Rockefeller University

Program for the Human Environment

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COI evolves rapidly in salamanders, helping distinguish and discover species, still some taxonomists worry

Results so far in animals suggest the major limitation to DNA barcoding is very young species pairs. Young species pairs may not have accumulated enough differences in the 648 bp barcode region of COI to form distinct lineages in neighbor-joining analysis. Because overall rates of mitochondrial DNA evolution differ among animal groups, and the relative rates of specific mitochondrial genes also differ, it may turn out that COI barcoding will be more effective in separating young species pairs in some groups than in others.

20 My of genetic divergence and morphologic stasis 

In April 2006 Systematic Biology Mueller compares complete mitochondrial genomes of 27 salamander species. The genetics of salamanders are particularly important as they are notoriously difficult to distinguish and classify due to morphologic stasis and frequent homoplasy. Many new species of salamanders have been discovered and described on the basis of mitochondrial divergence. Mueller found that COI has the highest rate of evolution among all mitochondrial genes in salamanders, suggesting it will be especially effective at resolving young species in this group. Despite these very encouraging results, the paper ends with a worried discussion about using COI for DNA barcoding of salamanders, because its evolutionary rate varies between lineages.

A better appreciation of the power of a standardized genetic approach for amphibians is Ron et al.’s paper in May 2006 Molecular Phylogenetics and Evolution which uses mitochondrial DNA to look at phylogeny and new species in the Neotropical tungara frog genus Engystomops. The authors observe that “the use of genetic markers in systematics has an enormous potential to facilitate the global inventory of biodiversity”, and conclude, based on their results and those in similar studies, that “the increasing use of molecular techniques will lead to the discovery of a vast number of species of Neotropical amphibians.”

New species descriptions could benefit from DNA barcodes

Jones et al 2005 Science 308:1161A year ago in Science, Jones et al. described a new species of African monkey, Lophocebus kipunji, documenting their report with field observations, sound recordings, and photographs. This led to legalistic wrangling over whether the species could be said to exist if there was no specimen! Fortunately, the suspense is relieved by Davenport et al. in this month’s Science, in which they provide morphologic and DNA information based on a specimen recovered from a farmer’s trap.  Although the authors relied on mitochondrial DNA evidence to establish the monkey belongs in a new genus, Rungwecebus, the actual sequence data is not listed among diagnostic characters in the species or genus description. Routine inclusion of DNA barcode sequences could improve the usefulness of formal species descriptions, assisting primate conservation efforts that monitor bushmeat trade, for example.

 

Where is my barcode?

To rapidly map biodiversity, stomatopods suggest start with DNA

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 Squilla maculata, Dictionaire D'Histoire Naturelle, Orbigny, 1849a 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 Stomatopod larva, https://www.dnr.sc.gov/marine/sertc/gallery.htmsequences 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. 

Zooplankton sequenced at sea, illuminating life in the dark

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. 

Clio pyramidata, one of the species sequenced at sea by CMarZ scientistsAccording 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.”  

Serious Games

Our longstanding interest in Serious Games extended during the past year to the Reinventing Public Diplomacy Through Games Competition organized by Josh Fouts and Doug Thomas at USC sponsored by the Lounsbery Foundation. First place went to PeaceMaker, a cross-cultural political video game simulation of the Israeli-Palestinian conflict which can be used to promote a peaceful resolution among Israelis, Palestinians and young adults worldwide. Congratulations to Asi Burak and PeaceMaker team members at Carnegie-Mellon.

A little history of our involvement with gaming: Swedish economist Ingolf Stahl first involved Jesse in interactive gaming in 1980-1981, when Ingolf, Jesse, Jennifer Robinson, and John Lathorp built a board game and two computer games about carbon dioxide emissions and global warming (described in Jennifer Robinson and Jesse H. Ausubel, A Game Framework for Scenario Generation for the CO2 Issue, Simulation and Games 14(3):317-344). The 1981 paper, Ingolf Stahl and Jesse H. Ausubel, Estimating the Future Input of Fossil Fuel CO2 into the Atmosphere by Simulation Gaming (IIASA Working Paper-81-107, published in Beyond the Energy Crisis-Opportunity and Challenge, Rocco.A. Fazzolare and Craig B. Smith, eds., Oxford, Pergamon, 1981) was the first paper to introduce the idea of greenhouse gas emission trading. Jesse’s 1988 book with Robert Herman, Cities and their Vital Systems: Infrastructure Past, Present, and Future, found its way to the brilliant young Will Wright, and Will made terrific use of it in his first 1989 release of SimCity, for which Jesse had the great opportunity to be a beta tester. Jesse wonders whether he still somewhere has the diskettes of the beta version. Will opened Jesse’s eyes to modern simulation and helpfully advised Jesse and Bill Massey on the creation of the university simulator, Virtual U . (For the game history: https://phe.rockefeller.edu/jesse/vupenn.pdf). Virtual U provided the kernel around which the enterprising Ben Sawyer (https://www.dmill.com) and Dave Rejeski nucleated the Serious Games initiative. Jesse still hopes to find a programmer who would take the 1981 Greenhouse Effect board game and turn it into an on-line game.

NYTIMES Newspaper Circulation

On 9 May 2006 The New York Times reported the decline in daily US newspaper circulation from 63 million in 1984 to 45 million in March 2006. The associated fall in demand for wood pulp affirms our vision of the great restoration of forests now underway and analysed in our numerous papers on forests and land use.

French CoML Slide Show

The French newspaper, Liberation, assembled a slide show of photos of plankton from the Bermuda triangle cruise of the Census of Marine Life by superb photographer and scientist Russell Hopcroft. (click “A voir” to view).

Inspired by Mars exploration, DNA sequencing gets much smaller, may be ready for field work soon

Blazej et al PNAS 103:7240, 2006ABI’s smallest sequencer is about the size and weight of a house air conditioning unit [ABI 310: 95 kg (208 lbs); 61 x 56 x 86 cm (24 x 22 x 34 in)]. Researchers who developed the Mars Organic Analyzer for detecting extraterrestrial life recently turned their attention to DNA sequencing. In 9 May 2006 PNAS Blazej, Kumaresan, and Mathies from the University of California, Berkeley, report on a microfabricated DNA sequencer comprised of three 10 cm glass wafers. Using 1 femtomole of DNA template and a 250 nanoliter reaction chamber, the device performs thermal cycling, DNA purification, and capillary electrophoresis, generating reads of up to 556 bases with 99% accuracy. Based on their results “the template/reagent requirements can be reduced an additional 100-fold, and a fully integrated microfluidic genomic sequencing system should also lead to significant infrastructure and labor savings.”

Faster, cheaper, more portable sequencing should facilitate “point-of-use” DNA barcoding devices for identifying specimens in the field, detecting invasive species at the customs station, and sorting through museum drawers for undescribed species, for example.