Data from: Navigating the scales of diversity in subtropical and coastal fish assemblages ascertained by eDNA and visual surveys

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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.

1. 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

2. Date of data collection: 2021

3. Geographic location of data collection: northern Taiwan, West Pacific

4. Funding sources that supported the collection of the data: Ocean Conservation Administration of Taiwan, Ministry of Science and Technology of Taiwan

5. 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 THE DATA AND FILE STRUCTURE

DATA & FILE OVERVIEW

1. 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.

2. 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)

METHODOLOGICAL INFORMATION

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).

DATA-SPECIFIC INFORMATION

Hsuetal_dataset_Site.csv

1. Number of variables/columns: 6

2. Number of cases/rows: 22

3. Missing data codes

   None

4. 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

5. Abbreviations used

   • for Area:
     • C: Coastal sites along the northern coast
     • I: Outlying islands

Hsuetal_dataset_DOV.csv

1. Number of variables/columns: 6

2. Number of cases/rows: 429

3. Missing data codes

   None

4. 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

Hsuetal_dataset_UVC.csv

1. Number of variables/columns: 6

2. Number of cases/rows: 591

3. Missing data codes:

   None

4. 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

Hsuetal_dataset_eDNA.csv

1. Number of variables/columns: 6

2. Number of cases/rows: 1704

3. Missing data codes

   None

4. 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

Hsuetal_dataset_BV.csv

1. Number of variables/columns: 11

2. Number of cases/rows: 22

3. Missing data codes

   None

4. 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

Hsuetal_dataset_level.csv

1. Number of variables/columns: 2

2. Number of cases/rows: 483

3. Missing data codes

   None

4. Variable List

   • Column A – Species
   • Column B – level: species' vertical positions in the water column

5. Abbreviations used:

   • for level
     • B: benthic
     • P: pelagic +BP: bentho-pelgic

Hsuetal_dataset_Lw_ab.csv

1. Number of variables/columns: 3

2. Number of cases/rows: 129

3. Missing data codes

   None

4. Variable List

   • Column A – Species
   • Column B – mean_a: averaged coefficient a
   • Column C – mean_b: averaged coefficient b

Hsuetal_dataset_flow.csv

1. Number of variables/columns: 4

2. Number of cases/rows: 22

3. Missing data codes

   None

4. 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

Hsuetal_dataset_gd.csv

1. Number of variables/columns: 21

2. Number of cases/rows: 22

3. Missing data codes

   None

4. Variable List

   • Column A – Site
   • Column B to V – Code of the 21 survey sites