DNA barcodes and reliable molecular identifications in a diverse group of invasive pests: lessons fromBactrocerafruit flies on variation across the COI gene, introgression, and standardization

Abstract

The utility of a universal DNA ‘barcode’ fragment of 658 base pairs of the Cytochrome C Oxidase I (COI) gene for the recognition of all animal species has been a widely debated topic on theoretical and practical levels. Regardless of its challenges, large amounts of COI sequence data have been produced in the last two decades. To optimally use the data towards reliable species identification will require further steps to validate the method and reference libraries. The fruit fly tribe Dacini holds about a thousand species, of which eighty are pests of economic concern, including some of the world’s foremost fruit and vegetable pests, and there are many morphologically cryptic species complexes in the tribe. Where previous studies showed limited success in using COI to identify Dacini, our results with a highly curated morphological dataset indicate high congruence between morphology and COI: 90% of the species in our 5,576 sequences, 262-species global dataset can be identified with COI alone based on a monophyly criterion. However, in some key pest species belonging to complexes that were previously thought diagnosable with COI, we found that expanded sampling and independent validation of identifications using genomic data revealed introgression of mitochondrial DNA. We find that the informative SNPs are uniformly distributed across the COI gene, and we provide recommendations for standardization. We conclude that reliable molecular identifications with COI require extensive species coverage, population sampling, and genomics-supported reference identifications before they can be validated as a “diagnostic” marker for specific groups.

Complete mitochondrial genome of Dacus vijaysegarani and phylogenetic relationships with congeners and other tephritid fruit flies (Insecta: Diptera)

“…Based on cox1 gene [2] and concatenation of cox1 and six nuclear genes [8], D. vijaysegarani from Vietnam is closely related to D. ancoralis from Sri Lanka. The Vietnam taxon of D. vijaysegarani also forms a monophyletic COXI cluster with specimens from Bangladesh resembling D. jacobi from India [39]. Our present study based on near complete cox1 gene shows a large genetic distance of 9.15 % between the Vietnam and Malaysia taxa of D. vijaysegarani.…”

Novel lures and COI sequences reveal cryptic new species of Bactrocera fruit flies in the Solomon Islands (Diptera, Tephritidae, Dacini)

“…All flies were identified to species using available keys (Drew 1989;Drew and Romig 2001). We pulled one or two legs from specimens that were selected for DNA extraction (for further details on DNA extraction methods see Doorenweerd et al 2020). All holotypes and all, or a subset of, the paratypes were double-mounted to be stored as dry specimens in collections for permanent future reference.…”

“…Notes. Bactrocera allodistincta was included as B. spnSol01 in Doorenweerd et al (2020). (Malloch), only distinguished by a subtle difference in wing infuscation in the presence of a light fuscous tinge as a broad, somewhat triangular area covering much of the middle of the wing, including the areas bordering r-m and dm-cu (Fig.…”

“…Notes. Bactrocera geminosimulata was included as B. spSol12 in Doorenweerd et al (2020). Differential diagnosis.…”

Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths

“…We used PyCOIStats v1.3 (Doorenweerd et al, 2020) to calculate the number of haplotypes distinct to each respective species, that is without considering missing data (Ns) and ambiguous base-calls such as Y, W, N, etc. as differences in the assignment of each haplotype (for further details see the readme document at https://doi.org/10.5281/zenodo.4123683).…”