Biologists Construct Groundbreaking Tree of Life Using 1.8 Billion Letters of Genetic Code

Tree of Life Colorful Artistic Illustration

A new study by 279 scientists, led by the Royal Botanic Gardens, Kew, has updated our understanding of the flowering plant tree of life by analyzing genetic data from over 9,500 species. This research, involving an international collaboration and significant technological advancements, provides crucial insights for plant classification, conservation, and medicinal discovery. The findings are freely accessible, promising to enhance future botanical studies and applications.

Scientists have constructed a groundbreaking tree of life using 1.8 billion letters of genetic code.

A recent study published in the journal Nature by an international team of 279 scientists, including three biologists from the University of Michigan, provides the latest insights into the flowering plant tree of life.

Using 1.8 billion letters of genetic code from more than 9,500 species covering almost 8,000 known flowering plant genera (ca. 60%), this achievement sheds new light on the evolutionary history of flowering plants and their rise to ecological dominance on Earth.

Led by scientists at the Royal Botanic Gardens, Kew, the research team believes the data will aid future attempts to identify new species, refine plant classification, uncover new medicinal compounds, and conserve plants in the face of climate change and biodiversity loss.

The major milestone for plant science, involving 138 organizations internationally, was built on 15 times more data than any comparable studies of the flowering plant tree of life. Among the species sequenced for this study, more than 800 have never had their DNA sequenced before.

Technological Challenges and Solutions

The sheer amount of data unlocked by this research, which would take a single computer 18 years to process, is a huge stride toward building a tree of life for all 330,000 known species of flowering plants—a massive undertaking byKew’s Tree of Life Initiative.

“Analyzing this unprecedented amount of data to decode the information hidden in millions of DNA sequences was a huge challenge. But it also offered the unique opportunity to reevaluate and extend our knowledge of the plant tree of life, opening a new window to explore the complexity of plant evolution,” said Alexandre Zuntini, a research fellow at Royal Botanic Gardens, Kew.

Tom Carruthers, postdoctoral researcher in the lab of U-M evolutionary biologist Stephen Smith, is co-lead author of the study with Zuntini, who he previously worked with at Kew. U-M plant systematist Richard Rabeler is a co-author.

Anigiosperm Tree of Life

Angiosperm Tree of Life. Credit: RBG Kew

“Flowering plants feed, clothe, and greet us whenever we walk into the woods. The construction of a flowering plant tree of life has been a significant challenge and goal for the field of evolutionary biology for more than a century,” said Smith, co-author of the study and professor in the U-M Department of Ecology and Evolutionary Biology. “This project moves us closer to that goal by providing a massive dataset for most of the genera of flowering plants and offering one strategy to complete this goal.”

Smith had two roles on the project. First, members of his lab—including former U-M graduate student Drew Larson—traveled to Kew to help sequence members of a large and diverse plant group called Ericales, which includes blueberries, tea, ebony, azaleas, rhododendrons and Brazil nuts.

Second, Smith supervised the analyses and construction of the project dataset along with William Baker and Felix Forest of the Royal Botanic Gardens, Kew, and Wolf Eisenhardt of Aarhus University.

“One of the biggest challenges faced by the team was the unexpected complexity underlying many of the gene regions, where different genes tell different evolutionary histories. Procedures had to be developed to examine these patterns on a scale that hadn’t been done before,” said Smith, who is also director of the Program in Biology and an associate curator in biodiversity informatics at the U-M Herbarium.

New Insights into Evolution

As co-leader of the study, Carruthers’ main responsibilities included scaling the evolutionary tree to time using 200 fossils, analyzing the different evolutionary histories of the genes underlying the overall evolutionary tree, and estimating rates of diversification in different flowering plant lineages at different times.

“Constructing such a large tree of life for flowering plants, based on so many genes, sheds light on the evolutionary history of this special group, helping us to understand how they came to be such an integral and dominant part of the world,” Carruthers said. “The evolutionary relationships that are presented—and the data underlying them—will provide an important foundation for a lot of future studies.”

The flowering plant tree of life, much like our own family tree, enables us to understand how different species are related to each other. The tree of life is uncovered by comparing DNA sequences between different species to identify changes (mutations) that accumulate over time like a molecular fossil record.

