DNA barcoding: bane or boon (or both) for taxonomy?

Donal A. Hickey,

Concordia University, Montreal.

Collaborators: Mehrdad Hajibabaei and Gregory Singer

Hajibabaei et al., 2006

Cowan et al. (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants.

Taxon 55: 611-616

DNA barcodes have been successfully applied to a limited number of animal groups with the application of the mitochondrial gene, cytochrome c oxidase subunit 1. Recently two DNA regions, the plastid trnH-psbA spacer and nuclear ribosomal ITS region, have been shown to have potential as an identification barcode for land plants, although with some significant drawbacks. The ideal barcode should be relatively short in length (∼700 bp), more variable between than within species, and easily amplifiable with universal primers. Building on current success, ongoing investigations are searching for the best barcode to apply to all land plants. Once established, a plant barcode may be effectively used in biodiversity inventories, conservation assessments, and applied forensic investigations. Advances in sequencing technology and the completion of the DNA barcode library have the potential to provide the public with increased access to information about the natural world.

Is DNA barcoding:

- a taxonomic tool?

- a phylogenetic tool?

- a tool for simply assigning unidentified specimens to known species?

- all of the above?

- none of the above?

Testing DNA barcoding as a phylogenetic tool:

Let’s see how barcoding works in a case where we know the answer (or, at least most of us think we know the answer).

The CBOL brochure:

What is wrong with this picture?

Benchmarking DNA barcodes: an assessment using available

primate sequences

By using high bootstrap values, most of the branching pattern collapses, but the species resolution remains.

The two closely related species of chimpanzee can be resolved by reducing the bootstrap cut-off to 95%

Or, we can retain the 100% bootstrap and increase the sequence length – it’s a simple trade-off .

In this case the “barcode” was extended to 1,500 bp

The relationship between barcode length and diagnostic value

(Lepidopteran dataset)

“The goal is to make all of biodiversity Google-searchable”.

Conclusions.DNA barcoding can be used to put names on individual specimens

It should not be used for:

- putting names on species

- or for assessing phylogenetic relationships between species.

In other words, it can create an entry point to Taxonomic e-Science for the non-specialist.

( But it can be very useful for specimen identification, especially for immature stages and damaged specimens)

Sperling FA, Anderson GS, Hickey DA. (1994)

A DNA-based approach to the identification of insect species used for postmortem interval estimation.

J Forensic Sci. 39: 418-427.

DNA fragments were amplified using the polymerase chain reaction (PCR), followed by direct DNA sequencing of the amplification products. Based on these abundant DNA sequence differences, we can unambiguously identify the immature larval stages of these insects.

These DNA sequence differences were also used to predict species-specific, diagnostic restriction sites in the amplified DNA, and these predictions were verified by digestion with nine restriction enzymes.