DNA Barcodes from types

Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavorable for DNA preservation, success in sequence recovery has been uncertain.

Earlier studies have shown that standard molecular methods can also be applied to type material of soft-bodied insects but success is rather mixed. Dried, mounted specimens can yield viable DNA even over 100 years after collection from as little as a single leg. Past studies usually included a number of PCR reactions to generate a set of short amplicons which could be assembled into a barcode contig. The problem is that templates can be depleted before the full sequence is recovered especially when many amplification reactions are required. This is extremely problematic if only one type specimen for a species is available.

In a new study coming out of BIO my colleagues used multiplex PCR to generate short amplicons covering the barcode region and then Next Generation Sequencing (NGS) for their characterization. They started with conventional Sanger sequencing of 1820 type specimens of the moth family Geometridae from the Natural History Museum,London as part of a project to develop a strongly validated taxonomic system to support species inventories and studies of host plant use in Papua New Guinea. For their comparative NGS run the colleagues picked single representatives from 30 different genera of the family, all between 102 and 123 years old.

They were able to recover sequence information from all specimens with average read lengths ranging from 458bp to 610bp which is impressive. But the inevitable question is if such an approach is not cost-prohibitive at this point. This is what the study authors have to say and I find that very encouraging:

By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.