Genetic diversity and population structure of penis fish ( Urechis unicinctus ) based on mitochondrial and nuclear gene markers

Abstract

Urechis unicinctus is distributed only in Bohai Gulf of China and Korean and Japanese coast. The wild populations of this species have sharply declined in China and Japan. We collected 105 samples from six localities of Bohai Gulf and Korea coast, and investigated genetic diversity and population structure with mitochondrial COI, 16S-rRNA and nuclear 28S-rRNA gene fragments. Genetic diversity of U. unicinctus based on COI sequences was still high (Hd: 0.9595, π: 0.0101), however, 28S-rRNA gene sequences showed low level of genetic diversity (Hd: 0.4084, π: 0.0007). Based on COI sequences, F values between populations ranged from -0.00204 to 0.05210, and 99.12% genetic diversity was contributed by different individuals within population. Both phylogenetic trees and median-joining network did not show clear geographic cluster, haplotypes from different populations were mixed. Our results indicated low level of genetic divergence among different localities of U. unicinctus, and this species should be treated as a whole population among China, Japan and Korea coast during species conservation.

Genetic Diversity and Population Structure of Acanthochiton rubrolineatus (Polyplacophora) Based on Mitochondrial and Nuclear Gene Markers

“…The gene segments of COI, 16SrRNA and 28SrRNA were amplified respectively with a polymerase chain reaction (PCR) technique using the primers listed in Table S1. The PCR reaction system was same as that described in Gong et al [37]. The PCR procedures were listed in Table S1.…”

“…Mitochondrial COI and 16S rRNA sequences were extensively used to assess the genetic diversity of marine invertebrate species [28,37,[56][57][58][59][60][61]. Combining previous reports, the mitochondrial DNA diversity of A. rubrolineatus was relatively high.…”

“…In general, the genetic diversity of A. rubrolineatus is characterized by high haplotype diversity and low nucleotide polymorphism ( Table 2, Table S4). Many marine invertebrate species that have experienced population decline and following expansion showed this type of genetic diversity [37,58,59], because haplotype diversity may increase rapidly in a short period of time by accumulating mutations, while nucleotide polymorphism cannot return to the original level in the same time [74].…”

“…In the quaternary glacial epoch, there were at least four subglacial and interglacial periods in China. Previous studies on population structures of many marine invertebrate species from Chinese seacoasts [37,[78][79][80][81] showed that Pleistocene glaciation was the main driving force to shape the genetic structures of marine mollusks in China. The dramatical shrinkage of the China Sea and temperature decrease in the subglacial periods led to the population decline or extinction of many marine invertebrate species in some regions.…”

“…Population genetic diversity and structure can reveal the evolutionary history of the species [32,33]. Mitochondrial gene markers, especially the cytochrome c oxidase subunit I gene (COI) and 16S ribosomal RNA gene (16S-rRNA), are commonly used in genetic diversity analyses of marine invertebrates [34][35][36][37][38]. Now, the genetic diversity and population structure of A. rubrilineatus in the whole distribution region is still unclear, though samples from Bohai Bay have been analyzed with COI sequences [39].…”