Skip to Main Content
 

Global Search Box

 
 
 
 

Files

File List


NTM_Dissertation.pdf (13.77 MB)

ETD Abstract Container

Abstract Header

Advancing Genetic Analyses and Implementing eDNA Metabarcoding for Invasive Species Detection and Macroinvertebrate Community Composition

Marshall, Nathaniel T
http://rave.ohiolink.edu/etdc/view?acc_num=toledo1556893201129347

Abstract Details

2019, Doctor of Philosophy, University of Toledo, Biology (Ecology).
The number and rate of species introductions are rising worldwide, and invasion genetics provides a valuable approach to trace introduction sources and routes over their temporal and spatial courses. Discerning what happens to an exotic species over the evolutionary span of introduction and establishment, over its ecological range and across its life stages offers an intriguing real-life experiment. This Ph.D. dissertation project sought to aid understanding of the population genetics and genomic detection underlying the evolution of the closely-related zebra (Dreissena polymorpha) and quagga (D. rostriformis) mussels, by evaluating populations across their > two decade-long temporal invasion courses from two allopatric North American populations in the Hudson River and Lake Erie (Laurentian Great Lakes). Results indicate that temporal divergence has been most pronounced in the zebra mussel’s Hudson River population, showing significant allelic turn-over during the middle time-point (2003). This suggests near complete population replacement, with overall genetic diversity levels remaining similar over time. Samples of veliger larvae from the zebra mussel also significantly differed from the local adult population, which appears attributable to gene flow from adjacent areas and possible genetic admixture. Identifying species and population genetic compositions of these biological invasions at early life stages and/or from environmental (e)DNA using targeted highthroughput sequencing (HTS) metabarcode assays offers powerful and cost-effective detection means. This dissertation develops, tests, and applies a targeted assay to analyze genetic variation from a diagnostic sequence region of the mitochondrial (mt)DNA cytochrome oxidase I (COI) gene, to assess temporal and spatial inter- and intra-specific genetic variability of invasive zebra and quagga mussels. Experiments evaluated its accuracy and performance using: (i) mock laboratory communities containing known DNA quantities per taxon, (ii) aquaria containing mixed species/haplotype compositions of adults, and (iii) field-collected water and plankton versus traditional sampling of adult communities. Results successfully delineated species compositions, relative abundances, and population-level diversity differences among ecosystems, habitats, time series, and life stages from two allopatric concurrent invasions in Lake Erie and the Hudson River. Species compositions and diversity of macroinvertebrates comprise a primary focus for monitoring aquatic communities, serving as possible sentinel indicators of ecosystem health. In this study, a suite of targeted metabarcode HTS assays were used to characterize the macroinvertebrate communities from eDNA water samples along the Maumee River. Metabarcode results were compared with a traditional sampling, identification, and enumeration survey done by a government agency (the Ohio Environmental Protection Agency) for multiple alpha (richness, Shannon-Wiener diversity, Simpson’s index, and evenness) and beta (Bray-Curtis and Jaccard dissimilarities) diversity measures. Targeted metabarcoding uncovered greater gamma richness, delineating 183 Operational Taxonomic Units (OTUs) versus 173 taxa from the conventional survey. eDNA and traditional sampling data displayed similar trends, showing comparable alpha diversity patterns and community compositions among habitat type and habitat quality scores along the river. Findings illustrate the utility of eDNA sampling and targeted HTS metabarcode assays, to enhance and complement environmental assessment of aquatic ecosystems for invasive species and biodiversity management. In conclusion, this dissertation study sought to help "pave the way" for the growing toolkit of biotechnology in revealing the evolutionary and ecological population changes. It is hoped that these approaches will be useful for helping to conserve, preserve, and improve our aquatic fauna for generations to come.
Carol Stepien, PhD (Committee Chair)
Jeanine Refsnider, PhD (Committee Member)
W. Von Sigler, PhD (Committee Member)
Jeffrey Ram, PhD (Committee Member)
David Strayer, PhD (Committee Member)
217 p.
Aquatic Sciences; Ecology; Environmental Science; Molecular Biology

Recommended Citations

Citations

  • Marshall, N. T. (2019). Advancing Genetic Analyses and Implementing eDNA Metabarcoding for Invasive Species Detection and Macroinvertebrate Community Composition [Doctoral dissertation, University of Toledo]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1556893201129347

    APA Style (7th edition)

  • Marshall, Nathaniel. Advancing Genetic Analyses and Implementing eDNA Metabarcoding for Invasive Species Detection and Macroinvertebrate Community Composition. 2019. University of Toledo, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=toledo1556893201129347.

    MLA Style (8th edition)

  • Marshall, Nathaniel. "Advancing Genetic Analyses and Implementing eDNA Metabarcoding for Invasive Species Detection and Macroinvertebrate Community Composition." Doctoral dissertation, University of Toledo, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1556893201129347

    Chicago Manual of Style (17th edition)

toledo1556893201129347
160
© 2019, some rights reserved.Creative Commons License Advancing Genetic Analyses and Implementing eDNA Metabarcoding for Invasive Species Detection and Macroinvertebrate Community Composition by Nathaniel T Marshall is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by University of Toledo and OhioLINK.