DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs

Abstract

This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes.

DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds

“…Thus, for species complexes where maximum intraspecific distance exceeds the distance to the nearest neighbor, species-level identification becomes ambiguous (Jinbo, Kato, & Ito, 2011;Sun et al, 2016). The accuracy of DNA metabarcoding identification depends on the "barcode gap," the existence of a gap between interspecific and intraspecific genetic divergence.…”

“…The accuracy of DNA metabarcoding identification depends on the "barcode gap," the existence of a gap between interspecific and intraspecific genetic divergence. Thus, for species complexes where maximum intraspecific distance exceeds the distance to the nearest neighbor, species-level identification becomes ambiguous (Jinbo, Kato, & Ito, 2011;Sun et al, 2016). There are various reasons resulting in the lack of large interspecific divergence, such as hybridization between closely related species, short time since speciation, and incomplete lineage sorting (Lin et al, 2015).…”

Molecular Approach to Identify Gobioid Fishes, “Nike” and “Hundala” (Local Name), from Gorontalo Waters, Indonesia

“…The COI gene is recommended as the standard barcoding marker for most animals (Renxie et al, 2018). Based on COI barcoding, high rates of species-level identification are well documented in many animal species, for instance, 95.27% for numerous northwestern pacific mollusks (Sun et al, 2016) and 98% for marine fishes (Ward, 2009). In addition, many studies have shown that intraspecific variation of COI barcodes is generally pretty small and clearly discriminable from interspecific variation (Hubert et al, 2008;Steinke et al, 2009;Ward et al, 2009;Bucklin et al, 2011).…”

Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA

“…The neotropical skipper butterfly Astraptes fulgerator is the best example (Hebert et al, ). Other animals, such as the bumble bee (Scriven, Whitehorn, Goulson, & Tinsley, ), mollusk (Sun et al, ), frog (Stuart, Inger, & Voris, ), and fish (Borsa, Hsiao, Carpenter, & Chen, ; Feulner, Kirschbaum, Schugardt, Ketmaier, & Tiedemann, ; Rosser, ), were also revealed to contain sympatric cryptic species as detected through mtDNA sequence analysis. The COI sequence is usually used as DNA barcoding for species identification with the criterion of 2% or 3% sequence divergence (e.g., Costa et al, ; Hebert et al, ; Loh, Bond, Ashton, Roberts, & Tibbetts, ; Shen, Guan, Wang, & Gan, ; Ward et al, ).…”

“…Other animals, such as the bumble bee (Scriven, Whitehorn, Goulson, & Tinsley, 2016), mollusk (Sun et al, 2016), frog (Stuart, Inger, & Voris, 2006), and fish (Borsa, Hsiao, Carpenter, & Chen, 2013;Feulner, Kirschbaum, Schugardt, Ketmaier, & Tiedemann, 2006;Rosser, 2015),…”