Friday 9 June 2006 Jesse presents a progress report on the Census of Marine Life to a Long Island chapter of The Nature Conservancy.
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DNA barcoding snake venoms helps toxinologists save lives
If you hear this sound 
watch your step–a venomous rattlesnake may be nearby! Prompt administration of the correct antivenom can be life-saving.
The essential first step in toxinological research is reproducible analyses of venom toxins. However, in December 2005 Toxicon 46: 711-715 Pook and McEwing, University of Wales, report that reproducibility of toxin analyses is commonly compromised by “misidentification of species due to insufficient or changing knowledge of current snake systematics.”
Their article describes a breakthrough in toxinological research: DNA barcoding of dried venoms to provide an accurate, permanent “label” that is independent of future taxonomic changes. This short article is a powerful demonstration of how a standardized approach to identifying species by DNA that uses a public database linked to vouchered specimens, i.e. DNA barcoding, can benefit science and society. While some taxonomists will continue to wring their hands, others may be excited by this work, as it demonstrates how DNA barcoding ADDED TO (and not replacing) standard systematic practice can improve the accessibility and usefulness of ongoing taxonomic work for the larger biological community. I believe this article is enormously important, and I quote here at length.
From the Introduction: “Erroneous or uncertain taxonomy confuses the interpretation of results with respect to intraspecific and interspecific variation. Genuine logistical problems are encountered by non-specialists in taxonomy and snake systematics, in being able to keep up with taxonomic changes. The main hindrances include unresolved taxonomy for some species groups, and new data that change the definition of taxonomic units in others, with the result that the use of systematic information in the toxinological and clinical literature is disorganised. The problem is compounded further by changes in the concept of a particular species, and hence the interpretability of the venom used. Taxonomic confusion, however, has serious implications in snake venom research. The development of effective antivenom treatments and treatment strategies for envenomized patients necessitates a sound taxonomic framework. Accurate clarification of the identity of a given venom is paramount, even after taxonomic revisions involving the species concerned.”
Pook and McEwing “propose a solution to the long-term problem of species identification in toxinological work, utilising mitochondrial haplotypes isolated directly from snake venoms to provide a means of identification that will remain useful even in the face of radical changes in our understanding of the species concerned.”
From the conclusion: “The barcode strategy is dependent on the availablity of known mtDNA haplotype standards against which the sequences being investigated can be compared. Mitochondrial haplotype standards should be gene sequences from snakes of confirmed identity, which have been accessioned to a museum collection as voucher specimens.”
Stressful leisure
The analysis that Jesse Ausubel and Arnulf Gruebler published in 1995 on Working Less and Living Longer: Long-Term Trends in Working Time and Time Budgets is cited in an article on “Stressful Leisure†in World Magazine, a Christian weekly.  We had read the January 2006 report by Mark Aguiar and Eric Hurst on “Measuring Trends in Leisure: The Allocation of Time over Five Decades†as well as its foil, “A Century of Work and Leisure†by Valerie Ramey and Neville Francis (June 2005) and recommend both. We continue to believe that changes in total life hours worked merits more attention.
Oklahoma Wind Power
The 17 May New York Times quoted Jesse about windpower. For an exposition of the problem, see “Nuclear and Renewable Heresies” posted 19 March 2005.
Salamanders support standardization
In Barcoding Life, Illustrated we suggested that “standardization typically lowers costs and lifts reliability…and should help accelerate construction of comprehensive, consistent reference library of DNA sequences and development of economical technologies for species identification.” However, some have been doubtful about the benefits of standardization. This reflects in part the balkanized nature of taxonomic science, as most systematists specialize on groups of related organisms and have limited scientific interactions with those studying other groups. Last year Jesse Ausubel and Paul Waggoner outlined some of the concerns raised by the growth of DNA barcoding in Barcoding Worries and Limits. The final item asks whether “it is too soon to standardize on a very few localities”. The salamander paper discussed in last week’s post seems to support this concern, as it implies that the relative rates of evolution of mitochondrial genes differ between animal groups. According to the paper, in salamanders COI evolves much more rapidly than other mitochondrial protein-coding genes.
However, as detailed below, my analysis indicates that salamanders are unexceptional in terms of COI differences. I find evolutionary divergences are widely distributed in mitochondrial protein-coding genes and the patterning of these differences is similar in diverse invertebrate and vertebrate organisms, including salamanders. First, I used PipMaker (percent identity plot) to examine the distribution of sequence differences in complete mitochondrial genomes. A representative PipMaker plot, shown above, compares the mitochondrial genomes of 2 plethodontid salamanders, Desmognathus fuscus and D. wrighti, revealing a typical pattern of widely distributed sequence differences. As in most vertebrates, in salamanders COI is slightly LESS divergent (14%) than other protein-coding regions, including cytochrome b (CYTB) (17%).
Second, I compiled differences between closely-related species pairs in CYTB and COI. For historical reasons, CYTB has been the single most common locus used to analyze differences in vertebrate species, and COI has been the single most common single locus for invertebrates. As shown below, these genes show highly correlated differences in deeply divergent lineages of invertebrates and vertebrates, including salamanders.
Species examined include Demospongiae (sponges); Platyhelminthes (tapeworms); Echinodermata (starfish); Arthropoda (ticks; fruit flies; mosquitos; shrimp); Mollusca (octopi; mantis shrimp) Vertebrata (turtles; eels; coelecanths; elephants; wolves; apes; and 5 pairs of congeneric salamanders)
These findings support standardizing on COI as the primary DNA barcode for multicellular animals. As discussed in earlier posts, there will of course be cases in which the primary barcode does not resolve closely-related species and a secondary barcode(s) may be needed.
DNA barcoding identifies invasive pests, appears ready for agricultural application
Pest and invasive species in agricultural crops and shipped goods pose enormous economic and biosecurity threats. Rapidly and reliably identifying pests and invasives in all life stages is likely to be one of the most economically important applications of DNA barcoding. In March 2006 Ann Entomol Soc Am 99: 204 Scheffer, Lewis, and Joshi from the USDA and the Philippine Department of Agriculture apply DNA barcoding to invasive leafminer flies in the Philippines. 
They analyzed 258 specimens from the Philippines and compared these to a database of 307 sequences previously collected from worldwide populations. Bootstrap values for all species were 100%. In addition, a total of 7 distinct clusters
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with 98-100% bootstrap support were found in 3 “morphospecies”, suggesting discovery of new species, similar to findings of unrecognized biodiversity in all DNA barcode surveys to date. They conclude “DNA barcoding of economically and medically important species offers a powerful means of rapid identification”.
With DNA barcoding, all can identify this Liriomyza sativae pupae
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
A 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 
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.
JIE Celebrated 10th Anniversary
On Thursday, May 11, 2006 the Journal of Industrial Ecology celebrated its 10th anniversary and inclusion in the Science Citation Index with a seminar and festive program. Jesse was one of three honorees, for PHE’s work on Dematerialization, carried out with Robert Herman and Iddo Wernick.