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Trophic Relationships, Distribution and Interactions Among Invasive And University of Windsor Scholarship at UWindsor Electronic Theses and Dissertations Theses, Dissertations, and Major Papers 9-27-2018 Trophic relationships, distribution and interactions among invasive and native Laurentian Great Lakes biota assessed using metabarcoding of stomach content DNA (scDNA) and environmental DNA (eDNA) Justin Glenn Mychek-Londer University of Windsor Follow this and additional works at: https://scholar.uwindsor.ca/etd Recommended Citation Mychek-Londer, Justin Glenn, "Trophic relationships, distribution and interactions among invasive and native Laurentian Great Lakes biota assessed using metabarcoding of stomach content DNA (scDNA) and environmental DNA (eDNA)" (2018). Electronic Theses and Dissertations. 7549. https://scholar.uwindsor.ca/etd/7549 This online database contains the full-text of PhD dissertations and Masters’ theses of University of Windsor students from 1954 forward. These documents are made available for personal study and research purposes only, in accordance with the Canadian Copyright Act and the Creative Commons license—CC BY-NC-ND (Attribution, Non-Commercial, No Derivative Works). Under this license, works must always be attributed to the copyright holder (original author), cannot be used for any commercial purposes, and may not be altered. Any other use would require the permission of the copyright holder. Students may inquire about withdrawing their dissertation and/or thesis from this database. For additional inquiries, please contact the repository administrator via email ([email protected]) or by telephone at 519-253-3000ext. 3208. Trophic relationships, distribution and interactions among invasive and native Laurentian Great Lakes biota assessed using metabarcoding of stomach content DNA (scDNA) and environmental DNA (eDNA) by Justin Glenn Mychek-Londer A Dissertation Submitted to the Faculty of Graduate Studies Through the Great Lakes Institute for Environmental Research In Partial Fulfilment of the Requirements for The Degree of Doctor of Philosophy At The University of Windsor Windsor, Ontario, Canada 2018 © Justin G. Mychek-Londer Trophic relationships, distribution and interactions among invasive and native Laurentian Great Lakes biota assessed using metabarcoding of stomach content DNA (scDNA) and environmental DNA (eDNA) by Justin G. Mychek-Londer APPROVED BY: __________________________________________________ N. Collins, External Examiner University of Toronto __________________________________________________ T. Johnson Ontario Ministry of Natural Resources __________________________________________________ H. J. MacIsaac Great Lakes Institute for Environmental Research __________________________________________________ A. T. Fisk Great Lakes Institute for Environmental Research __________________________________________________ D. Heath, Advisor Great Lakes Institute for Environmental Research September 17, 2018 DECLARATION OF CO-AUTHORSHIP AND PREVIOUS PUBLICATION I. Co-Authorship Declaration I hereby declare that this dissertation incorporates material resultant from joint research, as follows: This dissertation also incorporates collaboration under the supervision of my supervisor Dr. Daniel D. Heath and co-collaborators. Collaborations were in Chapter 3 with co-collaborator Subba Rao Chaganti, and Chapter 5 with co-collaborator Katherine D. Balasingham at the time of this submission. In all cases, key ideas, primary contributions, experimental designs, and data analysis and interpretation were performed by me with additional contributions to field and data samples, data analysis and interpretation and written discussion by co-authors. I am aware of the University of Windsor Senate Policy on Authorship and certify I have properly acknowledged contributions of other researchers to my dissertation and have obtained written permission from each of the co-author(s) to include the above material(s) in my dissertation. I certify that, with above qualifications, this dissertation and research to which it refers, is the product of my own work. II. Declaration of Previous Publication Submission This thesis includes material from an original paper from Chapter Two submitted for publication to a peer reviewed journal. Although rejected it is likely to be submitted again after recommendations of reviewers have been fully addressed and is as follows: Publication title: “Mychek-Londer, J.G., MacIsaac, H.J. and D.D. Heath., 2017, “Metabarcoding primers for invasive invertebrates in the Laurentian Great Lakes.” Submitted to The Journal of Great Lakes Research, August 20, 2017. I certify that I have obtained written permission from copyright owner(s) to include above materials previously submitted in Chapter Two and those