A two-step DNA barcoding approach for delimiting moth species: moths of Dongling Mountain (Beijing, China) as a case study

Abstract

DNA barcoding, based on a fragment of cytochrome c oxidase I (COI) mtDNA, is as an effective molecular tool for identification, discovery, and biodiversity assessment for most animals. However, multiple gene markers coupled with more sophisticated analytical approaches may be necessary to clarify species boundaries in cases of cryptic diversity or morphological plasticity. Using 339 moths collected from mountains surrounding Beijing, China, we tested a pipeline consisting of two steps: (1) rapid morphospecies sorting and screening of the investigated fauna with standard COI barcoding approaches; (2) additional analyses with multiple molecular markers for those specimens whose morphospecies and COI barcode grouping were incongruent. In step 1, 124 morphospecies were delimited into 116 barcode units, with 90% of the conflicts being associated with specimens identified to the genus Hypena. In step 2, 55 individuals representing all 12 Hypena morphospecies were analysed using COI, COII, 28S, EF-1a, Wgl sequences or their combinations with the BPP (Bayesian Phylogenetics and Phylogeography) multigene species delimitation method. The multigene analyses supported the delimitation of 5 species, consistent with the COI analysis. We conclude that a two-step barcoding analysis pipeline is able to rapidly characterize insect biodiversity and help to elucidate species boundaries for taxonomic complexes without jeopardizing overall project efficiency by substantially increasing analytical costs.

Hidden Genetic Variability, Can the Olive Moth Prays oleae (Lepidoptera: Yponomeutidae or Praydidae?) be a Species’ Complex?

“…DNA barcoding is an extremely powerful tool and it was long established that the mitochondrial gene cytochrome c oxidase I (COI) is the core of the global identification system for animals [27]. However, the use of a mitochondrial amplicon only has also inherent limitations, including on hybrid identification for example [31,32]. Also, in phylogeography, mitochondrial DNA (mtDNA) has been extensively used due to its fast substitution rate, lack of recombination, small effective population size resulting in fast lineage sorting, and high sensitivity to demographic events (e.g.…”

The first record of Cucullia umbratica (Lepidoptera: Noctuidae) from Japan

“…If this genetic difference corresponds to the genetic differentiation between European and Asian populations of Cucullia umbratica , the present result provides support for the possibility that the Japanese population of this moth was introduced from Europe. However, the genetic distance, greater than 3% between European and Chinese populations, is far beyond the range of generally recognised intraspecific variations of Lepidoptera (Hebert et al 2004) and the basis of the species identification for the Chinese specimen was not provided (Jin et al 2018). Therefore, it might be possible that the COI barcode of Chinese Cucullia umbratica (Genbank accession number KJ183425) has been obtained from a misidentified specimen.…”

Sixteen Years of DNA Barcoding in China: What Has Been Done? What Can Be Done?

“…Chinese scientists have used these approaches in their DNA barcoding studies. The last decade, however, has also witnessed significant progress in the methodology of DNA barcoding given many new approaches proposed by Chinese scientists (Zhang et al, 2008(Zhang et al, , 2012a(Zhang et al, ,b, 2017Yu et al, 2012;Liu et al, 2013Liu et al, , 2017Jin et al, 2018;Shi et al, 2018). The main advances include both algorithm development and the optimization of sequencing strategies, as summarized below.…”

“…groups in China (Figure 8A), indicating that the COI region has been consistently important for the general use of DNA barcodes of animal groups due to the fact that COI barcodes perform excellently in most animal groups (e.g., Hebert et al, 2003a,b;Rougerie et al, 2009;Steinke et al, 2009). Although other markers, such as 16S rRNA, Cytb, ITS2, etc., have also been used in some studies of animal groups, they were coanalyzed with COI in most cases (e.g., Li et al, 2010;Jin et al, 2018;Huang et al, 2019). Similarly, ITS genes are the most commonly used molecular markers ( Figure 8C) in studies that focus on microorganisms, while other genes are used relatively infrequently and are generally used as auxiliary barcodes.…”