News

Harvesting wild animals for sale as food is a large, mostly illegal business that threatens wild animal populations and puts humans at risk for exotic infections, witness the SARS outbreak in 2003. Regulations and treaties exist, but before these can be enforced, one needs to establish the species origin of bushmeat and other derived marketplace products. Here DNA can help. In 1 September 2009 Conservation Genetics (open access article) researchers from University of Colorado, Barnard College, and American Museum of Natural History describe DNA barcodes for 23 species of South American and Central African primates, ungulates, and reptiles regularly harvested for bushmeat. Equally important as the DNA sequences, Eaton and colleagues report high success (179/204 samples (87.7%)) with primer cocktails first developed for fish DNA barcoding by Ivanova et al 2007, demonstrating these can serve as universal vertebrate primer cocktails. Intraspecific variation was low (mean 0.24%) and differences among congeneric species was generally high (average 9.77%), making assignment to known species straightforward using either tree-based maximum likelihood or character methods.

This report is focused on documenting barcodes of bushmeat species, using well-identified vouchered specimens (1 vouchered specimen labeled as Melanosuchus niger (Black caiman) was found to be Caiman yacare (Yacare caiman).  The researchers did test a handful of unknown or partially identified specimens; all with recoverable COI sequences could be assigned to known species in the data set using the tree-based or character methods as described. Remarkably, Eaton and colleagues were able to recover COI DNA from 1 of 5 leather goods, which had been impounded by the US Fish and Wildlife Service as likely of CITES species origin. This proved to be Crocodylus niloticus (Nile crocodile). Recovering DNA from leather suggests many unsuspected household items have legible DNA barcodes.

I only wish the research report could have included pictures–there is so much more we might learn. There is an AMNH webpage describing the project which has several interesting images, although these are unlabeled and not referred to by the text. Perhaps we need a “mash-up” utility into which one could insert a scientific paper, which then would pull in relevant material–images, maps, links. Along these lines, there is a very neat Encyclopedia of Life NameLink utility which automatically detects scientific names and inserts hyperlinks to relevant EOL pages–try it!

The horse-chestnut leaf miner moth Cameraria ohridella (link to Encyclopedia of Life species page), first described as an apparent endemic in Macedonia in 1984, has steadily expanded its range over the past 25 years, turning once attractive stands of horse-chestnut trees in many urban areas across Europe into unsightly arrays. The damage results from larvae feeding on the leaf interior (ie “leaf mining), causing extensive mottling and leaf loss. C. ohridella is an “invasive pest” in Europe and the subject of an international symposium in Prague in 2004 aimed at identifying biocontrol methods. For such a well-known and important organism, one might expect that scientific information would be readily available. As above, there is an excellent EOL species page, but I was unable to find the original species description online (Deschka G, Dimic N. 1986. Acta Entomologica Jugoslavica, 22, 11-23). A number of museums and universities have print copies of this journal, and I could request a photocopy through Rockefeller University inter-library loan, although of course that service is not available to the public.  I did find a complete set of AEJ available from antique bookseller (the journal ceased publication in 1990) for about $500 US!  For wider access, I hope that EOL pages will include links to original species descriptions when available as out-of-copyright or open-access.

This leads to report in July 2009 Mol Ecol by researchers from France, Switzerland, Hungary, and Canada, using mitochondrial and microsatellite DNA markers to trace origin of C. ohridella. For this remarkably wide-ranging study, the researchers analyzed 486 specimens from 88 localities in 22 European countries, collecting a single individual per leaf per tree, and if possible, from 30 different trees at each collecting site. To skip to the conclusion, consistent with historical pattern of spread north and west through Europe, the invasive form of the moth appears to be derived from populations infecting wild horse-chestnut trees in the southern Balkans. The genetic diversity was greatest in natural forests in Macedonia, Greece, and Albania, whereas the individuals collected from all “artificial” habitats (ie planted trees in parks, gardens, and roadsides across Europe) had nearly identical COI barcode sequences, consistent with recent expansion from a single source. The important practical conclusion is that biocontrol agents in the form of natural parasitoids are most likely to be found in wild stands of horse-chestnut in southern Balkans. I look forward to more studies on detecting and monitoring invasive species with DNA.

Tardigrades, commonly called water bears, are tiny (0.1-1.5 mm) water-dwelling invertebrates found in diverse environments. About 1000 species are known. Morphologic identification is difficult and may be limited to certain life stages–some species can be identified only from eggs, for example. Tardigrades can transform into a dormant state with remarkable ability to withstand extreme drying, cold, and radiation for prolonged periods, making them of interest for persons studying biology of tissue repair, aging and other fields.

Tardigrade Barcoding Project has just launched their website at www.tardigradebarcoding.org. The project will “provide a set of indispensible tools for the identification of marine, freshwater, and terrestrial tardigrade species, and will greatly aid taxonomists and ecologists. It will also enhance understanding on the evolution, ecology, life-history and extraordinary tolerance of physical extremes for these animals.” I add that COI barcodes are likely to reveal great genetic diversity hidden within morphologically defined species (eg Blaxter et al 2003).

I look forward to learning more about tardigrades!

In this week’s Proc Natl Acad Sci USA, CBOL Plant Working Group, which included 52 researchers from 25 institutions, announced agreement on a DNA barcode for land plants. The authors tell their story:

“DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL and matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.”

The Working Group concludes: ” There is little doubt that the approaches used in plant DNA barcoding will be refined in the future. However, the key foundation step for plant barcoding is in reaching agreement on a standard set of loci to enable large-scale sequencing and the development of a global plant barcoding infrastructure. The broad community agreement presented here, to sequence rbcL and matK as a standard 2-locus barcode, is thus an important step in establishing a centralized plant barcode database as a tool for taxonomy, conservation, and the multitude of other applications that require identification of plant material.”

In the same issue of PNAS, a Commentary by Jesse Ausubel traces the development of DNA barcoding, from a proposal in 2003 for a standardized DNA-based approach to species identification, using mitochondrial COI gene for animal species. Adopting COI as a standard was the essential first step, leading to a rapidly growing library now with over 620,000 specimens from over 58,000 species, enabling high-school students to become identification experts for store-bought fish items and shedding new light on species diversity. With the publication of this paper, DNA-based identification for land plants is now poised to expand rapidly, with benefits to science and society. Ausubel views DNA barcoding enterprise as an urgently needed “macroscope” for probing ecological and evolutionary patterns on a broad scale. He concludes with a call “to accept the invitation of the 52 authors led by Hollingsworth to use the standard two-locus barcode of matkK and rbcL to join in building a powerful botanical macroscope.”