Sessile Benthic Marine Invertebrate Biodiversity at Ningaloo Reef, Muiron Islands, and Exmouth Gulf, Western Australia: A Review and Gap Analysis
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsI have finished reviewing the paper titled "A Comprehensive Review and Gap Analysis of Sessile Benthic Biodiversity at Ningaloo Reef, Muiron Islands, and Exmouth Gulf." The study examines biodiversity in these regions through an extensive literature review. This work is valuable because it compiles and harmonizes data from various sources in these areas. Such studies are essential for synthesizing existing knowledge and identifying gaps that can inform future research and ecosystem management. The results are significant and will likely attract considerable interest and citations.
Overall, the study is well-executed, from the compilation and analysis of data to the presentation, which includes clear photographs exemplifying key species, and well-written text. However, I have one major criticism regarding the discussion of the results, which I believe should be further developed (see the attached PDF for details). I also have a few minor comments and suggestions, which I have detailed in the PDF.
Comments for author File: 
Comments.pdf
Author Response
Thanks for your feedback, please find the responses below.
Reviewer 1.
Title
Including "Australia" at the end of the title would be beneficial. Some readers may not know where these locations are, and including it could help the paper appear in more bibliographic searches.
RESPONSE: We have added Western Australia to the title.
Abstract
Those who are not familiar with this area may not understand the connection between these locations and those mentioned in the title.
RESPONSE: We have revised the intro sentences to: “This paper provides a comprehensive review of sessile benthic biodiversity across three interconnected marine areas in Western Australia’s Gascoyne and southern Pilbara regions: Ningaloo Reef (a UNESCO World Heritage site), the nearby Muiron Islands to its north, and Exmouth Gulf to its east. The study aims to identify taxonomic and spatial knowledge gaps and establish a baseline biodiversity record for the broader region.”
Introduction
Line 57 This font is larger than the others.
Do you have any references that support or illustrate these management strategies?
RESPONSE: Font size has been changed to align with other text.
RESPONSE: The following reference was added to explain ecosystem management framework as applied in Western Australia: Fletcher, W, Shaw, J, Metcalf, S J, and Gaughan, D J. (2010), An Ecosystem Based Fisheries Management framework: the efficient, regional-level planning tool for management agencies. Marine Policy, 34 (6), 1226-1238.
Line 126 Could you explain how you approached this aim? It is difficult to understand how you achieved it.
RESPONSE: Thanks for this comment, this is more of a future objective rather than a specific aim so we have removed it as an aim and incorporated it into the discussion in lines 502-204.
Methods
Fig. 1 does not include the names of these regions or their borders.
RESPONSE: Figure one shows the Ninglaoo Reef and marine park boundaries along with Exmouth Gulf and the Muiron Islands. These are the regions of interest in this study.
Lines 173 - It would be better to use the recommended citation from the Worms website. 'WoRMS Editorial Board (2024). World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. Accessed xxxx-xx-xx. doi:10.14284/170'
RESPONSE: Citation revised as recommended.
Line 173 - Font size is different
RESPONSE: Font size corrected.
Line 178 - Please clarify this explanation. As it stands, it is difficult to understand.
RESPONSE: The sentence has been revised for clarity as follows “Morphospecies delineations were treated as verified records because these specimens had been assessed by taxonomic experts, who confirmed that they were morphologically distinct from described species.”
Table 1 - Why did you choose to group the species this way? Some are grouped by phylum (e.g., Porifera), while others are not.
RESPONSE: Grouping taxa into categories spanning Phylum (e.g., Porifera, Bryozoa), Subphylum (Tunicata), Class (Octocorallia, Zoantharia, Hydrozoa), and Order (e.g., Scleractinia, Actinaria, Antipatharia, Ceriantharia, Corallimorpharia) enabled analyses at ecologically meaningful levels, striking a balance between taxonomic resolution and ecological functionality. We have added the taxonomic level to Table 1 and ordered the taxa according to hierarchy to assist with interpretation and added this justification to the end of the methods section.
Line 193 - This could be due to your grouping, as you are comparing a phylum with groups of lower taxonomic levels. For example, if you compare Porifera and Cnidaria, Cnidaria is likely to be more well represented. You should justify or clarify this grouping rationale.
RESPONSE: Thanks for this valid comment – we have revised the result to not say the porifera were the “most speciose group” but rather to just focus on how many verified species of sponge were recorded.
Table 2 formatting
RESPONSE: Table 2 has been revised to improve formatting
Figure 2 - The decimal places on the y-axis are unnecessary.
RESPONSE: The figure has been updated to remove the decimal places and to convert the y-axis to proportions.
Lines 211 onwards - I believe that, as an interpretation of your results, this part is more suitable for a discussion section than for here.
RESPONSE: This section of the sponge results has been incorporated in to section 4.1 of the discussion.
Line 221 - A number should not be used to start a sentence. If you used a number at the start of a sentence, as you did in other sentences of the manuscript, spell out the number.
RESPONSE: This number has been written in full.
