Skip to main content
PLOS ONE logoLink to PLOS ONE
. 2024 Aug 8;19(8):e0296188. doi: 10.1371/journal.pone.0296188

Diversity patterns of the South African azooxanthellate scleractinians (Cnidaria: Anthozoa), with considerations of environmental correlates

Zoleka N Filander 1,2,*, Kerry J Sink 3,4, Marcelo V Kitahara 5,6, Stephen D Cairns 6, Amanda T Lombard 4
Editor: Carlo Nike Bianchi7
PMCID: PMC11309500  PMID: 39116158

Abstract

Azooxanthellate scleractinian corals, a group of species that lack a symbiotic relationship with dinoflagellates, are influenced by environmental variables at various scales. As the global commitment to sustainably manage ocean ecosystems and resources rises, there is a growing need to describe biodiversity trends in previously unsampled areas. Benthic invertebrate research in South Africa is a developing field, and many taxa in deep water environments remain inadequately characterized. Recently, the South African azooxanthellate scleractinian fauna was taxonomically reviewed, but their distributional correlations with physical parameters have not been studied. Here we aim to understand the biodiversity gradients of the South African azooxanthellate coral fauna by analysing the environmental correlates of museum samples. The associated coordinate data were georeferenced and depth obtained from a national bathymetric dataset, prior to undertaking a multivariate analysis. This analysis encompassed several steps, including the grouping of the longitude and depth data (environmental data), identifying families characteristic of the group variability, and examining the correlation of the associated data with the biological data. Additionally, the analysis involved quantifying diversity patterns along the environmental gradients. Overall, our results confirmed two longitudinal groups (eastern margin [Group A] vs southern and western margin [Group B]) and 11 depth categories represented within two bathymetric zones (shallow [50–200 m] and deep [300–1000 m]). Caryophylliids, flabellids, and dendrophylliids contributed the most towards distinguishing longitudinal and depth gradients. Both abiotic variable (longitudinal and depth) partially explained coral distribution patterns, with depth being highly correlated to the species variation observed. Data limitations within our data set resulted to unexplained variance, however, despite these limitations, the study demonstrates that historical museum samples provide a valuable data source that can fill research sampling gaps and help improve the understanding of biodiversity patterns of the coral fauna in under sampled marine ecosystems.

1. Introduction

The distribution of azooxanthellate corals, a group of scleractinian species that lack a symbiotic relationship with photosynthetic dinoflagellates, is influenced by environmental variables at various scales [15]. Physical and chemical oceanographic factors, as well as geomorphologic settings affect food supply and, consequently, benthopelagic coupling [3]. Overall, depth might be used as a variable linked to several oceanographic factors that influence species distributions. For example, coral species have preferred thermal ranges [4], and a global azooxanthellate coral richness trend has been documented between 200 and 1000 m. This depth range often coincides with shelf and slope features, which may provide suitable substrate for larval settlement and habitats for azooxanthellate coral species to colonise [3, 6]. Furthermore, long-term environmental stability appears to be important for the occurrence/distribution of deep water stony coral species. In addition to the temporal and spatial stability of an environment, it is well established that life history patterns, including reproduction strategies and relationship to substrate, are of utmost importance for a species’ distribution [7]. For instance, attached deep water scleractinians require consolidated substrates to survive, whilst unattached forms are found on or in unconsolidated sediments [2, 3].

Given the difficulty of sampling in deep-water marine ecosystems, the mapping and classification of biodiversity into spatial units (which then act as surrogates for unmapped biodiversity) is a common approach in spatial planning [812]. Considering the growing concern regarding declining ocean health, voluntary commitments to reach a national 30% area protection by 2030, and the United Nations call for better ocean governance [1315], such spatial classifications are powerful tools to guide conservation and management strategies to support the achievement of the United Nations 14th Sustainable Development Goals (SDGs).

Despite early marine collections along South Africa’s shores in the 1700’s [16, 17], ocean resource management is still constrained by the poor state of knowledge of key invertebrate species, particularly offshore [18]. Endeavouring to address such species data gaps, local research advancements have recently been initiated by re-examining natural history collections [1923]. Some of these studies have informed the national map of marine ecosystem types developed by Sink et al. [18, 24] for the National Biodiversity Assessment (NBA). The NBA used pelagic and benthic data, including biological information (macrofauna, epifauna, and fish) to produce an expert-driven ecosystem type map for national assessment and reporting. Absent, however, from this national spatial classification map is a holistic consideration of the South African azooxanthellate scleractinian fauna, as their distribution patterns had not yet been investigated. The NBA does however report on some distribution records of potential Vulnerable Marine Ecosystem indicator taxa, which includes records of two reef-building azooxanthellate coral taxa (Dendrophylliidae [25] and Caryophylliidae [26]).

Cairns [6] grouped the available literature on azooxanthellate Scleractinia into broad geographic regions, although not a biodiversity analysis, this output served as a starting point for emerging taxonomists in the field. Cairns and Keller [27] summarised depth affiliations within the southwest Indian Ocean, in which South African taxa reported off the eastern and southern margins were represented. Apart from these two publications [6, 27], the South African azooxanthellate Scleractinia distribution pattern, in relation to physical variables, has not been investigated. This study therefore aims to understand the biodiversity gradients of the South African azooxanthellate coral fauna by analysing the environmental correlates of museum samples. To achieve this, an approach was needed to source and standardize such data from 11 surveys, including those conducted a century ago.

2. Material and methods

Data considered for this study were based on a subset of species distribution records for the South African azooxanthellate scleractinian fauna recently reported by Filander et al. [28]. Samples without co-ordinate were omitted from the Filander et al [28] dataset, resulting in 761 occurrence records (Fig 1 and S1 Appendix: Occurrence data). These coral occurrence data were predominately collected during six historical dredge surveys undertaken between 1898 and 1990, listed below with the vessel or expedition name and depth range represented by the collection in parenthesis. These were Research Vessel (RV) Anton Bruun [50–1000 m], Benguela IV [100 m], RV Meiring Naude [50–1000 m], RV Pieter Faure [50–400 m, and 1000 m], RV Sardinops [50 m], and University of Cape Town Ecological Surveys [50–300 m and 500–600 m]). The recent surveys undertaken in the 21st century are represented by two trawl (NANSEN [50–200 m] and Department of Environment, Forestry and Fisheries/South African Environmental Observation Network demersal surveys [50–1000 m]) and three dredge surveys (ACEP: Deep–Secrets [200–500 m, 700 m and 1000 m]; IMIDA [100–200 m] surveys and Department of Environment, Forestry and Fisheries [200–500 m]).

Fig 1. Study domain and spatial coverage of the coral records forming the basis of the analysis.

Fig 1

The historical data sets had a varying degree of reliability in terms of associated data and, therefore, required data sourcing in some cases and validation in others. Consequently, all the occurrence records were first geo-referenced using ArcGIS 10.1. This step involved overlaying the coral point data on the NBA marine ecosystem types map [18, 24]. Records that were recovered on the coastline were moved to the closest polygon boundary of the ecosystem types with the near command in ArcGIS 10.1. This process was particularly beneficial for the Pieter Faure stations, which had positions in degrees magnetic North (not true North); whereby land bearings were used as a reference. In the next step, the spatial join tool was used to assign depth in relation to the most recent national bathymetric dataset [29] to each of the coral records, irrespective of whether depth was reported in the coral archive data set or not. The reason for this change is that modern mapping techniques have significantly improved historical bathymetric data, which were often either missing or erroneous [30]. Depth contours started at 50 m and were plotted at 100 m isobath intervals to a maximum of 1000 m, then further grouped according to shallow or deep zone. The resulting data set consisted of 95 of the total 108 azooxanthellate scleractinian species known from South Africa [28].

