DNA barcoding in floral and faunal research

Abstract

As I write this chapter in mid 2012, the context in which floral and faunal research is done is changing rapidly. Demand for biodiversity information, especially to understand global change, is increasing. The technologies that are available for carrying out biodiversity research and for disseminating the results are changing dramatically. The funding processes and organisational cultures of the institutions that have been the traditional homes of such research are evolving. This creates new challenges and opportunities for floral and faunal research. This chapter will focus on the intersection of DNA barcoding with floral and faunal research, the opportunities that DNA barcoding offers for increasing the quality and quantity of such work, and its connectivity with related activities. I will discuss the opportunities for DNA barcoding and then provide an example from my own research. The essay focuses on plants and animals, but will include some reference to other organisms. Because of the rapid evolution of the underlying technologies, and the related social changes, this essay represents a 'slice of time', and I expect some of the conclusions will be out of date before it is published. While challenges remain, I believe this is an exciting time of renaissance for taxonomy (Miller, 2007).A DNA barcode is a short gene sequence taken from standardised portions of the genome, used to identify species. Being DNA based, it can be used for specimens without morphological characters necessary for traditional identifications, such as roots or immature insects. Being a short sequence, it can be extracted from material that has not been specially preserved, and can often be extracted from standard museum or herbarium specimens. Being from a standardised region allows the use of universal primers for unknown taxa and allows rapid compilation of a global reference library. The choice of gene regions has focused on species level identification. While barcoding is not intended as a tool for higher classification research or for population genetics research, sometimes the barcoding gene regions have useful information at those levels (Craft et al., 2010). The present status of DNA barcodingWhile molecular diagnostics have been used for many years, DNA barcoding as a global initiative started by Hebert et al. (2003), who, among other things, pointed out that a standardised choice of gene region for species-level diagnosis allows individual projects of whatever scale to contribute to a global reference library that becomes increasingly more powerful over time. Mitochondrial Cytochrome c oxidase I (COI) had been widely used in animals since Folmer et al. (1994) and was quickly adopted as a community standard following Hebert et al. (2003). Standardised gene regions for plants proved more challenging for technical reasons, but are now designated as rbcL and matK, with additional research on trnH-psbA (Hollingsworth et al., 2009). The nuclear ribosomal internal transcribed spacer (ITS) region has been selected as a universal DNA b...

Documenting trumpet leaf-miner moths (Tischeriidae): new Neotropical Coptotriche and Astrotischeria species, with notes on Sapindaceae as a host-plant family

“…With the development of new technologies and the need to complete biodiversity inventories faster, integration of DNA COI barcoding or other molecular methods into ongoing taxonomic inventories has been propagated (notably Janzen et al 2009;Miller 2015;Miller et al 2016;Aagaard et al 2017). However, during the last few years, some very controversial attempts rejecting the usual standards for species description have been undertaken to speed species descriptions.…”

DNA Barcodes of Lepidoptera Reared from Yawan, Papua New Guinea

“…Methods for handling the Lepidoptera are described by Miller (2015), Miller et al (2003), and Novotny et al (2010). DNA sequencing (COI barcode) followed standard methods at the Biodiversity Institute of Ontario, University of Guelph , Wilson 2012, using legs and the LepF1 and LepR1 primers.…”

Challenges facing systematic biology

“…Another type of inventorying that appears destined toward success is the Barcode of Life (BoL) project (Hebert & al., 2003; Stoeckle & Hebert, 2008; Vernooy & al., 2010; Miller, 2015). The concept of assigning a barcode to all life forms, based on short DNA sequences, is one that is intuitively understood by all persons.…”