Line 232- I believe this should be placed in the discussion.
RESPONSE: These parts of the scleractinian results have been combined into relevant parts of section 4.1 and 4.2 of the discussion.
Line 257 onwards I believe this should be placed in the discussion.
RESPONSE: These parts of the octocoral results have been combined into relevant parts of section 4.1 and 4.2 of the discussion.
Figure 3 - You should reference this figure in the text. See the comment below regarding Figure 5.
RESPONSE: This Figure is now referred two four times.
Figure 4 - This figure is not referenced in the text. See the comment below regarding Figure 5.
RESPONSE: The sponge picture should have been placed before the corals, hence figure 5 is now figure 3 and is now cited in the text.
Figure 5 - This figure is referenced only as Figures 5A and 5B in the text. A reference to all photos of Figure 5 should be present in the text. This also applies to all other figures with photos. I believe including the figure number following the introductory sentence of the respective section could solve this issue. For example, "A total of 23 species of anemone from 15 families have been verified in the region. Examples are shown in Figure 5 (A–G)." In sum, every photo should be referenced in the text.
RESPONSE: Thanks for this advice, we have now included this “examples are shown…” statement in each section. In aligning figure citations, we realized that Octocorals were illustrated in the figure before Scleractinia, so we changed the order of that section in text. Similarly, we changed the order of Bryozoa, Tunicata and Hydrozoa to match the Figure plates.
Line 298 - ? and Line 317 – unclear wording
RESPONSE: Wording revised
Discussion - The discussion, particularly sections 4.1 and 4.2, is quite brief, as evidenced by the lack of references. For example, you should compare this areas' biodiversity with that of other areas and present some benefits of this biodiversity assessment, such as the discovery of bioactive compounds, improved ecosystem functioning, and better ecosystem management.
RESPONSE: These sections have now been expanded by including information that was previously in the results. However, we are loathe to do direct comparisons to species diversity beyond this region due to the inherent biases of the opportunistic sampling designs used in the various studies and the fact that few comparative studies documenting contemporary compilations of species-records from other regions exist.
Line 371 – strikethrough text
RESPONSE: Strikethrough text removed
Line 378 - Could you confirm this number (632)? As I understand it, 586 + 22 + 14 + 5 = 627. Have I overlooked something?
RESPONSE: The reviewer is correct, however we decided to remove this statement as we are treating Muirons separately from Ningaloo Reef in this study.
Additional RESPONSE: Overall editing, polishing and rewording has been undertaken to improve the clarity and flow of the manuscript.
Reviewer 2 Report
Comments and Suggestions for AuthorsReview for the paper “A Comprehensive Review and Gap Analysis of Sessile Benthic Biodiversity at Ningaloo Reef, Muiron Islands, and Exmouth Gulf” by Zoe Trisha Richards and co-authors submitted to “Diversity”.
The authors of this review conducted a comprehensive analysis of sessile benthic biodiversity within Ningaloo Reef, Muiron Islands, and Exmouth Gulf. The study focused on cataloging species, identifying taxonomic and spatial gaps, and establishing a foundational biodiversity baseline for the region. Notably, Ningaloo Reef emerged as a biodiversity hotspot, exhibiting a significantly higher species richness compared to Exmouth Gulf and the Muiron Islands. The research also identified critical gaps in existing biodiversity data, particularly in under-surveyed areas such as Ningaloo South and the Muiron Islands. These findings have important implications for biodiversity conservation strategies and management in the region.
Recommendations.
Abstract.
L 17. Consider replacing “30 meters depth” with “30 m depth”
Introduction.
L 47-48. The authors noted that the ecosystems under consideration "present stark contrasts in environmental conditions, oceanographic factors, and human impacts." However, the text does not provide data on the oceanographic regime at these sites, such as temperature and salinity fluctuations over seasonal and interannual scales.
L 72. The authors mentioned that the Muiron Islands are ecologically connected to Ningaloo Reef but have distinct soft coral communities. They should clarify what factors drive these differences in species composition compared to Ningaloo Reef.
L 104. The name of this RV should be in italics as accepted in scientific literature.
Materials and Methods.
L 129. The authors should include a brief justification for focusing on sessile benthic organisms from specific phyla (Porifera, Cnidaria, Bryozoa, and Chordata).
L 136. The authors should clarify why a depth limit of 30 m was chosen and whether deeper habitats in the region were excluded for logistical reasons or due to research objectives.
L 147. The authors should provide citations for these online data sources.
Results.
Currently, the paper is descriptive in nature. To achieve synthesis, provide a wider context, and improve data interpretation, it would be useful to conduct a statistical analysis based on the presence/absence matrix to reveal patterns in biodiversity across the study area. Calculating the Chao2 index for each site would also be useful.
L 214. Consider replacing “occurring Australia” with “occurring in Australia”
Figures 3-6. The authors should provide scale bars for these photographs if this information is available.
Discussion.
