Tuesday, January 12, 2016

Finding the Goby

Environmental DNA (eDNA) allows us to detect the presence of organisms without direct observation. Plants and animals shed cellular material in their surrounding environment, and this material can be collected and analyzed. Traces of DNA extracted from environmental samples can be used to determine if a target species has been in the vicinity of a sampling site.

Many colleagues think that eDNA monitoring approaches could considerably improve our ability to detect of rare, endangered and invasive species but because this methodology is rather new we need more studies in which new approaches are compared with traditional techniques.

And here is a new oneThe primary objective of this research was to use a multimethod occupancy modelling framework to compare method-specific detection probabilities between eDNA techniques and traditional seining for monitoring tidewater goby.

The tidewater goby (Eucyclogbobius newberryi) is a small fish that occurs in patches along a large stretch of California's coastline. It is a low dispersal species that was already listed as endangered in 1994. About 1/6 of the historically documented populations have disappeared and an estimated 50% of the remaining populations are considered vulnerable to extinction because of habitat loss.

Using eDNA as a monitoring approach for tidewater goby was conceived as an alternative to traditional field methods primarily because of the difficulty of using traditional field monitoring approaches (e.g. seines and minnow traps) in sloughs and estuaries along California's northern coast. Also, tidewater goby populations vary considerably in annual abundance and may be unevenly distributed throughout a site. Thus, eDNA techniques may provide an efficient and noninvasive means of detection at low abundance.

The colleagues used eDNA approaches and traditional seining methods at 29 sites, including multiple paired subsampling locations at each site. In addition they applied eDNA methods only at a total of 39 sites and analysed the data using a hierarchical occupancy model to evaluate three levels of uncertainty associated with collecting spatial replicate water samples within study sites and performing replicate qPCRs.

Analysis using a multimethod occupancy modelling framework indicated that the probability of detection using eDNA was nearly double (0.74) the rate of detection for seining (0.39). The higher detection rates afforded by eDNA allowed determination of tidewater goby occupancy at two locations where they have not been previously detected and at one location considered to be locally extirpated. Additionally, eDNA concentration was positively related to tidewater goby catch per unit effort, suggesting eDNA could potentially be used as a proxy for local tidewater goby abundance.


  1. Hi; Did any of the 39 non-seined sites not have goby eDNA?

  2. Pretty interesting. If you have the time, check out my website


  3. Another paper on eDNA detection in gobies has been published: http://dx.doi.org/10.1371/journal.pone.0147558