Date of Award
2026
Degree Type
Thesis
Degree Name
Master of Science (MS)
Department
Bioinformatics & Computational Biology
First Advisor
Yoel Stuart
Abstract
Freshwater ecosystems cover less than 1% of Earth’s surface and contain only 0.01% of its water, but support nearly a third of its vertebrate species, including over half of all fish. These systems harbor unique and vulnerable taxa and are among the most imperiled habitats globally. Urban rivers are especially degraded, as channelization, industrialization, and infrastructure simplify habitats, reduce native biodiversity, and disrupt ecological function. For example, historical wetland drainage, industrial development, and canalization have transformed the Chicago River into a highly modified, hardened waterway. In recent years, restoration efforts have aimed to reintroduce ecological function to this urban system. The Wild Mile project, led by the nonprofit Urban Rivers, uses floating treatment wetlands with the hope of improving water quality, increasing habitat complexity, and providing habitat for wildlife. Evaluating the ecological outcomes of such interventions requires sensitive and scalable monitoring approaches. Environmental DNA (eDNA) metabarcoding offers a non-invasive way to detect a broad range of taxa, commonly used for biodiversity monitoring, rare species detection, and ecosystem assessment, though its effectiveness depends on the completeness of reference databases. This thesis integrates genomic resource development and eDNA metabarcoding to better monitor and understand freshwater biodiversity. Aim 1 addresses gaps in reference databases by developing a reproducible bioinformatic pipeline to assemble complete mitochondrial genomes from both open-source and in-house sequencing data. As a proof of concept, this workflow produced the first known mitogenome for the Spring Cavefish (Forbesichthys agassizii), a species of Greatest Conservation Need in Illinois, thereby providing a resource for improving eDNA assay design to detect cryptic taxa. Aim 2 applies eDNA metabarcoding to assess how habitat restoration influences vertebrate and mussel communities within the Chicago River’s restored Wild Mile corridor. Water samples from ten restored and ten unrestored sites were analyzed using vertebrate and mussel-specific primers, detecting forty-seven vertebrate species and two mussel species. While overall species richness did not differ inside and outside the Wild Mile, community composition shifted with restoration: vegetation-associated species were more prevalent in restored sections, whereas disturbance-tolerant species were more prevalent in unrestored areas. Together, these studies demonstrate the importance of genomic resources development and how restoration interventions can shape freshwater communities. This work highlights the potential of eDNA as a non-invasive tool for monitoring ecological responses to habitat restoration and provides a framework for integrating genomic and ecological approaches for conservation.
Recommended Citation
Patel, Richa, "Assessing Ecosystem Restoration Using Environmental DNA Metabarcoding: A Case Study of the Chicago River’s ‘Wild Mile’" (2026). Master's Theses. 4584.
https://ecommons.luc.edu/luc_theses/4584
