cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5063/f19g5jxp
title: biodiversity quadrat surveys of rocky intertidal ecosystems

description: The Baseline surveys of rocky intertidal ecosystems (SC) project includes both Long-Term Monitoring and Biodiversity Surveys done in the South Coast of California. Long-Term Monitoring Surveys use fixed plots to document changes in percent cover, or abundance of targeted species or species assemblages. This fixed-plot approach allows the dynamics of rocky intertidal species to be monitored with reasonable sampling effort and provides sufficient statistical power to detect changes over space or time. Biodiversity Surveys provide detailed information about biodiversity and community structure. These surveys were designed to measure diversity and abundance of algae and invertebrates found within rocky intertidal communities on the western coast of temperate North America. This metadata record documents the Biodiversity Quadrat Surveys done as part of the SC Baseline surveys of rocky intertidal ecosystems. Biodiversity Quadrat sampling consists of recording the number of mobile invertebrate species within thirty-three 0.5m x 0.5m quadrats placed along 11 transects of variable length extending from the upper intertidal to the low intertidal. Biodiversity Surveys are comprised of three biological components, all sampled along the same transects: (1) point contact estimates of intertidal cover and substrate characteristics, (2) swath transects to estimate the density of sea stars and abalone, and (3) quadrat sampling to estimate the density of mobile invertebrates. Biodiversity Surveys are done throughout the year at sites ranging from Southeast Alaska to Baja California Sur, Mexico. Selected sites are resampled on a 3-5 year cycle. A site is defined as a contiguous rocky bench of at least 30m.
DOI: 10.5063/f15q4t7t
title: biodiversity swath surveys of rocky intertidal ecosystems

description: The Baseline surveys of rocky intertidal ecosystems (SC) project includes both Long-Term Monitoring and Biodiversity Surveys done in the South Coast of California. Long-Term Monitoring Surveys use fixed plots to document changes in percent cover, or abundance of targeted species or species assemblages. This fixed-plot approach allows the dynamics of rocky intertidal species to be monitored with reasonable sampling effort and provides sufficient statistical power to detect changes over space or time. Biodiversity Surveys provide detailed information about biodiversity and community structure. These surveys were designed to measure diversity and abundance of algae and invertebrates found within rocky intertidal communities on the western coast of temperate North America. This metadata record documents the Biodiversity Swath Surveys done as part of the SC Baseline surveys of rocky intertidal ecosystems. Biodiversity Swath sampling consists of recording the number of seastars and abalone on eleven 2m wide transects of variable length extending from the upper intertidal to the low intertidal. Biodiversity Surveys are comprised of three biological components, all sampled along the same transects: (1) point contact estimates of intertidal cover and substrate characteristics, (2) swath transects to estimate the density of sea stars and abalone, and (3) quadrat sampling to estimate the density of mobile invertebrates. Biodiversity Surveys are done throughout the year at sites ranging from Southeast Alaska to Baja California Sur, Mexico. Selected sites are resampled on a 3-5 year cycle. A site is defined as a contiguous rocky bench of at least 30m.
DOI: 10.5063/f1x63k2z
title: long-term monitoring photo plot surveys of rocky intertidal ecosystems

