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In another seeming step towards Jurassic Park, two groups of researchers recovered full-length mitochondrial DNA sequences from 22,000 to 44,000 year-old bones of extinct European and North American bears. Full-length mtDNA has been recovered from similarly ancient specimens, but in those cases frozen tissues preserved in permafrost were used. Both groups used specialized PCR protocols employing several hundred primer pairs designed to recover short fragments, rather than one of the newer sequencing technologies, demonstrating the continued power of DNA amplification.

In 28 july 2008 BMC Evol Biol Proc a group of 18 researchers led by Johannes Krause, Max Planck Institute, Germany, recovered full-length mtDNA from a 44,000 year old Ursus spelaeus (European cave bear) bone found in an Austrian cave, and from a 22,000 year-old skull of Arcdotus simus (American giant short-faced bear) from Eldorado Creek, Canada. In 11 november 2008 Proc Natl Acad Sci USA, 14 researchers led by Jean-Marc Elalouf, Institute de Biologie et Technologies de Saclay, France, report full-length U. spelaeus mitochondrial genome from a 32,000 year-old bone from the legendary Chauvet-Pont d’Arc Cave, home to the oldest rock art pictures ever found.  

If we found a bone from one of these extinct bears in our backyard, could it be identified by its COI barcode? Submitting the long-ago bears’ COI barcode region sequences (positions 48 to 705) to BOLD ID engine flags both species as not in database, with a NJ tree similar to that created by full-length genomes (ie the extinct U. spelaeus is sister to U. arctos (Brown bear) and U. maritimus (Polar bear), and extinct Arcdotus simus is sister to Tremarctos ornatus (Spectacled bear). Of course it would be difficult to recover a full-length sequence–what about the 130 base pair “mini barcode” proposed for broad-scale biodiversity analysis? This is within the size range(ie < 180 bp) that Elalouf and colleagues report best for recovery of ancient DNA. Remarkably, A. simus mini-barcode submitted to BOLD ID engine gives NJ tree correctly showing T. ornatus as its sister species and U. spelaeus mini-barcode correctly picks out U. arctos and U. maritimus as most closely-related species.

Recovering DNA from ancient bones leads to CSI-like thoughts of where else we might usefully recover DNA for species identification. DNA has been recovered from naturally shed feathers, flakes of seal skin at breathing holes in polar ice, hair and saliva left by predators of sheep, bird faeces, and, turning to world of commerce, ancient and modern processed leather goods (Long 2007). I look forward to analyses of the many processed foods with what is currently an unverifiable “list of ingredients.”

In Cladistics 25 Sept 2007, Steven Trewick from Massey University, New Zealand applies mtDNA to help sort out endemic flightless grasshoppers in genus Sigaus, which are restricted to mountainous alpine habitat on New Zealand’s South Island. Here we might expect a complex pattern of diversification. These are small, terrestrial, flightless, presumably non-vagile (ie don’t travel far) animals in a deeply fragmented habitat. Their habitat lies in New Zealand’s central mountains, the Southern Alps, formed by a geologically recent uplift 5 to 2 million years ago. Like other organisms restricted to elevated mountain terrain, they are effectively living on “sky islands.” In this setting, we might expect a plethora of relatively young species with very narrow ranges, with difficulty determining which forms merit species-level status.

Trewick focused on Sigaus australis species complex, which includes the apparently widely-distributed S. australis, and 5 sympatric or parapatric species with much narrower ranges (S. childi, S. obelisci, S. homerensis, and 2 undescribed species). Within this complex he analyzed 160 individuals collected at 26 locations (mostly S. australis (136 individuals) and 1-13 individuals for the more restricted species). For mtDNA analysis, an approximately 600 bp region of 12-16S and about 500 bp of 3′ COI (ie not overlapping COI barcode region!) were examined.

Although the 3′ COI fragment analyzed in this grasshopper paper has been utilized in a number of invertebrate mtDNA studies, it is just one of many mtDNA targets that give essentially equivalent phylogenetic information (eg, in this study COI and 12S-16S gave same results). The hodgepodge of mtDNA regions analyzed in species-level animal work means that most data cannot be compared or combined. In my view, ALL animal mtDNA studies should include the standard COI barcode (defined relative to the mouse mitochondrial genome as the 648 bp region that starts at position 58 and stops at position 705; https://barcoding.si.edu/PDF/DWG_data_standards-Final.pdf), plus of course any other regions of interest. Standardization on the barcode region ensures long-term usefulness, both as a reference for identification and for comparisons across the diversity of animals. In addition to a defined genic target region, DNA barcode standards have other advantages, including that records are linked to voucher specimens and list primer sequences and include bidirectional trace files and quality scores.

