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)

• Main Author: Mychek-Londer, Justin Glenn
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: University of Windsor 2018
• Subjects: endangered species; Great Lakes; invasive species; metabarcoding; metagenomics; molecular ecology; Cottus cognatus; Slimy sculpin
• Online Access: https://scholar.uwindsor.ca/etd/7549; https://scholar.uwindsor.ca/context/etd/article/8550/viewcontent/uc.pdf

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 (Leptodiaptomus sicilis, Limnocalanus macrurus, and ...