description: The Baseline surveys of rocky intertidal ecosystems (SC) project includes both Long-Term Monitoring and Biodiversity Surveys done in the SouthCoast of California. Long-Term Monitoring Surveys use fixed plots to document changes in percent cover, or abundance of targeted species or species assemblages. This fixed-plot approach allows the dynamics of rocky intertidal species to be monitored with reasonable sampling effort and provides sufficient statistical power to detect changes over space or time. Biodiversity Surveys provide detailed information about biodiversity and community structure. These surveys were designed to measure diversity and abundance of algae and invertebrates found within rocky intertidal communities on the western coast of temperate North America. This metadata record documents the Long-Term Monitoring Photo Plot Surveys. Photoplots are used to monitor abundance of organisms within target assemblages. In general, 5 replicate plots (50 x 75 cm) are placed in a stratified random manner throughout the target species' zone of maximum abundance. Plots are photographed in the field, and are scored for percent cover using a grid of 100 points either in the field or in the lab from photos. A species, higher taxon, or substrate located below each of the 100 points is identified and recorded. Layering is not scored separately, so the total cover is 100 percent. Long-Term Monitoring Surveys are comprised of one or more of the following procedures: 1) Photoplots used to monitor percent cover in assemblages such as barnacles, mussels, and rockweed, as well as small, mobile species such as snails and hermit crabs, 2) Line transects used to estimate cover of surfgrass, kelps and other algae not well-sampled by photoplots. 3) Irregular plots used for counts and sizes of large, mobile species such as seastars and limpets. Long-Term Monitoring Surveys are done throughout the year at sites ranging from Alaska to Southern California.
DOI: 10.5063/f1j1018r
title: long-term monitoring species count surveys of rocky intertidal ecosystems

description: The Baseline surveys of rocky intertidal ecosystems (SC) project includes both Long-Term Monitoring and Biodiversity Surveys done in the SouthCoast of California. Long-Term Monitoring Surveys use fixed plots to document changes in percent cover, or abundance of targeted species or species assemblages. This fixed-plot approach allows the dynamics of rocky intertidal species to be monitored with reasonable sampling effort and provides sufficient statistical power to detect changes over space or time. Biodiversity Surveys provide detailed information about biodiversity and community structure. These surveys were designed to measure diversity and abundance of algae and invertebrates found within rocky intertidal communities on the western coast of temperate North America. This metadata record documents the Long-Term Monitoring Species Count Surveys done as part of the SC Baseline surveys of rocky intertidal ecosystems. Species Count sampling is conducted by recording the number of a specific organism found in a permanent plot at a given site. For some species, at certain sites, size and color are also recorded. The type of plot and number of replicates monitored is dependent on the target species. Long-Term Monitoring Surveys are comprised of one or more of the following procedures: 1) Photoplots used to monitor percent cover in assemblages such as barnacles, mussels, and rockweed, as well as small, mobile species such as snails and hermit crabs, 2) Line transects used to estimate cover of surfgrass, kelps and other algae not well-sampled by photoplots. 3) Irregular plots used for counts and sizes of large, mobile species such as seastars and limpets. Long-Term Monitoring Surveys are done throughout the year at sites ranging from Alaska to Southern California.
DOI: 10.5281/zenodo.6082301
title: The 'dark matter' of protein variants carries a distinct DNA signature and predicts damaging variant effects

description: Data generated for the manuscript "The 'dark matter' of protein variants carries a distinct DNA signature and predicts damaging variant effects". Please consult the README file for detailed description of data files included in this dataset.
DOI: 10.5281/zenodo.4726168
title: The 'dark matter' of protein variants carries a distinct DNA signature and predicts damaging variant effects

description: Data generated for the manuscript "The 'dark matter' of protein variants carries a distinct DNA signature and predicts damaging variant effects". Please consult the README file for detailed description of data files included in this dataset.
DOI: 10.5063/f1np22kf
title: long-term monitoring transect surveys of rocky intertidal ecosystems

