Integrating a DNA barcoding project with an ecological survey:a case study on temperate intertidal polychaete communities in Qingdao,China

In this study,we integrated a DNA barcoding project with an ecological survey on intertidal polychaete communities and investigated the utility of CO1 gene sequence as a DNA barcode for the classification of the intertidal polychaetes.Using 16S rDNA as a complementary marker and combining morphological and ecological characterization,some of dominant and common polychaete species from Chinese coasts were assessed for their taxonomic status.We obtained 22 haplotype gene sequences of 13 taxa,including 10 CO1 sequences and 12 16S rDNA sequences.Based on intra-and inter-specific distances,we built phylogenetic trees using the neighbor-joining method.Our study suggested that the mitochondrial CO1 gene was a valid DNA barcoding marker for species identification in polychaetes,but other genes,such as 16S rDNA,could be used as a complementary genetic marker.For more accurate species identification and effective testing of species hypothesis,DNA barcoding should be incorporated with morphological,ecological,biogeographical,and phylogenetic information.The application of DNA barcoding and molecular identification in the ecological survey on the intertidal polychaete communities demonstrated the feasibility of integrating DNA taxonomy and ecology.

Species Identification of a Commonly Believed Sinarapan Fish Mystichtys luzonensis （Smith, 1902） in Lakes Buhi and Bato of Bicol Region

The paper aimed to determine the true identity of a presumed or commonly believed Sinarapan fish and compare their phylogenetic relationships by using DNA barcoding. The fish samples were collected by researchers from a fisheries research and development institution in April 2015 from four different lakes of Bicol Region, i.e., Lakes Buhi, Danao, Manapao and Bato. DNA was extracted using cetyl trimethyl ammonium bromide （CTAB） extraction buffer. The polymerase chain reaction （PCR） profile for the reaction was 94 ℃ for 10 min, followed by 35 cycles of 1 min at 94℃, 1 min at 48℃ and 1.5 min at 72℃, and a final extension of 10 min at 72℃. The CO 1 region with approximately 650 bp was amplified because of its capability to differentiate taxa. Sequencing was done by Macrogen while phylogenetic analysis was produced using a Molecular Evolutionary Genetics Analysis （MEGA） software version 6.0. The findings showed that CO1 can be used as a DNA marker in molecular identification of the fish samples. Samples from two of the four lakes were successfully sequenced. From basic local alignment search tool （BLAST） results, the maximum parsimony （MP） and neighbor-joining （N J） trees revealed that samples from Lakes Buhi and Bato are not species of Sinarapan but rather species of Leiopotherapon plumbeus and Rhinogobius giurinus, respectively. Furthermore, DNA barcoding is very useful in proving the true identity of unknown samples.