Students Use Expanse at UC San Diego to Study Bolivian Pink River Dolphins

Published October 18, 2024

ACCESS resources at SDSC and Purdue recently played a role in a Bolivian pink dolphin project, which included rescues.  Credit: Mauricio Herrea

By Naavya Ahuja and Kimberly Mann Bruch, SDSC Communications

Undergraduates from Towson University have used the Expanse computing system at the San Diego Supercomputer Center (SDSC) within the School of Computing, Information and Data Sciences at UC San Diego to explore the genomes of several Bolivian pink river dolphin individuals. Specifically, with compute power from Expanse, as well as Anvil at Purdue University, the students assembled and annotated the complete mitochondrial genomes of the pink dolphins, which can be used to study phylogenetic relationships as well as genetic variation among larger dolphin populations.

The Bolivian river dolphin (Inia boliviensis), which is endemic to the waters of the upper Madeira River basin of Bolivia, has been facing habitat degradation and fragmentation through the building of hydroelectric dams, deforestation and water diversion for agricultural irrigation. According to Towson Professor of Biological Sciences Jacqueline Doyle, who led the students in their work, these threats to the river dolphin populations provoked worldwide biologists, geographers, water rescue experts and veterinary researchers to come together on a project to better understand the taxonomic status of these animals. The students learned how to access Expanse and Anvil with Doyle’s guidance via allocations from the U.S. National Science Foundation (NSF) ACCESS program.

For several years, Doyle has specifically been working with worldwide teams ranging from the Noel Kempff Mercado Museum of Natural History in Bolivia to the Maryland Zoo in Baltimore and Saint Louis Zoo Institute for Conservation Medicine. The global team has succeeded in not only relocating several of the dolphins from closed bodies of water or shallow irrigational channels to safe waters, but also conducted well checks and collected small tissues for DNA extraction and subsequent whole-genome sequencing.

In conjunction with this fieldwork, Doyle utilized the data in one of her undergraduate classes at Towson to show a real-world usage of supercomputing resources like those found at SDSC and Purdue.

“Thanks to ACCESS allocations on Expanse and Anvil, the students were able to reconstruct the mitochondrial genomes of the Bolivian pink river dolphin from whole-genome sequencing data in order to build on the body of data that addresses whether this lineage represents a species distinct from the Amazon pink river dolphin,” Doyle said. “This research project not only provided the students with hands-on experience in genomics and bioinformatics but also has the potential to contribute to our understanding of the evolutionary history and taxonomic status of the Bolivian pink river dolphin.”

Computational work was funded by NSF ACCESS (grant no. BIO230100).