the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Standardized datasets of Brazilian reef diversity in space and time
Abstract. The Brazilian marine biogeographical province (SW Atlantic) hosts coral and rocky reefs that cover ~27 degrees of latitude and are distributed along a relatively narrow continental shelf and four oceanic islands and archipelagos. The broad gradients in temperature, productivity and salinity shape patterns of biodiversity and lead to distinct local communities within the province. Although existing research has helped to unveil spatiotemporal patterns of marine diversity in this province, data availability and scale have limited broader inferences on the main processes shaping biodiversity. Here, we bring together 16 datasets (n = 11 for reef fish, n = 5 for benthic reef organisms) comprising 22 years of research conducted across most of the Brazilian province. These datasets are unprecedented in terms of temporal, spatial, and taxonomic coverage. For example, eight datasets (six for reef fish, two for benthos) span seven (fish monitoring in Rio Grande do Norte) to 18 years (fish monitoring in Arraial do Cabo, Rio de Janeiro) of survey data. Also, these datasets contain data collected in priority areas for conservation in the Brazilian province, such as the Abrolhos Bank and the Trindade island. The data comprise detection and fish count/benthic cover data for 24,498 sampling events deployed at 55 locations, formatted according to the Darwin Core Standard, being therefore interoperable with other existing datasets. The 11 fish datasets comprise the detection and counting of 361 fish taxa (312 identified at species level, 49 identified at genus, subfamily and family) from 178 genera, 71 families and 2 classes (Teleostei and Elasmobranchii). The five benthic datasets comprise the description of the detection and cover of 81 taxa, 82 genera, 68 families, 15 classes, and 4 kingdoms (Animalia, Bacteria, Plantae, Chromista). By making this an open-access resource, we share with the public the result of two decades of federal and state funding for scientific research on Brazilian reefs.
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Status: open (until 21 Nov 2024)
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CC1: 'Comment on essd-2024-244', Miguel Mies, 16 Oct 2024
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review attached.
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RC1: 'Comment on essd-2024-244', João Feitosa, 22 Oct 2024
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The manuscript “Standardized datasets of Brazilian reef diversity in space and time”, submitted to Earth System Science Data, makes an exciting contribution to the field of reef ecology while falling within the scope of Earth System Science Data. The paper presents an outstanding collection of 16 datasets comprising both benthic and reef fish communities, spanning thousands of kilometers off the Brazilian coast while encompassing decades; all of the datasets are standardized as Darwin Core Archives, following the Global Biodiversity Information Facility recommendations, an excellent alternative for data sharing. Kudos to the authors for putting these datasets together and disseminating them to the scientific community; I am sure these will be put to excellent use by researchers worldwide. The manuscript per se is generally well-written, but I would like to point out some amendments for improvement. I recommend it for publication after a minor review, and the points I find necessary to be addressed can be found below.
Major comments
1 - Some Brazilian reef fish species have been historically misidentified as Caribbean species (e.g., several Labridae: Scarini species), and other very abundant fish were only described recently (e.g., Malacoctenus zaluari, in 2020). As the authors dealt with data as old as 2001, how did they standardize historical fish data for the species described/revalidated after sampling was performed? Supposing it was impossible to accomplish such standardization, authors should include caveats for these older datasets. If that is the case, I also suggest including a table indicating which taxa are likely missing from older samples as supplementary material; that way, users can identify samples where those taxa are truly absent.
2 - After downloading and inspecting some of the datasets, I found they had issues in meeting the standards of a Darwin Core Archive. I have checked some of the datasets with the data validator tool at the Darwin Core Archive Assistant (available @ https://www.gbif.org/tools/data-validator), and at least two datasets had problems detected (from about seven randomly chosen to check, out of the 16 datasets). The dwca-sisbiotamar_bentos-v2.1.zip and dwca-reefsyn_abrolhos_benthos-v2.2.zip had missing metadata (Error: "cvc-complex-type.2.4.b: The content of element 'project' is not complete. One of '{personnel}' is expected." for both files). I suggest the authors review all datasets carefully for these metadata omissions and meet Darwin Core Archive standards; I am sure these were minor omissions.
3 - I had trouble reading a particular dataset (dwca-reefsyn_fishes-v2.2, downloaded on Oct 22nd). I tried reading it both with the "flinch" R package and using the .txt measurements file. In both methods, the column "measurementType" is empty, and the column "measurementValue" seems to contain the misplaced content of what should be in the column "measurementUnit". I do not know if it was a repository/version problem, but the authors would not have much trouble correcting this since I could find the raw data for this dataset on the GitHub page provided. However, please review carefully the files provided.
Minor comments
Lines 55-60 - The transition between paragraphs about the working group and DCS could be more smooth. The authors should start the following paragraph by stating the importance of standardizing shared data and then introducing the reader to the DCS.
Figure 1 is unnecessary. All institutions are mentioned in the authors' affiliations, and Fig1B is not described at all (where does the data for the word cloud come from?). Actually, the authors have yet to call for Fig. 1 in the text. I recommend removing this image.
Lines 103-105 - Are these codes used in the datasets? I could not find them. They could be used to code "id" columns or else be removed from the text.
