Data from: Navigating the scales of diversity in subtropical and coastal fish assemblages ascertained by eDNA and visual surveys
This Hsuetal_2022_dataset_README.txt file was generated on 2022-08-05 by Tsai-Hsuan Tony Hsu (tonytsaihsuanhsu@gmail.com). Knit Hsuetal2022_Analysis.Rmd to generate html and extract R code.
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Author Information
First author Name: Tsai-Hsuan Tony Hsu Institution: Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
Second author Name: Dr. Wei-Jen Chen Institution: Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
Third & corresponding author Name: Dr Vianney Denis Institution: Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan Email: vianney.denis@gmail.com
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Date of data collection: 2021
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Geographic location of data collection: northern Taiwan, West Pacific
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Funding sources that supported the collection of the data: Ocean Conservation Administration of Taiwan, Ministry of Science and Technology of Taiwan
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Recommended citation for this dataset Hsu, Tsai-Hsuan Tony; Chen, Wei-Jen; Denis, Vianney (2023), Data from: Navigating the scales of diversity in subtropical and coastal fish assemblages ascertained by eDNA and visual surveys, Dryad, Dataset, https://doi.org/10.5061/dryad.3xsj3txk4
[Data and R script are also available through the GitHub repository https://github.com/vianneydenis/fish-survey.git in order to replicate our analyses]
- Description of dataset
These data were generated to navigate different scales of fish diversity and compare results of eDNA with those from visual surveys in northern Taiwan.
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File List
File 1: Hsuetal_dataset_Site.csv File 1 description: Information of the 21 sampling sites
File 2: Hsuetal_dataset_DOV.csv File 2 description: Fish abundance and total length data from diver-operated video surveys among the 21 sampling sites
File 3: Hsuetal_dataset_UVC.csv File 3 description: Fish abundance and total length data from underwater visual census surveys among the 21 sampling sites
File 4: Hsuetal_dataset_eDNA.xlsx File 4 description: Species annotation and read coverage for fish eDNA data among the 21 sampling sites
File 5: Hsuetal_dataset_BV.csv File 5 description: Count of benthic variables identified by the CoralNet among the 21 sampling sites
File 6: Hsuetal_dataset_level.csv File 6 description: Species' vertical position in the water column
File 7: Hsuetal_dataset_Lw_ab.csv File 7 description: Length-weight equation coefficients a and b retreived from FishBase to calculate biomass
File 8: Hsuetal_dataset_flow.csv File 8 description: Flow data recorded by a current meter, Marotte HS, at each site
File 9: Hsuetal_dataset_gd.csv File 9 description: Pairwise gepgraphic distance (km) between sites
File 10: Hsuetal_dataset_NGS.zip File 10 description: A zip file containing paired-end fastq files obtaining from NGS for the 21 sites and the filtration (FB) & extraction blanks (EB)
A detailed description of data acquisition and processing can be found in the published manuscript in the Ecological Indicators (https://doi.org/10.1016/j.ecolind.2023.110044).
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Number of variables/columns: 6
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Number of cases/rows: 22
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Missing data codes
None
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Variable List
- Column A - Date: sampling date
- Column B - Site: survey sites
- Column C - Code: abbreviation for each site
- Column D – Lattitude
- Column E – Longitude
- Column F – Area: Northern coast and outlying islands
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Abbreviations used
- for Area:
- C: Coastal sites along the northern coast
- I: Outlying islands
- for Area:
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Number of variables/columns: 6
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Number of cases/rows: 429
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Missing data codes
None
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Variable List
- Column A – Method
- Column B – Site: abbreviation for each site
- Column C – Family
- Column D – Species
- Column E – Length: total length of fish individuals
- Column F – Number: the number of fish individuals
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Number of variables/columns: 6
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Number of cases/rows: 591
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Missing data codes:
None
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Variable List
- Column A – Method
- Column B – Site: abbreviation for each site
- Column C – Family
- Column D – Species
- Column E – Length: total length of fish individuals (cm)
- Column F – Number: the number of fish individuals
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Number of variables/columns: 6
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Number of cases/rows: 1704
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Missing data codes
None
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Variable List
- Column A – Site: abbreviation for each site
- Column B – Family
- Column C – Species: species name automatically assigned by the MiFish pipeline
- Column D – Ratio: the coverage of the sequence reads among total reads in each site
- Column E – Valid_as: confirmed species name
- Column F – Chinese: Chinese name of the species
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Number of variables/columns: 11
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Number of cases/rows: 22
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Missing data codes
None
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Variable List
- Column A – Site: abbreviation for each site
- Column B – CCA: crustose oralline algae
- Column C – hard_coral: Scleractinain corals
- Column D – macroalgae: macroalgae
- Column E – other_life: other living organisms
- Column F – soft_coral: soft corals
- Column G – sponge: sponge
- Column H – sub_stable: stable substrates
- Column I – sub_unstable: unstable substrates
- Column J – turf: turf algae
- Column K – zoanthid: zoanthids
- Column L – other: other abiotic items
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Number of variables/columns: 2
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Number of cases/rows: 483
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Missing data codes
None
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Variable List
- Column A – Species
- Column B – level: species' vertical positions in the water column
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Abbreviations used:
- for level
- B: benthic
- P: pelagic +BP: bentho-pelgic
- for level
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Number of variables/columns: 3
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Number of cases/rows: 129
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Missing data codes
None
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Variable List
- Column A – Species
- Column B – mean_a: averaged coefficient a
- Column C – mean_b: averaged coefficient b
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Number of variables/columns: 4
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Number of cases/rows: 22
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Missing data codes
None
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Variable List
- Column A – Date: sampling date
- Column B – Site: survey sites
- Column C - Code: abbreviation for each site
- Column D – Speed: flow speed in m/s
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Number of variables/columns: 21
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Number of cases/rows: 22
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Missing data codes
None
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Variable List
- Column A – Site
- Column B to V – Code of the 21 survey sites