cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0nc625g
title: Long-term Coral Reef Monitoring Across Leeward Maui. In 100 Island Challenge Collection

description: The goal of this study is to document long-term patterns of change within Maui’s coral reef benthic communities. Maui’s reefs are subject to stress both from local factors (e.g., tourism, fishing, nutrient enrichment, and sedimentation) and global factors (climate change). Maui’s reefs experienced widespread bleaching in 2015 and 2019, which were among the first major bleaching events reported in the Hawaiian Islands. In the future, Maui’s reefs will face an increasing array of acute and chronic stressors, and data on the response of benthic communities to these stressors is critical to inform active management and conservation of coral reef ecosystems. The Smith Lab has been conducting research on Maui for nearly two decades and began collecting this long-term photographic dataset in 2014. This dataset can be used to better understand the effects of both local and global stressors on benthic community dynamics on this heavily populated island. This dataset consists of +20 forereef sites located along the leeward coast of Maui (stretching from Honokowai in the north to La Perouse Bay in the south). All sites are situated on hard bottom substrate and range from 3 to 14 m depth. Two sites are located within the submerged crater of the neighboring islet of Molokini, located 4.5 km offshore of Maui. Site selection was optimized to control for the influence of wave energy and depth on benthic community composition, and to align survey efforts with other long-term monitoring programs currently operating on Maui, including Hawaii's Coral Reef Assessment and Monitoring Program (CRAMP) and monitoring efforts by the Division of Aquatic Resources (DAR). A core group of 8-10 sites have been surveyed at approximately annual intervals since 2014, while the remaining sites have been surveyed at least twice (2014 and 2017). For repeat surveys, sites are re-located using permanent or invariant features of the reef to ensure that the same section of reef is surveyed through time.

We use large-area imaging techniques to describe the benthic composition from each reef. At each reef site, we take approximately 5,000 pictures of the reef benthos, and then stitch these pictures together into a 3D model using Structure from Motion technology. These models can be used to document the growth, structural complexity, spatial structure, and competitive dynamics of benthic taxa. This approach generates multiple digital products, including images collected in the field, composite 3D models, 2D orthorectified images of the 3D models, and annotations of the 2D orthorectified images. By re-visiting exact locations and reconstructing 3D models of multiple time points, we have the unprecedented opportunity to track the dynamics of individual corals and patches of algae. With advanced image analysis we can track how a reef community changes, addressing questions of coral growth, death, and competition that are currently unresolved. Furthermore, this data can be applied to address conservation and management challenges.
DOI: 10.25574/04993
title: Chandra X-ray Observatory ObsId 04993

description: Studying the effect of merging clusters in cosmological cluster samples
DOI: 10.25574/05813
title: Chandra X-ray Observatory ObsId 05813

description: MACS: The most massive galaxy clusters at z&gt;0.3
DOI: 10.15468/dl.gsmj44
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Siphlophis cervinus"
 ]
}

 The dataset includes 43 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003743-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/06109
title: Chandra X-ray Observatory ObsId 06109

description: Probing dark energy using the X-ray gas mass fraction in dynamically relaxed galaxy clusters
DOI: 10.25574/06172
title: Chandra X-ray Observatory ObsId 06172

description: Probing dark energy using the X-ray gas mass fraction in dynamically relaxed galaxy clusters
DOI: 10.5281/zenodo.18404794
title: Table 1 in Chrysobrycon eliasi, new species of stevardiine fish (Characiformes: Characidae) from the río Madre de Dios and upper río Manuripe basins, Peru

