Clemson Scientist’s Research Helps Build Massive Flowering Plant DNA Tree of Life

A person outside picking at a plant.
Clemson University

An international team of researchers — including Clemson University biologist Norman Wickett — have built the most extensive flowering plant tree of life to date.

The massive effort involved 279 scientists from 138 organizations in 27 countries, who analyzed DNA from plants both living and extinct. The project sheds new light on the complex evolutionary history of flowering plants and could help future conservation efforts in the face of climate change and biodiversity loss.

The research, led by the Royal Botanic Gardens, Kew, was published in the journal Nature.

The tree of life was built using 1.8 billion letters of genetic code from over 9,500 species covering almost 8,000 known flowering plant genera.

One of the plants sequenced, the Guadalupe Island olive (Hesperelaea palmeri), hasn’t been seen alive since 1875. Three other species included on the tree of life are already extinct. The researchers were able to sequence them using dried plant specimens in the world’s herbarium collections.

“What’s really cool is the DNA doesn’t have to be super high quality. That means we can go back to plant collections that were made 100 years ago or 200 years ago and take what DNA is left and match it to our probes and get these…sequences out of these plants,” said Norm Wickett, a professor in the Clemson Department of Biological Sciences.

Researchers successfully sequenced a specimen of sandwort (Arenaria globiflora) collected nearly 200 years ago in Nepal.

“It highlights the importance of having these collections,” Wickett said.

The botanist who collected the sandwort and deposited it in an herbarium 200 years ago would not have imagined what scientists today were able to do with it, Wickett said. “And, we don’t know what technology will be available 200 years from now.”

William Baker, senior research leader at Kew, said in many ways, this novel approach allowed today’s researchers to collaborate with botanists of the past.

“DNA was not even discovered in their lifetimes. Our work shows just how important these incredible botanical museums are to groundbreaking studies of life on Earth. Who knows what other undiscovered scientific opportunities lie within them?”

The flowering plant tree of life

Plants that fruit or flower are called angiosperms and account for about 90% of all known plant life on land. They are found virtually everywhere on the planet — from the steamiest tropics to the rocky outcrops of the Antarctic Peninsula.

The flowering plant tree of life, much like our own family tree, enables us to understand how different species are related to each other.

It also provides information about how the diversity of species have changed over time, said Wickett.

“A tree of life allows us to make links between what was going on in the environment and how that impacted the evolution of the species we’re studying,” he said.

Flowering plants originated over 140 million years ago, after which they rapidly overtook other vascular plants including their closest living relatives — the gymnosperms, which are non-flowering plants that have naked seeds such as cycads, conifers and ginkgo.

The research revealed that early flowering plants exploded in diversity, giving rise to over 80% of the major lineages that exist today, shortly after their origin. However, the trend declined to a steadier rate for the next 100 million years until another surge in diversification about 40 million years ago, coinciding with a global decline in temperatures.

“A tree of life allows us to make links between what was happening in past environments and how that impacted the evolution of the species that exist on Earth today,” said Wickett, whose work is focused on understanding the diversity of all land plants, from mosses to ferns and, of course, flowering plants.

Developing the tools

Wickett’s role in the research was to help develop the tools that were used to build the tree of life. The tree of life is uncovered by comparing DNA sequences between different species to identify changes, or mutations, that accumulate over time like a molecular fossil record.

In the past, researchers used no more than a handful of genes to build the tree. But research over the past 15 years has shown that not every gene matches the history of the species perfectly because individual parts of the genome evolve in different ways, Wickett said. With more genes, therefore, researchers are more likely to capture the entire evolutionary history of these plants.

“We designed an approach to capture the DNA sequences of 353 genes that are located throughout the genome, allowing us to look at both the overall pattern of evolution as well as how different parts of the genome may tell different stories. By looking at this overall pattern, we should avoid any artifacts that might come from just looking at one gene or one area of the genome,” he said.

The tree and data will be accessible to the public and scientific community.

The researchers said open access will help scientists to make best use of the data, such as combining it with artificial intelligence to predict which plant species may include molecules with medicinal potential. Similarly, the tree of life can be used to better understand and predict how pests and diseases are going to affect plants in the future.

Detailed findings were published in the prestigious scientific journal Nature in a paper titled, “Phylogenomics and the rise of the angiosperms.”

The Royal Botanic Gardens, Kew contributed to this article.

Written by Clemson University.