title: COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae).
abstract: The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, are often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers, thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Xia
authors.forename: Hai-Feng
authors.initials: HF
authors.lastname: Gu
authors.forename: Rui
authors.initials: R
authors.lastname: Peng
authors.forename: Qin
authors.initials: Q
authors.lastname: Chen
authors.forename: Yu-Chi
authors.initials: YC
authors.lastname: Zheng
authors.forename: Robert W
authors.initials: RW
authors.lastname: Murphy
authors.forename: Xiao-Mao
authors.initials: XM
authors.lastname: Zeng
mesh_terms: D029845:Amphibian Proteins / Q000235:genetics*; D000818:Animals; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D003576:Electron Transport Complex IV / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D014562:Caudata / Q000145:classification* / Q000235:genetics*
chemical_list: D029845:Amphibian Proteins; D012336:RNA, Ribosomal, 16S; D003576:Electron Transport Complex IV