Data from: Development and validation of rapid environmental DNA (eDNA) detection methods for bog turtle (Glyptemys muhlenbergii)

Bog turtles  Glyptemys muhlenbergii are listed as Species of
Greatest Conservation Need (SGCN) for wildlife action plans in every state
it occurs and multi-state efforts are underway to better characterize
extant populations and prioritize restoration efforts. However,
traditional sampling methods can be ineffective due to the turtle’s
wetland habitat, small size, and burrowing nature. Molecular methods, such
as qPCR, provide the ability to overcome this challenge by effectively
quantifying minute amounts of turtle DNA left behind in its environment
(eDNA). Developing such methods for bog turtles has proved difficult
partly because of the high sequence similarity between bog turtles and
closely-related, cohabitating species, most often wood turtles ( Glyptemys
insculpta ). Additionally, substrates containing bog turtle eDNA are often
rich in organics or other substances that frequently inhibit both DNA
extraction and qPCR amplification. Here, we describe the development and
validation of a qPCR assay, BT3, targeting the mitochondrial cytochrome
oxidase I gene that correctly identifies bog turtles with 100% specificity
and sensitivity when tested on 201 blood samples collected from six
species over a wide geographic range. We also developed a full-process
internal control employing a genetically modified strain of 
Caenorhabditis elegans  to improve DNA extraction methods, limit
false negative results due to qPCR inhibition, and measure total DNA
recovery from each sample. Using the internal control, we found that DNA
recovery varied by over an order of magnitude between samples and likely
explains the lack of bog turtle detection in some cases. Methods presented
herein are highly-specific and may offer a more cost effective,
non-invasive tool to supplement bog turtle population assessments in the
eastern United States. Poor or differential DNA recovery, which remains
unmeasured in the vast majority of eDNA studies, significantly reduced the
ability to detect bog turtle in their natural environment.