Environmental DNA - A New Tool for Population Monitoring

Project

Principal Investigator:

Frederic J. Janzen

Student Investigator:

Clare Adams

Collaborators:

 

Duration:

April 1, 2015 to March 31, 2016

Funding Source(s):

Iowa Department of Natural Resources (IDNR)

 

Goals and Objectives:

  • Use environmental DNZ to detect the presence/absence of C. picta
  • Quantify eDNA and relate it to turtle biomass, then create a statistical model based on this relationship for use in populations monitoring.

 

Progress:

Thusfar, we have placed turtles into three different ponds (B, C, D) at the Horticulture Farm of Iowa State University on 1 April 2015. One pond (A) received no turtles and is used as a control. All of these ponds have a different turtle biomass and different numbers of turtles. Sampling is an ongoing process. We sampled before turtles were placed in the ponds, every day for a week after turtles were placed in the ponds, and every three days thereafter. The week of everyday sampling was to look at accumulation rates of eDNA; testing the hypothesis that eDNA levels will rise for a short time frame after turtles are initially added. Sampling will continue until 30 June 2015.

Samples are currently being filtered with 0.7um glass microfiber filters. Soon, sample processing will start with cellulose nitrate filters as well (1 May 2015 thru 30 June 2015, once every 15 days). Sample processing has also begun for sodium acetate and ethanol DNA extractions.

C. picta specific primers have been designed and are working on species-specific tissue of this species. Universal turtle primers have also been designed, and amplicon sequencing has revealed species-specific differences – however because of such a short amplicon sequence (200bp), the results may not stand up to traditionally accepted sequence variation. eDNA has been successfully extracted and amplified from eDNA positive controls (very dirty C. picta laboratory water) with the universal primer.

 

Future Plans:

We shall continue sampling until the 30th of June, and then sample every day for a week after turtles are removed. The latter will inform us as to how eDNA degrades in a water sample over time, once animals are no longer present.

Once the QiaShredder is ordered and arrives, filtered samples can have their DNA extracted and all samples can start the amplification process via qPCR. qPCR will then show us the amount of eDNA per sample relative to series-diluted standards, for which we can then use in statistical modeling.  We plan on creating a statistical model relating the known turtle biomass per pond to eDNA quantities as amplified by qPCR. From this model, we shall sample at Ada Hayden Park in Ames, IA as well as Thomson River Causeway in Thomson, IL.

As for broader impacts, Clare has already taught undergraduate Rachel on how to filter eDNA and will be teaching undergraduate Morgan soon how to sample for eDNA and prepare samples. Once the fall semester arrives, it is possible that Clare will partner up with the herpetology class offered at Iowa State University to discuss novel methods in reptile population monitoring and conservation. It is also very likely Clare will talk to grade-school students at the Ames Catholic School about her research using a conservation perspective.

In the distant future, we hope to apply this technique to the endangered yellow mud turtle (Kinosternon flavescens) for continued population monitoring and informing conservation policy. On a broader note, we hope that wildlife agencies such as the Iowa DNR will be able to use eDNA to gather information about aquatic turtle populations of interest. 

Duration: 
04/01/2015 to 03/31/2016
Award Number: 
15CRDWBKKINK-0075