*4.3. DNA Confirmation of Selected Coral Species*

The genus *Acropora*, belonging to the family Acroporidae, is the most diverse and widespread coral genus. The species show both enormous intraspecific morphological variability and striking similarities between species within a geographical region, making species identification a challenge [84]. Consequently, for several species whose growth patterns and corallite arrangements appeared atypical, DNA barcoding was employed in parallel with morphological analysis. Notably, *A. aspera, A. digitifera,* and *A. gemmifera* were confirmed as present in Sri Lanka for the first time, although they have been widely recorded elsewhere in the Indian Ocean. The mitochondrial *COI* gene sequence of each species was found to have more than 99% similarity with the published genome sequences (Table 5). Sample COJP001 has a 99.69% similarity with the genomic region of the *A. aspera* and the morphological features also confirmed this identification (Table 5). Based on the description provided by Veron [43], *A. aspera* is a branching species with scale-like radial corallites. It is often confused with the similar species *A. millepora*; however, the corymbose clumps of colonies with branches and the two various sizes of axial corallites serve to differentiate *A. aspera* from *A. millepora*. Samples COJP002 and COJP004 were matched to samples of *A. gemmifera*, with the closest similarity being to a Malaysian sample *MG383839.1* [49]. COJP003 from the Valithoondal site was confirmed as *A. digitifera* and found to have the closest genetic relationship to a sample from the Egyptian coast of the Red Sea, *A. digitifera\_KR401100.1* (Table 5) [50]. This species is widely distributed in the Indian Ocean, Red Sea, and eastern Pacific Ocean [43] (Supplementary Table S2).

The colonies of *M. flabellata,* one of the world's uncommon species, were recorded on the Point Pedro reef front. They had an encrusting form, were blue and pinkish to brown in colour, and had prominent thecal papillae covering the colony. Septa could not be observed, making species separation from *M. undata* difficult. However, sequences from this species had the closest match with reference sequences from the Hawaiian Islands, HQ246603.1 [53]. The sample COJP007, which was confirmed as being of *Echinopora gemmacea,* was found only at Point Pedro and Inbarsitty. According to [43], *E. gemmacea* is an uncommon species. This specimen has the closest kinship to *E. gemmacea HE654561.1* from Yemen (Table 5) [52].

While the *COI* gene-based sequence relates to only a narrow portion of the genome, nevertheless, as found by others, it proved invaluable in confirming species-level identification of specimens from difficult to identify genera [33,85]. Apart from any intraspecific genetic variations, corals show a marked morphological plasticity that is considered to be largely adaptive [30]; molecular genetic studies are allowing a better understanding of this plasticity [86]. More generally, the use of DNA barcoding is enabling taxonomists to overcome the pitfalls of morphology-based identification and classification. In the present study, the use of barcoding has helped validate the finding of six scleractinian coral species new to Sri Lanka.

In summary, the northern coast of Jaffna Peninsula has the highest live coral cover among the regions of Sri Lanka; however, the reefs are prone to impacts from increasing fishing pressure and environmental pollution. These new insights into the coral biodiversity, distribution, and benthic biota of the coral reefs of the Jaffna Peninsula contribute knowledge required for future conservation and management. The present study indicates that the conservation of the coral reefs in Jaffna is critical, not only because of their direct ecological and economic importance, but because they may provide a reservoir of different coral species able to withstand the effects of future climate change.

**Supplementary Materials:** The following are available online at https://www.mdpi.com/article/10.3 390/oceans2030029/s1.

**Author Contributions:** Conceptualisation, A.A. and V.H.; data curation, A.A., V.H. and S.K.; funding acquisition, A.A. and V.H.; investigation, A.A. and A.U.; methodology, A.A., V.H., A.U. and A.H.; project administration, V.H.; resources, V.H.; supervision, V.H. and S.K.; validation, A.U.; visualisation, A.A., A.U. and A.H.; writing—original draft, A.A.; writing—review and editing, V.H. and S.K. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research received funding from IDEAWILD and from the Research Facilitation Fund (RFF) of the Postgraduate Institute of Agriculture, University of Peradeniya.

**Institutional Review Board Statement:** Samples were collected with permits from, and in compliance with, the laws and regulations of the Sri Lanka Department of Wildlife Conservation.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** Not applicable.

**Acknowledgments:** We acknowledge the International Coral Reef Society (ICRS) for granting a graduate fellowship to the senior author. We also thank the Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya for providing molecular laboratory facilities, the Department of Fisheries Science, Faculty of Science, University of Jaffna for their technical support We also thank the editor, Rupert Ormond, for extensive support in improving the text.

**Conflicts of Interest:** The authors declare that they have no known competing financial interest or personal relationship that could have appeared to influence the research studies presented in this paper.