2.1. Assumptions and sampling biases

Over 80% of the resulting data are of historical origin, and therefore pose some limitations. One of these limitations is sampling coverage bias, given that past national marine surveys focused mainly on accessible nearshore areas (intertidal ‐ ~40 m), whilst sampling in areas beyond the continental shelf [~ 50–150 m on the eastern margin, which progressively gets deeper (~ 200 m <) towards the western margin] mostly relied on international surveys (the Pieter Faure expeditions being an exception) [17]. These historical surveys represent decades of sampling effort but were not systematic and primarily offer presence data, with a degree of uncertainty regarding absence. The reliability of absence data in historical datasets is inherently non-linear and leads to acknowledged challenges in interpretation. This fit–for use limitation is acknowledged. However, in order to incorporate the occurrence data into the multivariate biodiversity analysis, it was necessary to make two assumptions. The first assumption involves presenting the data as presence–absence, and the second assumption involves extrapolating the occurrence of historical records to the modern day. In terms of the latter, this is a bias because anthropogenic activities (e.g., trawling) may have altered these habitats and some species may no longer be present in the historically noted area. Nonetheless, depth and co-ordinate information are the only two variables commonly associated with such datasets, noting these may be unreliable in some instances (the Pieter Faure collection).

Furthermore, the data preparation methodology does not follow the interpolation of the presence-absence matrix (if species occur between two extreme points, then occurrence is assumed in between) as conducted in preceding marine benthic invertebrate studies based on museum specimens [2123]. This approach would have yielded unrealistic conclusions in the absence of fine-scale seabed data- as substrate type is one of the primary drivers of coral settlement [3]. As substratum data (grab samples and multibeam do not sufficiently cover the available coral samples [18, 31] substrate data were not considered to support interpolation techniques. The only two variables considered in this paper are longitude and depth (S1 Appendix: Occurrence data).

2.2. Data analysis

A presence-absence matrix (S1 Appendix: presence-absence) of the coral occurrence data was compiled and all analyses were undertaken using the PRIMER 7 software package [32], with the PERMANOVA+ add on [33]. The matrix, consisting of 488 columns (stations/samples) and 95 rows (species), was converted to a resemblance matrix. The associated higher taxonomic classifications of these resulting species identifications were thereafter extracted from the World Register of Marine Species batch match online function [34] (S1 Appendix: Taxonomic attributes). Owing to the patchy nature of the data set, in which 30 species were represented by only one sample and 22 species by less than ten samples (S1 Appendix: Number of records per species), the Gamma+ dissimilarity matrix was selected- a measure based on average taxonomic distinctiveness. [35, 36]. This dissimilarity matrix is based on the average taxonomic distinctiveness (ATD) measure, which used the cophenetic distances derived from the phylogeny clades established in Kitahara et al. [37] and Stolarski et al. [38] (e.g. “Basal”, “Complex”, and “Robust”) (S1 Appendix: Taxonomic attributes). Owing to limited resolution regarding species relationships below family level, phylogenetic scores were not assigned beyond the known molecular clades. It is important to note that ATD is a diversity calculation method that considers the distance between each species and its closest relative outside the group. The resulting ATD value provides an estimation of the group’s evolutionary uniqueness, with higher values indicating greater distinctiveness. Such a procedure allowed for biotic distances among samples to be quantified even when they had zero or very few species in common [35].

The sample-specific data also required data preparation, which followed the biological data assessment. Longitude and depth are the two sample-specific variables considered to determine the environmental settings of the South African maritime domain (S1 Appendix: Sample-specific abiotic data). For instance if a sample was recorded at a 31° longitude, then it was collected in the Indian Ocean and influenced by the Agulhas Current. Each abiotic parameter was classified accordingly, before investigating the independent longitude and depth gradients (S1 Appendix: Sample-specific abiotic data). To classify the longitudinal data as a factor, an auto select k-R cluster mean analysis was run on the normalized longitudinal data [39]. A draftsman’s plot was produced to identify the number of longitudinal groups present and validate the cluster groups present (see Fig 2). On the other hand, the depth readings were grouped according to shallow (50–200 m) vs deep (300–1000 m) zones.

Fig 2.

Fig 2

A: The 50x50 km gridded cells with samples in relation to the longitudinal groups defined by the k-R cluster analysis. Group A represents samples collected off the eastern margin and Group B are samples collected off the southern and western margins. B: The draftsman’s plot results are also shown.

A standard approach was undertaken to investigate changes in family attributes along the longitudinal and depth gradients, whereby a SIMPER analysis was performed to evaluate respective contributing taxa [40]. Sampling effort (denoted by N), species richness (denoted by S), Shannon index (denoted by H’loge), and taxonomic distinctiveness (denoted by delta+) across the longitudinal and depth groups was quantified. The former was investigated by assigning coral records to 50x50 km grids created with the fishnet ArcGis function, whereby the grid size was guided by the boundary breaks of the k-R mean cluster groups and therefore provides information on spatial coverage of each group.

Subsequently, a RELATE routine was undertaken to evaluate if the combined longitude and depth spatial gradients correspond with those inferred from the coral species patterns [41]. Here we used the Gamma + matrix in relation to the associated depth and longitude information, which was normalised into a Euclidean distance resemblance matrix. The RELATE routine calculated a Spearman’s ρ rank correlation coefficient between all elements of the coral assemblage and environmental variable resemblance matrices, followed by a permutation test. Following this, a biota and/or environment matching (BEST) test was conducted to confirm which variable contributed the most to sample statistic given by the RELATE results [42]. A species accumulation model was lastly produced to assess how well the observed azooxanthellate stony coral data represents South Africa’s predicted coral diversity.

3. Results

3.1. Longitudinal gradient

The k-R (non-hierarchal) cluster analysis yielded two longitudinal groups (R = 0.94), whereby Group A encompasses samples from the eastern margin of South Africa and Group B are samples from the southern and western margins (Fig 2). The SIMPER results showed a distinction between families contributing the most to the cluster identities. Three dendrophylliids contributed the most to the similarity within group A; and the same number of caryophylliids defined Group B.

Overall, the number of samples between the two groups varied, whereby Group A (eastern margin) had more than twice the number of samples than Group B (southern and western margin) (Table 1). Contrary to this, the related area (number of grids) representing these samples was larger in Group B than in Group A (Table 1). Diversity followed the same pattern of higher measures in Group A as compared with Group B.

Table 1. Summary of sampling effort in relation to longitudinal gradient.

k-R cluster group Number of samples Number of 50x50 km grids Species richness Shannon’s Index Delta +
A (eastern margin) 569 37 86 3.964 90.907
B (southern & western margin) 192 43 37 3.249 89.289

3.2. Depth gradients

A direct relationship between the number of samples (N), species richness (S), and depth was observed (Fig 3). The highest number of samples and observed species richness occurred between depths of 50 and 200 m, with the greatest species richness and sample count recorded at 50 m. The same two measures (S and N) fluctuated in the deep zone (300–1000 m) where the highest coral diversity measures (S and N) were recorded at 1000 m and the lowest at 800 m. Average taxonomic distinctiveness (denoted by delta +), which takes into account species phylogeny, did not show a clear pattern in coral diversity with depth and species diversity was relatively constant from 50 to 200 m. However, according to this measure, coral diversity was slightly higher at 1000 m despite the usage of a smaller number of samples from this depth (42 samples compared to 269 samples at 50 m). Eight taxonomic families were recorded at 1000 m, while only seven were recorded at 50 m. In contrast, however, the conservative Shannon diversity index mirrored the pattern of species richness with depth (Fig 3).

Fig 3. The relationship between number of coral samples (N) and species richness (S) in conjunction with the average taxonomic distinctiveness (delta+) and Shannon diversity (H’loge) index measures across depth gradients.

Fig 3

The x-axis shows samples represented in depth values in metres and the y-axis shows values that represent diversity measures in arbitrary units. The inset shows the Shannon diversity (H’loge) index repeated on a Y axis of 1–4.

The SIMPER results of the coral species data according to family suggested that the caryophylliids, dendrophylliids, and flabellids were the main contributing taxa towards both shallow (50–200 m) and deep (300-1000m) stations. Whilst all three families collectively contributed towards the bathymetric zone comparisons (shallow vs deep) at a 70% cut, the Caryophylliidae representatives were more abundant at the deeper stations compared with the Dendrophylliidae and the Flabellidae in the shallow stations (S1 Appendix: Depth zones SIMPER results).

