The eDNA revolution & developing comprehensive aquatic biodiversity archives
But even where streams and lakes are heavily studied, those baselines typically exist only for the few large charismatic species we like to eat or play with by tethering ourselves to them via narrow strands of monofilament. We know very little that is very specific about where most aquatic species live, and even for those we think we know well, genetic techniques like DNA barcoding are sometimes revealing layers of unappreciated cryptic biodiversity and entirely new species (blog 53 and examples shown here by Hebert & colleagues). Sure, when we’re forced to we can draw crude polygons on maps and say that that’s the range of species x, y, or z (graphic 1). But that isn’t nearly precise enough to be useful in meaningful conservation planning or strategic investing because it doesn’t resolve the locations of individual populations or provide information at scales commensurate with those at which human activities alter landscapes. And because so much of conservation comes down fundamentally to choices about where to make investments, we need that granular level of biological information feeding into our decision making process. Compounding matters exponentially, we need high-resolution information for all species if we want to be serious about the biodiversity thing and not just give it lip service.
That’s a fantastically tall order to fill so hasn’t really been worth contemplating seriously until just the last few years. But with the revolution now being wrought by environmental DNA (eDNA) that vision is rapidly becoming a transforming reality. Most, by now, have heard about this seemingly magical new technology, but for those who haven’t, it is possible to detect fragments of DNA that have been shed from their parent organisms and to use that information in reliable determination of species locations. eDNA technology is especially powerful in aquatic environments where simple water samples can be taken from streams, lakes, or wetlands and analyzed to determine what lives there. Collecting eDNA samples in the field requires only inexpensive equipment and a small water pump that fits easily into a daypack. Costs to collect and process lab samples are already much lower than traditional sampling techniques and will continue to fall as the technology matures. Moreover, first generation eDNA technologies limited analyses to single species determinations, but next generation technologies are already becoming available to do multispecies assessments simultaneously. And not all the DNA contained in samples are destroyed during an analysis so what’s left over simply goes in the freezer where it can sit indefinitely to serve as a biodiversity archive for later queries if the need arises. Combine it all, and it’s possible not just to contemplate, but to begin actuating, geographically broad sampling campaigns designed to map all of aquatic critter-dom at the resolutions needed for conservation and management.
For a thorough recent review about aquatic eDNA applications, Thomsen & colleagues provide a good place to start (study hyperlinked here:https://www.researchgate.net/profile/Philip_Thomsen). But for those wishing a full aquatic eDNA immersion, the bibliography below hyperlinks to 79 recent studies, of which only 1 was published prior to 2011. And before you literally wade out to start collecting eDNA, here are a few basic pointers to help minimize any missteps (but please consult the real experts and expertise of those cited in the bibliography rather than relying overly much on the simplifications of this blogger).
1) First, a species-specific eDNA marker has to be developed before you can use the technology to determine the presence/absence of a target species. But new markers are being developed for more species by various labs all the time so the odds that a marker already exists for a species of interest are continually increasing. AFS, AFWA, and USFS maintain this eDNA clearinghouse website to make it easy to see what’s out there and to know who to contact: http://edna.fisheries.org/
2) If an eDNA marker doesn’t exist, it costs about $5k to develop one. But you (or someone) need to collect tissues from the target organism across a representative portion of its range (a great excuse for those electrofishing rodeos blog 30!) and send them to the lab vendor for marker development.
3) Once a marker exists, you can start collecting eDNA samples and sending them to the lab for processing. The field sampling protocols for aquatic eDNA collection are straightforward and several are listed in the bibliography below. Consult with your lab vendor as they will have a preferred protocol.
4) Depending on the species, the detection efficiency of eDNA may or may not be well understood. If it’s not well understood, you don’t want to run around collecting samples willy-nilly until you’ve conducted field trials to determine detection rates under field conditions. Otherwise, it’s impossible to determine what negative readings mean. It may be because the organism wasn’t there that day, or because it wasn’t close enough to where the sample was taken to put a detectable amount of DNA into the water. For some well-studied organisms, those detection efficiencies have been estimate (see studies below), but for most species they have not been. The general expectation, however, is that eDNA will usually have higher detection efficiencies (often much higher) than traditional sampling techniques.
5) Finally, eDNA is a new and sexy way to collect species occurrence data but it will yield valuable information in direct proportion to the quality of questions driving its application. As with any sampling technique, those questions are the foundation upon which logical sampling strategies are designed to determine where in space & time samples are collected. So don’t forget the basics!
As in any revolution, there will be abuses, overreaches, and unfulfilled promises, especially during these initial years as eDNA technology is being deployed and learned. But that will be worked through and those bits of DNA shrapnel floating through waterways around us will transform the way we do business and how we think about biology as surely as electricity brought day to night, the industrial revolution started warming the climate, and the internet and digital rivers of information now connect us. We’ll ultimately find that eDNA gives us a really big hammer and reveals a world full of nails. I suspect that the quality and quantity of information built by the aquatics army with that hammer will be remarkable when we look back on it someday. And because it’s so easy and inexpensive to collect eDNA samples, it presents a huge crowd-sourcing opportunity (blog 71) that can be used to engage school kids, anglers, grandpas, or your local congresswoman in discovering the joy of mucking around aqueous environments & uncovering underappreciated parts of nature. Before we know it, we will have constructed an accurate assessment of all aquatic critters everywhere and will have finished the maps started by the likes of Lewis & Clark, Jordan, and Evermann during the great geographical & fish expeditions of the 1800s (graphic 2). Those maps are the keys to designing comprehensive conservation strategies that allow us decide how to invest most cost effectively this century. Not surprisingly, we will be subject to a deluge of new data as this all unfolds and infrastructures capable of handling it will be needed—a topic that will be pondered next time in the pen-penultimate Climate-Aquatics blog.
