Mini-barcodes are equally useful for species identification and more suitable for large-scale species discovery in Metazoa than full-length barcodes

Abstract

20New techniques for the species-level sorting of millions of specimens are needed in 21 order to accelerate species discovery, determine how many species live on earth, 22 and develop efficient biomonitoring techniques. These sorting methods should be 23 reliable, scalable and cost-effective, as well as being largely insensitive to low-quality 24 genomic DNA, given that this is usually all that can be obtained from museum 25 specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well 26 they perform for species-level sorting when compared to full-length barcodes. This is 27 here tested based on 20 empirical datasets covering ca. 30,000 specimens and 28 5,500 species, as well as six clade-specific datasets from GenBank covering ca. 29 98,000 specimens for over 20,000 species. All specimens in these datasets had full-30 length barcodes and had been sorted to species-level based on morphology. Mini-31 barcodes of different lengths and positions were obtained in silico from full-length 32 barcodes using a sliding window approach (3 windows: 100-bp, 200-bp, 300-bp) and 33 by excising nine mini-barcodes with established primers (length: 94 -407-bp). We 34 then tested whether barcode length and/or position reduces species-level 35 congruence between morphospecies and molecular Operational Taxonomic Units 36 (mOTUs) that were obtained using three different species delimitation techniques 37 (PTP, ABGD, objective clustering). Surprisingly, we find no significant differences in 38 performance for both species-or specimen-level identification between full-length 39 and mini-barcodes as long as they are of moderate length (>200-bp). Only very short 40 mini-barcodes (<200-bp) perform poorly, especially when they are located near the 41 5' end of the Folmer region. The mean congruence between morphospecies and 42 mOTUs is ca. 75% for barcodes >200-bp and the congruent mOTUs contain ca. 75% 43 of all specimens. Most conflict is caused by ca. 10% of the specimens that can be 44 3 identified and should be targeted for re-examination in order to efficiently resolve 45 conflict. Our study suggests that large-scale species discovery, identification, and 46 metabarcoding can utilize mini-barcodes without any demonstrable loss of 47 information compared to full-length barcodes. 48 49 Keywords: DNA barcoding, mini-barcodes, species discovery, metabarcoding 50 51The question of how many species live on earth has intrigued biologists for 52 centuries, but we are nowhere close to having a robust answer. We do know that 53 fewer than 2 million have been described and that there are an estimated 10-100 54 million multicellular species on the planet (Roskov et al. 2018). We also know that 55 many are currently being extirpated by the "sixth mass extinction" (Ceballos et al. 56 2015; Sánchez-Bayo and Wyckhuys 2019), with potentially catastrophic 57 consequences for the environment (Cafaro 2015). Monitoring, halting, and perhaps 58 even reversing this process is frustrated by the "taxonomic impedime...

Mangroves are an overlooked hotspot of insect diversity despite low plant diversity

“…Given the large number of specimens collected, we only barcoded subsets that represented different taxa and ecological guild (see Materials and Methods; Table S3). The individually NGS-barcoded 140,000 specimens [55] were grouped into putative species, which then allowed for estimating species richness and abundance [56–58]. Contrary to expectations, we demonstrate that mangrove forests have a very distinct and rich insect fauna.…”

DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances

“…Mini-barcoding has been successfully used to identify traditional Chinese herbal ingredients such as Angelicae sinensis radix, Ligusticum sinense, and Notopterygium incisum, among others [102]. Currently, it has been applied to identify the traditional medicinal plant Rhodiola (Crassulaceae) [43], distinguish members of the Apiaceae family [104], and discovery of numerous species in Metazoa [105] and more natural herbal products [17]. Nonetheless, the few nucleotides often limit taxonomic discrimination using mini-barcoding, resulting in the main limitation of mini-barcoding being the resolution [97,106].…”

Three questions: How can taxonomists survive and thrive worldwide?

“…Data quality is an entirely different issue, unapproachable in this paper, as many COI pseudogenes are hosted online because authors simply did not check and mitochondrial heteroplasmy also can confound analyses. Regardless, to get these data, many studies rely on directly sequencing all specimens, which can take the majority of a project's work hours and funding (Tang et al 2015;Yeo et al 2019). Next-generation methods have been suggested as a highthroughput, lower-cost solution, but only now are powerful metabarcoding and metagenomic methods beginning to show promise for accurately quantifying richness in bulk samples (Lang et al 2019;Peel et al 2019;Piper et al 2019).…”