3.3. The correlation of sample-specific variables (longitude and depth groups) with coral distribution patterns

The RELATE results showed a marginal correlation (Rho-value = 0.087) but a significant difference (p-value = 0.001) when comparing the coral patterns modelled by the Gamma+ resemblance matrix with that of the Euclidean distance matrix (environmental variables ‐ longitude and depth). It is important to note that the null hypothesis in the RELATE function is that there is no correlation. Thus, although the correlation is closer to zero (unexplained variance), the p-value confirms that longitude and depth are good predictors for the coral distribution patterns. The BEST results further confirmed the influence of depth with an independent correlation value of 0.094, whilst both environmental parameters (longitude and depth) accounted for a correlation value of 0.097.

The majority of the species accumulation curves did not reach a plateau (Fig 4). All seven estimated curves, along with the observed or sampled species, started with a steep slope and indicated a rapid increase in the number of species observed with increasing sampling effort. Only two (MM and UGE) of the seven estimator curves followed the species observed pattern (Sobs), which appears to be levelling off as the sampling effort increases (Fig 4).

Fig 4. Species richness accumulation curve showing the species observed (Sobs = blue upright triangle) in relation to five estimators (Chao 1 = red downward triangle, Chao 2 = green square, Jacknife 1 = pink diamond, Jacknife 2 = blue circle, Bootstrap = grey cross).

Fig 4

Two pairs of curves overlap, whereby the UGE estimator curve follows the same pattern as the Sobs and the Chao1 has the same pattern as Chao 2.

4. Discussion

The results of the multivariate analyses indicate that the sample-specific factors (longitude and depth) play a significant role as predictor variables for the diversity of azooxanthellate Scleractinia corals. However, there is still some unexplained variation in the data. Further investigation revealed variability among the established longitude and depth groups, and specific coral families contributing to this observed pattern were identified.

An increasing species turnover along the west to east gradient was detected. Such distributional patterns have long been reported for other South African marine invertebrates fauna (e.g., [21, 23, 43]), suggesting that different oceanographic conditions are influencing the South African marine fauna. The accompanying current regimes may also govern these contrasting species profiles across the region. Thus, although the two longitudinal boundaries (Group A = eastern margin vs Group B = western margin) established by the k-R mean cluster analysis do not conform to the previously proposed oceanographic boundaries [44, 45], the margins correspond to varying oceanographic variables and currents, whereby the eastern margin (Group A) is situated within the oligotrophic waters of the Indian oceanic basin and influenced by the western boundary Agulhas Current. Interestingly, Group B encompasses the southern and western margins located in both the Indian and Atlantic basins respectively. At the southern margin, the Agulhas Current retroflects, moving away from the shelf, and introduces Indo-Pacific waters into the Atlantic Ocean, the latter being regulated by the northward flowing Benguela Current [46].

The SIMPER results detailed a clear taxonomic/ family distinction within these two longitudinal groups. Dendrophylliids contributed the most to the eastern margin group whereas caryophylliids characterised the western and southern fauna. Additionally, the exclusivity in families found between Group A and Group B aligns with the proposal that species have a temperature threshold [3, 6]. The physiological characteristics of azooxanthellate coral species are indeed influenced by the properties of ambient water temperature [47, 48]. For example, an ex-situ experiment undertaken on the reef-building corals D. pertusum and Madrepora oculata revealed that they respond differently when exposed to three temperatures (12, 9.0, and 6.0°C; [49]). The respiration response rates varied; M. oculata declined whereas D. pertusum was not affected by temperatures being lowered. Two other physiological responses (calcification and dissolved organic carbon) were measured, and neither showed a consistent trend when comparing the two species. Thus, species belonging to different families or even congeners are expected to exhibit varying thermal tolerance.

The recovered species longitudinal pattern of low sampling effort in Group A (eastern margin) but higher number of records and diversity observed herein, was particularly surprising as the western margin (which contributes to Group B) has a higher historic sampling effort [17]. The greater presence of coral species in the eastern Agulhas region (Group A) may be explained by the heterogenous seabed provided by the increased abundance of mesophotic reefs, submarine canyons and mosaic ecosystem types [18, 24]. Whilst the incising submarine canyons along the eastern continental margin [5053] may also give rise to a heterogenous environment, localised studies that classify different substrate types within and between canyons are needed to confirm this hypothesis [54]. Even though the Benguela Current in the South Atlantic (influencing the western passive margin) is unique in its interactions with the western boundary Agulhas Current [44], much of this region has a unconsolidated seabed, resulting in a more homogenous environment [31, 54, 55]. Thus the unconsolidated seabed, superimposed with the slow current speed (< 3 m/s) may be a constraint for coral presence. The presence of scleractinians is however influenced by multiple factors operating at different scales, and it is crucial to consider species-specific regional adaptation abilities to environmental gradients (dissolved oxygen) ‐ even for cosmopolitan species [56, 57]. Nonetheless, the prominence of anthropogenic activities that interact with the seabed in the Southern Benguela Upwelling area [58, 59] cannot be overlooked and may also influence the low number of species records in the area.

The southern margin is a unique area that exhibits high endemism [17]. In this region, the Agulhas Current injects Indo-Pacific waters into the Atlantic, down to depths of 2000 m in the form of anticyclonic rings [60], before retroflecting eastwards towards the Southern Indian Ocean Gyre and the Antarctic circumpolar current [61]. Schouten et al. [62] noted that the location of the retroflection loop is variable, but still within the southern region. Nonetheless, the Agulhas transport is estimated to increase from 65 Sv (1Sv ‐ 106 m 3s-1) at 32°S to 95 Sv at the southern tip of South Africa, as it breaks away from the shelf [63, 64]. Thus, the unpredictable behaviour and velocity of the Agulhas Current make this area challenging for sampling and, therefore, the low number of records here may be attributed to limited sampling effort.

The species depth gradient results complement the longitudinal species patterns whereby the univariant biodiversity measures peaked at 50 m, which corresponds to the accessible eastern margin of the South African continental maritime domain. In addition to the shelf being shallower (~ 50–150 m) and more accessible, the western boundary Agulhas Current (characteristic of this area) has been linked to the highly diverse biological properties in the Southwest Indian Ocean, where eddies can trap and transport material over long distances [65]. These complex oceanographic eddies can upwell deep nutrient-rich waters through surface divergence mechanisms [65], creating environments that favour the continuous inflow of potential coral food sources. Thus, these observations may provide grounds for a hypothesis to explain why azooxanthellate corals have a higher presence within this area. The multivariate taxonomic average distinctiveness measure (denoted by delta +) showed diversity along the depth gradients (50 to 1000 m) to be highest at 1000 m, in which eight of the 11 known South African coral families are represented. This result marginally aligns with the knowledge that the global azooxanthellate stony coral pattern has overall higher species diversity between the 200 and 1000 m [6]. Irrespective, the SIMPER analysis distinguished three major families to contribute to bathymetric zone delineation. The deeper depths (300–1000 m) were characterized by caryophylliids and flabellids, and the shallow zone (50–200 m) by dendrophylliids only. These results support the known depth affiliations of these families, in which Dendrophylliidae species occurrence is reported to peak at shallower depths (50 to 300 m) [66] and extant species of Caryophylliidae and Flabellidae are more prominent in the deeper waters (more than 200 m) [37].

The two sample-specific (depth and longitude) data sets were applied in combination to extrapolate ocean basin properties (nutrient content, salinity, temperature, etc.), which characterise the oceanographic settings influencing South African marine fauna (the colder Benguela current along the western margin, and the warmer Agulhas Current along the southern and eastern margin). In this context, the RELATE permutation model implies that longitude and depth are good predictors for coral distribution patterns. However, the close to zero R-values (R<0.5) suggests a non-linear relationship even though significant variability is evident in the species composition within the factorial groups. Whilst depth is noted to be one of the main drivers for coral distribution (as shown by BEST results), it is important to recognize that this parameter encompasses several other properties, such as the Aragonite Saturation Horizon (ASH) that is the depth below which calcium carbonate becomes unstable and tends to dissolve [1, 67]. Such a zone has been estimated at 700–1500 m depth range south of ~ 20°S [67]. Eight of the 11 known South African coral families are recorded within this depth range, suggesting these species are surviving within an aragonite saturation state. Interestingly, coral species have been previously reported to withstand saturating conditions [68]. The response of coral species to water properties, such as the ASH, are in no way consistent, highlighting the need for further research to comprehend the underlying environmental drivers of coral distribution.