Our understanding of the tree of life is improving rapidly in tandem with advances in DNA sequencing technology. For this study, new genomic techniques were developed to magnetically capture hundreds of genes and hundreds of thousands of letters of genetic code from every sample, orders of magnitude more than earlier methods.

Arenaria globilfora

Arenaria globilfora. Credit: RBG Kew

A key advantage of the team’s approach is that it enables a wide diversity of plant material, old and new, to be sequenced, even when the DNA is badly damaged. The vast treasure troves of dried plant material in the world’s herbarium collections, which comprise nearly 400 million scientific specimens of plants, can now be studied genetically.

“In many ways, this novel approach has allowed us to collaborate with the botanists of the past by tapping into the wealth of data locked up in historic herbarium specimens, some of which were collected as far back as the early 19th century,” said Baker, senior research leader for Kew’s Tree of Life Initiative.

“Our illustrious predecessors, such as Charles Darwin or Joseph Hooker, could not have anticipated how important these specimens would be in genomic research today. 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 science opportunities lie within them?”

Across all 9,506 species sequenced, more than 3,400 came from material sourced from 163 herbaria in 48 countries.

“Sampling herbarium specimens for the study of plant relationships makes broad sampling from diverse areas of the world much more feasible than if one had to travel to get fresh material from the field,” said U-M’s Rabeler, a research scientist emeritus and former collection manager at the U-M Herbarium.

For the tree of life project, Rabeler helped verify the identity of herbarium specimens selected for sampling and analyzed the resulting data.

Flowering plants alone account for about 90% of all known plant life on land and are found virtually everywhere on the planet—from the steamiest tropics to the rocky outcrops of the Antarctic Peninsula. And yet, our understanding of how these plants came to dominate the scene soon after their origin has baffled scientists for generations, including Darwin.

Flowering plants originated more than 140 million years ago after which they rapidly overtook other vascular plants including their closest living relatives—the gymnosperms (nonflowering plants that have naked seeds, such as cycads, conifers, and ginkgo).

Darwin was mystified by the seemingly sudden appearance of such diversity in the fossil record. In an 1879 letter to Hooker, his close confidant and director of the Royal Botanic Gardens, Kew, he wrote: “The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery.”

Using 200 fossils, the authors scaled their tree of life to time, revealing how flowering plants evolved across geological time. They found that early flowering plants did indeed explode in diversity, giving rise to more than 80% of the major lineages that exist today shortly after their origin.

However, this trend then 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. These new insights would have fascinated Darwin and will surely help today’s scientists grappling with the challenges of understanding how and why species diversify.

Global Collaboration and Open Access

Assembling a tree of life this extensive would have been impossible without Kew’s scientists collaborating with many partners across the globe. In total, 279 authors were involved in the research, representing many different nationalities from 138 organizations in 27 countries.

“The plant community has a long history of collaborating and coordinating molecular sequencing to generate a more comprehensive and robust plant tree of life. The effort that led to this paper continues in that tradition but scales up quite significantly,” said U-M’s Smith.

The flowering plant tree of life has enormous potential in biodiversity research. This is because, just as one can predict the properties of an element based on its position in the periodic table, the location of a species in the tree of life allows us to predict its properties. The new data will thus be invaluable for enhancing many areas of science and beyond.

To enable this, the tree and all of the data that underpin it have been made openly and freely accessible to both the public and scientific community, including through theKew Tree of Life Explorer.

Open access will help scientists to make the 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. Ultimately, the authors note, the applications of this data will be driven by the ingenuity of the scientists accessing it.

