10.5061/DRYAD.6N7675R
Kirtane, Anish
University at Buffalo, State University of New York
Wilder, Maxwell
SUNY College of Environmental Science and Forestry
Green, Hyatt
SUNY College of Environmental Science and Forestry
Data from: Development and validation of rapid environmental DNA (eDNA)
detection methods for bog turtle (Glyptemys muhlenbergii)
Dryad
dataset
2019
bog turtle
internal control
Glyptemys muhlenbergii
sample interference
qPCR inhibition
DNA recovery
2019-10-11T00:00:00Z
2019-10-11T00:00:00Z
en
https://doi.org/10.1371/journal.pone.0222883
217865 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
DNA partitioning experiment field data 2017 field data 2018 lysing matrix
optimization study reference DNA analysis
USA