description: Table 1. Morphometric data of holotype and 27 paratypes of Chrysobrycon eliasi from río Madre de Dios and Upper río Manuripe basins. n = number of specimens; SD = standard deviation. The values of the holotype are included in the range of males.
CharactersHolotypeMalesFemales and juvenilesnRangeMeanSDnRangeMeanSDStandard length (mm)34.251327.58-39.9035.08-1529.33-43.5035.71-Percentages of standard lengthDepth at dorsal-fin origin31.971329.02-34.4931.311.631526.94-31.1229.141.38Snout to dorsal-fin origin64.501362.56-64.8963.550.831561.15-65.8663.701.25Snout to pectoral-fin origin28.821327.21-29.4328.200.761526.71-28.1727.410.41Snout to pelvic-fin origin46.191344.48-49.5246.051.321543.81-48.1645.771.13Snout to anal-fin origin57.641356.81-61.2658.541.201557.11-60.7658.641.03Dorsal-fin to pectoral-fin length46.801344.27-50.1746.761.391544.27-47.8846.151.03Dorsal-fin to adipose-fin length25.281324.59-26.3125.420.601523.93-26.0425.290.59Dorsal-fin to hypurals complex length37.931336.32-41.1738.711.461536.62-40.1238.081.07Eye to dorsal-fin origin50.981349.74-52.1550.980.751548.07-52.9451.241.44Pectoral-fin to pelvic-fin length17.871315.76-22.6318.701.321516.13-20.7419.311.25Pelvic-fin to anal-fin length12.851312.85-15.8614.100.941512.12-16.6714.741.21Dorsal-fin length17.581316.26-21.6519.201.441517.75-20.6719.320.92Dorsal-fin base length11.591310.77-11.8511.330.361510.31-12.0111.000.42Pectoral-fin length26.011322.69-26.4024.801.241523.31-26.4724.670.74Pelvic-fin length16.531313.00-16.8215.401.181512.54-14.6613.750.60Anal-fin length18.361315.67-20.3417.811.041516.69-20.0518.140.94Anal-fin base length33.661331.48-35.7333.071.181530.23-34.3032.741.05Caudal peduncle depth11.621310.00-12.4611.390.78159.21-10.699.880.47Caudal peduncle length12.851312.48-15.7014.060.971511.39-14.1912.770.91Bony head length25.611324.36-25.9525.140.531522.90-25.3924.460.65Percentages of head lengthSnout length30.331327.83-30.4629.430.961526.96-31.2829.291.25Horizontal eye length33.181329.93-36.0033.001.821531.99-37.2134.561.57Postorbital head length39.681337.02-41.6639.441.731537.06-41.4638.821.33Maxillary length36.601333.76-38.0736.560.881535.36-38.7536.721.02Least interorbital width34.891334.58-38.4835.901.111534.97-39.5136.631.20Upper jaw length46.981344.51-48.5346.121.091541.83-49.3445.641.47
description: Published as part of Vanegas-Ríos, James Anyelo, Azpelicueta, María de las Mercedes & Ortega, Hernán, 2011, Chrysobrycon eliasi, new species of stevardiine fish (Characiformes: Characidae) from the río Madre de Dios and upper río Manuripe basins, Peru, pp. 739 in Neotropical Ichthyology 9 (4) on page 739, DOI: 10.1590/S1679-62252011000400004, http://zenodo.org/record/5423252
DOI: 10.5281/zenodo.18404795
title: Table 1 in Chrysobrycon eliasi, new species of stevardiine fish (Characiformes: Characidae) from the río Madre de Dios and upper río Manuripe basins, Peru