Figure 2 - This image's color codes could be more precise to distinguish. The authors should include different shapes for points (preferred) or change the colors (results will likely not be color-blind inclusive). Authors could also include the Roman numbers referring to datasets in the figure itself instead of using a color legend (it would be easier to read). I recommend referencing the Brazilian States in the maps (since authors often refer to them in the text).
Line 138 - "n = 20,561 for fish, and n = 3,937 for fish", please correct.
Table 1 - The values of Latitude and Longitude in this table are hard to follow. In each cell, I assume you mean "from, to", but the table formatting is not of any help. I suggest you include multiple columns for each metric, such as "Southernmost latitude" or "Northernmost latitude," or apply equivalent terms. Instead of using "Transect/plot" for all scales, why not use "transect" for visual surveys and "plot" for video plots? It does not make sense to me. The same is seen in Table 2, but it is even more ambiguous since it is given "Plot/point" for all photoquadrat datasets; it leaves the reader wondering whether the number of samples represents each quadrat or the number of points where organisms were identified.
Figure 3 - This image is the best to describe the temporal span of the datasets, but it could be improved. The cumulative number of sampling events is of little interest to readers. However, this image could provide more information on the beginning/end of a given dataset (much like sampling programs are already represented). It would be great if this figure could be placed earlier in the manuscript; I would suggest a composite image with the maps so a user looking for particular data in space and time could locate the dataset of interest in a breeze.
Figure 5 could inform the readers of the data type displayed in each dataset's "measurements" columns.
Line 374 - correct "Antias salmopunctatus" to "Anthias salmopunctatus"
Figure 6 legend - correct "foreach"
Taxonomic coverage - I suggest the authors review this section, particularly the species list. I found some errors for fish (e.g., "Goblioclinus kalisherae" [an extra "l"]; Anthias is missing) and for the benthic dataset, I suggest you replace the Division/Phylum Ochrophyta for the currently accepted Division/Phylum Heterokontophyta (see Guiry, M.D., Moestrup, Ø. & Andersen, R.A. (2023). Validation of the name Heterokontophyta. Notulae Algarum. 297: 1-5).
Conclusions - As an excellent data paper, the authors should better disclose their datasets' significance and applications to the current reef ecology knowledge. Brazilian reefs are singular in their morphological and geological formations, habor a fauna rich in endemics but with lower species diversity in a reef system that is also unique in its conditions: being highly turbid and dynamic, it differs greatly from the predominantly oligotrophic reefs elsewhere. By making these datasets available, the authors share unique data from a neglected system for researchers worldwide to account for in their work, which is indeed remarkable.
Additional Suggestions
The authors make a major contribution to reef science by sharing their excellent datasets. However, they left me wondering if a deeper detail could also be provided for future ecological studies applying their data: reef fish experts like myself often collect habitat descriptors while censusing fish, frequently offered as covariates in analytical procedures. Do the authors have this kind of data, and can those be included in the paper?
Citation: https://doi.org/10.5194/essd-2024-244-RC1
Data sets
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset XIV: Benthic communities from the Brazilian province (2.0) A. W. Aued et al. https://doi.org/10.25607/YR6DKC
Long-term Ecological Monitoring Research Brazilian Oceanic Islands (benthic community) (1.0) C. A. M. M. Cordeiro et al. https://doi.org/10.25607/YRFTHS
Long-term Ecological Monitoring Research Brazilian Oceanic Islands (reef fish) (1.0) C. M. M. Cordeiro et al. https://doi.org/10.25607/ROV4OR
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset II: Abrolhos Bank monitoring (1.1) R. Francini-Filho https://doi.org/10.25607/JQWG40
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset XII: Benthic communities’ monitoring in Abrolhos Bank (2.1) R. Francini-Filho https://doi.org/10.25607/JJM2EH
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset IX: Trophic interactions along the Western Atlantic (2.0) G. O. Longo and K. Y. Inagaki https://doi.org/10.25607/7VOMV6
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset XVI: Benthic communities from Rio Grande do Norte (2.0) G. O. Longo and N. C. Roos https://doi.org/10.25607/C2C37E
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset XI: Rio Grande do Norte monitoring (2.0) G. O. Longo et al. https://doi.org/10.25607/2DOYBV
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset X: Alcatrazes monitoring. Version 2.0 T. C. Mendes et al. https://doi.org/10.25607/4e5fuo
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset I: Fish communities from the Brazilian province (3.2) R. Morais et al. https://doi.org/10.25607/7NXV5V
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset V: Fish assemblages from Trindade and Martin Vaz (2.0) H. T. Pinheiro https://doi.org/10.25607/VVJWCV
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset VII: Fish assemblages from Guarapari (2.1) H. T. Pinheiro and T. Simon https://doi.org/10.25607/QYFWLO
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset VIII: Fish assemblages from Southern Espírito Santo (2.1) H. T. Pinheiro and T. Simon https://doi.org/10.25607/E8DONT
ReefSYN | Standardized datasets of Brazilian reef diversity in space and time - Dataset VI: Santa Catarina reef fish monitoring (2.0) J. Quimbayo et al. https://doi.org/10.25607/YS9KOA
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