Although the azooxanthellate coral data reported here represent an accumulation of samples over 30 years and are the best available representation of the South African fauna, all species richness estimator models did not plateau, demonstrating that the area is still not well sampled and may be much more diverse than currently known. Additional systematic sampling coverage will provide a clearer understanding of national coral diversity trends.

5. Conclusion and recommendations

This study examined the best available data for the South African azooxanthellate coral fauna and presented a pre-processing methodology that can provide standardised position and depth data for historical samples to allow analysis of distribution trends. Differences in azooxanthellate coral species distribution patterns across South Africa’s diverse and dynamic oceanographic conditions were revealed, whereby species turnover increased on a west to east axis. A species depth gradient was additionally observed, in which the multivariate diversity measure complemented the existing knowledge on taxa trends. Despite the sparsity and unbalanced nature of the sampling, knowledge has been advanced and gaps identified. A purposeful application for this existing coral data set will be its integration into multi-taxa biogeography analyses that will support more robust data-driven ecosystem classification, description, and delineation. This in turn will support spatial prioritisation and marine spatial planning, particularly alongside taxa that share similar abiotic requirements.

Supporting information

S1 Appendix

(XLSX)

pone.0296188.s001.xlsx (418.8KB, xlsx)

Acknowledgments

A sincere acknowledgement goes to Dr David Herbert (Department of Natural Sciences, National Museum Wales) who assisted with associated station data for the Meiring Naude and Sardinops collections. Dr Victoria Goodall (Nelson Mandela University) for reviewing the data analysis section. Mr Ashley Johnson and Dr Lauren Williams (Department of Fisheries, Forestry, and the Environment) provided words of encouragement and ArcGIS technical support; respectively.

Data Availability

All relevant data are within the paper and its Supporting Information files.

Funding Statement

The financial support for this research study was provided by the Department of Forestry, Fisheries, and Environment (DFFE). The funders had no role in study design, and analysis, decision to publish, or preparation of the manuscript. Some of the samples were acquired through DFFE research surveys led by lead author.

