Five years ago, I was a co-author on a consortium paper in PNAS that recommended two genes to serve as universal markers for DNA-based identification (DNA barcoding*) of plants. Five years ago, the world celebrated Charles Darwin’s 200th birthday. You might not think those two events are related, but they are. Here’s how.
The paper marked the end of a very long road. DNA barcoding as an international, standardized endeavor got underway in earnest around 2005, but the gene chosen and officially endorsed by the Consortium for the Barcode of Life (CBOL) to serve as the DNA barcode for animals, CO1, is not variable enough to discriminate among plant species. The CBOL Plant Working Group was formed to solve this problem by finding an alternative gene or genes (or between-gene region or regions) for plants. We spent four years generating, pooling, analyzing, and, hardest of all, making a decision based on a very large data set of PCR amplification success rates and DNA sequences from seven candidate genes (or regions) from 907 specimens from 550 species representing the major groups of land plants. You can learn more about the study, the results, and our recommendation to the DNA barcoding community in the (open access) paper in PNAS.
What you can’t learn more about in the paper is the story of the 138 specimens that a group of us from the Natural History Museum in London, where I was a postdoctoral researcher at the time, contributed towards that 907-specimen total. Because the paper was about what the combined data from multiple researchers could tell us about prospects for DNA barcoding in plants, it wasn’t the time or place to tell the stories of researchers’ individual projects. And because the narrative of a project can’t really be published on it’s own without (as yet unpublished) data to go along with it, I was afraid this meant the story of our project would go unpublished, which would be a real shame because it’s a good story.
You see, we had collected those 138 specimens during our project to repeat Charles Darwin’s 1855 botanical survey of Great Pucklands Meadow at Down House. It was one of a series of projects I helped coordinate as part of the Museum’s campaign to celebrate and extend Darwin’s legacy on the occasion of his 200th birthday. The aims of the re-survey were to detect any changes in the meadow flora since 1855 and work out protocols for combining the collection and management of plant specimens with DNA barcoding.
2010 came and went, then 2011. I moved back to the United States and became a member of faculty at the MDI Biological Laboratory. I had pretty much given up on telling the story of the meadow project when, in 2012, I was invited to contribute a chapter to an academic book on the topic of “Darwin-inspired learning” to be edited by Carolyn Boulter, Michael Reiss and Dawn Sanders. Contributors were challenged to “think about how their knowledge and expertise and the work of Charles Darwin intersect to provide new ways of thinking about teaching and learning”, to quote from the invitation email, and my chapter would “examine how scientists use Darwin’s ideas today in the context of current experiments/investigations/reviews”, drawing on my own work as a scientist. I asked the editors if they thought the meadow story would fit and they were enthusiastic.
The big news and the reason for the timing of this post is that Darwin-Inspired Learning – including my chapter about the Great Pucklands Meadow resurvey – was just published! You can purchase it in hardcover, paperback, or e-book from Sense publishers. I recommend the e-book as the quality is better, especially the images (color!) and tables.
To give you a taste of my chapter, and to outline the rest of the meadow story, here are some excerpts and images:
In June 1855 Charles Darwin wrote to Joseph Hooker that he intended to survey the 13-acre hay meadow (Great Pucklands) near Down House, and reported with delight – ‘Hurrah! Hurrah!’ – that he had identified his first grass (C.R. Darwin to J.D. Hooker, 5 June 1855). He and Miss Thorley, his children’s governess, began the survey that month (C.R. Darwin to J.D. Hooker, 15 June 1855)…
I love the “Hurrah! Hurrah!” part because it helps humanize Darwin, who is all to often portrayed as a boring, dusty Victorian, and demonstrates his lifelong love of learning.
The survey was, perhaps, among the first intentional, comprehensive species counts in a geographically defined area in history. In an age when rare specimens were prized above all, their aim was radical: to identify all of the plant species growing on a small, unremarkable plot.
