Skip to main content

Frequently Asked Questions

Find answers to the most common questions below. If you still can't find the answer you're looking for, you can get in touch at treeoflife@kew.org

Questions

What is PAFTOL?

PAFTOL is the Plant and Fungal Trees of Life Project at the Royal Botanic Gardens, Kew. PAFTOL aims to discover and disseminate the evolutionary history of all plant and fungal genera. You can find out more about PAFTOL here.

How was the tree of life built?

The tree presented in the Kew Tree of Life Explorer is based on DNA sequence data obtained from 353 nuclear genes. It is an output of the Plant and Fungal Trees of Life project at the Royal Botanic Gardens, Kew. To find out more about the project and our methods, follow the links to our About and Methods pages.

Where do the DNA sequence data come from?

Most of the DNA sequence data were generated by the PAFTOL project at the Royal Botanic Gardens, Kew using samples from Kew's collections and from PAFTOL's network of collaborators and partners. Laboratory work was conducted both at Kew and at commercial genomic service providers. In addition, several collaborators (such as the Genomics for Australian Plants project) provided data. We also mined data from public sources. For more information, please see our Methods page.

What do the numbers on the tree mean?

The numbers on the nodes are support values that indicate the degree of confidence we can have in each relationship. The support values are local posterior probabilities, which are calculated by ASTRAL III during the computation of the tree. A value greater than 0.95 is generally considered to indicate that the node is well supported and likely to be biologically meaningful. For more information see Sayyari & Mirarab (2016).

Why is the plant that interests me falling in an unexpected place?

One of the most frequently asked questions that we receive is “why is my favourite plant in the wrong place?”. The short answer is “it's complicated!” Here is a longer answer... Phylogenomic data are rich and powerful, yet their interpretation requires considerable nuance. While we can never fully rule out a genuinely incorrect placement due to mistakes such as misidentification of a sample or a lab error, unexpected placements can also arise from “correct” data. Firstly, the unexpected placement may reflect a genuine evolutionary discovery of hitherto unknown relationships - the tree presented here contains a wealth of new data that may challenge previous evidence and ideas. Alternatively, biological phenomena may be responsible. Complexities in molecular evolutionary history, such as ancient hybridization, horizontal gene transfer, incomplete lineage sorting or gene/genome duplication and loss, may result in mismatches between genetic signal and species history. Additionally, inadequacies in the data may limit our ability to recover relationships reliably; typically, these cases coincide with low support values. For example, rapid diversification or low molecular evolutionary rates may lead to insufficient evolutionary signal. Poor-quality sequence data can also result in erroneous phylogenetic inferences. Some groups of plants with unusual growth, such as parasitic or mycoheterotrophic plants, can be difficult to place accurately. They often yield low quality data or may be impacted by unusual molecular evolutionary constraints, both of which can lead to inaccurate phylogenetic results. Finally, the dataset is vast, rendering complete exploration of all possible trees impossible. We are constantly searching for improvements in analysis methods to ensure that the tree of life inferred here is ever more reliable.

Why are some placements flagged as inaccurately reflecting the phylogenetic relationships of the species?

We carefully scrutinise the tree of life at all stages of the analysis and take steps to ensure that only the most reliable data appear in the trees that we provide here. Some samples, however, continue to offer challenges to correct placement in the tree, despite the data themselves being correct. For example, the two genera Prosopanche and Hydnora are well-established as members of the order Piperales, based on other evidence, but do not fall in that order in our tree. This is likely due to their parasitic nature, which is known to impact their molecular evolution, which in turn may affect tree reconstruction and lead to incorrect placement in the tree of life.

Why is the plant that interests me given an unexpected name?

We standardise all botanical names to those reported in the latest release of the World Checklist of Vascular Plants (WCVP). The WCVP synthesises botanical names information from the latest scientific literature. A sample might have an unexpected name because the name has been recently updated or because opinion differs among botanists about which name should be used.

How was the identification of the samples verified?

As far as possible, we targeted samples for DNA sequence data production that had been verified by a botanical expert. We also worked with specialist communities that are expert on specific plant groups to obtain the best possible material. We included DNA barcoding and phylogenetic tests in our analytical pipeline to further validate identifications, at least to the family level. To the greatest extent possible, we have also ensured that a voucher specimen for every sample exists in a public herbarium, so that the original material may be re-examined. Many of these vouchers can be found at Kew. Links to specimen metadata are available via the species tab. Links through to images of many of the voucher specimens will soon be available. For externally sourced data, we refer the user to the original place of publication for further information on sample identity and verification.

How do I download data from the Explorer?

You can access and download the data from the Explorer in various ways. You can find all of the raw sequence data generated for the project in the European Nucleotide Archive and the National Center for Biotechnology Information Sequence Read Archive under bioproject number PRJEB35285. Public raw data that have been mined for the Explorer can be found following the links associated with each species. Metadata for all included species are available on the Species page of the Explorer and can also be downloaded there. Assembled genes, gene alignments, gene trees and species trees can be downloaded via our SFTP (see Access Data). The tree of life itself (and custom subtrees) can be downloaded in Newick and graphics formats from the Tree of Life page.

When can I expect the next update to the Kew Tree of Life Explorer?

The next release of the Kew Tree of Life Explorer is scheduled to be made public in late 2025.

Where can I find general information about the PAFTOL project?

You can find out more about the Plant and Fungal Trees of Life project here.

Where can I find out about the scientific outputs of the PAFTOL project?

Scientific papers and reports arising from the PAFTOL project can be accessed via the Royal Botanic Gardens, Kew research repository.

What teaching resources are available?

We have collaborated with YouTube channel Domain of Science to make an educational film on the plant tree of life - The Surprising Map of Plants. Teachers can find formal resources on plant evolution on Kew's free teaching resource platform Endeavour. For a more hands-on experience, why not come to Kew Gardens to enjoy the Agius Evolution Garden, a stunning series of garden rooms that tell the story of plant evolution from the time of the dinosaurs to the present day. A brand new audio guide will soon be released to help you get even more out of your visit.

Where can I explore the tree of life at Kew Gardens?

The wonders of plant evolution can be experienced throughout Kew Gardens, from which many of the samples sequenced for the Kew Tree of Life Explorer were sourced. In Kew's Agius Evolution Garden, the story of plant evolution is explained through beautiful horticulture and garden design that allows you to walk through the plant tree of life. We've also made an audio guide to help you get even more out of your visit.