystems, relative to the past 6000–35 000 yr, and spatial
 variability in the vulnerability of wildfire regimes and associated
 ecological processes to 21st-century climate change.
description: ScriptsFiguresThis archive contains the figures from the main text, available in 300 dpi .tif, .jpg and .fig (matlab) formats.DataClimateDataResults
DOI: 10.5061/dryad.kb5cb
title: Data from: Motion dazzle: a locust's eye view

description: Motion dazzle describes high-contrast patterns (e.g. zigzags on snakes,
 dazzle paint on World War I ships) that do not conceal an object, but
 inhibit an observer’s perception of its motion. However, there is limited
 evidence for this phenomenon. Locusts have a pair of descending
 contralateral movement detector (DCMD) neurons which respond to
 predator-like looming objects, and trigger escape responses. Within the
 network providing input to a DCMD, separate channels are excited when
 moving edges cause areas of the visual field to brighten or darken
 respectively, and these stimuli interact antagonistically. When a looming
 square has an upper half and lower half that are both darker than
 background, it elicits a stronger DCMD response than the upper half does
 alone. However, when a looming square has a darker-than-background upper
 half and a brighter-than-background lower half, it elicits a weaker DCMD
 response than its upper half does alone. This effect allows high-contrast
 patterns to weaken and delay DCMD response parameters implicated in escape
 decisions, and is analogous to motion dazzle. However, the motion dazzle
 effect does not provide the best means of motion camouflage because
 uniform bright squares, or low-contrast squares, elicit weaker DCMD
 responses than high-contrast, half dark, half bright squares.
description: RDS_BiolLett_Expt1Data from experiment 1RDS_BiolLett_Expt2Data from experiment 2
DOI: 10.5061/dryad.8h022
title: Data from: Reading the leaves: a comparison of leaf rank and automated areole measurement for quantifying aspects of leaf venation

description: The reticulate venation that is characteristic of a dicot leaf has excited
 interest from systematists for more than a century, and from physiological
 and developmental botanists for decades. The tools of digital image
 acquisition and computer image analysis, however, are only now approaching
 the sophistication needed to quantify aspects of the venation network
 found in real leaves quickly, easily, accurately, and reliably enough to
 produce biologically meaningful data. In this paper, we examine 120 leaves
 distributed across vascular plants (representing 118 genera and 80
 families) using two approaches: a semiquantitative scoring system called
 “leaf ranking,” devised by the late Leo Hickey, and an automated
 image-analysis protocol. In the process of comparing these approaches, we
 review some methodological issues that arise in trying to quantify a vein
 network, and discuss the strengths and weaknesses of automatic data
 collection and human pattern recognition. We conclude that subjective leaf
 rank provides a relatively consistent, semiquantitative measure of areole
 size among other variables; that modal areole size is generally consistent
 across large sections of a leaf lamina; and that both
 approaches—semiquantitative, subjective scoring; and fully quantitative,
 automated measurement—have appropriate places in the study of leaf
 venation.
description: Supplementary
 ArchiveThis archive consists of
 a single tarball holding a file hierarchy that contains our images, data,
 and processing scripts. See the associated readme file for more
 detail.Green_et_al.2014.APPS_data_archive.tgz
DOI: 10.5061/dryad.ss7kp
title: Data from: Sexual selection targets cetacean pelvic bones

description: Male genitalia evolve rapidly, probably as a result of sexual selection.
 Whether this pattern extends to the internal infrastructure that
 influences genital movements remains unknown. Cetaceans (whales and
 dolphins) offer a unique opportunity to test this hypothesis: since
 evolving from land-dwelling ancestors, they lost external hind limbs and
 evolved a highly reduced pelvis which seems to serve no other function
 except to anchor muscles that maneuver the penis. Here we create a novel
 morphometric pipeline to analyze the size and shape evolution of pelvic
 bones from 130 individuals (29 species) in the context of inferred mating
 system. We present two main findings: 1) males from species with
 relatively intense sexual selection (inferred by relative testes size)
 have evolved relatively large penises and pelvic bones compared to their
 body size, and 2) pelvic bone shape diverges more quickly in species pairs
 that have diverged in inferred mating system. Neither pattern was observed
 in the anterior-most pair of vertebral ribs, which served as a negative
 control. This study provides evidence that sexual selection can affect
 internal anatomy that controls male genitalia. These important functions
 may explain why cetacean pelvic bones have not been lost through
 evolutionary time.
description: Whale
 pelvicsThis zipped archive
 contains all the .xyz files (the original laser scans of all the bones in
 the study) and all associated scripts and programs for calling landmarks.
 The general workflow is to run the Python scripts prepended with 13.1,
 13.2, 14, and 15 in order. Contact Matt Dean
 (matthew-dot-dean-at-usc-dot-edu) if assistance is
 required.WHALE_PELVIC_BONES.tar.gz
DOI: 10.5061/dryad.tq525v7
title: Data from: Quantification and optimization of ADF-STEM image contrast for beam sensitive materials

