DOI: 10.5061/dryad.j0zpc86nz
title: Data from: Drivers of coastal benthic communities in a complex environmental setting

description: Analyzing the environmental factors affecting benthic communities in
 coastal areas is crucial for uncovering key factors that require
 conservation action. Here, we collected benthic and environmental
 (physical-chemical-historical and land-based) data for 433
 transects in Taiwan. Using a k-means approach, five communities
 dominated by crustose coralline algae, turfs, stony corals,
 digitate, or bushy octocorals were first delineated.
 Conditional random forest models then identified physical,
 chemical, and land-based factors (e.g., light intensity, nitrite,
 and population density) relevant to community delineation and
 occurrence. Historical factors, including typhoons and
 temperature anomalies, had only little effect. The prevalent turf
 community correlated positively with chemical and land-based
 drivers, which suggests that anthropogenic impacts are causing a benthic
 homogenization. This mechanism may mask the effects of climate
 disturbances and regional differentiation of benthic assemblages.
 Consequently, management of nutrient enrichment and terrestrial runoff is
 urgently needed to improve community resilience in Taiwan amidst
 increasing challenges of climate change.
description: Full details on sample collection and analyses are available in
 the published manuscript. Lin, Y.V., Château, P.-A,
 Nozawa, Y., Wei, C.-L, Wunderlich, R.F., Denis, V. (2024) Drivers of
 coastal benthic communities in a complex environmental setting. Marine
 Pollution Bulletin 203, 116462. https://doi.org/10.1016/j.marpolbul.2024.116462
description: # Data from: Drivers of coastal benthic communities in a complex
 environmental setting --- This README.md was generated on 2024-06-03 by
 Yuting Vicky Lin
 ([vicky.linyuting@gmail.com](mailto:vicky.linyuting@gmail.com)). 1.
 **Author Information** * First author * Name: Dr. Yuting Vicky Lin *
 Institution: Institute of Oceanography, National Taiwan University, Taipei
 10617, Taiwan * Second author * Name: Prof. Pierre-Alexandre Château *
 Institution: Department of Marine Environment and Engineering, National
 Sun Yat-Sen University, Kaohsiung 80420, Taiwan * Third author * Name:
 Prof. Yoko Nozawa * Institution: Tropical Biosphere Research Center,
 University of the Ryukyus, Okinawa 905-0227, Japan Biodiversity Research
 Center, Academia Sinica, Taipei 11529, Taiwan Department of Marine
 Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro,
 Semarang 50275, Indonesia * Fourth author * Name: Prof. Chih-Lin Wei *
 Institution: Institute of Oceanography, National Taiwan University, Taipei
 10617, Taiwan * Fifth author * Name: Dr. Rainer Ferdinand Wunderlich *
 Institution: Department of Bioenvironmental Systems Engineering, National
 Taiwan University, Taipei 10617, Taiwan & 5INRAE, UR EABX, 33612
 Cestas, France * Sixth & corresponding author * Name: Prof. Vianney
 Denis * Institution: Institute of Oceanography, National Taiwan
 University, Taipei 10617, Taiwan * Email:
 [vianneydenis@ntu.edu.tw](mailto:vianneydenis@ntu.edu.tw) 2. **Date of
 data collection**: 2016-2020 3. **Geographic location of data
 collection**: Taiwan, West Pacific 4. **Funding sources that supported the
 collection of the data**: Marine National Park of Taiwan, National Science
 and Technology Council of Taiwan, Ocean Affairs Council of Taiwan 5.
