DNA barcoding in the Southeast Pacific marine realm: Low coverage and geographic representation despite high diversity

Abstract

The Southeast Pacific comprises two Large Marine Ecosystems, the Pacific Central-American Coastal and the Humboldt Current System; and is one of the less well known in the tropical subregions in terms of biodiversity. To address this, we compared DNA barcoding repositories with the marine biodiversity species for the Southeast Pacific. We obtained a checklist of marine species in the Southeast Pacific (i.e. Colombia, Ecuador, Chile, and Peru) from the Ocean Biodiversity Information System (OBIS) database and compared it with species available at the Barcoding of Life Data System (BOLD) repository. Of the 5504 species records retrieved from OBIS, 42% of them had at least one registered specimen in BOLD (including specimens around the world); however, only 4.5% of records corresponded to publicly available DNA barcodes including specimens collected from a Southeast Pacific country. The low representation of barcoded species does not vary much across the different taxonomic groups or within countries, but we observed an asymmetric distribution of DNA barcoding records for taxonomic groups along the coast, being more abundant for the Humboldt Current System than the Pacific Central-American Coastal. We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. Our results highlight the critical need for increasing taxonomic sampling effort, the number of trained taxonomic specialists, laboratory facilities, scientific collections, and genetic reference libraries.

Species Delimitation of Southeast Pacific Angel Sharks (Squatina spp.) Reveals Hidden Diversity through DNA Barcoding

“…All efforts to quantify the impact of fisheries in South American angel sharks will be unsuccessful without a precise identification of the species. The use of molecular approaches, such as DNA barcoding, has a potential to quickly identify undescribed species in poorly studied regions like the Southeast Pacific [78]; and in ecologically and economically important groups like Elasmobranchii that hold a high level of taxonomic uncertainties [78].…”

Revision and annotation of DNA barcode records for marine invertebrates: report of the 8thiBOL conference hackathon

“…To date, the ever-growing libraries have been deposited mostly in two large and public molecular databases, namely (i) GenBank (Sayers et al 2021), a repository with data usually released after publication, and (ii) the Barcode of Life Data Systems (BOLD, Ratnasingham and Hebert 2007), a workbench in which data can be validated and analyzed before being released. Parallel with this growth, instances of inaccurate or discordant data have been increasingly reported (Lis et al 2016, Meiklejohn et al 2019, Ramirez et al 2020, Fontes et al 2021, particularly when comparing data of morphological and molecular origin. This is recognized as a pertinent issue for the reliability of current and prospective DNA-based biomonitoring (Leese et al 2018).…”

Classification of Fish Species with Image Data Using K-Nearest Neighbor

“…Species classification has four parts. First, differences in individual, gender, geography, phenotypic plasticity, and genetic variability can lead to misclassification [6]. Second, there is ecological damage to the environment and human activities that cause damage to the fishery environment, making it difficult to collect fish species [7,8].…”