description: Table 1. Morphometric data of holotype and 27 paratypes of Chrysobrycon eliasi from río Madre de Dios and Upper río Manuripe basins. n = number of specimens; SD = standard deviation. The values of the holotype are included in the range of males.
CharactersHolotypeMalesFemales and juvenilesnRangeMeanSDnRangeMeanSDStandard length (mm)34.251327.58-39.9035.08-1529.33-43.5035.71-Percentages of standard lengthDepth at dorsal-fin origin31.971329.02-34.4931.311.631526.94-31.1229.141.38Snout to dorsal-fin origin64.501362.56-64.8963.550.831561.15-65.8663.701.25Snout to pectoral-fin origin28.821327.21-29.4328.200.761526.71-28.1727.410.41Snout to pelvic-fin origin46.191344.48-49.5246.051.321543.81-48.1645.771.13Snout to anal-fin origin57.641356.81-61.2658.541.201557.11-60.7658.641.03Dorsal-fin to pectoral-fin length46.801344.27-50.1746.761.391544.27-47.8846.151.03Dorsal-fin to adipose-fin length25.281324.59-26.3125.420.601523.93-26.0425.290.59Dorsal-fin to hypurals complex length37.931336.32-41.1738.711.461536.62-40.1238.081.07Eye to dorsal-fin origin50.981349.74-52.1550.980.751548.07-52.9451.241.44Pectoral-fin to pelvic-fin length17.871315.76-22.6318.701.321516.13-20.7419.311.25Pelvic-fin to anal-fin length12.851312.85-15.8614.100.941512.12-16.6714.741.21Dorsal-fin length17.581316.26-21.6519.201.441517.75-20.6719.320.92Dorsal-fin base length11.591310.77-11.8511.330.361510.31-12.0111.000.42Pectoral-fin length26.011322.69-26.4024.801.241523.31-26.4724.670.74Pelvic-fin length16.531313.00-16.8215.401.181512.54-14.6613.750.60Anal-fin length18.361315.67-20.3417.811.041516.69-20.0518.140.94Anal-fin base length33.661331.48-35.7333.071.181530.23-34.3032.741.05Caudal peduncle depth11.621310.00-12.4611.390.78159.21-10.699.880.47Caudal peduncle length12.851312.48-15.7014.060.971511.39-14.1912.770.91Bony head length25.611324.36-25.9525.140.531522.90-25.3924.460.65Percentages of head lengthSnout length30.331327.83-30.4629.430.961526.96-31.2829.291.25Horizontal eye length33.181329.93-36.0033.001.821531.99-37.2134.561.57Postorbital head length39.681337.02-41.6639.441.731537.06-41.4638.821.33Maxillary length36.601333.76-38.0736.560.881535.36-38.7536.721.02Least interorbital width34.891334.58-38.4835.901.111534.97-39.5136.631.20Upper jaw length46.981344.51-48.5346.121.091541.83-49.3445.641.47
description: Published as part of Vanegas-Ríos, James Anyelo, Azpelicueta, María de las Mercedes & Ortega, Hernán, 2011, Chrysobrycon eliasi, new species of stevardiine fish (Characiformes: Characidae) from the río Madre de Dios and upper río Manuripe basins, Peru, pp. 739 in Neotropical Ichthyology 9 (4) on page 739, DOI: 10.1590/S1679-62252011000400004, http://zenodo.org/record/5423252
DOI: 10.25574/09379
title: Chandra X-ray Observatory ObsId 09379

description: Probing Dark Energy with Relaxed Galaxy Clusters
DOI: 10.15468/dl.ke5cp7
title: Occurrence Download

description: A dataset containing 5247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sorbus",
 "OccurrenceStatus is Present",
 "Geometry POLYGON((8.4 44.6, 11.5 44.6, 11.5 46.7, 8.4 46.7, 8.4 44.6))"
 ]
}

 The dataset includes 5247 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003742-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/10785
title: Chandra X-ray Observatory ObsId 10785

description: Probing Dark Energy with Relaxed Galaxy Clusters
DOI: 10.25574/11719
title: Chandra X-ray Observatory ObsId 11719

description: MACSJ0358.8-2955: much more distant and exciting than we thought
DOI: 10.25574/12244
title: Chandra X-ray Observatory ObsId 12244

description: The Bullet Cluster Reloaded? An in-depth study of two post-collision cluster mergers
DOI: 10.25574/12300
title: Chandra X-ray Observatory ObsId 12300

description: An in-depth study of dark matter in the massive cluster merger MACSJ0358.8-2955
DOI: 10.25574/13194
title: Chandra X-ray Observatory ObsId 13194

description: An in-depth study of dark matter in the massive cluster merger MACSJ0358.8-2955
DOI: 10.5061/dryad.931zcrjs4
title: PacBio HiFi based haplotype-aware assemblies of tomato hybrid varieties Funtelle and Maxeza

