Area of Research: DNA Barcoding

In “Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae” (FirstCite early online publication in Proceedings Royal Society Biology) Paul Barber and Sarah Boyce, Boston University, look at a what is thought to be a well-understood group, stomatopods, commonly known as mantis shrimp. Stomatopods are marine crustaceans distinct from true shrimp and are thought to include about 400 species worldwide. Like many marine species, they have a bipartite life cycle where dispersal is achieved through a planktonic larval developmental stage. However, larval stages are notoriously difficult to identify morphologically. Barber and Boyce first established a database of COI DNA barcodes from adult forms of nearly all known species. They then applied DNA barcoding to planktonic larvae collected in light traps at locations in the Pacific Ocean and Red Sea. Comparison of sequences from 189 larval forms revealed 22 distinct larval operational taxonomic units (OTUs), but a minority of these matched known species, suggesting that stomatopod species diversity is underestimated by a minimum of 50% to more than 150%. Their results support general use of DNA barcoding as a rapid, relatively-inexpensive first step in cataloging marine species with planktonic larvae. A similar approach has been applied on land by Smith et al “DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar“.

DNA barcode OTUs, such as found in these studies, are not equivalent to species descriptions and are not sufficient to establish systematic phylogeny. In my view, these studies indicate that DNA barcodes can be permanent indexers for filing and retrieving biologic information in the encyclopedia of life.  Routinely incorporating DNA barcoding into biological surveys will enhance the long-term value of expensive field work. 

The deep oceans are the largest biotic space on earth, but remain largely unexplored.  Census of Marine Life scientists recently trawled the Atlantic between the southeast US coast and the Mid-Atlantic ridge, focusing on the zone of perpetual darkness that lies below about 1000 m, to inventory and photograph the variety and abundance of zooplankton–the tiny sea animals that form a vital link in ocean food chains. The 20 day cruise completed April 20 is part of the ambitious gobal inventory of zooplankton by 2010 (Census of Marine Zooplankton (CMarZ), a Census of Marine life initiative. As reported in Science, for the first time DNA sequencing was performed on the rolling seas, telescoping into just three weeks what would normally represent years of laboratory work. 

According to Ann Bucklin, lead scientist for CMarZ and Head of the University of Connecticut Marine Sciences Department, “we are just starting to realize how little we know about species variety. We used to think we knew many species well, but the advent of DNA barcoding has radically altered that perception.  Genetically distinctive species of zooplankton are being found with increasing frequency.”  

The lead story in the US National Museum of Natural History 2005 Annual Report: New Tools for Understanding Nature, entitled “Barcoding the Planet” highlights the museum’s organizational and research involvement in the international scientific effort “to develop a system for rapidly and inexpensively identifying the approximately 1.7 million known flora and fauna species, and creating an electronic database for the estimated 10 million species across the planet”.  As outlined by Cristian Samper, Museum Director, “the use of DNA barcoding in identifying and distinguishing species could revolutionize the way we do science”. The article concludes with an observation from Lee Weigt, Manager of the Museum’s Laboratories of Analytical Biology “What the human genome research can do for medicine, DNA barcoding can do for biology”

In 1998, as part of biodiversity survey to assess the health of New York City’s Central Park, researchers at the American Museum of Natural History collected leaf litter samples. After sorting, the museum sent a collection of Central Park millipedes and centipedes to Richard L. Hoffman, curator for invertebrates at the Virginia Museum of Natural History. After study, Dr. Hoffman sent several specimens he could not identify to scientists in Italy. In July 2002, Italian scientists announced the Central Park centipede was a new species, and named it Nannarrup hoffmani in honor of Dr. Hoffman. In October 2003, Foddai, Bonato, Pereira, and Minelli published the species description in Journal of Natural History. As of April 2006, the journal issue containing the description is available to subscribers or by payment per article.

My summary: 1 new species, found across the street from one of the world’s premier natural history research institutions, recognized as a new species 4 years later, published description year 5, awaiting public access year 8.  I believe that DNA barcoding can provide taxonomists with scientific tools and help attract funding to accelerate this process.

Many shark species are threatened by overfishing, including the filter-feeding whale shark Rhincodon typus. The Ocean Conservancy reports “many sharks fall victim to finning, the process of slicing off a shark’s fins and tossing it back into the water. Highly prized for use in the delicacy shark fin soup, shark fins support a very lucrative market. Although the U.S. Shark Finning Prohibition Act of 2000 made this practice illegal in all U.S. waters, finning remains legal in most parts of the world.” In The USA regulations prohibit possession of any part of protected species, but how to identify dried fins? The National Oceanographic and Atmospheric Administration recently confiscated a ton of dried shark fins and brought charges against dealers based on DNA identification of protected shark species.  A DNA barcode library together with rapid, portable methods for sequence analysis will empower enforcement of regulations for many protected species.