References

  • 1.Guinotte J, Orr J, Cairns S, Freiwald A, Morgan L, George R. Will human‐induced changes in seawater chemistry alter the distribution of deep‐sea scleractinian corals?. Frontiers in Ecology and the Environment. 2006; 4(3), 141–146. 10.1890/1540-9295(2006)004[0141:WHCISC]2.0.CO;2. [DOI] [Google Scholar]
  • 2.Hovland M.. Deep-water coral reefs: Unique biodiversity hot-spots. Springer Science & Business Media. 2008. [Google Scholar]
  • 3.Roberts J, Wheeler A, Freiwald A. Cairns S. Cold-water corals: the biology and geology of deep-sea coral habitats. Cambridge University Press. 2009. [Google Scholar]
  • 4.Davies A, Guinotte J. Global habitat suitability for framework-forming cold-water corals. PloS one. 2011; 6(4), p.e18483. doi: 10.1371/journal.pone.0018483 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Angeletti L, Castellan G, Montagna P, Remia A, Taviani M. The “Corsica Channel Cold-Water Coral Province”(Mediterranean Sea). Frontiers in Marine Science. 2020; p.661. 10.3389/fmars.2020.00661. [DOI] [Google Scholar]
  • 6.Cairns SD. Deep-water corals: an overview with special reference to diversity and distribution of deep-water scleractinian corals. Bulletin of Marine Science. 2007; 81(3):311–22. https://repository.si.edu/handle/10088/7536. [Google Scholar]
  • 7.Oakham V. Deep-Sea Coral Reefs: Distribution, Ecology and Anthropogenic Impacts. 2009. The Plymouth Student Scientist, p. 203–211. [Google Scholar]
  • 8.Waters J. Driven by the West Wind Drift? A synthesis of southern temperate marine biogeography, with new directions for dispersalism. Journal of Biogeography. 2008; 35(3), 417–427. 10.1111/j.1365-2699.2007.01724.x. [DOI] [Google Scholar]
  • 9.Costello M. Distinguishing marine habitat classification concepts for ecological data management. Marine Ecology Progress Series. 2009; 397, 253–268. 10.3354/meps08317. [DOI] [Google Scholar]
  • 10.Reygondeau G, Dunn D. Pelagic biogeography. Encyclopedia of Ocean Sciences. 2018; 588–598. 10.1016/B978-0-12-409548-9.11633-1. [DOI] [Google Scholar]
  • 11.Reygondeau G. Current and future biogeography of exploited marine exploited groups under climate change. In Predicting Future Oceans: Sustainability of Ocean and Human Systems Amidst Global Environmental Change. Elsevier Inc. 2019. 10.1016/B978-0-12-817945-1.00009-5. [DOI] [Google Scholar]
  • 12.Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, et al. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. Elife. 2022;11:e78129. doi: 10.7554/eLife.78129 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.United Nations. Revised Roadmap for the UN Decade of Ocean Science for Sustainable Development. 2018. Available online at: http://www.fao.org/3/CA0463EN/ca0463en.pdf.
  • 14.United Nations. Revised draft text of an agreement under the United Nations Convention on the Law of the Sea on the conservation and sustainable use of marine biological diversity of areas beyond national jurisdiction, Intergovernmental conference on an international legally binding instrument under the United Nations Convention on the Law of the Sea on the conservation and sustainable use of marine biological diversity of areas beyond national jurisdiction (fourth session, New York, 23 March–3 April 2020). UNGA: New York. 2019.
  • 15.United Nations Environment Program Convention on Biological Diversity. Zero draft of the post-2020 global biodiversity framework. 2020. Available online at: https://www.cbd.int/doc/c/efb0/1f84/a892b98d2982a829962b6371/wg2020-02-03-en.pdf.
  • 16.Day JH. Marine biology in South Africa. In: Brown AC, editor. A history of scientific endeavour in South Africa. Cape Town: Royal Society of South Africa. 86–108. 1977.
  • 17.Griffiths C, Robinson T, Lange L, Mead A. Marine biodiversity in South Africa: an evaluation of current states of knowledge. PloS one. 2010; 5(8), p.e12008. doi: 10.1371/journal.pone.0012008 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Sink K, van der Bank M, Majiedt P, Harris L, Atkinson L, Kirkman S, et al. In: South African National Biodiversity Assessment 2018 Technical Report Volume 4: Marine Realm. South African National Biodiversity Institute, Pretoria. South Africa. 2019. Available from: http://hdl.handle.net/20.500.12143/6372. [Google Scholar]
  • 19.Biccard A. Taxonomy, systematics and biogeography of South African Cirripedia (Thoracica). M.Sc. Thesis, University of Cape Town. 2012. Available from: http://hdl.handle.net/11427/10163.
  • 20.Laird M. Taxonomy, systematics and biogeography of South African actiniaria and corallimorpharian. PhD. Thesis. University of Cape Town, South Africa, 236 pp. 2013. Available from: http://hdl.handle.net/11427/6117.
  • 21.Filander Z. Systematics and biodiversity of South African sea urchins. M.Sc. Thesis University of Cape Town. 2014.
  • 22.Boonzaaier MK. Diversity and zoogeography of South African Bryozoa. Doctoral thesis, University of Western Cape. 2017. Available from: http://hdl.handle.net/11394/6308.
  • 23.Landschoff J. Contributions to the taxonomy of South African hermit crabs (Crustacea: Decapoda: Paguroidea)–integrating microCT scanning and barcoding. PhD. Thesis. University of Cape Town, South Africa, 242 pp. 2018. Available from: http://hdl.handle.net/11427/28431.
  • 24.Sink KJ, Adams LA, Franken M-L, Harris LR, Currie J, Karenyi N, et al. Iterative mapping of marine ecosystems for spatial status assessment, prioritization, and decision support. Frontiers in Ecology and Evolution. 2023; 11:1108118. doi: 10.3389/fevo.2023.1108118 [DOI] [Google Scholar]
  • 25.Gray J.. An outline of an arrangement of stony corals. Annals of Natural History. 1847; (1)19: 120–128. 10.1080/037454809496460. [DOI] [Google Scholar]
  • 26.Dana J. Zoophytes. Volume VII of the United States Exploring Expedition during the years 1838, 1839, 1840, 1841, 1842, under the command of Charles Wilkes, USN. Lea & Blanchard, Philadelphia, 740 pp. 1846. Available from: 10.5962/bhl.title.70845. [DOI] [Google Scholar]
  • 27.Cairns S, Keller N. New taxa distributional records of azooxanthellate Scleractinia (Cnidaria, Anthozoa) from the tropical southwest Indian Ocean, with comments on their zoogeography and ecology. Annals of the South African Museum. 1993; 103, 213–292. [Google Scholar]
  • 28.Filander Z, Kitahara M, Cairns S, Sink K, Lombard A. Azooxanthellate Scleractinia (Cnidaria, Anthozoa) from South Africa. ZooKeys. 2021. doi: 10.3897/zookeys.1066.69697 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.de Wet WM, Compton JS. Bathymetry of the South African continental shelf. Geo-Marine Letters. 2021; 41(3):40. [Google Scholar]
  • 30.Dierssen HM, Theberge AE, Wang Y. Bathymetry: History of seafloor mapping. Encyclopedia of Natural Resources. 2014; 2:564. [Google Scholar]
  • 31.Cawthra HC, Bergh EW, Wiles EA, Compton JS. Late Quaternary deep marine sediment records off southern Africa. South African Journal of Geology. 2021; 124(4), 1007–1032. [Google Scholar]
  • 32.Clarke K, Gorley R, Somerfield P, Warwick R. Change in marine communities: an approach to statistical analysis and interpretation. Primer-E Ltd. 2014. [Google Scholar]
  • 33.Anderson MJ, Gorley RN, Clarke KR. PERMANOVA+ for PRIMER: guide to software and statistical methods. Plymouth, UK: PRIMER-E; 2008. [Google Scholar]
  • 34.WoRMS Editorial Board. World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. 2023. Accessed 2023-02-17. doi:10.14284/17.
  • 35.Clarke K, Warwick R. The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels. Marine Ecology Progress Series. 1999; 184, 21–29. [Google Scholar]
  • 36.Clarke K, Somerfield P, Chapman M. On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray–Curtis coefficient for denuded assemblages. Journal of Experimental Marine Biology and Ecology. 2006; 330(1), 55–80. [Google Scholar]
  • 37.Kitahara VM. Morphological and molecular systematics of scleractinian corals (Cnidaria, Anthozoa), with emphasis on deep-water species. PhD. Thesis‥ James Cook University. 2011.
  • 38.Stolarski J, Kitahara MV, Miller DJ, Cairns SD, Mazur M, Meibom A. The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals. BMC evolutionary biology. 2011; 11:1–1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Clarke k, Somerfield P, Gorley R. Clustering in non–parametric multivariate analyses. Journal of Experimental Marine Biology and Ecology, 2016; 483, 147–155. 10.1016/j.jembe.2016.07.010. [DOI] [Google Scholar]
  • 40.Clarke K. Non‐parametric multivariate analyses of changes in community structure. Australian Journal of Ecology, 1993; 18(1), pp.117–143. 10.1111/j.1442-9993.1993.tb00438.x. [DOI] [Google Scholar]
  • 41.Somerfield P, Clarke K, Gorley R. A generalised analysis of similarities (ANOSIM) statistic for designs with ordered factors. Austral Ecology, 2021; 46(6), 901–910. 10.1111/aec.13043. [DOI] [Google Scholar]
  • 42.Clarke K, Somerfield P, Gorley R. Testing of null hypotheses in exploratory community analyses: similarity profiles and biota–environment linkage. Journal of Experimental Marine Biology and Ecology, 2008; 366(1–2), 56–69. 10.1016/j.jembe.2008.07.009. [DOI] [Google Scholar]
  • 43.Lange L. Use of demersal bycatch data to determine the distribution of soft-bottom assemblages off the West and south coasts of South Africa. PhD. Thesis. University of Cape Town). 2012. Available from: http://hdl.handle.net/11427/10899. [Google Scholar]
  • 44.Longhurst A. Ecological Geography of the Sea, Second Edition. Academic Press. 2007:1–17. [Google Scholar]
  • 45.Spalding M, Fox H, Allen G, Davidson N, Ferdaña Z, Finlayson M, et al. Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas. BioScience. 2007; 57(7), 573–583. 10.1641/B570707. [DOI] [Google Scholar]
  • 46.Shannon LV. The Benguela ecosystem. I: Evolution of the Benguela physical features and processes. Oceanography and Marine Biology. 1985; 23, 105–182. [Google Scholar]
  • 47.Gori A, Ferrier-Pagès C, Hennige SJ, Murray F, Rottier C, Wicks LC, et al. Physiological response of the cold-water coral Desmophyllum dianthus to thermal stress and ocean acidification. PeerJ. 2016; 4:e1606 doi: 10.7717/peerj.1606 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 48.Castellan G, Angeletti L, Taviani M, Montagna P. The yellow coral Dendrophyllia cornigera in a warming ocean. Frontiers in Marine Science. 2019; 6, p.692. [Google Scholar]
  • 49.Naumann MS, Orejas C, Ferrier-Pagès C. Species-specific physiological response by the cold-water corals Lophelia pertusa and Madrepora oculata to variations within their natural temperature range. Deep Sea Research Part II: Topical Studies in Oceanography. 2014; 99, 36–41. [Google Scholar]
  • 50.Green AN, Goff JA, Uken R. Geomorphological evidence for upslope canyon-forming processes on the northern KwaZulu-Natal shelf, SW Indian Ocean, South Africa. Geo-Marine Letters. 2007; 27(6), 399–40. [Google Scholar]
  • 51.Green A, Uken R. Submarine land sliding and canyon evolution on the northern KwaZulu-Natal continental shelf, South Africa, SW Indian Ocean. Marine Geology. 2008; 254(3–4), 152–170. [Google Scholar]
  • 52.Green A. Sediment dynamics on the narrow, canyon-incised and current-swept shelf of the northern KwaZulu-Natal continental shelf, South Africa. Geo-Marine Letters. 2009; 29(4), 201–219. [Google Scholar]
  • 53.Green A. Submarine canyons associated with alternating sediment starvation and shelf-edge wedge development: Northern KwaZulu-Natal continental margin, South Africa. Marine Geology. 2011; 284(1–4), 114–126. [Google Scholar]
  • 54.Filander Z, Smith AN, Cawthra HC, Lamont T. Benthic species patterns in and around the Cape Canyon: A large submarine canyon off the western passive margin of South Africa. Frontiers in Marine Science. 2022; 9. 10.3389/fmars.2022.1025113. [DOI] [Google Scholar]
  • 55.Dingle RV. Sedimentary basins and basement structures on the continental margin of southern Africa. Geological Survey Bulletin of South Africa. 1979; 63, 29–43. [Google Scholar]
  • 56.Hanz U, Wienberg C, Hebbeln D, Duineveld G, Lavaleye M, Juva K, et al. Environmental factors influencing benthic communities in the oxygen minimum zones on the Angolan and Namibian margins. Biogeosciences. 2019; 16(22), 4337–4356. [Google Scholar]
  • 57.Orejas C, Wienberg C, Titschack J, Tamborrino L, Freiwald A, Hebbeln D. Madrepora oculata forms large frameworks in hypoxic waters off Angola (SE Atlantic). Scientific Reports. 2021;11(1):15170. doi: 10.1038/s41598-021-94579-6 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 58.Atkinson LJ, Field JG, Hutchings L. Effects of demersal trawling along the west coast of southern Africa: multivariate analysis of benthic assemblages. Marine Ecology Progress Series. 2011; 430, 241–255. doi: 10.3354/meps08956 [DOI] [Google Scholar]
  • 59.Majiedt PA, Holness S, Sink KJ, Reed J, Franken M, van der Bank MG, et al. Chapter 4: Pressures on Marine Biodiversity. In: Sink KJ, van der Bank MG, Majiedt PA, Harris LR, Atkinson LJ, Kirkman SP, Karenyi N (eds). 2019. South African National Biodiversity Assessment 2018 Technical Report Volume 4: Marine Realm. South African National Biodiversity Institute, Pretoria. South Africa. 2019. Available from: http://hdl.handle.net/20.500.12143/6372. [Google Scholar]
  • 60.Beal L, De Ruijter W, Biastoch A, Zahn R, SCOR/WCRP/IAPSO Working group. On the role of the Agulhas system in ocean circulation and climate. Nature. 2011; 472, 429–436. 10.1038/nature09983. [DOI] [PubMed] [Google Scholar]
  • 61.Spalding MD, Agostini VN, Rice J, Grant SM. Pelagic provinces of the world): a biogeographic classification of the world’s surface pelagic waters. Ocean and Coastal Management, 2012; 60: 19–30. doi: 10.1016/j.ocecoaman.2011.12.016 [DOI] [Google Scholar]
  • 62.Schouten M, de Ruijter W, Van Leeuwen P, Lutjeharms J. Translation, decay and splitting of Agulhas rings in the southeastern Atlantic Ocean. Journal of Geophysical Research. 2000; 105(C9), 21913–21925p. 10.1029/1999JC000046. [DOI] [Google Scholar]
  • 63.Gordon A, Weiss R, Smethie W Jr, Warner M. Thermocline and intermediate water communication between the South Atlantic and Indian Oceans. Journal of Geophysical Research. 1992; 97(C5), 7223–7240. 10.1029/92JC00485. [DOI] [Google Scholar]
  • 64.Duncombe Rae C. Agulhas retroflection rings in the South Atlantic Ocean: an overview. South African Journal of Science. 1991; 11(1), 327–344. 10.2989/025776191784287574. [DOI] [Google Scholar]
  • 65.Halo I, Penven P, Backeberg B, Ansorge I, Shillington F, Roman R. Mesoscale eddy variability in the southern extension of the East M Madagascar Current: Seasonal cycle, energy conversion terms, and eddy mean properties. Journal of Geophysical Research. 2014; 119(10), 7324–7356. [Google Scholar]
  • 66.Cairns S. A generic revision and phylogenetic analysis of the Dendrophylliidae (Cnidaria: Scleractinia). Smithsonian Contributions to Zoology. 2001; 615, 1–75. 10.5479/si.00810282.615. [DOI] [Google Scholar]
  • 67.Jiang L, Feely R, Carter B, Greeley D, Gledhill D, Arzayus K. Climatological distribution of aragonite saturation state in the global oceans. Global Biogeochemical Cycles. 2015; 29(10), 1656–1673. 10.1002/2015GB005198. [DOI] [Google Scholar]
  • 68.Auscavitch SR, Lunden JJ, Barkman A, Quattrini AM, Demopoulos AW, Cordes EE. Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage. PeerJ. 2020; 8, p.e9523. doi: 10.7717/peerj.9523 [DOI] [PMC free article] [PubMed] [Google Scholar]