description: The Baseline surveys of rocky intertidal ecosystems (SC) project includes both Long-Term Monitoring and Biodiversity Surveys done in the SouthCoast of California. Long-Term Monitoring Surveys use fixed plots to document changes in percent cover, or abundance of targeted species or species assemblages. This fixed-plot approach allows the dynamics of rocky intertidal species to be monitored with reasonable sampling effort and provides sufficient statistical power to detect changes over space or time. Biodiversity Surveys provide detailed information about biodiversity and community structure. These surveys were designed to measure diversity and abundance of algae and invertebrates found within rocky intertidal communities on the western coast of temperate North America. This metadata record documents the Long-Term Monitoring Transect Surveys done as part of the SC Baseline surveys of rocky intertidal ecosystems. Permanent point-intercept transects are used to monitor percent cover of surfgrass, kelps, and other algae. In general, 3 replicate transects are established for each target species. Transects are generally 10 m long and percent cover is estimated by recording the taxa or substrate occurring under each 10 cm interval (for a total of 100 points). Long-Term Monitoring Surveys are comprised of one or more of the following procedures: 1) Photoplots used to monitor percent cover in assemblages such as barnacles, mussels, and rockweed, as well as small, mobile species such as snails and hermit crabs, 2) Line transects used to estimate cover of surfgrass, kelps and other algae not well-sampled by photoplots. 3) Irregular plots used for counts and sizes of large, mobile species such as seastars and limpets. Long-Term Monitoring Surveys are done throughout the year at sites ranging from Alaska to Southern California.
DOI: 10.5063/f1057d2p
title: Reef_Check_algae_surveys

description: The Reef Check Foundation’s California program (RCCA), trains, tests and certifies experienced recreational scuba divers to collect scientifically robust survey data on rocky reef species. All of RCCA’s volunteers go through a rigorous four-day training and annual recertification program. RCCA’s monitoring program gathers economically and ecologically important data, and educates the public about scientific methods and environmental stewardship. Over the baseline monitoring period of 2011/2012, RCCA conducted 91 surveys at its long-term monitoring sites in the South Coast Study Region. Many of these sites have been surveyed since 2006 or 2007 in order to track marine life populations and in anticipation of the establishment of MPAs in this study region. This metadata record documents the fish surveys that are part of RCCA’s South Coast MPA Baseline subtidal community surveys. Subtidal community structure surveys are conducted annually at sites during the summer or early fall, and quantify substrate type and relief, benthic cover, abundance of 73 species or species groups of macroalgae, invertebrates, and fishes. Spatial allocation of sampling is designed to measure year-to-year site-wide variability in species abundances and community structure. A site is defined as a fixed stretch of coastline, occupying approximately 250m. Each site is comprised of six core transects along which fish, invertebrate, algae and substrate are sampled and 12 additional fish transects. Transects are stratified across the two depth zones and fish transects are placed around the core transects. Dimensions for all algae transects are 30m long x 2m wide. For a complete description of the Reef Check California sampling protocol see: http://reefcheck.org/rcca/monitoring_protocol.php.
DOI: 10.5063/f1vd6wk0
title: Reef_Check_fish_surveys

description: The Reef Check Foundation’s California program (RCCA), trains, tests and certifies experienced recreational scuba divers to collect scientifically robust survey data on rocky reef species. All of RCCA’s volunteers go through a rigorous four-day training and annual recertification program. RCCA’s monitoring program gathers economically and ecologically important data, and educates the public about scientific methods and environmental stewardship. Over the baseline monitoring period of 2011/2012, RCCA conducted 91 surveys at its long-term monitoring sites in the South Coast Study Region. Many of these sites have been surveyed since 2006 or 2007 in order to track marine life populations and in anticipation of the establishment of MPAs in this study region. This metadata record documents the fish surveys that are part of RCCA’s South Coast MPA Baseline subtidal community surveys. Subtidal community structure surveys are conducted annually at sites during the summer or early fall, and quantify substrate type and relief, benthic cover, abundance of 73 species or species groups of macroalgae, invertebrates, and fishes. Spatial allocation of sampling is designed to measure year-to-year site-wide variability in species abundances and community structure. A site is defined as a fixed stretch of coastline, occupying approximately 250m. Each site is comprised of six core transects along which fish, invertebrate, algae and substrate are sampled and 12 additional fish transects. Transects are stratified across the two depth zones and fish transects are placed around the core transects. Fish sampling consists of visual surveys by scuba divers that record the number of individuals and their size (in three size classes) of 35 species of ecologically or economically important fishes on "transects" along the seafloor. Dimensions for all fish transects are 30m long x 2m wide x 2m high (off the seafloor).
DOI: 10.5063/f1qn64vn
title: Reef_Check_invertebrate_surveys

