The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata.

Adrian Kannan,Yoon-Yen Yow,Suganiya Rama Rao,Shyamala Ratnayeke

doi:10.7717/peerj.8755

Abstract

Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as ‘barcodes’ to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06–6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.

Highlights

Cryptic species are often subject to ambiguous and erroneous species classification in the field of biological taxonomy
We evaluated the effectiveness of both mitochondrial markers of c oxidase subunit I (COI) and 16S ribosomal deoxyribonucleic acid (rDNA) for DNA barcoding of Pomacea spp. in Peninsular Malaysia
Sizes of amplified fragments of these regions were in the range of 669 bp to 714 bp and 528 bp to 550 bp for the COI and 16S rDNA regions respectively

Summary

Introduction

Cryptic species are often subject to ambiguous and erroneous species classification in the field of biological taxonomy. In the case of cryptic speciation, the identification of genetically distinct species is masked empirically by their indistinguishable morphology which renders traditional taxonomy sometimes impractical (Bickford et al, 2007). The increasing significance of molecular genetics in modern taxonomy has uncovered hidden or cryptic biodiversity to aid and improve the resolution of morphological-based species delimitation (Bickford et al, 2007), since the introduction of DNA barcoding (Hebert et al, 2003). Prone to pitfalls (Will, Mishler & Wheeler, 2005; Waugh, 2007), DNA barcoding is sometimes considered a valuable tool because it complements traditional morphological taxonomy facilitating an integrated approach of species delimitation (Sheth & Thaker, 2017). The role of DNA barcoding as a diagnostic tool for cryptic diversity in conservation biology is useful, since it plays a crucial role in managing invasive alien pests (Armstrong & Ball, 2005)

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