Decision Letter 0

Carlo Nike Bianchi

14 Jul 2023

PONE-D-23-17495The application of historic sample-specific variables in evaluating the biodiversity patterns of the South African azooxanthellate scleractinians (Cnidaria: Anthozoa).PLOS ONE

Dear Dr. FILANDER,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Aug 28 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Carlo Nike Bianchi

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at 

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Thank you for stating the following financial disclosure: 

   "The financial support for this research study was provided by the Department of Forestry, Fisheries, and Environment (DFFE)."

Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 

If this statement is not correct you must amend it as needed. 

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

3. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability.

"Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized.

Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access.

We will update your Data Availability statement to reflect the information you provide in your cover letter.

4. We note that Figure 1 and 3 in your submission contain [map/satellite] images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (a) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (b) remove the figures from your submission:

a. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license.  

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#+K49

Natural Earth (public domain): http://www.naturalearthdata.com/

Additional Editor Comments:

The ms has been red by two independent reviewers, from two countries and belonging to different academic schools. Both reviewers asked for major changes, underlining severe flaws in writing and editing. The ms needs to be largely rewritten before reconsideration by the same or other reviewers. I strongly recommend that the authors take into careful consideration all commenys of the two reviewers.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: No

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: In general the ms should be rearranged in material and methods and it should be cleared some points and doubts that I have outlined in the notes inside the .pdf.

Some points are not clear in the methods and the methods should be well understood and it should be replicable.

I suggest the ms should not be accepted in the present form.

Reviewer #2: I started reading this manuscript in detail and making notes where the English was awkward and needed editing, but soon ran out of time and energy to do this. The data are quite thin, although are worthy of presentation, but i feel that the existing MS is way too long and complicated to present what is available. It also needs severe editing, not only to make it shorter and simpler but also to correct a whole lot of minor editorial inconsistencies. For example to consistently capitalize proper names such as Agulhas Current, to consistently give numbers over 10 as numerals not words and the names of taxonomic families consistently in either lower case English form or capitalized Latin format (preferred).

The reference list is also a mess, firstly i do not understand why references are numbered when they are referred to by name and not number in the text . Secondly there is every type of formatting error here, from a mixture of abbreviated and non- abbreviated journal titles, to missing publication information, to spelling, spacing and punctuation errors! In short this all needs to be done a lot more carefully!

As regards the actual factual contend i think this does have merit and that a shorter, simpler and better edited version would be worthy of publication. I would particularly like to see though, some better analysis of the relationships between habitat area, number of samples taken and numbers of taxa found - for example it appears that huge swathes of deeper water on the east coast are not or hardly sampled - it would be nice to know how big these areas are and how many samples (even if zero) are available from each depth zone.This would better inform whether there are indeed few spcies or just few or no samples here.

By the way i thought the figures were overly garishly coloured!

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Andrea Peirano

Reviewer #2: No

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachment

Submitted filename: Peirano rev. PONE-D-23-17495_reviewer.pdf

pone.0296188.s002.pdf (2.5MB, pdf)
PLoS One. 2024 Aug 8;19(8):e0296188. doi: 10.1371/journal.pone.0296188.r002

Author response to Decision Letter 0


29 Sep 2023

Nelson Mandela University

University Way

Summerstrand

Gqeberha

6019

South Africa

15 September 2023

PLOS ONE

1265 Battery Street, Suite 200

San Francisco,

CA 94111

United states of America

Dear Dr Carlo Nike Bianchi (Academic Editor)

Re: Rebuttal Letter for Manuscript ID [PONE-D-23-17495]

Title of Your Manuscript: The application of historic sample-specific variables in evaluating the biodiversity patterns of the South African azooxanthellate scleractinians (Cnidaria: Anthozoa).

I hope this letter finds you well. I would like to express my gratitude for the careful consideration and feedback provided by the reviewers on the above-mentioned manuscript submitted to PLOS ONE. I appreciate the time and effort the reviewers and the editorial team have invested in evaluating my work and their constructive suggestions.

I have thoroughly considered the reviewers' comments and suggestions, and I would like to demonstrate how we have addressed their concerns and provide clarifications on the points raised. Below, I have outlined each major concern and the corresponding response.

Regards, Zoleka Filander (on behalf of co-authors)

Reviewer 1

Reviewer #1 overview: In general the ms should be rearranged in material and methods and it should be cleared some points and doubts that I have outlined in the notes inside the .pdf.

Some points are not clear in the methods and the methods should be well understood and it should be replicable. I suggest the ms should not be accepted in the present form.

Authors response: We thank the reviewer for the suggestion and have rearranged the manuscript, provided clarity on the methods, and made changes with a view to ensuring that the methods are repeatable by other studies.

Response to comments in pdf

Reviewer #1 comment: Line 37 (now line 44 in updated manuscript) = I suggest to change into a more apropriate

deep water coral. You examine depth between 50 and 700 m.

Authors response: “stony Cold water” in the keywords has been updated to deep water as suggested.

Reviewer #1 comment: Line 66-71 (now 95-100 in updated manuscript) = I do not agree with these sentence. biological pattern in deep area have been described in quite all the oceans around the word. Perhaps you mean in South Africa ? I suggest to change coral species instead of species.

Authors response: We thank the reviewer for this feedback and have updated this sentence to reflect the reference to coral species and have also updated citations.

Reviewer #1 comment: Line 90-91 (now line 133-135 in updated manuscript) = I do not understand: a taxonomic revision doesn't mean that prevoius works cannot be reconsidered and corrected.

Authors response: We thank the reviewer for highlighting this, and have updated the sentence to provide improved clarity.