 **Recommended citation for this dataset** Lin YT, Château P-A, Nozawa Y,
 Wei C-L, Wunderlich RF, Denis V (2024), Data from: Drivers of coastal
 benthic communities in a complex environmental setting, Dryad, Dataset,
 [https://doi.org/10.5061/dryad.j0zpc86nz](https://doi.org/10.5061/dryad.j0zpc86nz) \[Data and R script are also available through the GitHub repository [https://github.com/NTU-FRELab/drivers-communities](https://github.com/NTU-FRELab/drivers-communities) in order to replicate our analyses] ## DESCRIPTION OF THE DATA AND FILE STRUCTURE ### DATA & FILE OVERVIEW 1. **Description of dataset** These data were used to identify distinct benthic communities around Taiwan and the important environmental drivers causing the difference. 2. **File List** File 1: Linetal_dataset_Benthic.csv: benthic cover estimates of the 433 sampling transects File 2: Linetal_dataset_Env.csv: data of 21 environmental drivers in the 433 sampling transects File 3: Linetal_dataset_Cor.csv: coordination and benthic information used to generate Figure 1b File 4: Linetal_dataset_TW.shp, .cpg, .dbf, .prj, .shx: a shapefile of Taiwan map used to generate Figure 1a ### METHODOLOGICAL INFORMATION A detailed description of data acquisition and processing can be found in the published manuscript in the Marine Pollution Bulletin ([https://doi.org/10.1016/j.marpolbul.2024.116462](https://doi.org/10.1016/j.marpolbul.2024.116462)). #### DATA-SPECIFIC INFORMATION ##### **Linetal\_dataset\_Benthic.csv** 1. Number of variables/columns: 28 2. Number of cases/rows: 434 3. Missing data codes None 4. Variable List Column A - transect Column B - ac_erect_single Column C - ag_articulated_calcareous Column D - ag_corticated_foliose Column E – ag_corticated_macrophyte Column F – cca_crustose Column G – cy_filamentous Column H – hc_arborescent Column I – hc_bushy Column J – hc_column Column K – hc_encrusting Column L – hc_foliose Column M – hc_massive Column N – hc_table Column O – oc_arborescent Column P – oc_bushy Column Q – oc_cluster Column R – oc_digitate Column S – oc_encrusting Column T – oc_lobate Column U – oc_massive Column V – sg Column W – sp_encrusting Column X – sp_massive Column Y – sp_repent Column Z – turf_filamentous Column AA – zo_encrusting Column AB – zo_massive 5. Descriptions The values in this .csv file are benthic covers estimated based on the relative probability of the top five identifications suggested by a trained deep neural network in CoralNet (Global ID: 22264). The descriptions of each variables are as below: ac_erect_single: an ascidian individual that is in the erect morphology; ac denotes to ascidian ag_articulated_calcareous: Articulated calcareous alga; ag denotes to alga ag_corticated_foliose: Corticated foliose alga ag_corticated_macrophyte: Corticated macrophyte cca_crustose: Crustose coralline alga; cca denotes to crustose coralline alga cy_filamentous: Filamentous cyanobacterium; cy denotes to cyanobacteria hc_arborescent: A stony coral colony with arborescent morphology; hc denotes to stony coral hc_bushy: A stony coral colony with bushy morphology hc_column: A stony coral colony with columnar morphology hc_encrusting: A stony coral colony with encrusting morphology hc_foliose: A stony coral colony with foliose morphology hc_massive: A stony coral colony with massive morphology hc_table: A stony coral colony with table morphology oc_arborescent: A octocoral colony with arborescent morphology; oc denotes to octocoral oc_bushy: A octocoral colony with bushy morphology oc_cluster: A octocoral colony with cluster morphology oc_digitate: A octocoral colony with digitate morphology oc_encrusting: A octocoral colony with encrusting morphology oc_lobate: A octocoral colony with lobate morphology oc_massive: A octocoral colony with massive morphology sg: Seagrass; sg denotes to seagrass sp_encrusting: A sponge colony with encrusting morphology; sp denotes to sponge sp_massive: A sponge colony with massive morphology