Global team of researchers, including three New York botanical garden scientists, publish ground-breaking study of plant evolution with many potential uses, from plant conservation to the discovery of new medicines
DNA of over 9,500 species sequenced to create largest-ever tree of life for flowering plants, mapping evolutionary and genetic relationships of plants
THE NEW YORK BOTANICAL GARDEN
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AN INTERNATIONAL TEAM OF RESEARCHERS, INCLUDING THREE NEW YORK BOTANICAL GARDEN (NYBG) SCIENTISTS, USED GENETIC CODE FROM MORE THAN 9,500 FLOWERING PLANT SPECIES TO CREATE THE MOST DETAILED EVOLUTIONARY TREE OF LIFE FOR THIS GROUP OF PLANTS TO DATE.
view moreCREDIT: ROYAL BOTANIC GARDENS, KEW
Bronx, NY—A new paper published today in the journal Nature by an international team of 279 researchers, including three New York Botanical Garden (NYBG) scientists, presents the most up-to-date understanding of the evolutionary and genetic relationships of the flowering plants, which represent about 90 percent of known plant life.
Using 1.8 billion letters of genetic code from over 9,500 species covering almost 8,000 plant genera (groups of closely related species), the research team was able to create the most detailed tree of life—a graphic depiction of species relationships similar to a genealogical family tree—to date for this group of plants, shedding new light on the evolutionary history of flowering plants and their rise to ecological dominance on Earth. The study’s authors believe the data will aid future attempts to identify new species, refine plant classification, uncover new medicinal compounds, and conserve plants in the face of the dual biodiversity and climate crises.
Contributing to this major milestone in plant science were Fabián Michelangeli, Ph.D., Abess Curator of Tropical Botany and Director of NYBG’s Institute of Systematic Botany; Gregory M. Plunkett, Ph.D., Director and Curator of NYBG’s Cullman Program for Molecular Systematics; and John D. Mitchell, NYBG Affiliated Scientist.
“While the main goals of this large-scale project were to understand the relationships of all flowering plant genera, it also sheds light on the timing of major events in the evolution of complex flower forms and life histories,” Dr. Michelangeli said. “Large analyses such as this can provide context for conservation strategies, sustainable agriculture, and many other applications that need basic biodiversity knowledge. Understanding how organisms are related is the building block of all biodiversity science and applications.”
The research team—led by the Royal Botanic Gardens, Kew, and involving 138 organizations internationally—used 15 times more data than any comparable studies of the flowering plant tree of life. Among the species included in the study, the DNA of more than 800 had never been sequenced before. The sheer amount of data unlocked by this research, which would take a single computer 18 years to process, is a huge stride towards building a tree of life for all 330,000 known species of flowering plants.
Drs. Michelangeli and Plunkett and Mr. Mitchell provided expertise on the plant families they study as well as expertly identified samples for a variety of plant groups, with a large proportion coming from the Melastomataceae family of tropical plants, which is Dr. Michelangeli’s specialty, and the Apiaceae (parsley or carrot) and Araliaceae (ginseng) families, which Dr. Plunkett studies.
Unlocking Historic Herbarium Specimens for Cutting-Edge Research
The flowering plant tree of life, much like a family tree, enables scientists 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. Science’s 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.
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, preserved plants in the world’s herbarium collections, which comprise nearly 400 million specimens, can now be studied genetically. Using such specimens, the team successfully sequenced a sandwort (Arenaria globiflora) collected nearly 200 years ago in Nepal and, despite the poor quality of its DNA, were able to place it on the tree of life. The team even analysed extinct plants, such has the Guadalupe Island olive (Hesperelaea palmeri), which has not been seen alive since 1875. In fact, 511 of the species sequenced are already at risk of extinction, according to the Red List, the authoritative compilation of the world’s threatened plant, fungal, and animal species maintained by the International Union for Conservation of Nature.
Across all 9,506 species sequenced, over 3,400 came from material sourced from 163 herbaria in 48 countries. Additional material from plant collections around the world such as DNA banks, seeds, and living collections have been vital for filling key knowledge gaps to shed new light on the history of flowering plant evolution. The team also benefited from publicly available data for over 1,900 species, highlighting the value of the open science approach to future genomic research.
Illuminating Darwin’s “Abominable Mystery”
Flowering plants account for about 90 percent 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 Charles Darwin. Flowering plants originated over 140 million years ago after which they rapidly overtook other vascular plants, including their closest living relatives—the gymnosperms, non-flowering 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 Joseph Dalton 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 researchers scaled their tree of life to time, revealing how flowering plants evolved across geological time. They found that early flowering plants exploded in diversity, giving rise to over 80 percent 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.
Assembling a tree of life this extensive would have been impossible without the collaboration of scientists across the globe. In total, 279 authors were involved in the research, representing many different nationalities from 138 organizations in 27 countries. International collaborators shared their unique botanical expertise as well as many invaluable plant samples from around the world that could not be obtained without their help. The comprehensive nature of the tree is in no small part a result of this wide-ranging partnership.
“Efforts like this show how the international scientific community can come together to collaborate and produce something that no one research group or institution can do alone,” Dr. Michelangeli said.
Putting the Flowering Plant Tree of Life to Good Use
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 scientists 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 the Kew Tree of Life Explorer. The study’s authors believe such open access is key to democratising access to scientific data across the globe.
Open access will also 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 might affect the world’s plants in the future. Ultimately, the authors note, the applications of the data will be driven by the ingenuity of scientists.
About The New York Botanical Garden
The New York Botanical Garden (NYBG) has been a connective hub among people, plants, and the shared planet since 1891. For more than 130 years, NYBG has been rooted in the cultural fabric of New York City, in the heart of the Bronx, its greenest borough. NYBG has invited millions of visitors to make the Garden a part of their lives, exploring the joy, beauty, and respite of nature. NYBG’s 250 acres are home to renowned exhibitions, immersive botanical experiences, art and music, and events with some of the most influential figures in plant and fungal science, horticulture, and the humanities. NYBG is also a steward of globally significant research collections, from the LuEsther T. Mertz Library collection to the plant and fungal specimens in the William and Lynda Steere Herbarium, the largest such collection in the Western Hemisphere.
The plant people of NYBG—dedicated horticulturists, enthusiastic educators, and scientific adventurers—are committed to helping nature thrive so that humanity can thrive. They believe in their ability to make things better, teaching tens of thousands of kids and families each year about the importance of safeguarding the environment and healthy eating. Expert scientists work across the city, the nation, and the globe to document the plants and fungi of the world—and find actionable, nature-based solutions to the planet’s dual climate and biodiversity crises. With eyes always looking forward, they train the next generation of botanists, gardeners, landscape designers, and environmental stewards, ensuring a green future for all. At NYBG, it’s nature—or nowhere.
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JOURNAL
Nature
METHOD OF RESEARCH
Data/statistical analysis
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
Phylogenomics and the rise of the angiosperms
ARTICLE PUBLICATION DATE
24-Apr-2024
Vast DNA tree of life for flowering plants revealed by global science team
Scientists use 1.8 billion letters of genetic code to build groundbreaking tree of life
UNIVERSITY OF MICHIGAN
The most up-to-date understanding of the flowering plant tree of life is presented in a new study published today in the journal Nature by an international team of 279 scientists, including three University of Michigan biologists.
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.
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 by Kew'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.
"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.
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.
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.
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 the Kew 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.
Study: Phylogenomics and the rise of the Angiosperms (DOI: 10.1038/s41586-024-07324-0)
Written by Royal Botanic Gardens, Kew.
JOURNAL
Nature
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