Reviewer #1 comment: Line 103-105 (now line 146-150 in updated manuscript) = this last sentence should be more specific on the author's study and its objectives

you may consider some sentences in the in material and method and/or abstract

Authors response: We thank the reviewer for this suggestion and have added a summary of the overall objectives at the end of this paragraph.

Reviewer #1 comment: Line 112 (now line 179-186 in updated manuscript) = please add the range of sample depth for each cited cruise

Authors response: We thank the reviewer for this suggestion and depth ranges represented by the samples from each cruise have now been added as a table.

Reviewer #1 comment: Line 127 (now line 193 in updated manuscript) = move the references to the end of the sentence.

Authors response: The citation has been added to the end of the sentence.

Reviewer #1 comment: Line 126-127 (now line 190 in updated manuscript) = please describe the GIS system. For example what is a polygon boundary ? why you decide to '..move the sampling points to the closest polygon ? You can add a paragraph to describe the GIS architecture.

Authors response: We thank the reviewer for bringing ambiguity to our attention, and have therefore refined the opening of the sentence to provide rationale for undertaking the ArcGis steps.

Reviewer #1 comment: Line 127-128 (now line 195-197 in updated manuscript) = this should be moved in results

Authors response: This is statement was not a result reached through this study, but rather an explanation/supporting statement as to why some of the records fell on

land/coastline and is therefore not moved or changed.

Reviewer #1 comment: Line 131-132 (now line 225-227 in updated manuscript) = this sentence sounds very strange .Some lines above you write you move to a polygon, (I think taking no account of the depth sampling) Now you say that recorded sampling depth were not taken in account.

These considerations should be well argued because the value of a sample (also from a hystorical point of view) is based on the data recorded (Where, When and How it was sampled) mainly vessel position and depth. From your sentences this data seems to have no value.

Authors response: We thank the reviewer for this feedback and would like to clarify that the reasons to standardize the depths associated with each record is not to discount historical datasets but rather to establish a uniform methodology across the dataset – especially considering that such datasets are known to have various degrees of reliability.

Furthermore, in the assumption and sampling biases sections, specifically line 233-247 of updated manuscript, we are talking about the sampling footprint in South Africa, which is higher in the nearshore areas vs the offshore areas. Historically, the latter relied on international surveys and samples are mostly hosted at international institutions (e.g., Natural history museum in London). Please take note that this paragraph (line 233-247 now in updated manuscript) is different to the previous paragraph (line 190-230 in updated manuscript) - which is explaining why the two-part ArcGis approach was undertaken. We have clarified this by adding a sentence outlining the improvement of current bathymetry data vs historical techniques

Reviewer #1 comment: Line 139 (now 235-237 in updated manuscript) = depth range ?

Authors response: We thank the reviewer for the suggestion and have updated by adding the depth ranges.

Reviewer #1 comment: Line 142 (now line 238-239 in updated manuscript) = why they are biased

Authors response: We assume the data to be presence-absence in the multivariate analysis, when in actual fact the data are presence-only. However, collections, and the resolution of collected data, depend on the expertise onboard on any given expedition. In other words, just because a coral specimen was not recorded/preserved, it doesn’t mean that it was not present at a sampled station. We have therefore left this statement as is and no changes have been made.

Reviewer #1 comment: Line 146-147 (now line 244-247 in updated manuscript) = this could be an error. Hystorical data can give informations on the appearance/disappearance of species in time. For example, the hystorical occurence/not occurrence of a species is now used as a method to evaluate cliatic changes in biological communities.

Authors response: We thank the reviewers for this comment and have updated to clarify the reasoning. As additional information- we are assuming that the records are where they were historically recorded, and this might not be the case considering the footprint of anthropogenic activities. Whilst historical datasets can be used to investigate changes in biological communities, the anthropogenic footprint needs to be considered. This has been difficult to isolate.

Reviewer #1 comment: Line 153-154 (now line 261-264 in updated manuscript) = this interpolation is not a general assupmtion. It depends on the geographical scale.

Authors response: We agree, it does depend on scale, but this approach was not considered due to the uneven availability of substrate information in South Africa - as highlighted in lines 266-271.

Reviewer #1 comment: Line 155-157 (now line 264-271in updated manuscript) = In this part is introduced the bottom characteristcs and discussed, it is the first time that bottom characteristic is cited

I suggest to indroduce at the start of the material and methods all parameters collected in the hystorical paper research or published literature, than discuss each one ( depth, species, latitude/longitude, type of bottom etc) and why and how was included in your dataset

Authors response: in the Introduction (now lines 78-82) in the updated manuscript) we mention the importance of habitat/ substrate/sediment type to the survival of coral. These sentences (lines 264-271) are included to support why the interpolation technique was not applied. This has been clarified by adding a sentence that highlights that the only two variables used in this paper are longitude and depth (bearing in mind that this section is outlining the assumptions made and the biases of the dataset, before unpacking the multivariate analysis conducted and the subsequent results).

Reviewer #1 comment: Line 161 (now line 271 in updated manuscript) = what is a substrate level ? Do you mean substrate type ? Or level is a matrix level or GIS data level ?

Authors response: We have clarified that substrate refers to characteristics of the seabed (i.e., sediment/substrate data). The updated paragraph (264-272) reflects the uneven representation of substrate information in South Africa.

Reviewer #1 comment: Line 163 = please describe ATD

Reviewer #1 comment: Line 164-174 = this part is a conclusion ?

Authors response: We have clarified that Average Taxonomic distinctiveness is a diversity measure that considered phylogenetic data, and added sentences on how this is quantified, along with reasoning for using ATD.

This paragraph has been deleted in the “assumption and biases: section and important information on ATD incorporated into the first paragraph of the data analysis section (now line 340-351 in updated manuscript).

Reviewer #1 comment: Line 210-21 (now line 367-368 in updated manuscript) = this approach should be introduced early, where you describe the database and/or the GIS approach.

Authors response: We thank the reviewer for this suggestion and have refined the existing sentence in line 228-229 (in updated manuscript), whilst also keeping it in this section (line 367-368 in updated manuscript) for ease of reading, we see this section to be also appropriate in the data analysis.

Reviewer #1 comment: Line 380 (now line 762 in updated manuscript) = Madrepora

Authors response: We thank the reviewer for bringing out attention to this typo, which has now been updated.

Reviewer #1 comment: Line 438 (now 836-837 in updated manuscript) = in the material and methods you write there are two great dividion 50-200 and 200-1000 with steps of 100 m.

Hence, the eigth families are between 900 and 1000 m ?

Authors response: We thank the reviewer for the comment and have updated the sentences to reflect that the diversity gradients were quantified based on the associated sample depth data. Thus eight families are represented at 1000 m - this statement is independent of the zone groupings (i.e., 50-200 m vs 300-1000 m) used/needed in the SIMPER analysis to evaluate the characteristic species of the zones which is discussed in the following sentences (now line 840-849 in updated manuscript).

Reviewer #1 comment: Line 443-445 (now line 843-849 in updated manuscript) = so, if i have understood you find that dendrophyllidae fhave a range limited to a maximum of 200 m if compared with Cairns (2001)

Authors response: Our findings support Cairn’s (2001) statement that dendrophylliids are most abundant in the 50-300 m depth. We have clarified this in the manuscript by amending the sentence to reflect this.

Reviewer 2

Reviewer #2 comment: I started reading this manuscript in detail and making notes where the English was awkward and needed editing, but soon ran out of time and energy to do this. The data are quite thin, although are worthy of presentation, but i feel that the existing MS is way too long and complicated to present what is available. It also needs severe editing, not only to make it shorter and simpler but also to correct a whole lot of minor editorial inconsistencies. For example to consistently capitalize proper names such as Agulhas Current, to consistently give numbers over 10 as numerals not words and the names of taxonomic families consistently in either lower case English form or capitalized Latin format (preferred).

Authors response: We have severely edited this manuscript and thank the reviewer for the recommendations to simplify and improve the manuscript. The manuscript has been shortened and simplified by –

1. Removing the ANOSIM methodology and results, thus focusing on the gradients of each variable (longitude and depth) and the corelation between the biological vs environmental (i.e., longitude and depth) data.

2. Removing the paragraph on the species characteristic of the factors being tested (longitude and depth) and focusing on the family distinction only.

