Reply to Hendawitharana et al. Comment on “Arulananthan et al. The Status of the Coral Reefs of the Jaffna Peninsula (Northern Sri Lanka), with 36 Coral Species New to Sri Lanka Confirmed by DNA Bar-Coding. Oceans 2021, 2 , 509–529”

We appreciate the comments made by Hendawitharana et al [...]

ClustalW [18].The aligned outputs were queried to identify the species, and the reference sequences of various coral species were retrieved from the National Center for Biotechnology Information (NCBI) [19][20][21][22], GenBank, and Barcode of Life Data System (BOLD) [23] by using the Basic Local Alignment Search Tool (BLAST).Those sequences corresponding to the genotype were analyzed for homologies with sequences in the NCBI database by performing BLAST and BOLD workbench.From the BLAST analysis, all samples provided a greater than 99.5% similarity.Nevertheless, we did discuss the limitations of this method in the Discussion Section of our paper [1].
In most cases, Veron's [1] "keys for genera and species" proved satisfactory for the robust identification of the corals observed.Identification of seven samples proved more challenging; these were Acropora aspera (COJP001), Acroposra digitifera (COJP003), and two specimens from two different locations representing Acropora gemmifera (COJP002, COJP004), Acropora hyacinthus (COJP006), Echinopora gemmacea (COJP007), and Montipora flabellate (COJP009), which was present only in small colony form.Even though we accept that the COI is not definitive for Acropora species, the best fitting morphological descriptions from Corals of the World [2], and we have chosen the best fitting BLASTn output to conclude the identification.It should also be noted that even though, unsurprisingly, the COI sequences of COJP001, COJP002, and COJP006 did not discriminate between them, the indicated identity reinforced the identification previously made from the study of the sample's morphological parameters, including corallite structure (axial, radial, exserted radial), as well as colony form.
More generally, we are aware that the conventional classification of scleractinian corals based on their morphology alone has been called into question based on both molecular and small-scale morphological data, resulting in frequent revisions to their classification at all levels [8,[13][14][15][24][25][26].Advances in molecular analysis have revealed clearer inconsistencies between previously accepted coral taxonomy and their apparent evolutionary past.Further, the term "accepted" may also be used to gloss over significant differences in name games with corals.For example, Acropora danai, which is now considered a junior synonym of Acropora abrotanoides, as described in Wallace, 1999 [27], and Veron, 2000 [2].Acropora nobilis is now considered a junior synonym of A. intermedia, as documented in Wallace, 1999, andVeron et al., 2022 [3,28].
Our study described the status of the reefs in the Jaffna Peninsula, from both a conservation and a bio-geographic point of view.The results of the biogeographic study were relevant because the database of already published work from the Indian Ocean and Red Sea regions indicated that most if not all the species that we recorded were present within these regions [29][30][31][32][33][34][35][36] (Table 1).While acknowledging the fact that Hendawitharana et al. (2023) found our tile misleading, we would like to state the following.The phrase "Confirmed by DNA-Bar coding" referred only to the genetic confirmation of the eight newly recorded species studied in this way to check their identity.We do not believe that the title misleads the readership and trust that disagreement on this point can be disregarded.We accept the possibility that a few of the identifications based on confirmation by barcoding may turn out not to be as robust as we would hope, but we do stand by the validity of the identifications described in our paper.In summary, our study holds significant value in its exploration of previously unstudied taxa and geographic regions, as well as in shedding light on the potential existence of new species records, albeit with acknowledged methodological limitations.Moreover, through this initial investigation, our goal was to raise awareness regarding the area's potential significance and to propose further research with enhanced methodologies for robustly validating our discoveries.We also recognize the challenges associated with conducting comprehensive species occurrence inventories and the circumstances where their approaches may prove beneficial.

Table 1 .
Details of scleractinian corals reported to be new to Sri Lanka, with notes on their taxon update details and known geographical distribution (individual closest locations near by Indian territory already clearly presented in our published article).