DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters

Abstract

The application of DNA barcoding represents a complementary and efficient approach to identifying specimens at all stages of their life cycle when used in combination with traditional morphological methods. Due to difficulties obtaining samples from the deep sea (> 200 m), these methods have been less frequently applied to deep-water taxa. We used DNA-barcoding techniques to enhance large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico, a region that has recently been identified as one of the world’s four most hyperdiverse ocean ecosystems. This study was conceptualized in direct response to the Deepwater Horizon Oil Spill in 2010, which identified major knowledge gaps in our understanding of deep-sea biodiversity. We employed traditional Sanger sequencing and a genomic skimming approach to target the mitochondrial ribosomal large subunit 16S and the protein-coding cytochrome oxidase subunit 1 (COI). Alongside these molecular approaches, traditional taxonomic investigations allowed for advancements in biodiversity, evolutionary relationships, cryptic species complexes, and distributional records across four abundant and common deep-pelagic orders (Amphipoda, Euphausiacea, Lophogastrida, and Decapoda). DNA barcodes were successfully obtained from 82 species for a total of 158 and 169 new 16S and COI sequences, respectively. Evidence of cryptic diversity has been found in the genera EucopiaDana, 1852 (Lophogastrida) and Allosergestes Judkins & Kensley, 2008 (Decapoda). New records for the Gulf of Mexico of species of LanceolaSay, 1818 (Amphipoda), Eupasiphae Wood-Mason in Wood-Mason & Alcock, 1893, PasiphaeaSavigny, 1816, and MeningodoraSmith, 1882 (Caridea) are presented. Preliminary results allow us to reconsider the current classification and evolutionary relationships of several lineages. The urgency to document biodiversity in the deep-pelagic is pressing against a backdrop of future threats including oil spills and deep-sea drilling.

A Mysterious World Revealed: Larval-Adult Matching of Deep-Sea Shrimps from the Gulf of Mexico

“…Newly generated larval sequences were aligned with a subset of data generated in [35] alongside other sequences from previously published studies (Supplementary Table S1) to help identify the unknow larvae. The Multiple Sequence Alignment Tool (MAFFT) with the E-INS-i algorithm [57] was used to align the DNA sequences.…”

“…Our DNA barcoding efforts resulted in a total of 25 de novo 16S sequences and nine de novo COI sequences from these larvae. Using a subset of the dataset generated from [35] and previous studies, in combination with these newly generated larval sequences (Supplementary Table S1), the final tree (16S + COI) included 51 total species from the infraorder Caridea and suborder Dendrobranchiata (Figure 3). Using this phylogeny, we were able to successfully match 14 larval and juvenile species (=16 developmental stages) with their adult counterparts.…”

“…In this paper, we have a juvenile Funchalia villosa which was identified using sequences obtained by [35]. This species is pelagic, and it is known to perform diel vertical migrations, descending to 2608 m deep during the day and migrating to shallow water of around 50 m deep at night [84,85].…”

“…Although rearing experiments have facilitated the taxonomic identification of larvae from plankton samples, most are difficult (or impossible) to breed and maintain in the laboratory. Molecular approaches, such as DNA barcoding, can be an excellent alternative or complementary method for larval identifications [32][33][34][35]. This method does require a reliable database of adult barcodes that are linked to vouchered museum specimens in zoological collections.…”

“…16S and COI) and phylogenetic trees. A very recent barcoding study on adult deep-pelagic crustaceans was conducted in the Gulf of Mexico and adjacent waters [35], and we plan to use this dataset (alongside previously published datasets) to match unknown larvae collected on research expeditions into the northern Gulf of Mexico and adjacent waters over the past 5 years.…”