3. A substantial edit to reduce unnecessary text and shorten the manuscript as far as possible.

Proper nouns have been updated and are capitalized, and the number over 10 has been updated to a numerical.

In terms of the taxonomic families, the English and Latin format has been maintained, as this provides concise reading. Using both has been done in other published work. See -

https://doi.org/10.1016/S1055-7903(03)00162-3

https://doi.org/10.1016/j.ympev.2022.107565

https://doi.org/10.1038/s41598-020-77763-y

Reviewer #2 comment: The reference list is also a mess, firstly i do not understand why references are numbered when they are referred to by name and not number in the text .

Authors response: Thank you for the comment, we have maintained the numbering as the journal guidelines require references to be numbered

Secondly there is every type of formatting error here, from a mixture of abbreviated and non- abbreviated journal titles, to missing publication information, to spelling, spacing and punctuation errors! In short this all needs to be done a lot more carefully!

Authors response: We apologise for this oversight and have updated each reference with increased attention to detail.

Reviewer #2 comment: As regards the actual factual contend i think this does have merit and that a shorter, simpler and better edited version would be worthy of publication. I would particularly like to see though, some better analysis of the relationships between habitat area, number of samples taken and numbers of taxa found - for example it appears that huge swathes of deeper water on the east coast are not or hardly sampled - it would be nice to know how big these areas are and how many samples (even if zero) are available from each depth zone.This would better inform whether there are indeed few spcies or just few or no samples here.

Authors response: We sincerely appreciate the reviewer’s comment and would like to bring to their attention that detailed information regarding the geographical representation of each longitudinal group can be found in Table 1, which is included within the text. Additionally, the depth bar graph (Fig. 4) illustrates the distribution of records/species across the different isobaths.

We would like to clarify that the data presented in our study is presence only data, but for the purposes of the multivariate analysis, it is considered as presence-absence. Consequently any absence of of data should not be interpreted as a true representation of the dataset. We kindly request that an absence analysis of the dataset is not pursued.

Reviewer #2 comment: By the way i thought the figures were overly garishly coloured!

Authors response: We thank the reviewer for his comment and have changed the colour to monochrome where possible.

Attachment

Submitted filename: Rebuttal.docx

pone.0296188.s003.docx (28.9KB, docx)

Decision Letter 1

Carlo Nike Bianchi

15 Nov 2023

PONE-D-23-17495R1The application of historic sample-specific variables in evaluating the biodiversity patterns of the South African azooxanthellate scleractinians (Cnidaria: Anthozoa).PLOS ONE

Dear Dr. FILANDER,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

 Please submit your revised manuscript by Dec 30 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Carlo Nike Bianchi

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

One of the former reviewers, while appreciating that the ms has been improved, thinks that some work of revision is still necessary. Apart from the specific points indicated, the ms is considered lengthy. The Authors are therefore required to be more synthetic.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: (No Response)

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: a large number of revisions and corrections have been made to this version which now reads much more clearly (although still long in relation to the data content in my opinion!

I spotted only a small number of points that still need correction as follows ( indicated by line number):

83 - i presume you mean 'since the 1700's'

98- it is not necessary of useful to insert 'i.e. ' when detailing a set of items in brackets. This happens many times in MS and should be removed

101-103 i suggest merging these two sentences instead or repeating the reference

149 - data are pleural ( of datum), so 'are' not 'is'

288- space needed before m

Refs 8-9 words in the one title given with caps, in the other in lower case - which is correct format?

ref 27 - in different font to others

587 - there is a spare M in this line

596 full stop needed after title

623 Seconded? do you mean Second Edition?

643 i think title is Research not Res, which is abbreviation

644 no journal given for this ref

Ref 92 why are words capitalised in this title

Figs 1 and 2 could easily be combined by adding blacks to the first figure

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #2: Yes: Charles Griffiths

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2024 Aug 8;19(8):e0296188. doi: 10.1371/journal.pone.0296188.r004

Author response to Decision Letter 1


4 Dec 2023

Nelson Mandela University

University Way

Summerstrand

Gqeberha

6019

South Africa

01 December 2023

PLOS ONE

1265 Battery Street, Suite 200

San Francisco,

CA 94111

United states of America

Dear Dr Carlo Nike Bianchi (Academic Editor)

Re: Rebuttal Letter for Manuscript ID [PONE-D-23-17495]

Initial title of manuscript: The application of historic sample-specific variables in evaluating the biodiversity patterns of the South African azooxanthellate scleractinians (Cnidaria: Anthozoa).

Revised title of manuscript: Diversity patterns of the South African azooxanthellate scleractinians (Cnidaria: Anthozoa), with considerations of environmental correlates.

I trust this correspondence finds you in good health. I want to convey my appreciation for the meticulous evaluation and feedback given by the reviewer(s) regarding the submitted manuscript to PLOS ONE. The dedication of both the reviewer and the editorial team in assessing this work and providing constructive suggestions is genuinely valued.

We have carefully examined the reviewers' comments and suggestions, and I wish to illustrate our responsiveness to their concerns. Below, we have delineated each major concern along with its corresponding response.

Regards,

Zoleka Filander (on behalf of co-authors)

Reviewer 2

Reviewer #2 overview: a large number of revisions and corrections have been made to this version which now reads much more clearly (although still long in relation to the data content in my opinion!

Authors response: We thank the reviewer for the suggestion to compress the contents within the manuscript. This has prompted improved referencing of the methodology and the elimination of redundant/repetitive information. The manuscript has undergone rearrangement, resulting in a reduction of the text from 33 to 31 pages. To enhance representation and reference convenience, Figure 2 has been integrated with the draftsman's plot results, and the permutation histogram of the RELATE results has been omitted. These comprehensive edits have necessitated a title change, aligning more accurately with the manuscript's refined content.

Reviewer #2 comment: I spotted only a small number of points that still need correction as follows ( indicated by line number):

• 83 - i presume you mean 'since the 1700's'

• 98- it is not necessary of useful to insert 'i.e. ' when detailing a set of items in brackets. This happens many times in MS and should be removed

• 101-103 i suggest merging these two sentences instead or repeating the reference

• 149 - data are pleural ( of datum), so 'are' not 'is'

• 288- space needed before m

• Refs 8-9 words in the one title given with caps, in the other in lower case - which is correct format?

• ref 27 - in different font to others

• 587 - there is a spare M in this line

• 596 full stop needed after title

• 623 Seconded? do you mean Second Edition?

• 643 i think title is Research not Res, which is abbreviation

• 644 no journal given for this ref

• Ref 92 why are words capitalised in this title

• Figs 1 and 2 could easily be combined by adding blacks to the first figure

Authors response: All the aforementioned suggestions have been incorporated, with revisions made to rectify these errors, and the manuscript has undergone significant editing..

Attachment

Submitted filename: Rebuttal.docx

pone.0296188.s004.docx (18.5KB, docx)

Decision Letter 2

Carlo Nike Bianchi

8 Dec 2023

Diversity patterns of the South African azooxanthellate scleractinians (Cnidaria: Anthozoa), with considerations of environmental correlates.

PONE-D-23-17495R2

Dear Dr. FILANDER,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Carlo Nike Bianchi

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Acceptance letter

Carlo Nike Bianchi

2 Jul 2024

PONE-D-23-17495R2

PLOS ONE

Dear Dr. Filander,

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team.

At this stage, our production department will prepare your paper for publication. This includes ensuring the following:

* All references, tables, and figures are properly cited

* All relevant supporting information is included in the manuscript submission,

* There are no issues that prevent the paper from being properly typeset

If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps.

Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

If we can help with anything else, please email us at customercare@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Carlo Nike Bianchi

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Appendix

    (XLSX)

    pone.0296188.s001.xlsx (418.8KB, xlsx)
    Attachment

    Submitted filename: Peirano rev. PONE-D-23-17495_reviewer.pdf

    pone.0296188.s002.pdf (2.5MB, pdf)
    Attachment

    Submitted filename: Rebuttal.docx

    pone.0296188.s003.docx (28.9KB, docx)
    Attachment

    Submitted filename: Rebuttal.docx

    pone.0296188.s004.docx (18.5KB, docx)

    Data Availability Statement

    All relevant data are within the paper and its Supporting Information files.


    Articles from PLOS ONE are provided here courtesy of PLOS

    RESOURCES