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Growing a giant phylogenetic tree at Kew Gardens

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A wing of the Jodrell Laboratory at Kew Royal Botanical Gardens in the UK, with an artist’s interpretation of the DNA double helix in the foreground. The steel installation was built in 2003 to commemorate the discovery of the double helix by James Watson and Francis Crick.

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Félix Forest, Head of the Molecular Systematics Lab at the Jodrell Lab, Kew Gardens.

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Plant material is processed for DNA analysis inside the Jodrell Lab at Kew.

By Dr Genevieve Thompson, Postdoctoral Researcher, SAEON Fynbos Node

The current patterns of botanical diversity in any region are a reflection of two major dynamics over the ages - the influence of the environment on the capacity of plant populations to coexist locally; and the historical diversification of lineages that culminates in the botanical taxa that we see today.

Determining the Who, What, When, Where and Why of these two processes is incredibly challenging (even in species depauperate environments) and is unlikely to be completely resolved during any of our life-times. Nevertheless, as scientists we have to start somewhere, especially when we are privileged enough to live in a country that houses one of the most botanically renowned floras in the world.

Unfortunately our flora, and many other species-rich environments across the globe are being threatened by a myriad of impacts including habitat destruction, species introductions and global change as a consequence of human activities. Understanding these impacts and predicting vegetation responses in species-rich, heterogeneous landscapes requires a holistic approach that “tackles eco-evolutionary dynamics in a multispecies and a spatial context and therefore provides a more realistic, and potentially more accurate approach to predicting future changes” (Urban et al., 2012).

A baseline for natural change

An approach that concurrently considers a range of driving variables (e.g. evolutionary, environmental or stochastic drivers) will help to establish a baseline for what would be considered natural change, versus change that is human induced. To establish such a baseline, we need to have a better understanding of the natural change in floral diversity in South Africa.

Our aim is to produce a map of South Africa detailing the distribution of plant phylogenetic diversity relative to priority conservation areas, protected areas, areas of high human density and a range of other impact-related variables.

"Our aim is to produce a map of South Africa detailing the distribution of plant phylogenetic diversity relative to priority conservation areas, protected areas, areas of high human density and a range of other impact-related variables."

Phylogenetic diversity, or the cumulative evolutionary history of a species, can be measured using phylogenetic trees built with genetic sequence data, and mapped in space using occurrence records from a range of South African databases (e.g. PRECIS and POSA).

Potential correlates of phylogenetic diversity can then be identified by comparing the spatial distribution of phylogenetic diversity to a range of environmental variables such as temperature, rainfall and soil type. This information has a range of applications, from the development of networks for monitoring and detecting global change impacts through to conservation planning.

Reconstructing a phylogenetic tree

The reconstruction of a phylogenetic tree that encompasses such a diversity of species requires a range of technical and theoretical expertise. This brought together a team of people including Félix Forest (Kew Gardens, UK), Jonathan Colville (South African National Biodiversity Institute - SANBI), Tony Verboom (University of Cape Town), Jasper Slingsby and Genevieve Thompson (SAEON Fynbos Node).

Genevieve visited the Jodrell Lab at Kew Royal Botanical Gardens to work with Félix on the technical analyses associated with the construction of large phylogenetic trees. Félix is the Head of the Molecular Systematics Lab at Kew, and is a well-published plant phylogenetics guru, with an excellent knowledge of South African flora. The June research trip was funded by SANBI (thanks to Jonathan Colville and John Donaldson for facilitating this).

Genevieve arrived ready to soak up some science, armed with a swath of genetic data that needed to be refined and processed. During the visit, almost three and a half thousand genetic sequences were processed, representing the bulk of the two and a half thousand native and introduced genera that occur in South Africa.

Genetic data of two gene regions commonly used in DNA barcoding were employed (matK and rbcL) to construct a phylogenetic tree. The measurement of phylogenetic diversity requires a tree that is calibrated (has an evolutionary time scale) using fossil records. Eighteen speciation events, linked to well-studied fossil records, were used to create a calibrated phylogenetic tree and calculate phylogenetic diversity for the sampled South African genera. The next steps in the project continue back at the Fynbos Node in Cape Town, and the project is due to be completed in December 2013.

Overall, a wealth of information was gained during the trip to Kew, and good progress was made on the project.

Reference:

Urban, M.C., De Meester, L., Vellend, M., Stoks, R. & Vanoverbeke, J. (2012). A crucial step toward realism: responses to climate change from an evolving metacommunity perspective. Evolutionary Applications, 5, 154-167.

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