description: The Reef Check Foundation’s California program (RCCA), trains, tests and certifies experienced recreational scuba divers to collect scientifically robust survey data on rocky reef species. All of RCCA’s volunteers go through a rigorous four-day training and annual recertification program. RCCA’s monitoring program gathers economically and ecologically important data, and educates the public about scientific methods and environmental stewardship. Over the baseline monitoring period of 2011/2012, RCCA conducted 91 surveys at its long-term monitoring sites in the South Coast Study Region. Many of these sites have been surveyed since 2006 or 2007 in order to track marine life populations and in anticipation of the establishment of MPAs in this study region. This metadata record documents the fish surveys that are part of RCCA’s South Coast MPA Baseline subtidal community surveys. Subtidal community structure surveys are conducted annually at sites during the summer or early fall, and quantify substrate type and relief, benthic cover, abundance of 73 species or species groups of macroalgae, invertebrates, and fishes. Spatial allocation of sampling is designed to measure year-to-year site-wide variability in species abundances and community structure. A site is defined as a fixed stretch of coastline, occupying approximately 250m. Each site is comprised of six core transects along which fish, invertebrate, algae and substrate are sampled and 12 additional fish transects. Transects are stratified across the two depth zones and fish transects are placed around the core transects. Dimensions for all invertebrate transects are 30m long x 2m wide. For a complete description of the Reef Check California sampling protocol see: http://reefcheck.org/rcca/monitoring_protocol.php.
DOI: 10.5063/f13x84r7
title: Reef_Check_UPC_surveys

description: The Reef Check Foundation’s California program (RCCA), trains, tests and certifies experienced recreational scuba divers to collect scientifically robust survey data on rocky reef species. All of RCCA’s volunteers go through a rigorous four-day training and annual recertification program. RCCA’s monitoring program gathers economically and ecologically important data, and educates the public about scientific methods and environmental stewardship. Over the baseline monitoring period of 2011/2012, RCCA conducted 91 surveys at its long-term monitoring sites in the South Coast Study Region. Many of these sites have been surveyed since 2006 or 2007 in order to track marine life populations and in anticipation of the establishment of MPAs in this study region. This metadata record documents the Uniform Point Contact (UPC) surveys that are part of RCCA’s South Coast MPA Baseline subtidal community surveys. Subtidal community structure surveys are conducted annually at sites during the summer or early fall, and quantify substrate type and relief, benthic cover, abundance of 73 species or species groups of macroalgae, invertebrates, and fishes. Spatial allocation of sampling is designed to measure year-to-year site-wide variability in species abundances and community structure. A site is defined as a fixed stretch of coastline, occupying approximately 250m. Each site is comprised of six core transects along which fish, invertebrate, algae and substrate are sampled and 12 additional fish transects. Transects are stratified across the two depth zones and fish transects are placed around the core transects. UPC transects are 30m long and data is collected at 30 points uniformly spaced along the transects. For a complete description of the Reef Check California sampling protocol see: http://reefcheck.org/rcca/monitoring_protocol.php.
DOI: 10.5063/f1pk0d82
title: SCR_Aerial_AnacapaIsland_10142012_IntClass

