DNA speeds discovery of overlooked species

Just as new telescopes reveal previously hidden details of the universe, genetic surveys regularly reveal previously hidden (aka cryptic) species. Of course these species are cryptic only in the sense that morphological analysis is not the right tool to “see” them with. To my ear the word “cryptic” suggests camouflaged organisms that blend in with the environment, such as the Dead leaf butterfly Kallima inachus. Unlike camouflage, which is presumably a protection adaption, it is my impression there is nothing biologically special about morphologic crypsis except for the difficulty we have in recognizing it; that is, what we call cryptic species exhibit the same sorts of distinct ecological and behavioral adaptations found in those whose differences are more visible to the human eye.

To restate the above, when multiple individuals are examined for gene(s) that reflect species-level differences (this is the essence of DNA barcoding), many animal and at least some plant species are discovered to be comprised of two or more genetic clusters, each carrying diagnostic nucleotide substitutions. When appropriate analytic tools are applied, these within-species clusters are often found to be reciprocally monophyletic lineages that have been reproductively isolated for hundreds of thousands to millions of years. In studies where the painstaking work of natural history observation has been carried out, these genetic clusters usually show ecological and behavioral differences and sometimes previously overlooked morphological distinctions, consistent with species-level status. In short, DNA analysis speeds discovery of new species. In many cases, it reveals species that would otherwise probably remain unrecognized indefinitely.

The premise of DNA barcoding is that a very short segment (ie for animals 648 bp COI barcode region) is usually sufficient to screen for new species and to assign specimens to known species. Of course, more sequencing is always of interest, but the added discriminatory value for detecting species-level differences is small compared to the added cost. Moving backwards in evolutionary time, a neighbor joining tree constructed with 648 bp barcode sequences often groups genera and families correctly; however it generally does not contain enough information to establish branching order or uncover deeper-level associations that are the heart of phylogenetic study, so there is plenty for systematists to do.

Now for some data. In 25 december 2008 Mol Phylo Evol researchers from University of Gothenburg and University of Florida report on Lumbriculus variegatus Muller, 1774, a segmented freshwater worm widely distributed in Europe and North America, commonly used as a model laboratory organism, in environmental toxicology, and sold as pet food for fish and amphibians under name “blackworm.” Part of the laboratory interest in L. variegatus lies in its remarkable ability to re-generate after fragmentation; any of the approximately 200 segments can re-form a complete adult worm; most populations reproduce through auto-fragmentation. Given that L. variegatus is a common, widely-distributed organism described over 200 years ago and is regularly used in scientific study, one might not expect any taxonomic surprises.

Gustafsson and colleagues were initially studying a neuropeptide gene FMRFamide using L. variegatus purchased from a commercial supplier in California, with puzzling results suggesting polyploidy with multiple gene copies.  This lead them to further characterize approximately 50 individuals collected at multiple sites in Europe and North America.  Sequencing of COI, 16S, and ITS sorted the specimens into 2 phylogenetically distinct (maximum parsimony and Bayesian analysis) clades with 17% mean difference in COI, with the same genetic structure in mitochondrial COI/16S as nuclear ITS. Both clades were found in North America and Europe, sometimes at the same site. The authors conclude “it thus seems reasonable to regard these two main lineages within the L. variegatus complex as different species, regardless of which species concept one adheres to.”  Of course, it may be they have rediscovered a named species; they caution that more study needs to be done including sampling the other named species in genus Lumbriculus (see EOL page). 

DNA barcoding is an efficient instrument for revealing species-level differences. Routine application of DNA barcoding can enhance quality control in work with model organisms, cell lines, and collected specimens, and the long-term value of species descriptions.