description: Modern commercial varieties of tomato (Solanum lycopersicum) are typically
 F1 hybrids that are genetically heterozygous. Here we generated
 haplotype-aware assemblies of two different tomato commercial hybrids
 (Funtelle and Maxeza) using PacBio HiFi reads. The HiFi data was assembled
 using the Hifiasm assembler allowing for the generation of contigs that
 distinguish the two parental haplotypes (haplotype-aware assembly).
 Reference based scaffolding was used to generate the chromosome-scale
 assemblies available here. It should be noted that although the raw
 assembly manages to fully distinguish haplotypes we did not test whether
 the working reference sequence we make available here is fully phased at
 the chromosome level.
description: The raw PacBio HiFi sequencing reads of the both varieties
 studied here are available via the European Nucleotide Archive under
 project numbers PRJEB62442 (Funtelle) and PRJEB62443 (Maxeza).
 For scientific correspondence please contact Charles Underwood
 (cunderwood[@]mpipz.mpg.de)
description: # PacBio HiFi based haplotype-aware assemblies of tomato hybrid varieties
 Funtelle and Maxeza
 [https://doi.org/10.5061/dryad.931zcrjs4](https://doi.org/10.5061/dryad.931zcrjs4) Organism name: *Solanum lycopersicum* Cultivar name: Funtelle Assembly level: Reference-anchored contigs Assembler: hifiasm + RagTag Sequencing technology: PacBio HiFi European Nucleotide Archive project: PRJEB62442 Organism name: *Solanum lycopersicum* Cultivar name: Maxeza Assembly level: Reference-anchored contigs Assembler: hifiasm + RagTag Sequencing technology: PacBio HiFi European Nucleotide Archive project: PRJEB62443 MD5sum: Funtelle-1.fasta 87a62db087f03992c278fdd56dcd10d7 Funtelle-2.fasta 6c465e49d5072f4003477d0852ad7829 Maxeza-1.fasta 078a41440661f66be779ff6d2b721ff1 Maxeza-2.fasta 6e3100ec131cb8ccec932eea5e6f07ef Assembly Statistics: Funtelle1 Contigs 1,155 Total length (Mb) 875.2 Max length (Mb) 76.1 N50 length (Mb) 56.5 N90 length (Mb) 1.3 L50 7 L90 29 Funtelle2 Contigs 651 Total length (Mb) 839.5 Max length (Mb) 69.8 N50 length (Mb) 41.3 N90 length (Mb) 1.8 L50 8 L90 34 Maxeza1 Contigs 1,488 Total length (Mb) 869.4 Max length (Mb) 73.2 N50 length (Mb) 55.7 N90 length (Mb) 2.1 L50 7 L90 25 Maxeza2 Contigs 689 Total length (Mb) 846.2 Max length (Mb) 74.8 N50 length (Mb) 39.4 N90 length (Mb) 4.6 L50 8 L90 27
DOI: 10.25574/14012
title: Chandra X-ray Observatory ObsId 14012

description: Understanding the connection between radio halos and cluster mergers
DOI: 10.25574/18285
title: Chandra X-ray Observatory ObsId 18285

description: Building a Cheap and Cheerful SZ-selected sample of galaxy clusters with the Planck Catalogue.
DOI: 10.25574/21703
title: Chandra X-ray Observatory ObsId 21703

description: X-ray Emission from z=6 galaxies
DOI: 10.25574/22856
title: Chandra X-ray Observatory ObsId 22856

description: X-ray Emission from z=6 galaxies
DOI: 10.15468/dl.ae9uzh
title: Occurrence Download

description: A dataset containing 1041 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Raneya brasiliensis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 1041 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003745-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4v8vzc
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Humboldtia decurrens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 16 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003746-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cszpn5
title: Occurrence Download

description: A dataset containing 14482 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "Geometry POLYGON((-74.9891 1.17613,-74.10321 0.18199,-73.52962 0.63129,-74.41232 1.6062,-74.4888 1.54886,-74.9891 1.17613))"
 ]
}

