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

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

Bibliographic Details
Main Author: Marshall, Nathaniel T.
Language:English
Published: University of Toledo / OhioLINK 2019
Subjects:
Aquatic Sciences
Ecology
Environmental Science
Molecular Biology
Online Access:http://rave.ohiolink.edu/etdc/view?acc_num=toledo1556893201129347
id ndltd-OhioLink-oai-etd.ohiolink.edu-toledo1556893201129347
record_format oai_dc
collection NDLTD
language English
sources NDLTD
topic Aquatic Sciences
Ecology
Environmental Science
Molecular Biology
spellingShingle Aquatic Sciences
Ecology
Environmental Science
Molecular Biology
Marshall, Nathaniel T.
Advancing Genetic Analyses and Implementing eDNA Metabarcoding for InvasiveSpecies Detection and Macroinvertebrate Community Composition
author Marshall, Nathaniel T.
author_facet Marshall, Nathaniel T.
author_sort Marshall, Nathaniel T.
title Advancing Genetic Analyses and Implementing eDNA Metabarcoding for InvasiveSpecies Detection and Macroinvertebrate Community Composition
title_short Advancing Genetic Analyses and Implementing eDNA Metabarcoding for InvasiveSpecies Detection and Macroinvertebrate Community Composition
title_full Advancing Genetic Analyses and Implementing eDNA Metabarcoding for InvasiveSpecies Detection and Macroinvertebrate Community Composition
title_fullStr Advancing Genetic Analyses and Implementing eDNA Metabarcoding for InvasiveSpecies Detection and Macroinvertebrate Community Composition
title_full_unstemmed Advancing Genetic Analyses and Implementing eDNA Metabarcoding for InvasiveSpecies Detection and Macroinvertebrate Community Composition
title_sort advancing genetic analyses and implementing edna metabarcoding for invasivespecies detection and macroinvertebrate community composition
publisher University of Toledo / OhioLINK
publishDate 2019
url http://rave.ohiolink.edu/etdc/view?acc_num=toledo1556893201129347
work_keys_str_mv AT marshallnathanielt advancinggeneticanalysesandimplementingednametabarcodingforinvasivespeciesdetectionandmacroinvertebratecommunitycomposition
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spelling ndltd-OhioLink-oai-etd.ohiolink.edu-toledo15568932011293472021-08-03T07:11:00Z Advancing Genetic Analyses and Implementing eDNA Metabarcoding for InvasiveSpecies Detection and Macroinvertebrate Community Composition Marshall, Nathaniel T. Aquatic Sciences Ecology Environmental Science Molecular Biology The number and rate of species introductions are rising worldwide, and invasiongenetics provides a valuable approach to trace introduction sources and routes over theirtemporal and spatial courses. Discerning what happens to an exotic species over theevolutionary span of introduction and establishment, over its ecological range and acrossits life stages offers an intriguing real-life experiment. This Ph.D. dissertation projectsought to aid understanding of the population genetics and genomic detection underlyingthe evolution of the closely-related zebra (Dreissena polymorpha) and quagga (D.rostriformis) mussels, by evaluating populations across their > two decade-long temporalinvasion courses from two allopatric North American populations in the Hudson Riverand Lake Erie (Laurentian Great Lakes). Results indicate that temporal divergence hasbeen most pronounced in the zebra mussel’s Hudson River population, showingsignificant allelic turn-over during the middle time-point (2003). This suggests nearcomplete population replacement, with overall genetic diversity levels remaining similarover time. Samples of veliger larvae from the zebra mussel also significantly differed from the local adult population, which appears attributable to gene flow from adjacentareas and possible genetic admixture.Identifying species and population genetic compositions of these biologicalinvasions at early life stages and/or from environmental (e)DNA using targeted highthroughputsequencing (HTS) metabarcode assays offers powerful and cost-effectivedetection means. This dissertation develops, tests, and applies a targeted assay to analyzegenetic variation from a diagnostic sequence region of the mitochondrial (mt)DNAcytochrome oxidase I (COI) gene, to assess temporal and spatial inter- and intra-specificgenetic variability of invasive zebra and quagga mussels. Experiments evaluated itsaccuracy and performance using: (i) mock laboratory communities containing knownDNA quantities per taxon, (ii) aquaria containing mixed species/haplotype compositionsof adults, and (iii) field-collected water and plankton versus traditional sampling of adultcommunities. Results successfully delineated species compositions, relative abundances,and population-level diversity differences among ecosystems, habitats, time series, andlife stages from two allopatric concurrent invasions in Lake Erie and the Hudson River.Species compositions and diversity of macroinvertebrates comprise a primaryfocus for monitoring aquatic communities, serving as possible sentinel indicators ofecosystem health. In this study, a suite of targeted metabarcode HTS assays were used tocharacterize the macroinvertebrate communities from eDNA water samples along theMaumee River. Metabarcode results were compared with a traditional sampling,identification, and enumeration survey done by a government agency (the OhioEnvironmental Protection Agency) for multiple alpha (richness, Shannon-Wienerdiversity, Simpson’s index, and evenness) and beta (Bray-Curtis and Jaccard dissimilarities) diversity measures. Targeted metabarcoding uncovered greater gammarichness, delineating 183 Operational Taxonomic Units (OTUs) versus 173 taxa from theconventional survey. eDNA and traditional sampling data displayed similar trends,showing comparable alpha diversity patterns and community compositions among habitattype and habitat quality scores along the river. Findings illustrate the utility of eDNAsampling and targeted HTS metabarcode assays, to enhance and complementenvironmental assessment of aquatic ecosystems for invasive species and biodiversitymanagement. In conclusion, this dissertation study sought to help "pave the way" for thegrowing toolkit of biotechnology in revealing the evolutionary and ecological populationchanges. It is hoped that these approaches will be useful for helping to conserve,preserve, and improve our aquatic fauna for generations to come. 2019-08-28 English text University of Toledo / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=toledo1556893201129347 http://rave.ohiolink.edu/etdc/view?acc_num=toledo1556893201129347 unrestricted This thesis or dissertation is protected by copyright: some rights reserved. It is licensed for use under a Creative Commons license. Specific terms and permissions are available from this document's record in the OhioLINK ETD Center.

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