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DNA barcodes

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On a glorious, sunny day in late June, a small team of entomologists convened at the Kenai National Wildlife Refuge to do what entomologists do best: collect insects.

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They had come to take part in a rapid ecological assessment of arthropod biodiversity, where we collect as many species as possible in a short time. 

Our goals were twofold. We sought to greatly augment the list of arthropods known to live on the refuge and to build a corresponding library of DNA barcodes for those species. The project is a blending of old-fashioned collecting in the spirit of 19th century explorers and cutting edge, CSI-style DNA work.

The whole idea is to work myself out a job.

Though the ecological importance of insects is plainly evident (consider the spruce bark beetle or see last week’s Refuge Notebook article on defoliators) and though their quick responsiveness to environmental change makes them ideal candidates as indicators of environmental quality, the trouble with insects is that they are hard to identify.

It took years to sort through the over 15,000 specimens collected as part of the Refuge’s Long Term Ecological Monitoring Program from 2004 to 2006, and many of these remain unidentified to this day. If insect diversity is to be monitored feasibly, then this problem of identification must be surmounted.

Our plan for the near future is to take bulk samples of perhaps hundreds of insects, liquefy them in a blender, extract the insects’ DNA from the slurry, and obtain a list of species that were present in the sample using next-generation DNA barcoding methods. DNA barcoding is the use of a short section of DNA for species identification, not unlike recognizing products in a store by their black-and-white barcode labels. These methods will make monitoring of insects much more feasible by eliminating the tedious task of sorting and identifying insects using forceps, microscope, and identification keys.

However, these next-generation methods require that a library of DNA barcodes from known, identified specimens be established beforehand. Otherwise, barcodes obtained from a slurry of pulverized insects would be nothing more than barcodes. We began building this library last winter by sequencing specimens already in the Kenai National Wildlife Refuge’s entomology collection, but our small collection included 208 species, only a small portion of the arthropod diversity present on the Refuge.  This June, we sought to build upon this collection.

We had help from an all-star team of entomologists from around the state:  Dr. Dan Bogan, aquatic entomologist from the University of Alaska Anchorage and his student, Jeff Skaza; Dr. Derek Sikes, curator of insects at the University of Alaska Museum in Fairbanks and an avid coleopterist (a person who studies beetles); and Dr. David Wartinbee, professor of biology at Kenai Peninsula College in Soldotna and a specialist on Chironomid midges.

Together, we traveled over the Refuge, visiting as many different kinds of habitats as possible within the four days allotted. We first surveyed the forest, muskeg, and lake shore near Refuge headquarters. The next day we toured habitats along the shore of Skilak Lake by skiff. For the final two days, we were dropped off at Emerald Lake on the south side of Kachemak Bay, where we camped overnight and sampled the productive subalpine thickets, meadows, waters, and alpine habitats accessible from the lake. 

We employed a wide variety of collecting methods (sweep nets, beat sheets, aerial nets, malaise traps, pan traps, sieves, aquatic nets, streamside washing, and searching under stones, logs, and under bark by hand), each of us focusing on the methods and insect groups we knew best.

Thankfully, we were blessed with beautiful weather, which was not only pleasant for us, but made our efforts more productive as innumerable insects responded to the sunshine with great activity.

I am presently cataloging the many vials, bags, and containers of insects obtained this June.  I do not have an estimate of the number of specimens and species we collected yet as this would be little more sophisticated than guessing the number of beans in a set of jars, but I can say that at least thousands of specimens were collected, representing probably hundreds of species. Incidentally, we found a Northern Holly Fern near Emerald Lake, a plant species not previously recorded on the Refuge.

The insect specimens will be sorted and mailed to various specialists for identification and, later this winter, they will be sent out for DNA barcoding. Specimen data from this project is being posted on the internet in near real-time via the Arctos database (http://arctos.database.museum/knwr_ento). As we obtain DNA barcodes, these will be deposited in GenBank, where they will be useful not only to us, but to any study identifying insects using DNA barcodes. Our efforts will allow National Parks, National Forests, and other refuges to rapidly assess insect diversity on their respective pieces of Alaska.

Matt Bowser serves as Entomologist at the Kenai National Wildlife Refuge. More photos from this project (with captions) are available at https://picasaweb.google.com/KenaiWildlifeRefuge/2011ArthropodRapidEcologicalAssessment

For more detailed information about the Refuge, you can check our website at http://kenai.fws.gov or on Facebook at http://www.facebook.com/kenainationalwildliferefuge

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