Using DNA metabarcoding to describe biodiversity and disease dynamics

• Main Author: Massey, Aimee L.
• Other Authors: Levi, Taal, Kavanaugh, Maria, Sharpton, Thomas, Jolles, Anna, Betts, Matt, Fisheries and Wildlife
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Oregon State University
• Subjects: Archipelago; Canis lupus; Alaska
• Online Access: https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/ws859p027

Land-use change, particularly in the form of the conversion of primary forest to forest-matrix systems, alters species communities and species interactions. Describing these often complex and nuanced species responses is one of the great challenges in ecology. Another complementary challenge is finding and using the most efficient means for collecting quality data necessary for understanding ecological relationships. For my PhD dissertation, I utilized the emerging molecular method of DNA metabarcoding to profile species communities and answer landscape level questions about the effects of forest loss on species. DNA metabarcoding is the high-throughput DNA sequencing of taxonomically informative barcode genes to profile the diversity found using environmental samples such as water, scat, soil, or pollen. Metabarcoding can also be used with direct sources of DNA such as the bloodmeals or carrion meals from insects, which is referred to as iDNA or insect-derived DNA. I utilized both eDNA (from scat samples) and iDNA (from carrion flies, sandflies, and mosquitos) to help validate and develop metabarcoding for diversity surveillance. In Chapter 2, I profiled the diet of Alexander Archipelago wolves (Canis lupus ligoni) across an island archipelago system in southeast Alaska using both DNA metabarcoding from prey DNA in scat samples and mechanical sorting of the same scat samples. Although I found similar relative abundances of the primary and secondary prey species across the methods, DNA metabarcoding revealed a greater diversity and relative abundance of alternate prey species than had been described with mechanical sorting of scats both in our study and in previous studies. Additionally, I found that disagreement in species assignment between the two methods could be attributed to false positives from mechanical sorting due to misassignment of degraded hair. Lastly, I found that both fresh and degraded scats yielded quality DNA sequence data suggesting that metabarcoding is sensitive enough to determine prey ...