sp_repent: A sponge colony with repent morphology turf_filamentous: Filamentous turf alga; turf denotes to turf alga zo_encrusting: A zoanthid colony with encrusting morphology; zo denotes to zoanthid zo_massive: A zoanthid colony with massive morphology ##### **Linetal\_dataset\_Env.csv** 1. Number of variables/columns: 26 2. Number of cases/rows: 434 3. Missing data codes None 4. Variable List * Column A - Region * Column B - Site * Column C - Depth * Column D - Latitude * Column E – Longitude * Column F – Mean_SST * Column G – SD_SST * Column H – Light_intensity * Column I – Wave_exposure * Column J – Wave_height * Column K – Mean_chl_a * Column L – SD_chl_a * Column M – Nitrate * Column N – Nitrite * Column O – Phosphate * Column P – DHW * Column Q – DHW_recovery * Column R – Typhoon_disturbance * Column S – Typhoon_recovery * Column T – Typhoon_frequency * Column U – Anthropogenic_land_use * Column V – Forest_land_use * Column W – Population_density * Column X – Tourist_visitors * Column Y – Unstable_substrate_cover * Column Z – Management_status 5. Descriptions The environmental data in 433 benthic sampling transects around the coastline of Taiwan. The descriptions of each variables are as below: Region: Region in Taiwan where the benthic sampling was conducted Site: Name of the sampling site Depth: Depth where the benthic sampling was conducted. Unit: meter Latitude: Latitude where the benthic sampling was conducted Longitude: Longitude where the benthic sampling was conducted Mean_SST: Mean sea surface temperature extracted from NOAA Global Coral Bleaching Monitoring. Unit: °C. Mean sea surface temperature is abbreviated to Mean_SST SD_SST: Standard deviation of sea surface temperature extracted from NOAA Global Coral Bleaching Monitoring. Unit: °C. Standard deviation of sea surface temperature is abbreviated to SD_SST Light_intensity: Light intensity calculated from Aqua MODIS, NPP, L3SMI, Global, 4km. Unit: E x m-2 x year-1 Wave_exposure: Wave exposure extracted from Yeager et al. (2017). Unit: kW x m-1 Wave_height: Wave height extracted from Open Whether Data, Central Weather Bureau, Taiwan. Unit: meter Mean_chl_a: Mean chlorophyll a extracted from Global Ocean Chlorophyll, PP and PFT from Satellite Observations: Monthly and Daily Interpolated. Unit: mg x m-3. Mean chlorophyll a is abbreviated to Mean_chl_a SD_chl_a: Standard deviation of chlorophyll a extracted from Global Ocean Chlorophyll, PP and PFT from Satellite Observations: Monthly and Daily Interpolated. Unit: mg x m-3. Standard deviation of chlorophyll a is abbreviated to SD_chl_a Nitrate: Nitrate concentration data downloaded from iOcean, Ocean Conservation Administration, Taiwan. Dongsha's data was provided by the laboratory of Prof. Fuh-Kwo Shiah in Academia Sinica, Taipei, Taiwan. Unit: μm Nitrite: Nitrite concentration data downloaded from iOcean, Ocean Conservation Administration, Taiwan. Dongsha's data was provided by the laboratory of Prof. Fuh-Kwo Shiah in Academia Sinica, Taipei, Taiwan. Unit: μm Phosphate: Phosphate concentration data downloaded from iOcean, Ocean Conservation Administration, Taiwan. Dongsha's data was provided by the laboratory of Prof. Fuh-Kwo Shiah in Academia Sinica, Taipei, Taiwan. Unit: μm DHW: Degree heating week extracted from NOAA Global Coral Bleaching Monitoring. Unit: °C-weeks. Degree heating week is abbreviated to DHW DHW_recovery: Recovery time from the last extreme heat event. The time gap between the year the maximum DHW occurred and the year of sampling, and the data of the maximum DHW were downloaded from NOAA Global Coral Bleaching Monitoring. Unit: year. Recovery time from the last extreme heat event is abbreviated to DHW_recovery Typhoon_disturbance: Maximum wind speed for the last severe typhoon, and the wind speed data were from CWB observation data inquire system, Central Weather Bureau, Taiwan. Dongsha's data was provided by Prof. Po-Hsiung Lin in the Department of Atmospheric Science, National