Accelerated Spider Identification at Kean Skylands

Sam Charlie

 Co-Presenters: John Loaisiga-Mora
College: Dorothy and George Hennings College of Science, Mathematics and Technology
Major: Biology
Faculty Research Mentor: Jesus Ballesteros Chavez
 

Abstract:

Accurately identifying biological specimens is the first most essential task for revealing major ecological and evolutionary dynamics in any ecosystem. Traditionally, this requires taxonomists as their expertise specializes in specific organism groups. However, developing this skill takes years to accomplish, and it is often undervalued, leading to a decline in taxonomists, also known as the "taxonomist" crisis. Yet, the necessity of naming and describing species persists. DNA barcoding has been proposed to ameliorate this taxonomy crisis by allowing swift specimen identification and classification by comparing short DNA sequences with curated barcode databases. The traditional barcoding approach has nevertheless fallen short to the challenge, because of its limited sequencing output, of little or no use besides the specimen identification, and the time, costs implied for running such project at any productive scale. This study explores Oxford Nanopore long read sequencing technology (ONT), coupled with standard DNA extraction protocols to produce shotgun sequencing libraries to recover barcode regions bio-informatically. Importantly, additional sequences (bycatch) have the potential of enriching and prolonging the utility of the sequencing experiment, providing a broader representation of the pan-genome associated with that specimen. As proof of concept, we surveyed the spider fauna at Kean Skylands Campus during the Fall 2024 semester. We collected spiders at night, using standard collecting techniques, such as sweeping nets and hand collecting. Spiders represent a good group to test this approach because specimens are abundant, encompassing diverse families and the U.S. fauna is relatively well known and documented; at the same time, it represents the typical challenges of most biodiversity surveys, for example where juveniles are the most abundant and only adults can be identified by non-molecular approaches. This allows cross-validation of the barcode identifications compared with traditional morphology-based approaches. Here we present the preliminary results of this survey and discuss the effectiveness of the general protocol in recovering the nominal species barcoding reads with comments on the effects source material, sample management and library preparations. While the challenges of training and supporting professional taxonomists remain, this study emphasizes the relevance, value, and urgency of such expertise in rapidly changing ecosystems.