In the present study single-strand conformation polymorphism (SSCP) of a 380 bp 12S fragment was used to screen for differences, and then individuals with different SSCP results were subjected to sequencing, so in the end just 40 of 160 Sigaus sp grasshoppers were sequenced for COI. This also means that there is voucher data in GenBank for just these 40 individuals. Continuing down the DNA barcode standard checklist, primer sequences are not easily accessible (there is a published reference for the primers, but access requires article purchase), it is not stated if bidirectional sequencing was done, and trace files and quality scores are not provided. I hope that future studies on New Zealand orthopterans will include the 5′ COI region and the remaining information, as I believe this will increase their long-term utility both as an identification reference and for comparisons across diversity of animal life (>520,00K individuals representing >50,000 species in BOLD so far). There is a big opportunity for grasshopper specialists to contribute–the BOLD taxonomy browser contains records for only 191 of the approximately 10,000 species in family Acrididae! 

To skip to the conclusion, the sequence analysis gave an entirely different picture than existing morphologic taxonomy. 12S-16S and COI gave identical results: four well-supported geographically-structured clades within the widespread S. australis morphospecies, 3 of which had partly overlapping ranges. The 5 described or proposed species in the complex nested within these clusters, with shared or similar mtDNA haplotypes to S. australis from the same region.

The author concludes that the results show that “haplotype sharing and paraphyly essentially invalidate the DNA barcoding approach.” I disagree. To my reading, the most parsimonious explanation is that 1) morphologic taxonomy has overlooked deeply divergent genetic lineages, which likely represent different species, in S. australis for over 100 years, and 2) a number of morphologically distinctive forms have arisen very recently.

In support of the first point I note that in April 2008 report “Diversity and taxonomic status of some New Zealand grasshoppers” by the same author and Simon Morris, “Attention needs to be given to the spatial distribution of diversity within [S. australis complex]…Further morphological study may support the splitting of one or more of the groups indicated by phylogenetic analysis of mtDNA sequences.” 

Regarding point 2, genetic methods including DNA barcoding may not resolve very young species. For Sigaus sp. grasshoppers, nuclear sequence data will help sort out whether these are young species or the products of recent hybridization or introgression. 

In this regard, I am struck by the apparent variability in some grasshopper species, as in the color morphs of S. childi shown above. It brings to my mind the extraordinary transformations from solitary grasshoppers to swarming locusts (these are members of the same Acrididae family as Sigaus). Perhaps grasshopper genetics include analogous latent “switches” that might enable relatively rapid evolutionary transformations.
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The DNA barcode initiative aims to establish a universal identification system for plant and animal species by analyzing a standardized genetic locus (or for plants, a small set of loci). In addition to making analysis cheaper, standardizing on one or a few loci enables a diverse assemblage of researchers to work together to build an interoperative library.

If there were no Human Genome Project, researchers working gene by gene might eventually have decoded the human genome sometime during this century, albeit at much slower pace using more expensive and less accurate technology. For a genetic library of biodiversity, a concerted effort is essential. The various taxon-specific genetic initiatives, which are typically aimed at reconstructing deep evolutionary history, are too limited in scope (ie number of species and individuals per species analyzed) and too expensive in terms of cost per species to completely catalog animal and plant life. In addition, because different groups analyze different gene regions, it is impossible to stitch together the results into single database, for instance one that could be used to identify an unknown specimen without knowing beforehand what group it belongs to. The DNA barcoding initiative offers the necessary framework for constructing a genetic reference database for species. In addition as a large-scale project it should help drive technological improvements analogous to those spawned by the Human Genome Project which enabled its completion for a fraction of the originally projected cost. 

As of today, researchers have deposited 516,134 barcode records from 50,138 species in Barcode of Life Database (BOLD) www.barcodinglife.org. According to my analysis of GenBank shown in figure, this puts COI BOLD records far above the totals for any other single gene for animals. Thus five years of a concerted, standardized approach has leapt ahead of 30 years of incremental analysis. If the proof is in the pudding, this to me is a pudding that proves the value of the DNA barcoding initiative. Comparison of the totals indicates that most BOLD COI records are not yet in GenBank, although some aspects are visible through ID engine and Taxonomy Browser, so there is work to help move these fully into the public domain and at the same time ensure appropriate academic credit. Congratulations to all those moving this effort forward.

GPS devices for civilian use were first introduced 1982. The TI 4100 from Texas Instrument Company cost $150,000, weighed 50 lbs, and had heavy demand from land surveyors (GPS World, December 2004). Thanks to steady improvements in cost, size, and power demand, GPS technology is now a standard feature in cellular phones, meeting such daily needs as finding the nearest coffeeshop. The simplicity of everyday use is undergirded by an enormous investment in technology. In a 1997 report, RAND corporation estimated approximately $8 billion had been spent to develop, launch, and maintain the 24-satellite system that provides GPS signals, and the ongoing costs were $300 million/y.