Reference: “Phylogenomics and the rise of the angiosperms” by Alexandre R. Zuntini, Tom Carruthers, Olivier Maurin, Paul C. Bailey, Kevin Leempoel, Grace E. Brewer, Niroshini Epitawalage, Elaine Françoso, Berta Gallego-Paramo, Catherine McGinnie, Raquel Negrão, Shyamali R. Roy, Lalita Simpson, Eduardo Toledo Romero, Vanessa M. A. Barber, Laura Botigué, James J. Clarkson, Robyn S. Cowan, Steven Dodsworth, Matthew G. Johnson, Jan T. Kim, Lisa Pokorny, Norman J. Wickett, Guilherme M. Antar, Lucinda DeBolt, Karime Gutierrez, Kasper P. Hendriks, Alina Hoewener, Ai-Qun Hu, Elizabeth M. Joyce, Izai A. B. S. Kikuchi, Isabel Larridon, Drew A. Larson, Elton John de Lírio, Jing-Xia Liu, Panagiota Malakasi, Natalia A. S. Przelomska, Toral Shah, Juan Viruel, Theodore R. Allnutt, Gabriel K. Ameka, Rose L. Andrew, Marc S. Appelhans, Montserrat Arista, María Jesús Ariza, Juan Arroyo, Watchara Arthan, Julien B. Bachelier, C. Donovan Bailey, Helen F. Barnes, Matthew D. Barrett, Russell L. Barrett, Randall J. Bayer, Michael J. Bayly, Ed Biffin, Nicky Biggs, Joanne L. Birch, Diego Bogarín, Renata Borosova, Alexander M. C. Bowles, Peter C. Boyce, Gemma L. C. Bramley, Marie Briggs, Linda Broadhurst, Gillian K. Brown, Jeremy J. Bruhl, Anne Bruneau, Sven Buerki, Edie Burns, Margaret Byrne, Stuart Cable, Ainsley Calladine, Martin W. Callmander, Ángela Cano, David J. Cantrill, Warren M. Cardinal-McTeague, Mónica M. Carlsen, Abigail J. A. Carruthers, Alejandra de Castro Mateo, Mark W. Chase, Lars W. Chatrou, Martin Cheek, Shilin Chen, Maarten J. M. Christenhusz, Pascal-Antoine Christin, Mark A. Clements, Skye C. Coffey, John G. Conran, Xavier Cornejo, Thomas L. P. Couvreur, Ian D. Cowie, Laszlo Csiba, Iain Darbyshire, Gerrit Davidse, Nina M. J. Davies, Aaron P. Davis, Kor-jent van Dijk, Stephen R. Downie, Marco F. Duretto, Melvin R. Duvall, Sara L. Edwards, Urs Eggli, Roy H. J. Erkens, Marcial Escudero, Manuel de la Estrella, Federico Fabriani, Michael F. Fay, Paola de L. Ferreira, Sarah Z. Ficinski, Rachael M. Fowler, Sue Frisby, Lin Fu, Tim Fulcher, Mercè Galbany-Casals, Elliot M. Gardner, Dmitry A. German, Augusto Giaretta, Marc Gibernau, Lynn J. Gillespie, Cynthia C. González, David J. Goyder, Sean W. Graham, Aurélie Grall, Laura Green, Bee F. Gunn, Diego G. Gutiérrez, Jan Hackel, Thomas Haevermans, Anna Haigh, Jocelyn C. Hall, Tony Hall, Melissa J. Harrison, Sebastian A. Hatt, Oriane Hidalgo, Trevor R. Hodkinson, Gareth D. Holmes, Helen C. F. Hopkins, Christopher J. Jackson, Shelley A. James, Richard W. Jobson, Gudrun Kadereit, Imalka M. Kahandawala, Kent Kainulainen, Masahiro Kato, Elizabeth A. Kellogg, Graham J. King, Beata Klejevskaja, Bente B. Klitgaard, Ronell R. Klopper, Sandra Knapp, Marcus A. Koch, James H. Leebens-Mack, Frederic Lens, Christine J. Leon, Étienne Léveillé-Bourret, Gwilym P. Lewis, De-Zhu Li, Lan Li, Sigrid Liede-Schumann, Tatyana Livshultz, David Lorence, Meng Lu, Patricia Lu-Irving, Jaquelini Luber, Eve J. Lucas, Manuel Luján, Mabel Lum, Terry D. Macfarlane, Carlos Magdalena, Vidal F. Mansano, Lizo E. Masters, Simon J. Mayo, Kristina McColl, Angela J. McDonnell, Andrew E. McDougall, Todd G. B. McLay, Hannah McPherson, Rosa I. Meneses, Vincent S. F. T. Merckx, Fabián A. Michelangeli, John D. Mitchell, Alexandre K. Monro, Michael J. Moore, Taryn L. Mueller, Klaus Mummenhoff, Jérôme Munzinger, Priscilla Muriel, Daniel J. Murphy, Katharina Nargar, Lars Nauheimer, Francis J. Nge, Reto Nyffeler, Andrés Orejuela, Edgardo M. Ortiz, Luis Palazzesi, Ariane Luna Peixoto, Susan K. Pell, Jaume Pellicer, Darin S. Penneys, Oscar A. Perez-Escobar, Claes Persson, Marc Pignal, Yohan Pillon, José R. Pirani, Gregory M. Plunkett, Robyn F. Powell, Ghillean T. Prance, Carmen Puglisi, Ming Qin, Richard K. Rabeler, Paul E. J. Rees, Matthew Renner, Eric H. Roalson, Michele Rodda, Zachary S. Rogers, Saba Rokni, Rolf Rutishauser, Miguel F. de Salas, Hanno Schaefer, Rowan J. Schley, Alexander Schmidt-Lebuhn, Alison Shapcott, Ihsan Al-Shehbaz, Kelly A. Shepherd, Mark P. Simmons, André O. Simões, Ana Rita G. Simões, Michelle Siros, Eric C. Smidt, James F. Smith, Neil Snow, Douglas E. Soltis, Pamela S. Soltis, Robert J. Soreng, Cynthia A. Sothers, Julian R. Starr, Peter F. Stevens, Shannon C. K. Straub, Lena Struwe, Jennifer M. Taylor, Ian R. H. Telford, Andrew H. Thornhill, Ifeanna Tooth, Anna Trias-Blasi, Frank Udovicic, Timothy M. A. Utteridge, Jose C. Del Valle, G. Anthony Verboom, Helen P. Vonow, Maria S. Vorontsova, Jurriaan M. de Vos, Noor Al-Wattar, Michelle Waycott, Cassiano A. D. Welker, Adam J. White, Jan J. Wieringa, Luis T. Williamson, Trevor C. Wilson, Sin Yeng Wong, Lisa A. Woods, Roseina Woods, Stuart Worboys, Martin Xanthos, Ya Yang, Yu-Xiao Zhang, Meng-Yuan Zhou, Sue Zmarzty, Fernando O. Zuloaga, Alexandre Antonelli, Sidonie Bellot, Darren M. Crayn, Olwen M. Grace, Paul J. Kersey, Ilia J. Leitch, Hervé Sauquet, Stephen A. Smith, Wolf L. Eiserhardt, Félix Forest and William J. Baker, 24 April 2024, Nature.
DOI: 10.1038/s41586-024-07324-0