L 356. Consider replacing “30 meters” with “30 m”
L 357-389. The authors should provide more context on habitat differences among Ningaloo Reef, the Muiron Islands, and Exmouth Gulf, particularly with regard to environmental factors such as turbidity, depth variation, and sediment composition.
L 445. The authors noted that coral communities in Exmouth Gulf have lower growth and reproductive fitness compared to clear-water habitats. They should clarify what specific environmental factors in Exmouth Gulf contribute to these differences.
Citations should be formatted according to the Instructions for Authors and included as numbers in square brackets. References must also be formatted according to the MDPI standard.
Author Response
Thanks for your feedback. Please find our responses below:
Abstract.
L 17. Consider replacing “30 meters depth” with “30 m depth”
RESPONSE: Edit made
Introduction.
L 47-48. The authors noted that the ecosystems under consideration "present stark contrasts in environmental conditions, oceanographic factors, and human impacts." However, the text does not provide data on the oceanographic regime at these sites, such as temperature and salinity fluctuations over seasonal and interannual scales.
RESPONSE: This sentence has been revised to give examples of these differences – more details about these points and references are in the three paragraphs that follow.
L 72. The authors mentioned that the Muiron Islands are ecologically connected to Ningaloo Reef but have distinct soft coral communities. They should clarify what factors drive these differences in species composition compared to Ningaloo Reef.
RESPONSE: Additional information has been added to this paragraph to explain that it is likely the higher turbidity levels, nutrient levels and lower wave impact that drives these differences. Plus too extra references have been added - Lowe et al., 2015; Vabderklift et al., 2020).
L 104. The name of this RV should be in italics as accepted in scientific literature.
RESPONSE: Edit made
Materials and Methods.
L 129. The authors should include a brief justification for focusing on sessile benthic organisms from specific phyla (Porifera, Cnidaria, Bryozoa, and Chordata)
RESPONSE: We focus on these groups due to their functional role as habitat providers and their other ecosystem services such as nutrient cycling. To clarify this, we have added further justification to the introduction.
L 136. The authors should clarify why a depth limit of 30 m was chosen and whether deeper habitats in the region were excluded for logistical reasons or due to research objectives.
RESPONSE: The 30 m depth contour was chosen due to the geomorphological constraints of Exmouth Gulf, which lacks habitats beyond this depth. This boundary enables a comparable sampling effort using scuba across regions while focusing on ecologically significant shallow reef communities. This extra information has been added to the methods.
L 147. The authors should provide citations for these online data sources.
RESPONSE: Citations for ALA, iNaturalist, DBCA, PMCP and WAMSI sources have been included.
Results
Currently, the paper is descriptive in nature. To achieve synthesis, provide a wider context, and improve data interpretation, it would be useful to conduct a statistical analysis based on the presence/absence matrix to reveal patterns in biodiversity across the study area. Calculating the Chao2 index for each site would also be useful.
RESPONSE: The data underpinning this study are derived from opportunistic specimen collection efforts rather than systematic, quantitative surveys. As such, the dataset reflects uneven and non-standardized sampling effort across sites, which limits the reliability of site-based comparisons and quantitative metrics like the Chao2 index. Undertaking statistical analyses based on presence/absence data in this context risks generating misleading interpretations driven more by sampling bias than true ecological patterns. Our focus is therefore on providing a comprehensive descriptive synthesis of available records to establish a baseline for future, more systematic and quantitative biodiversity assessments. Further reinforcement of this has been added to section 4.4 to prevent mis-interpretation of the data.
L 214. Consider replacing “occurring Australia” with “occurring in Australia”
RESPONSE: Edit made
Figures 3-6. The authors should provide scale bars for these photographs if this information is available.
RESPONSE: Scale bars are not available for these field photographs.
Discussion.
L 356. Consider replacing “30 meters” with “30 m” L 357-389. The authors should provide more context on habitat differences among Ningaloo Reef, the Muiron Islands, and Exmouth Gulf, particularly about environmental factors such as turbidity, depth variation, and sediment composition.
RESPONSE: edit made and additional information added.
L 445. The authors noted that coral communities in Exmouth Gulf have lower growth and reproductive fitness compared to clear-water habitats. They should clarify what specific environmental factors in Exmouth Gulf contribute to these differences.
RESPONSE: Clarification added to this sentence to clarify that this is due to the elevated turbidity
Citations should be formatted according to the Instructions for Authors and included as numbers in square brackets. References must also be formatted according to the MDPI standard.
RESPONSE: Citations now numbered.
Additional RESPONSE: Overall editing, polishing and rewording has been undertaken to improve the clarity and flow of the manuscript.
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsI have finished reviewing the revised manuscript, ‘Sessile Benthic Marine Invertebrate Biodiversity at Ningaloo Reef, Muiron Islands, and Exmouth Gulf, Western Australia: A Review and Gap Analysis’. The authors have addressed all my comments and suggestions. Where they did not adopt a recommendation, their explanations were satisfactory. The revisions to the text were well executed, and these improvements have clearly benefited the manuscript.
