Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan

Taha Soliman; Okuto Takama; Iria Fernandez-Silva; James D Reimer

doi:10.7717/peerj.2410

Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan

PeerJ. 2016 Sep 28:4:e2410. doi: 10.7717/peerj.2410. eCollection 2016.

Authors

Taha Soliman¹, Okuto Takama², Iria Fernandez-Silva³, James D Reimer⁴

Affiliations

¹ Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan; National Institute of Oceanography and Fisheries, Alexandria, Egypt; Microbiology and Biochemistry of Secondary Metabolites Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.
² Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus , Nishihara , Okinawa , Japan.
³ Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan; Section of Ichthyology, California Academy of Sciences, San Francisco, CA, USA; Department of Biochemistry, Genetics and Immunology, Campus Universitario, University of Vigo, Vigo, Spain.
⁴ Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan; Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan.

Abstract

The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan.

Keywords: 16S ribosomal DNA; Okinawa Island; Sea cucumber; Stichopus chloronotus; mtDNA.

Grants and funding

TS was supported by Ministry of Higher Education of the Egyptian Government during this study in Japan. JDR was funded by a Japan Society for the Promotion of Science (JSPS) ‘Zuno-Junkan’ grant entitled ‘Studies on origin and maintenance of marine biodiversity and systematic conservation planning.’ IF-S was funded by a JSPS postdoctoral fellowship for overseas researchers and the European Union Seventh Framework Programme (FP7/2007-2011) under grant agreement PIOF-GA-2011-302957. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.