**1. Introduction**

Corals are foundational species that appeared 425 million years ago and are responsible for creating the structural complexity and high productivity of coral reef ecosystems [1]. They have radiated into more than 1500 species and nearly 900 scleractinian corals. Almost all reef corals are hermatypic, that is, they contain in their tissues photosynthetic algae of the family Symbiodiniaceae [1–3], which, living in a symbiotic relationship with corals, are ultimately responsible for the high biomass and productivity of reef habitats [1,4]. The high species diversity of coral reefs has led to their designation as oceanic "rain forests" [5]. However, unprecedented declines in live coral cover and phase shifts in coral reef ecosystems have arisen from the impacts of anthropogenic activities. The most recent widespread degradation of coral reefs, involving coral bleaching and the consequent death and loss of corals, is mostly due to climate change and ocean acidification [6,7]. Averting the effects of climate change will be a considerable challenge if we are to secure the ecological, economic, and social values of coral reefs in the marine biome.

**Citation:** Arulananthan, A.; Herath, V.; Kuganathan, S.; Upasanta, A.; Harishchandra, A. 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. https://doi.org/ 10.3390/oceans2030029

Academic Editor: Rupert Ormond

Received: 12 March 2021 Accepted: 16 July 2021 Published: 26 July 2021

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Considering the global nature of these ongoing threats to coral reefs, we investigated the most neglected coral reef area on the Island of Sri Lanka (SL), which is located 40 km away from the southeast coast of the Indian mainland and has 1338 km of open coastline and 2791 km located within coastal lagoons [8]. Fringing-type coral reefs occupy about 2% of the coast and cover 475.70 sq km of Sri Lankan territorial waters [9], with more extensive and well-developed fringing reefs being present on the north-western and northern coasts than in the southern and eastern regions [10,11]. The first detailed records of these coral reefs date from the 19th century and were provided by Ridley (1883) and Ortmann (1889) [12,13]. Subsequently, further studies of Sri Lankan reefs were published through the 20th century [14–19], but most of these concerned the western, south-western, southern, and north-western parts of the country [20,21]. In contrast, the northern region of SL has, in the recent past, received very little attention, due to the decades of civil war. As a result, little is known about the distribution and diversity of corals in that area, yet the region includes the largest coral reef ecosystem in SL, located near the Gulf of Mannar and known as "Bar Reef". It is recognised as a "High Regional Priority Area" by the International Union for the Conservation of Nature (IUCN)/National Oceanic and Atmospheric Administration (NOAA) USA "World Heritage Biodiversity" Project [22,23]. Further north lie Palk Strait and Palk Bay, which are highly productive shallow water areas containing coral reefs, seagrass beds, coastal lagoons, estuaries, mangroves, and salt marshes [22–27].

At the northernmost end of Sri Lanka is the Jaffna Peninsula, with around 293 km of coastline. Extensive fringing coral reefs are present along the northern coast of the peninsula and around the adjacent islands [28], many of which were previously unsurveyed. However, during and following the decades of civil war (which ended in 2009), these reefs were exposed to destructive fishing practices, such as the use of explosives, as well as over-fishing of many species, including ecologically important herbivorous fish and invertebrates, the loss of which has often been associated with a phase shift from coral dominated to algal dominated reefs [24–26]. Studying the ecology and biogeography of northern Sri Lanka represents a considerable challenge, since access presents problems and little information is available about the marine topography and substratum [29].

The present study aimed to report on the current status of reefs around the Jaffna Peninsula and to extend our knowledge of the understudied benthic community, including the diversity of coral species. To do so, we combined molecular tools and traditional morphometric approaches [30–32] and used DNA barcoding, which is known to have revolutionised the understanding of the evolution and systematics of scleractinian corals and resulted in an extensive taxonomic revision of the order [33–37]. Our surveys revealed that the coral reefs of the Jaffna Peninsula have a relatively high percentage of live coral cover and a greater diversity of scleractinian corals than other parts of the country.
