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Knowledge of how species are distributed is essential for understanding evolution and ecology, and monitoring enables detecting invasive species and recognizing effects of biological and physical environmental change. That’s easy to say, but many species are small, secretive, or difficult to distinguish from one another, so mapping species distributions requires enormous human effort and ongoing monitoring requires even more. I venture a guess that we have good monitoring for 10,000 or so plant and animal species, mostly large animals and those plants and animals of economic importance, and static distribution maps for about 100,000 species, out of a total of 1.7 million named species and not counting the projected total of 10 million species that might eventually be recognized when surveying biodiversity approaches completion. 

Just as high-resolution satellite mapping has surpassed most ground surveys in accuracy, speed, and cost, we need efficient technologies that can help detect and monitor species from environmental samples. In 9 April 2008 Early Online Biol Lett researchers from Universite Joseph Fourier and Universite de Savoie, France, and Universita Milano Bicocca, Italy, apply high-sensitivity DNA analysis to detect presence or absence of American Bullfrog Rana catesbeiana, a globally invasive species. PCR amplification of a diagnostic 79 bp fragment of mitochondrial gene cyt b using species-specific primers (no amplification of samples from the 5 locally native Rana sp). Three 15 mL water samples were collected from each of 9 ponds (surface area 1000-10,000 m^2) in France, including “three ponds where bullfrogs were present at low density (one to two adults seen, no reproduction), three ponds where bullfrogs were present at high density (dozens of adults and thousands of tadpoles), and three ponds where bullfrogs have never been detected.” Each sample was analyzed 3-5 times, giving 9-15 repeats per pond. R. catesbiana DNA was never detected in the ponds with no bullfrogs and was detected in water samples from all three high-density ponds, with most (79%) of replications positive. Bullfrog DNA was also detected in all low-density ponds, although fewer of the replications were postive ( 37%).

Ficetola et al observe “our approach allows the reliable detection of secretive organisms in wetlands without direct observation.”  The authors conclude “The ongoing effort to develop DNA barcodes for identifying species  from degraded DNA (Hajibabaei et al 2006; Taberlet et al 2007) will make our approach applicable to more and more plant and animals species…These factors will soon make possible the assessment of the current biodiversity of macro-organisms from environmental samples.” 

Like satellite mapping 20 years ago, DNA-based environmental monitoring of biodiversity, aided by growing DNA barcode libraries, is set to expand rapidly.

Alien species sometimes damage native landscapes. In Voyage of the Beagle, in entry dated September 19, 1832, Darwin describes the spread of an introduced European thistle Cyanara cardunculus in Banda Oriental, now Uruguay: “very many (probably several hundred) square miles are covered by one mass of these prickly plants, and are impenetrable by man or beast. Over the undulating plains, where these great beds occur, nothing else can live…I doubt whether any case is on record, of an invasion on so grand a scale of one plant over the aborigines.”

The challenge is to recognize invasive species before they become established. In 11 January 2008 Polar Biology researchers from Stellenbosch University and University of Western Ontario apply DNA barcoding to otherwise unrecognizable moth larvae on sub-Antarctic Marion Island. The indigenous Lepidoptera on Marion Island comprises 2 or 3 flightless moths, and the occassional adult winged moths or butterflies have been assumed to be transients arrived on fresh produce.

In April 2004, 3 noctuid moth larvae were found in an abandoned Wandering Albatross nest, a common habitat for one of the indigenous moth species. The larvae could be tentatively identified only to genus level and so rearing was attempted, with one larva dying after several months of pupating (as an aside, this is one example of how morphologic identifications can be laborious and/or incomplete, even for experts). The final larva was killed and preserved for DNA study; COI DNA barcode region was amplified using standard Folmer primers. The Marion Island moth larva barcode clustered with the 40 or so Black Cutworm Agrotis ipsilon sequences in BOLD, and was distinct from COI sequences of the other 18 Agrotis species in BOLD. Agrotis ipsilon is a common pest that feeds on a wide variety of plants. The authors conclude that Agrotis ipsilon is an established alien species with the potential to disrupt local ecosystems and that “steps be taken to eradicate the species from Marion Island.”

It is easy to predict that rapid identification of potential invasive alien species will be a major application of DNA barcoding, with direct economic and ecosystem benefits.

Just posted, a freshly minted home page for Barcode of Life activities at Program for the Human Environment, The Rockefeller University, with expanded links to partners and downloadable pdfs and powerpoint files for illustrated flyers “Top Ten Reasons for Barcoding Life” and “Barcoding Life, Illustrated.” Enjoy!

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Just as DNA analysis regularly overturns seemingly solid eyewitness identifications in crime investigations, routine DNA analysis can also help biologists avoid blunders. In 28 August 2007 Mol Ecol, researchers from University of Colorado, New Mexico State University, Pisces Molecular, and Brigham Young University report that over 20 years of restocking efforts in western US aimed at restoring native populations of endangered greenback cutthroat trout Oncorhynchus clarkii stomias have mostly been restocking a non-native, non-endangered subspecies, Colorado River cutthroat trout O. c. pleuriticus.  They trace the confusion to repeated introductions beginning in the late 1800s of Colorado River cutthroat trout throughout the native range of greenback cutthroat trout. The authors analyzed mitochondrial (COI, ND2) and nuclear (microsatellites, AFLP) DNA from 365 individuals from 15 locations in 3 major river drainage systems in Colorado and surrounding states. Distinct mtDNA lineages corresponding to each subspecies were corroborated by nuclear microsatellite and AFLP data.  For another cautionary tale of repeated misidentification of a widely studied organism, see Siddall and colleagues’ entertaining June 2007 Proc R Soc paper scrutinizing commercially available medicinal leeches sold as Hirudo medicinalis. 

How might the future look with routine application of DNA ID as quality control? Incorporating DNA barcode analysis into Tree of Life studies is one useful approach, exemplified by two recent large-scale evolutionary studies published in January and April 2008 Syst Entomol, one on phylogenetic relationships in Saturnid silkmoths, and one on higher-level relationships among 12 families in ‘bombycoid complex’ of Lepidoptera. Both studies analyze COI barcodes of all specimens, “allowing confirmination of their identification for species present in the BOLD reference library and enabling future identifications of organisms whose identity is still pending.”

On February 27, 2008, Encyclopedia of Life (EOL), “a web page for every species” officially launched, with over 30,000 species pages, mostly fish so far, and a diversity of links to internet resources including Biodiversity Heritage Library (2.9 million pages digitized). In case you missed it, there is a thrilling, award-winning video.  Following Wikipedia model, EOL users are invited to become “curators” for one or more species pages, and later this year all are invited to submit content (photos, drawing, text, video, for example) for review. For an entertaining brief history of Wikipedia and why it keeps getting better see Nicholson Baker’s review of John Broughton’s Wikipedia: The Missing Manual in March 20, 2008 New York Review of Books.

Most near-sun comets are now discovered by amateurs, using images downloaded from the Solar and Heliospheric Observatory (SOHO), a satellite launched December 2, 1995 as part of international collaboration between European Space Agency (ESA) and National Aeronautics and Space Administration (NASA). I expect that EOL and other open-access databases will lead to many more persons contributing to biodiversity science.

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