Toward Speleogenomic Pipelines: Characterizing Biodiversity from Species to Communities
Document Type
Conference Proceeding
Publication Date
4-2025
Abstract
Low pass whole genome sequencing (LPWGS), also known as genome skimming, is both affordable and a viable alternative to traditional PCR based DNA Barcoding approaches for biodiversity inventories. From organismal samples, LPWGS enables the recovery of small genomes, such as mitochondria or plastids, as well as high copy nuclear genes commonly used in phylogenetics (e.g., 18S rRNA, 28S rRNA, etc.); while for environmental samples (e.g., sediment), community analyses from microbes to eukaryotes are simultaneously possible. While PCR based approaches are standard, LPWGS facilitates access to genomic data from taxa that are otherwise difficult to amplify due to PCR bias (e.g., primer specificity). For biodiversity inventories targeting multiple taxa or phyla in difficult-to-access environments, such as subterranean estuaries, LPWGS is particularly advantageous. The study presents speleogenomic pipelines to characterize individual organisms to communities generating robust data for multi-gene species delimitation, phylogenetic reconstruction, and wholistic community characterization.
Recommended Citation
Casias, Marci; Grizzle, Connor; and Rodriguez, Marco, "Toward Speleogenomic Pipelines: Characterizing Biodiversity from Species to Communities" (2025). Student Research Symposium 2025. 60.
https://digitalcommons.tamusa.edu/srs_2025/60
Comments
Poster Session 2
5:30-7:00 p.m.
BLH Lobby