Two Distinct Mitochondrial Genealogies and their Divergence Rate in the Sea Urchin Strongylocentrotus intermedius

Abstract

The sea urchin Strongylocentrotus intermedius (A. Agassiz, 1863) is an ecologically and economically important species inhabiting the shallow water hard substrates in the northwest Pacific including the East Sea. In this study we attempted to analyze the genetic structure of the sea urchin with samples from Jumunjin, east coast of Korea using mitochondrial DNA sequences. First, a total of 20 individuals were analyzed for their COI sequences, which resulted in 10 haplotypes. Phylogenetic tree of the haplotypes showed that there are two genetic groups. These two genealogies in S. intermedius were also found sympatrically in the northern part of the East Sea near Primorye, Russia. Secondly, the whole mitochondria genomes of the two haplo-groups were sequenced and compared gene by gene for examination of the divergence rate. Nucleotide sequence divergence was the highest in the ND5 gene of about 1.7% per site and the lowest in the ATP8 gene which showed no nucleotide substitution. Among the 13 coding genes, amino acid changing nucleotide substitution occurred only in ND1 (1 substitution), ND2 (2), ATP6 (1), ND4 (3), and ND5 (8). This study will help understand what kind of selection is acting on the evolution of the sea urchin mitochondrial DNA, and how long this polymorphism have been maintained in the S. intermedius species.ted to analyze the genetic structure of the sea urchin with samples from Jumunjin, east coast of Korea using mitochondrial DNA sequences. First, a total of 20 individuals were analyzed for their COI sequences, which resulted in 10 haplotypes. Phylogenetic tree of the haplotypes showed that there are two genetic groups. These two genealogies in S. intermedius were also found sympatrically in the northern part of the East Sea near Primorye, Russia. Secondly, the whole mitochondria genomes of the two haplo-groups were sequenced and compared gene by gene for examination of the divergence rate. Nucleotide sequence