Darwin and Thorley ultimately recorded 142 seed plant species growing in the 13-acre meadow. These belonged to 108 genera and 32 orders of plants. What did we find in our resurvey?
In 2005 and 2006 the NHM team recorded 160 seed plants and one fern, the seed plants belonging to 112 genera, 44 families and 27 orders; in 2007 the NHM team re-found and collected 140 of the seed plants and the fern, the seed plants belonging to 106 genera, 44 families and 27 orders.
So we found about the same number of plant species, but were they the same species Darwin found?
Darwin must have made a list of the species he recorded in the meadow, for he wrote of comparing the flora of Great Pucklands with that of Ashdown Common in Sussex…. Alas, Darwin’s species list is yet to be discovered (Randal Keynes, pers. comm.). Therefore it is only possible to compare the number of species, genera and orders recorded by Darwin with the number recorded during the repeat survey.
It is difficult to convey in words how much that “alas” pains me. I live in hope that the list may yet be found, perhaps through the important and careful work being done by the Darwin Manuscripts Project. Isn’t there anything we can learn from the number of species, though, even without knowing their identity?
The number of seed plant species and genera collected by the NHM team in 2007 (140 and 106, respectively) is similar to the number Darwin reported finding in 1855 (142 and 108, respectively). At the level of order, however, the numbers diverge; the NHM team’s collection spanned 27 orders while Darwin’s survey spanned 32 orders. On first consideration, this might seem to suggest that the similarity between the numbers of species and genera is coincidence, and that the flora Great Pucklands meadow changed significantly between 1855 and 2007. However, there is another potential explanation: the flora has remained relatively constant, and the NHM team and Darwin found largely the same species, but British plant taxonomy has changed in the interim, such that the orders to which those species are assigned have changed or been combined and/or renamed.
The next paragraph is a rather wonderfully geeky (if I do say so myself) comparison of the different floras available to Darwin in 1855. I spent a lot of weekends on it. I think and hope that British botanists will enjoy it.
Speaking of British botanists, this last excerpt acknowledges the fantastic people with whom I had the great pleasure of working on this and other projects at the Natural History Museum. Had this book chapter been a paper in a peer-reviewed journal, their contribution most certainly would have warranted co-authorship.
The author thanks Down House and its staff for access to Great Pucklands meadow in 2005, 2006 and 2007, and other members of the team from the Natural History Museum in London who helped design and carry out the repeat survey, sample collection and processing, DNA barcoding, and analysis, including Frederick Rumsey, Mark Spencer, Mark Carine, Anna Dennis, Christopher Davis, Steve Russell, Michael Grundmann, Julia Llewellyn-Hughes, Johannes Vogel, and Harald Schneider. Randal Keynes and David Kohn kindly provided expert assistance with locating and interpreting historical information. Sandra Knapp provided counts of families and orders from Stace (1997). Funding for the project was provided by the Natural History Museum and Whatman International, Ltd.
*If you want to learn more about DNA barcoding, you can visit the Barcode of Life website, the Wikipedia entry, or, for something with a little more cheek, my explanation of biodiversity and DNA barcoding using only the thousand most common words in the English language.
CBOL Plant Working Group (2009). A DNA barcode for land plants, Proceedings of the National Academy of Sciences, 106 (31) 12794-12797. DOI: http://dx.doi.org/10.1073/pnas.0905845106
Boulter, C. J., Reiss, M.J. and Sanders, D.L, Eds. Darwin-Inspired Learning. Sense, 2014. Print and Ebook.
Darwin, C.R., Letter to Hooker, J.D. 5 June 1855. Darwin Correspondence Project Database. http://www.darwinproject.ac.uk/entry-1693/ (letter no. 1693; accessed 21 February 2010).
Darwin, C.R., Letter to Hooker, J.D. 15 June 1855. Darwin Correspondence Project. http://www.darwinproject.ac.uk/entry-1700 (letter no. 1700; accessed 21 February 2010).