Genetic investigation on the population structure of the harbour porpoise phocoena phocoena (Linnaeus, 1758) living in Turkish waters

It is known that 10 species have been living in Turkish Seas belonging to Ordo: Cetacea (dolphins and whales). Harbour Porpoise, Phocoena phocoena (Linnaeus, 1758) is one of the most common species of cetaceans in Turkey. Harbour porpoise is a cosmopolitan species distributed in the Northern Hemisphere. It is known to be widespread in the North Atlantic, North Pacific and Black Sea, and rarely in the Sea of Marmara. Live observation, live and dead stranding records have been reported in the Aegean Sea. The species is not recorded in the Mediterranean Sea anymore. Harbour porpoises are divided into three sub-species; Phocoena phocoena vomeria in the North Pacific, Phocoena phocoena phocoena in the North Atlantic and Phocoena phocoena relicta in the Black Sea. In addition, the porpoise population which lives in Iberia and Mauritania coasts has been suggested to be represented by a different subspecies which is named; Phocoena phocoena meridionalis. The Black Sea harbour porpoise population is found to be morphologically and genetically separated from the Atlantic harbour porpoise population and represented by the Phocoena phocoena relicta Abel, 1905. Genetic structure of this species has been studied using mtDNA and nuclear DNA markers in Turkey. The unique haplotype detected in some individuals in the Marmara Sea, especially in the Gulf of Izmit, indicates that the porpoises in this area may be genetically differentiated, in other words, there might be an isolated harbour porpoise population in the Marmara Sea. The aim of this study is to isolate DNA from the skin tissues of harbour porpoises sampled in Turkish coasts between 1999-2018, and investigate the genetic structure of the species using mitochondrial DNA (mtDNA) and nuclear DNA (RAD sequencing) markers. In this study, a total of 88 (Western Black Sea: 48, Eastern Black Sea: 19, Turkish Straits System (TSS): 19, Aegean Sea: 2) harbour porpoise mtDNA sequences are obtained. The presence of 14 different mtDNA haplotypes are revealed and five of these haplotypes are found to be new that were not found in any other previous studies. According to Φst calculations, it is shown that the harbour porpoise subpopulation in the Marmara Sea show a statistically significant differentiation from other subpopulations in the Black Sea. The highest haplotype and nucleotide diversity is observed in the TSS. Haplotype and nucleotide diversity in the Western Black Sea subpopulation is also found to be the highest after the TSS subpopulation. According to the double digest RAD (ddRAD) sequencing results, the highest genetic diversity is observed in the Western Black Sea (SNP ratio: 28%), followed by the Turkish Straits System (TSS) (with the ratio of 24%). It is identified that the individuals with the unique XVIII haplotype is separated from other individuals. Structure analysis results support the phylogenetic tree analysis results. As a result of mtDNA and ddRAD analysis results, it is mentioned that there is a harbour porpoise subpopulation in the Marmara Sea. In order to preserve the existence of the unique haplotype in the area, a sensitive conservation strategy is required for the harbour porpoise supopulation in the Marmara Sea. The finding of new mtDNA haplotypes, that are only found in this study, will allow the comparison of data between further studies both in Turkey and in the world. This study is the first study, in which the RAD sequencing is used in harbour porpoise samples in the Turkish Straits System (TSS) and the Aegean Sea in order to determine the genetic structure of the species. This study is supported by Scientific Research Projects Coordination Unit of Istanbul University. Project number: 51782.