The GPS history suggests viewing the current drive to establish a DNA reference library for millions of plant and animal species as infrastructure investment, analogous to the GPS satellite system. It is relatively expensive but once established will enable diverse new applications for society and science. What uses will improvements in DNA sequencing married to a robust DNA barcode library bring? 

Food authentication is likely to be one major application, including a wide array of products such as fish, olive oil, and packaged mixtures such as soups and pet food.

In Hidrobiologica March 2008 researchers from El Colegia de la Frontera Sur, Universidad Autonoma Metropolitana, Iztapalapa, Mexico, describe a new species of Cladocera from temporary pools in a semi-desert region. Cladocera, commonly known as “water fleas,” are minute crustaceans mostly limited to fresh water; Daphnia sp are the best known. Cladocera are of practical importance as water quality indicators.  

Similar to that for other invertebrates, the species description for this minute (0.4 mm) crustacean Leberis chihuahuensis comprises about 4 pages of mysterious text and 2 pages of equally enigmatic illustrations. In addition, the DNA barcode of the type specimen is provided, as well as the more usual NJ tree, in this case showing 14% sequence divergence from its sister species L. davidi. 

By including both kinds of characters, ie DNA barcode and morphology, Elias-Gutierrez and Valdez-Moreno provide what seems to me a model for any new species description, one that will enable specialists and non-specialists alike to make the most use of their findings.

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In 2003, Paul Hebert and colleagues proposed a universal identification system employing short DNA sequences as identifiers for animal and plant species. Inspired by the Universal Product Code labels that stores use to track merchandise, he named these short sequences “DNA barcodes.” My colleagues and I set down thoughts inspired by this new name:

“Commercial barcodes and the barcode of life

Jesse Ausubel, Mark Stoeckle, Paul Waggoner

September 2004 

Although new methods of sequencing and visualization have displaced the one that produced autoradiographs that show blurry gray stripes of a gel indicating presence or absence of particular bits of DNA, the analogy between the commercial barcode and the barcode of life may be traced to it. However, the power of the analogy comes from other similarities: large capacities to differentiate mind-boggling diversity, ability of digits to distinguish unambiguously, rapidity and economy of identification, ability of parts of the code to distinguish categories, and avoidance of a Tower of Babel by uniformity. We elaborate briefly.

Without the final digit that checks accuracy, the quartets of bars and spaces in the Universal Product Code (UPC) have 10 alternatives at 11 locations, creating an ample 1011 capacity to identify manufacturers and their products. Instead of operating in quartets, sequences of CATG operate in trios that specify synthesis of an amino acid. Each trio of the four alternative CATG has 43 or 64 alternatives. A 600-unit sequence of DNA comprising 200 trios with 64200 alternatives opens ample capacity to identify millions of species. Such large capacities are needed to differentiate the diversity of an economy or a forest.

Because one product number in a UPC differs from another by discrete, digital steps rather than by the shades of verbal descriptions, the numbers identify the product–unambiguously. A barcode of life written as a sequence of CATG along a uniform locality of genomes differs from another by four discrete, unambiguous steps rather than by gradations of words, shapes, and colors. Barcodes gain power because digital beats analogue at making unambiguous distinctions.

Speed and economy also propel use of barcodes. Behind the beep of a UPC scanner lies orchestration that began with the initial conception of bars for numbers a half-century ago. Users and inventors orchestrated optics, electronics, and software to develop miniature, robust equipment that made the barcode an affordable master key to supermarket inventories and suppliers (Swartz 1999). Now that the price of DNA identification of a species has fallen to about $10 (Randhawa 2004), the orchestration can begin to provide a barcode of life. Uniformity fosters frequent use and thus learning and economy.

Product codes can identify products with increasing resolution. At the first level of resolution, the first bars of a UPC on a carton resolve the manufacturer. At the second level, the last bars resolve the product line. Opening the box and reading the serial number would resolve the individual. In analogous manner, extending a DNA barcode through more and more sequences would resolve from kingdoms to species, subspecies, and finally individuals. For our goal, Ockham’s razor prescribes as short a barcode of life as suffices to distinguish species.

Uniformity bestows the universality implied by the U in UPC. Scanners in hardware, grocery, and convenience stores must all call the same light bulb by the same 12 digits. Recently agreement between America and Europe added a thirteenth digit, made uniformity more widespread, and brought universality closer to realization (NY Times 12 July 2004, page C1). The power of standardization, whether in railroad gauges or typewriter keyboards, is one of the strongest lessons of the history of technology.

Finally, the success of a short DNA sequence distinguishing species will rest on reasoning, testing, and agreement, not just an appealing analogy. Reasoning will select a uniform locality on genomes that varies enough but not too much among species, testing will establish whether barcodes of that uniform locality correspond to established binomial names across several species, and then agreement will foster an expanding compilation of matching barcodes and binomial names.”