10 Comments on "Biologists Construct Groundbreaking Tree of Life Using 1.8 Billion Letters of Genetic Code"

  1. Traders’ pet scientists may be unleased to replicate more artificial species and health unsafe products for profit and trade in the market. Rules and regulations don’t work.

    • Torbjörn Larsson | May 1, 2024 at 9:03 am | Reply

      There are no “pet” scientists, such personal conspiracy theories have nothing to do with science.

  2. Why so many coauthors…might be a record

    • Torbjörn Larsson | May 1, 2024 at 9:05 am | Reply

      The major milestone for plant science, involving 138 organizations internationally, was built on 15 times more data than any comparable studies of the flowering plant tree of life.

  3. Blasphemy!!

  4. The world should be moved by arts, sciences, technologist. People with new views new discoveries studies. The world is moved by wrong individuals mostly liars and thieves politicians delinquents all of them greedy pathological monkey’s not even closed to the real human level. Only studies will launch civilization into a new gardens of new worlds and conquest of space is a primordial fact to reach a tree of life getting us closer all to the reality of god and the infinite to discover…

  5. Dania Siddiqui | April 30, 2024 at 9:36 pm | Reply

    Exploring world and understanding lineages in universe is one of the most respectable thing to do… Beautiful work done .. May Allah guide us towards positive usage of knowledge

    • Torbjörn Larsson | May 1, 2024 at 9:06 am | Reply

      Superstition suits a science site ill. Can we not just appreciate nature’s processes and science usefulness!?

  6. Much of human history is plagued by religious stories made up by humans, after which we try to find evidence that support these made up stories. Here is real science at work. Anyone can verify the genomic sequence of their favorite plant, and dispute or confirm these results. As Torbjörn Larsson says, this is the horse (evidence) pulling the cart (belief), rather than the other way round (what religion does).

  7. Such an awesome achievement!
    Wow. One of the great achievements by mankind.

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