Scylla serrata (Forskal, 1775) is an important crab resource for aquaculture and coastal fisheries in India. Study on population differentiation and population history of this economically important crab species is very much essential for conservation and management. Wild S. serrata samples were collected from 18 different locations in India including Andaman coastal waters. Population structure and demographic history of S. serrata was evaluated using 425bp of cytochrome b and 562bp of 16S rRNA genes. Only nine and three haplotypes were obtained by the analysis of cytochrome b and 16S rRNA gene respectively. Low level of haplotype diversity, nucleotide diversity, non significant F ST values for16S rRNA gene (F ST = 0.0133) and negative non significant F ST values for cytochrome b gene (F ST = −0.0063) were confirming the lack of population structure in Indian coastal waters. The maximum likelihood tree of cytochrome b gene showed that there were only 2 clusters and one cluster had only one representative (Hap8). The haplotypes of 16S rRNA gene were also clustered in to two groups with haplotype 1 (Hap1) as a separate group in maximum likelihood tree. The present study clearly figure out the S. serrata populations in Indian waters can be considered as a single stock during conservation and management programme.
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