INCREASING LIMITS OF ENVIRONMENTAL DNA DETECTION USING THE ENDANGERED ATLANTIC WHITEFISH (COREGONUS HUNTSMANI) AS A TEST CASE

Abstract

Environmental (e)DNA analysis offers a non-invasive alternative to traditional aquatic monitoring, but it can struggle to detect species at very low abundances. Here, I developed a novel eDNA marker targeting the SmaI-corII SINE and compared its detection capabilities to the mitochondrial marker ND4 using the endangered Atlantic Whitefish (Coregonus huntsmani) as a test case. My results showed that the SINE marker, which is 190x and 82x more abundant than ND4 in gDNA and eDNA samples, respectively, enhanced species detection in eDNA samples compared to the mitochondrial marker. I also investigated the use of SINEs to assess genetic diversity within eDNA samples. My analysis revealed 5 SmaI-corII variants within Atlantic Whitefish gDNA, all of which were also detected in eDNA samples. Additionally, I identified two variants unique to Lake Whitefish (Coregonus clupeaformis) eDNA samples. This study demonstrates that SINEs serve as sensitive eDNA markers with both intra- and interspecific variation. Given that SINEs and other transposable elements are present in most organisms, these findings have implications for supporting the ongoing management of at-risk aquatic species.