description: Many functional materials are difficult to analyze by Scanning
 Transmission Electron Microscopy (STEM) on account of their beam
 sensitivity and low contrast between different phases. The problem becomes
 even more severe when thick specimens need to be investigated, a situation
 that is common for materials that are ordered from the nanometer to
 micrometer length scales or when performing dynamic experiments in a TEM
 liquid cell. Here we report a method to optimize annular dark-field (ADF)
 STEM imaging conditions and detector geometries for thick and
 beam-sensitive low-contrast specimen using the example of a carbon
 nanotube/polymer nanocomposite. We carried-out Monte Carlo simulations as
 well as quantitative ADF-STEM imaging experiments to predict and verify
 optimum contrast conditions. The presented method is general, can be
 easily adapted to other beam-sensitive and/or low-contrast materials, as
 shown for a polymer vesicle within a TEM liquid-cell, and can act as an
 expert guide on whether an experiment is feasible and to determine the
 best imaging conditions.
description: MC simulations
 dataFolder contains Monte
 Carlo simulations data generated from GATE, sample mac file used to run MC
 simulations, sample m file used to generate angular distribution from the
 raw data.rsos_repository.zip
DOI: 10.5061/dryad.8rc4r
title: Data from: Integrative taxonomy recognizes evolutionary units despite widespread mitonuclear discordance: evidence from a rotifer cryptic species complex

description: Mitonuclear discordance across taxa is increasingly recognized as posing a
 major challenge to species delimitation based on DNA sequence data.
 Integrative taxonomy has been proposed as a promising framework to help
 address this problem. However, we still lack compelling empirical evidence
 scrutinizing the efficacy of integrative taxonomy in relation to, for
 instance, complex introgression scenarios involving many species. Here, we
 report remarkably widespread mitonuclear discordance between about 15
 mitochondrial and four nuclear Brachionus calyciflorus groups identified
 using different species delimitation approaches. Using coalescent-,
 Bayesian admixture-, and allele sharing-based methods with DNA sequence or
 microsatellite data, we provide strong evidence in support of
 hybridization as a driver of the observed discordance. We then describe
 our combined molecular, morphological, and ecological approaches to
 resolving phylogenetic conflict and inferring species boundaries. Species
 delimitations based on the ITS1 and 28S nuclear DNA markers proved a more
 reliable predictor of morphological variation than delimitations using the
 mitochondrial COI gene. A short-term competition experiment further
 revealed systematic differences in the competitive ability between two of
 the nuclear-delimited species under six different growth conditions,
 independent of COI delimitations; hybrids were also observed. In light of
 these findings, we discuss the failure of the COI marker to estimate
 morphological stasis and morphological plasticity in the B. calyciflorus
 complex. By using B. calyciflorus as a representative case, we demonstrate
 the potential of integrative taxonomy to guide species delimitation in the
 presence of mitonuclear phylogenetic conflicts.
description: 1_Haplotype_alignments1_Alignments.zip2_jModelTest2_results2_jModelTest2.zip3_MrBayes_infiles_outfiles3_MrBayes.zip4_RAxML_oufilies4_RAxML.zip5_BEAST_infiles_outfiles5_BEAST.zip6_Delimitations_resultsFor mtCOI, nu28S, and nuITS1 includes results of the methods: ABGD, GMYC-BEAST, GMYC-PATHd8, GMYC-r8s, bGMYC, and PTP. In the case of nu28S, and nuITS1 also chromatogram information (inside the haplowebs folder) and in the case of nuITS1 also heterozygosities and the files for the haplowebs method.6_Delimitations.zip7_JML_tests_infiles_outfilesAlso includes infiles and outfiles of the starBEAST simulations7_JML_tests.zip8_STRUCTURE_NewHybrids_infiles_outfiles8_STRUCTURE_NewHybrids.zip9_Rotifer_microphotographsAppendix_1Appendix_2