Identifying the Genetic Distance Threshold for Entiminae (Coleoptera: Curculionidae) Species Delimitation via COI Barcodes

Abstract

The subfamily Entiminae is the largest group in the family Curculionidae, and it has long represented a challenge in traditional and molecular classification. Here, we analyzed intra- and interspecific genetic distances of 621 public COI barcode sequences (658bp) from 39 genera and 110 species of Entiminae, to determine parameters most congruent in retaining established species. We found that the mean intraspecific genetic distance (3.07%) was much smaller than the mean interspecific one (21.96%), but there is a wide range of overlap between intra- and interspecific genetic distances (0.77–18.01%), indicating that there is no consistent, universal barcoding gap. Specifically, DNA barcoding gap analysis for morphospecies revealed that 102 of 110 morphospecies had barcoding gaps, and 9.18% was the optimum threshold of genetic distances for 97 species delimitation. We further confirmed this threshold with barcodes from 27 morphologically identified specimens (including 21 newly reported barcodes) sequenced from five genera and seven species. We also identified thresholds to delimit congeneric species within 14 selected genera (species > 2), which varied from 7.42% (Trichalophus) to 13.48% (Barypeithes). We herein present optimal parameters for species identification in the Entiminae. Our study suggests that despite no universal genetic distance threshold value in subfamily Entiminae, 9.18% is optimal for most species. We recommend a wider sampling of geographic populations to better account for intraspecific distance variation, and that genetic distance thresholds for species delimitation should be refined at the genus level.

Comprehensive DNA barcode reference library and optimization of genetic divergence threshold facilitate the exploration of species diversity of green lacewings (Neuroptera: Chrysopidae)

“…, 2021; Ma et al. , 2022). However, the repeated inferences of optimal threshold would restrict wide utility of a regional DNA barcode reference library, and whether the threshold significantly changes with the expansion of reference library requires further investigation.…”

“…As evolutionary histories vary among taxonomic groups (Davison et al, 2009;Zhang et al, 2017), the empirical threshold of 2.00%, which was inferred based on Lepidoptera (Hebert et al, 2003), may not be applicable in other insects, leading to overestimation or underestimation of species diversity (Zhang et al, 2017). Moreover, several studies pointed out that the optimal threshold should be estimated independently for each reference library within the same taxonomic group, as the genetic diversity among different regional lineages may not be uniformly shaped (Attiná et al, 2021;Ma et al, 2022). However, the repeated inferences of optimal threshold would restrict wide utility of a regional DNA barcode reference library, and whether the threshold significantly changes with the expansion of reference library requires further investigation.…”

“…, 2006; Ma et al. , 2022). Accordingly, the threshold of genetic distance to define the boundary of species should be optimized for a specific group that includes only the species with close phylogenetic relationships (Davison et al.…”

“…The empirical threshold, that is, 2.00% or 3.00% of genetic divergence of the COI DNA barcodes (Hebert et al, 2003;Hajibabaei et al, 2006), is frequently used to distinguish whether a variation of the DNA barcode region is intraspecific or interspecific (Zhang et al, 2017). However, such criteria cannot be universal because the evolutionary rate of a gene may greatly vary among distantly related groups (Meier et al, 2006;Ma et al, 2022). Accordingly, the threshold of genetic distance to define the boundary of species should be optimized for a specific group that includes only the species with close phylogenetic relationships (Davison et al, 2009;Gadawski et al, 2022).…”

A novel biological sources consistency evaluation method reveals high level of biodiversity within wild natural medicine: A case study of Amynthas earthworms as “Guang Dilong”

“…As the discrimination result of subsequent commercial samples implied, it was feasible to stabilize the species origin of wild TCM by controlling their geographical origin. This study also provided an identification tool for earthworm medical materials, such as mini-barcode primers pair and reasonable species genetic distance threshold 92 . Combined with the power of DNA metabarcoding, it could support the large-scale sampling needed for time- and cost-efficient assessment of commercial materials.…”