Whistlers highlight the unreliability of DNA barcodes

Genomic data and plumage patterns do not agree with mtDNA in the Western Whistler.

Imagine being able to identify any species by quickly scanning a section of their DNA. That is the rationale behind DNA barcoding where each species is linked to a specific DNA sequence (mostly the mitochondrial gene COI). This approach – introduced by Paul Hebert and his colleagues – sounds promising but has several shortcomings and pitfalls. An opinion paper on insect taxonomy succinctly summarized the situation: “While we do believe that barcode clusters are indeed useful as grouping statements, there is no compelling reason why they should be described as species.” I could not agree more: DNA barcodes can generate taxonomic hypotheses, but these remain to be confirmed with additional data, such as genomics, morphology or behavior. Taxonomy is a pluralistic practice that requires expert knowledge, and cannot be condensed into an automated procedure of scanning DNA barcodes. The possible problems with only relying in DNA barcodes were nicely illustrated by a recent Emu paper on the taxonomy of Australian Whistlers (genus Pachycephala).

Genomics and Plumage Patterns

In 2014, Leo Joseph and his colleagues argued to split the Golden Whistler (P. pectoralis) into two, adding the Western Whistler (P. occidentalis) to the checklist of Australian birds. This decision was largely based on analyses of the mitochondrial DNA which separated the western populations of the Western Whistler (then classified as the subspecies P. pectoralis fuliginosa) from all other populations of the Golden Whistler. Interestingly, the mtDNA of eastern populations of P. pectoralis fuliginosa was different from the western populations, leading the researchers to include them in the Golden Whistler. The nuclear markers (eight loci) in these analyses did not provide any additional insights. Hence, the researchers decided to recognize only the western populations as a separate species: the Western Whistler.

This taxonomic arrangement is now called into question by a recent genomic study (again by Leo Joseph and his colleagues). Using almost 20,000 genetic markers, the researchers identified three main clusters:

  1. Eastern mainland and Tasmanian subspecies of the Golden Whistler (pectoralis, youngi and glaucura)
  2. Western subspecies of the Golden Whistler (fuliginosa)
  3. Western Whistler (P. occidentalis)

More importantly, the latter two clusters – the western subspecies and the Western Whistler – are closely related to each other. This genetic connection is further strengthened by morphological data. In the eastern subspecies, adult females and immatures have grey chests and bellies accompanied by yellow or white under-tail coverts. The plumage patterns are quite different in the western subspecies and the Western Whistler where adult females and immatures are cinnamon from the chest to the under-tail coverts (see drawings on the figure below).

A principal component analyses based on genomic data clusters the Western Whistler (P. occidentalis) and the western populations of the Golden Whistler (P. p. fuliginosa) together, separating them from the eastern populations of P. pectoralis. From: Joseph et al. (2021).

Mitochondrial Introgression

These patterns present a taxonomic conundrum: based on genomic data and plumage patterns, the fuliginosa subspecies clusters with the Western Whistler, while mtDNA places it with the eastern populations. The most parsimonious explanation for these findings entails that what had been retained in the 2014 paper as the fuliginosa subspecies of the Golden Whistler P. pectoralis is most closely related to what the same paper called the Western Whistler P. occidentalis. This population was isolated in southwestern Australia, but has received mtDNA from the mainland eastern populations of Golden Whistler through introgressive hybridization. Based on this scenario, the researchers propose that the Western Whistler should be expanded to include what was the fuliginosa subspecies of P. pectoralis. Because the name P. fuliginosa Vigors & Horsfield, 1827 has priority over P. occidentalis Ramsay, 1878, the scientific name of the Western Whistler will be changed to P. fuliginosa. Possibly, introgression is still in progress and has not yet reached the western populations of the Western Whistler that now become known as P. fuliginosa occidentalis. However, it is more likely that 200 kilometers of unsuitable habitat between the two subspecies of P. fuliginosa poses a significant barrier.

Apart from this taxonomic bookkeeping, this finding carries an important warning on the use of DNA barcodes. Solely relying on mtDNA and a few incompletely sorted nuclear loci for delineating species led to the wrong classification among these whistlers. The analyses of genomic data and plumage patterns provided the complete picture. To reiterate the message from the start of this blog post: DNA barcodes can generate taxonomic hypotheses, but these remain to be confirmed with additional data.

References

Joseph, L., Campbell, C. D., Drew, A., Brady, S. S., Nyári, Á., & Andersen, M. J. (2021). How far east can a Western Whistler go? Genomic data reveal large eastward range extension, taxonomic and nomenclatural change, and reassessment of conservation needs. Emu-Austral Ornithology121(1-2), 90-101.

Featured image: Golden Whistler (P. pectoralis) © J.J. Harrison | Wikimedia Commons

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s