Taiwan University, Taipei, Taiwan. Unit: m x s-1. Maximum wind speed for the last severe typhoon is abbreviated as Typhoon disturbance Typhoon_recovery: Recovery time from the last severe typhoon. It was calculated by the time gap between the year the nearest severe typhoon occurred and the year of sampling. Data were from CWB observation data inquire system, Central Weather Bureau, Taiwan. Unit: year. Recovery time from the last severe typhoon is abbreviated to Typhoon_recovery Typhoon_frequency: Number of severe typhoons in the last decade. Data were from CWB observation data inquire system, Central Weather Bureau, Taiwan. Unit: decade-1. Number of severe typhoons in the last decade is abbreviated to Typhoon frequency Anthropogenic_land_use: The area of the agricultural, aquacultural, and urban land use in the township located within a 10 km radius of sampling locations. Data were from MOI Open Data, Ministry of Interior, Taiwan. Unit: km2 Forest_land_use: The area of the forest land use in the township located within a 10 km radius of sampling locations. Data were from MOI Open Data, Ministry of Interior, Taiwan. Unit: km2 Population_density: The average population density within a 10 km radius of sampling locations. Data were from Gridded Population of the World (GPW), v4, 2015, Socioeconomic data and application center, NASA. Unit: people x 10km-radius-1 Tourist_visitors: The number of visit times in the scenic spots located within a 10 km radius of sampling locations. Data were from Tourism statistics database of the Taiwan Tourism Bureau, Taiwan. Unit: visits Unstable_substrate_cover: Covers of unstable subtract (i.e., sand, rubbles) on the canopy layer of reefs. Data were extracted from each of 433 transects. Unit: Percentage (absolute cover). Management_status: The marine protected status of sampling locations was classified into “fully no-take,” “open access,” and “restrictions on fishing gear, catch size, species, and/or any recreational activities." Data were from the marine protected area database of Functional Reef Ecology Laboratory, Taiwan Yeager LA, Marchand P, Gill DA, Baum JK, McPherson JM (2017) Marine Socio-Environmental Covariates: queryable global layers of environmental and anthropogenic variables for marine ecosystem studies. Ecology 98:1976-1976 ##### **Linetal\_dataset\_Cor.csv** 1. Number of variables/columns: 14 2. Number of cases/rows: 88 3. Missing data codes None 4. Variable List * Column A - Region * Column B - Site * Column C - Depth * Column D - Latitude * Column E – Longitude * Column F – 1 * Column G – 2 * Column H – 3 * Column I – 4 * Column J – 5 * Column K – y * Column L – x * Column M – Label1 * Column N – Label2 5. Descriptions Coordination, depth and benthic composition of each sampling transect. All these information was used to generate the Figure 1. Abbreviations used for variables are as below: 1: CCA Community 2: Turf & Stony Coral Community 3: Turf Community 4: Digitate Community 5: Bushy Community y: The vertical position of the pie chart x: The horizontal position of the pie chart Label1: The number of sampling sites used in Figure 1a Label2: The number of sampling sites used in Figure 1b ##### **Linetal\_dataset\_TW\.shp, .cpg, .dbf, .prj, .shx** 1. Geometry type: MULTIPOLYGON 2. Spatial boundary: latitude - 20.69750 to 25.63431; longitude - 116.71000 to 122.10850 3. Missing data codes None 4. Spatial reference: WGS 84 5. Descriptions This shapefile contains spatial polygons within the specified spatial boundary, which is used for generating the map of Taiwan. ## Usage notes R and QGIS can be used to view Linetal_dataset_TW.shp. Linetal_dataset_TW.cpg, Linetal_dataset_TW.dbf, Linetal_dataset_TW.prj, and Linetal_dataset_TW.shx are the companion files for Linetal_dataset_TW.shp that can not be opened individually but are part of the shapefile data. Microsoft Excel can be used to view Linetal_dataset_Benthic.csv, Linetal_dataset_Env.csv, and Linetal_dataset_Cor.csv.