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.

Catalogue of the Type Specimens of Amphibians and Reptiles in the Herpetological Museum of the Chengdu Institute of Biology, Chinese Academy of Sciences: II. Hynobiidae (Amphibia, Urodela)

“…Comments: Previously, P. jinfo was considered as a population of P. flavomaculatus (Fei et al, 2006), Zeng et al (2006) suggested it is a cryptic species based on the molecular data, and Wei et al (2009) Huang et al (1992) and Fei et al (2006) considered that the diagnosis of the genus Liua cannot effectively distinguish the genus Liua from the genus Ranodon, so the genus Liua was not valid, and R. shihi should be assigned in the genus Ranodon. However, the molecular data supports the validity of the genus Liua (Li et al, 2004;Wang et al, 2005;Zeng et al, 2006;Zhang et al, 2006;Xia et al, 2012). In addition to the listed 699 specimens of L. shihi, whose populations are affirmed by molecular data, 52 other specimens have (Liu and Hu, 1966).…”

“…Classification of taxa mainly follows Fei et al (2006), AmphibiaWeb (2012) and Xia et al (2012). All information for each type specimen of the seven species is presented in the following format: genus name, species name, information of the original description, the catalog number of holotype, sex, type locality, information of allotype (if any) and paratype, number and distribution of deposited specimens, except Pseudohynobius kuankuoshuiensis.…”

DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae)

“…DOI: 10.3109/19401736.2015.1041113 DNA barcoding of Rhacophoridae 5 the more overlap between intraspecific genetic variation and interspecific divergence the less effective barcoding became. Overlap also occurs in other species, such as in blue butterflies (Wiemers & Fiedler, 2007), corals (Shearer & Coffroth, 2008), gastropods (Puillandre et al, 2009) and hynobiids (Xia et al, 2012). Regardless, existence of a DNA barcoding gap remains controversial.…”

“…However, effective DNA barcoding relies on a universal gene and COI serves this purpose (Hebert et al, 2003). COI has a faster evolutionary rate than 16S, and, thus, it identifies species better and helps to discover cryptic species (Xia et al, 2012). Smith et al (2007) found that COI barcoding could identify 94% of amphibian species correctly.…”

Molecular barcoding of venomous snakes and species-specific multiplex PCR assay to identify snake groups for which antivenom is available in Thailand

“…The gene most commonly used as a marker for the barcode is the mitochondrial COI gene because it has been studied in many vertebrates and exhibits interspecific nucleotide divergence that is greater than its intraspecific nucleotide divergence (Chaves et al, 2008). Other mitochondrial genes, such as Cytb and 16S rRNA (Xia et al, 2012;Nicolas et al, 2012), have also been employed as barcodes with varying levels of success. Snake DNA barcodes based on COI, Cytb, and 12S rRNA genes are well established in India, China, and the USA (Wong et al, 2004;Pook and McEwing, 2005;Dubey et al, 2011;Gaur et al, 2012).…”