 The dataset includes 14482 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003747-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fxpnvx0zk
title: Data from: Anti-predator defenses are linked with high levels of genetic differentiation in frogs

description: Predator-prey interactions have been suggested as drivers of diversity in
 different lineages, and the presence of anti-predator defences in some
 clades is linked to higher rates of diversification. Warning signals are
 some of the most widespread defenses in the animal world, and there is
 evidence of higher diversification rates in aposematic lineages. The
 mechanisms behind such species richness, however, are still unclear. Here,
 we test whether lineages that use aposematism as anti-predator defense
 exhibit higher levels of genetic differentiation between populations,
 leading to increased opportunities for divergence. We collated from the
 literature &gt; 3,000 pairwise genetic differentiation values across
 more than 700 populations from over 60 amphibian species. We find evidence
 that, given the same geographic distance, populations of species of
 aposematic lineages exhibit greater genetic divergence relative to species
 that are not aposematic. Our results support a scenario where the use of
 warning signals could restrict gene flow, and suggest that anti-predator
 defences could impact divergence between populations and potentially have
 effects at a macro-evolutionary scale.
description: Data was collected from publications as described in the
 manuscript. It was processed using R but raw values can be found in the
 original publications used. 
description: # Anti-predator defenses are linked with high levels of genetic
 differentiation in frogs 
 Dataset from literature collection of genetic divergence values (Fst) and
 geographic distances. Geographic distances were calculated from location
 coordinates using the topodist package, meaning they are topographic
 distances. ## Description of the data and file structure Each row in the
 dataset corresponds to a comparison between two populations of the same
 species. Each row has information of the species used for comparisons, the
 geographic distance between populations, the marker used to estimate
 genetic differentiations and the genetic differentiation calculated as an
 Fst value. We also include information on the average sample size for each
 study. ## Sharing/Access information Data was derived from the sources
 listed in Ref-species file.
DOI: 10.15468/dl.94hjvp
title: Occurrence Download

description: A dataset containing 51085 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Astronium graveolens"
 ]
}

 The dataset includes 51085 records from 400 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003679-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gb5mkkwwj
title: Custom script for feature extraction from Genbank files

description: Microbes are thought to be distributed and circulated around the world,
 but the connection between marine and terrestrial microbiomes is largely
 unknown. We use Plantibacter, a representative plant-associated genus, as
 our research model to show the global distribution and adaptation of
 plant-related bacteria in plant-free environments, especially in the
 remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and
 their plant-associated relatives shared over 98% whole-genome average
 nucleotide identity (ANI), indicating recent divergence and ongoing
 speciation from plant-related niches to marine environments. Comparative
 genomics revealed that the marine strains acquired new genes via
 horizontal gene transfer from non-Plantibacter species and refined
 existing genes through positive selection to improve adaptation to new
 habitats. Meanwhile, marine strains retained the ability to interact with
 plants, such as modifying root system architecture and promoting
 germination. Plantibacter species were further found to be widely
 distributed in marine environments, revealing an unrecognized phenomenon
 that plant-associated microbiomes have colonized the ocean, which could
 serve as a reservoir for plant growth-promoting microbes. This study
 demonstrates the presence of an active reservoir of terrestrial plant
 growth-promoting bacteria in remote marine systems and advances our
 understanding of the microbial connections between plant-associated and
 plant-free environments at the genome level.
description: The script was written in Python to extract isolation source in a
 genbank file.
description: # Custom script for feature extraction from Genbank files
 The script is used to
 extract isolation source from GenBank files and can be adjusted to extract
 other features as well. This script can help extract the relevant
 information batch rather than manually copy the information one by one.
 The script contains all the information needed to perform the information
 extraction. GenBank file (x.gb) to be processed should be provided by
 users. An example GenBank file for test is included in this dataset
 ([16S_plantibacter_isolates.gb](https://datadryad.org/stash/downloads/file_stream/2637428)). ## Description of the data and file structure The script was written in Python and is Linux compatible. Biopython should be installed in the system to run this script. Steps to run this script on Linux system are as below. 1\. First download the GenBank file (x.gb) into the same location where the script is. 2\. Then change the gb file name to the one written in the script or change the gb file name in the script to the one you use. 3\. Run the script by typing ./feature_extr.py. 4\. Output will be produced at the same location. ## Sharing/Access information NA ## Code/Software The script was written in Python and is Linux compatible. Biopython should be installed in the system to run this script. Steps to run this script on Linux system are as above.