expected for publication submission for Chapter Three and Chapter Five. I certify that the above material describes work completed during my registration as a graduate student at the University of Windsor. I declare that, to the best of my knowledge, my dissertation does not infringe upon anyone’s copyright nor violate any proprietary rights and that any ideas, techniques, quotations, or any other material from the work of other people included in my dissertation, for work already submitted or expected to be submitted for publication are fully acknowledged in accordance with the standard referencing practises. I declare that this is a true copy of my dissertation, including any final revisions, as approved by my thesis committee and the Graduate Studies office, and that this thesis has not been submitted for a higher degree to any other University or Institution. iii ABSTRACT As aquatic invasive species (AIS) proliferate, they pose serious threats to native taxa, foodwebs and ecosystems. Massively-parallel, high-throughput, next-generation sequencing (NGS) and metabarcoding of environmental DNA (eDNA) and predator stomach content DNA (scDNA) are new approaches to detect AIS and can facilitate detailed analyses of AIS impacts. Using such technology, degraded and digested samples, and cryptic taxa can be identified with high sensitivity. The Laurentian Great Lakes (Great Lakes) are highly invaded and to determine occurrence patterns of AIS and native species inhabiting them I used a shortened portion of Cytochrome Oxidase One (CO1) and NGS metabarcoding. I developed, optimized and validated novel target-species CO1 PCR primer sets for AIS invertebrates: Bythotrephes longimanus, Cercopagis pengoi, Dreissena rostriformis bugensis, Dreissena polymorpha, and Hemimysis anomala. I tested primer set sensitivities, specificities, and multiplexing and used these with universal primer sets to analyze field-sampled scDNA and eDNA. I analyzed influences of abiotic (spatiotemporal) and biotic (predator species and size) variables in relation to prey occurrences in scDNA. The lowest AIS DNA in detected with novel primer sets in PCRs was: B. longimanus = 2.07; C. pengoi = 0.0002; D. r. bugensis = 0.0009; D. polymorpha = 0.103; and H. anomala = 0.127 (Chapter 2). Detection limits within mixes of interfering DNA (as percentage of total DNA) were: B. longimanus = 3.90 %, C. pengoi = 0.003 %, D. r. bugensis = 0.020 %, D. polymorpha = 0.170 % and H. anomala = 0.019 %. To determine invertebrate AIS roles in Lake Michigan, I metabarcoded scDNA from alewife (Alosa pseudoharengus), bloater (Coregonus hoyi), ninespine stickleback (Pungitius pungitius), rainbow smelt (Osmerus mordax) and slimy sculpin (Cottus cognatus) sampled Spring 2009 and 2010 at 73-128 m depths from three offshore sites. I detected multiple occurrences of target AIS and three native prey iv (Leptodiaptomus sicilis, Limnocalanus macrurus, and Mysis diluviana; Chapter 3). Driving variation in occurrences of the AIS and native taxa in scDNA was sample site, highlighting localized ecological and foodweb differences in ongoing AIS roles and impacts. Predator species effects likely reflected realized ecological feeding niches. To metabarcode scDNA from Lake Erie commercially fished predator species walleye (Sander vitreus), white bass (Morone chrysops), white perch (Morone americana) and yellow perch (Perca flavescens), I used novel AIS primer sets (Chapter Two) and a universal primer set to target fishes. Three invertebrate AIS including C. pengoi, B. longimanus, and D. r. bugensis, and AIS prey fishes gizzard shad (Dorosoma cepedianum), rainbow smelt and round goby (Neogobius melanostomus), and native prey fishes channel catfish (Ictalurus punctatus) and emerald shiner (Notropis athernoides) were detected, and all were relatively common components of scDNA. Occurrence patterns varied significantly with season, predator species, year, and predator size; however, the significances of factors also varied with prey species. Prey occurrences revealed dynamics among native and AIS prey and predators, potential competition, or prey selectivity which varied by way of these factors (Chapter 4). In 2013, 43 sites each in the Sydenham and Grand Rivers were sampled and metabarcoded for invertebrate eDNA using a universal primer set. Data revealed spatial patterns of AIS at sites within and among each river. Key AIS identified were: D. r. bugensis, Branchiura sowerbyi, Potamothrix moldaviensis, Craspedacusta sowerbyi and Skistodiaptomus pallidus. Further, I identified rare native mollusks including Quadrula quadrula and Villosa fabalis - threatened and endangered species in lower and middle reaches of the Sydenham. Novel results and information will provide important guidance to those tasked with ongoing challenges of
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