The Barcode Blog

Two papers in early online Mol Ecol Notes report large scale COI surveys of tropical bats and North American birds. In the first paper, Clare et al examined 840 specimens representing 87 (72%) of 121 known bat species in Guyana, each derived from vouchered specimens held at Royal Ontario Museum, including multiple individuals (range 2-74) from 73 (84%) of species. 81 of 87 species had distinct COI barcodes with average intraspecific variation of 0.6%. In the remaining 6 species, 15 distinct mitochondrial lineages were found which likely represent overlooked cryptic species. 

As most bats are small brown animals that fly around at night emitting noises that humans cannot hear, it is not surprising that some have been overlooked, and it seems probable many new species will be found lurking in museum drawers. Even in relatively bat-poor temperate regions there may be hidden diversity. It was not until 1997 that Europe’s most abundant and best studied bat, the Pipistrelle (Pipistrellus pipistrellus, Schreber 1774) was suggested to be 2 species through DNA analysis, a hypothesis confirmed by biological covariants and official species designation in 1999. 

In the second paper, Kerr et al (I am a co-author) report a continental-scale survey of mtCOI sequences in North American birds, including 2590 individuals from 643 species, representing 93% of the breeding avifauna of Canada and the United States. 94% of species had distinct barcodes, and in the remaining 6%, barcode clusters corresponded to small sets of closely-related species, most of which hybridize regularly. Fifteen (2%) of currently-recognized species were comprised of two distinct barcode clusters, many of which may represent cryptic species.

Birds being conspicuous, vocal, diurnal animals it is surprising that there are what appear to be overlooked species, even in an intensively-studied temperate region with relatively few species.  Of course barcode clusters are not proof of species status, but to my knowledge all such divergent lineages either correspond to recognized species, or have subsequently been found to show biological covariants and have ultimately been granted species status.

Sequencing of large tissue collections housed in museums can be done relatively rapidly and inexpensively. It is a challenge on how to report results in a way that communicates the genetic findings in a timely fashion without trampling on the careful procedures designed to maintain order in taxonomy.

By using tissues derived from vouchered museum specimens, these barcoding studies lay the groundwork for subsequent taxonomic study. By analyzing a standardized region, DNA barcoding studies can be stitched together to create a large-scale map of biodiversity, a horizontal genomics approach mapping leaves on the tree of life.

I see the “barcode map of genetic diversity” as analogous to an astronomical sky map that uses just a slice of the electromagnetic spectrum. It does not contain all the information necessary to understand the universe, but by focusing on one part of the spectrum it enables results from various studies to be seamlessly combined and allows both large and small scale comparisions. 

In February 2007 Microbiology Today, scientists report on the Barcoding Protists Workshop held in Portland, Maine in November 2006, which was attended by 40 protist experts from 12 countries (Australia, Canada, Denmark, France, Germany, Japan, Malaysia, Netherlands, Norway, Russia, UK, and USA). The workshop was co-sponsored by the US National Center for Culture of Marine Phytoplankton and the UK NERC Culture Collection of Algae and Protozoa.

According to Williamson et al, “most original descriptions for [over 200,000 named] protist species are based on light microscopy and ink drawings, not only making species identification for some groups an inherently subjective and specialist occupation, but also potentially hiding major genetic diversity.”

Workshop participants agreed unanimously that “to help resolve many of the contradictions and uncertainties in protist taxonomy, genetic barcoding is the way forward, starting with material, particularly type strains, in internationally recognized culture collections.”

In early online 12 Jan 2007 Mol Ecol Notes researchers from Columbia University, American Museum of Natural History, and California State University analyze COI barcode region sequences of 131 individuals representing 19 species of Mopalia chitons. Chitons are molluscs with flattened segmented shells, and most of the 860 known world species are herbivores that graze in tidal zones, although some are found at depths up to 6000 meters.  According to the authors “much of the biology of [Mopalia sp] remains undiscovered” because many “are difficult to distinguish from one another by morphology alone”, making them a good test case for DNA barcoding.

Kelly et al compared three approaches for identifying Mopalia chitons by COI. First, they used a “character based assessment called characteristic attribute organization system (CAOS)”. In this approach, a “guide tree” is generated using maximum likelihood or parsimony, and CAOS identifies sets of characters for each node in the guide tree. CAOS then attempts to assign unknowns based on these characters. If there is insufficient information to assign the query sequence, CAOS stops the analysis. The authors compared CAOS to neighbor-joining distance analysis on Barcode of Life Data Systems (BOLD) site, and to BLAST algorithm. All three approaches had overall accuracy of 100% when provided with the entire data set. CAOS was superior to NJ and BLAST when a skeletonized reference set containing of 50% of the total sequences was used.  

CAOS automatically identifies diagnostic molecular characters, and this will help integrate DNA barcode data into traditional taxonomy. For practical use, diagnostic sequence differences may aid design of solid-state microarrays that detect species in environmental samples, such as the 0.1mm Mopalia mucosa planktonic larva shown here, which might be found floating in seawater, or in the stomach of a krill.