description: This raster dataset was developed for the Sea Grant South Coast MPA Baseline Program as part of the project “Nearshore Substrate Mapping and Change Analysis using Historical and Concurrent Multispectral Imagery” (#R/MPA 30 10-049). The study region is the South Coast Region (SCR). Imagery was acquired on October 14, 2012 at a spatial resolution of 0.3 meters using a Microsoft UltraCam-X digital camera acquiring in the red, green, blue and near-infrared bands. Information on the UltraCam-X camera system and wavelengths for each ban can be found in the file "The Microsoft Vexcel UltraCam X.pdf" included in the Support folder on the image data delivery media and on the OceanSpaces.org server. This image mosaic product is a result of the resampling of the 0.3 meter data to 2 meter GSD. Details on this system and the data processing are below in the Lineage section of this document. Individual UCX image tiles were mosaicked into sections based on the islands covered and local coastal regions as well as the SCR MPA zones in order to generate this multispectral image product. These imagery were subsequently used to generate habitat classification thematic maps of the SCR's intertidal zones and kelp beds from Point Conception to Imperial Beach, CA. The imagery files deliverd are in GeoTIFF format. More information on the classes resolved and processing methods are in the Lineage section of this document. This raster dataset contains a habitat classification of either offshore giant kelp beds and/or the intertidal zone along the California South Coast Region (SCR) from from Point Conception, CA down to Imperial beach, CA. This specific raster classification includes the Anacapa Island SMCA and Anacapa Island SMR.
DOI: 10.5063/f1736p06
title: SCR_Aerial_AnacapaIsland_10142012_KelpClass

description: These raster and vector dataset were developed for the Sea Grant South Coast MPA Baseline Program as part of the project “Nearshore Substrate Mapping and Change Analysis using Historical and Concurrent Multispectral Imagery” (#R/MPA 30 10-049). The study region is the South Coast Region (SCR). Imagery was acquired on October 14, 2012 at a spatial resolution of 0.3 meters using a Microsoft UltraCam-X digital camera acquiring in the red, green, blue and near-infrared bands. Information on the UltraCam-X camera system and wavelengths for each ban can be found in the file "The Microsoft Vexcel UltraCam X.pdf" included in the Support folder on the image data delivery media and on the OceanSpaces.org server. This image mosaic product is a result of the resampling of the 0.3 meter data to 2 meter GSD. Details on this system and the data processing are below in the Lineage section of this document. Individual UCX image tiles were mosaicked into sections based on the islands covered and local coastal regions as well as the SCR MPA zones in order to generate this multispectral image product. These imagery were subsequently used to generate habitat classification thematic maps of the SCR's kelp beds from Point Conception to Imperial Beach, CA. The imagery files deliverd are in GeoTIFF format. More information on the classes resolved and processing methods are in the Lineage section of this document. This raster dataset contains a habitat classification of either offshore giant kelp beds along the California South Coast Region (SCR) from from Point Conception, CA down to Imperial beach, CA. This specific raster classification includes the Anacapa Island SMCA and Anacapa Island SMR.
DOI: 10.6084/m9.figshare.19118204
title: Phylogenetic trees and supp. alignments for Altemose et al. 2021, T2T Consortium

description: Phylogenetic trees and supp. alignments are provided for a subset of supp. figures in Altemose et al. 2021 "Complete genomic and epigenetic maps of human centromeres". This dataset contains phylogenetic trees of αSat sequences (files with extension MTS) and alignments (files with extension MAS) in MEGA5 format. Phylogenetic analyses was performed using MEGA5 (https://www.megasoftware.net/older_versions).
DOI: 10.6084/m9.figshare.19118204.v3
title: Phylogenetic trees and supp. alignments for Altemose et al. 2021, T2T Consortium

description: Phylogenetic trees and supp. alignments are provided for a subset of supp. figures in Altemose et al. 2021 "Complete genomic and epigenetic maps of human centromeres". This dataset contains phylogenetic trees of αSat sequences (files with extension MTS) and alignments (files with extension MAS) in MEGA5 format. Phylogenetic analyses was performed using MEGA5 (https://www.megasoftware.net/older_versions).
DOI: 10.6084/m9.figshare.19118204.v2
title: Phylogenetic trees and supp. alignments for Altemose et al. 2021, T2T Consortium

description: Phylogenetic trees and supp. alignments are provided for a subset of supp. figures in Altemose et al. 2021 "Complete genomic and epigenetic maps of human centromeres". This dataset contains phylogenetic trees of αSat sequences (files with extension MTS) and alignments (files with extension MAS) in MEGA5 format. Phylogenetic analyses was performed using MEGA5 (https://www.megasoftware.net/older_versions).