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A new study published in the journal Nature by an international team of 279 scientists, including three biologists from the University of Michigan, provides new insights into the
A new study published in the journal Nature by an international team of 279 scientists, including three biologists from the University of Michigan, provides new insights into the flowering plant, the tree of life. Using 1.8 billion letters from more than 9,500 species, covering nearly 8,000 known genera of flowering plants (about 60%), this achievement sheds new light on the evolutionary history of flowering plants and their rise to ecological dominance on Earth.
The research team, led by scientists from the Royal Botanic Gardens, Kew, believes the data will aid future efforts to identify new species, improve plant taxonomy, discover new medicinal compounds and protect plants in the face of climate change and biodiversity loss.
This landmark study was created with the participation of 138 organizations from around the world, based on 15 times more data than any other comparative study on flowering plants on the tree of life. Among the species sequenced for this study, more than 800 had never had their DNA sequenced before.
The massive amount of data produced by this work, which would require a single computer to process for 18 years, is a major step towards creating a tree of life for all 330,000 known species of flowering plants, a major undertaking of the Kew Tree of Life Initiative.
“Analyzing this unprecedented amount of data to decipher the information hidden across millions of DNA sequences was a monumental task. But it also provided a unique opportunity to re-evaluate and extend our knowledge of the plant tree of life, opening a new window into the complexity of plant evolution,” said Kew Royal Botanist. Gardens research assistant Alexander Zuntini.
Tom Carruthers, a postdoctoral researcher in the laboratory of an evolutionary biologist at Stephen Smith University, co-authored the study with Zuntini, with whom he previously worked at Kew. UM plant taxonomist Richard Rabeler is co-author.
“When we enter the forest, flowering plants feed, clothe and welcome us. “Creating a flowering plant-tree of life has been a major challenge for the field of evolutionary biology for more than a century and has been a challenge for the field of evolutionary biology for more than a century,” said Smith, co-author of the study and a professor in the UM Department of Ecology and Evolutionary Biology. “This project brings us closer to that goal by providing a large data set for most flowering plant species and proposing a strategy to achieve that goal.”
Smith played two roles in the project. Initially, members of his lab, including former UT graduate student Drew Larson, traveled to Kew to help identify members of a large and diverse group of plants called Ericales, which includes blueberries, tea, ebony, azaleas, rhododendrons and Brazil nuts.
Secondly, Smith led the analysis and dataset creation of the project, together with William Baker and Felix Forrest of the Royal Botanical Gardens, Kew, and Wolf Eisenhardt of Aarhus University.
“One of the biggest challenges the team faced was the unexpected complexity underlying many gene regions, where different genes tell different evolutionary stories. Procedures had to be developed to study these patterns at scales that had not been done before,” said Michael J., who is also director of the Biology Program and curator of biodiversity informatics at the UM Herbarium. Smith, his assistant.
As co-leader of the study, Carruthers’ main responsibilities included scaling the evolutionary tree over time using 200 fossils, analyzing the different evolutionary histories of genes underlying the overall evolutionary tree, and estimating rates of diversification in different flowering plant lineages. 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 and helps us understand how they became such an integral and dominant part of the world,” Carruthers said. “The evolutionary relationships presented and the data underlying them will form an important basis for many future studies.”
The tree of life of flowering plants, like our family tree, helps us understand how different species are related to each other. The tree of life is discovered by comparing DNA sequences between different species to identify changes (mutations) that accumulate over time as molecular fossils.
With advances in DNA sequencing technology, our understanding of the tree of life is rapidly evolving. For this study, new genomic methods were developed to magnetically capture hundreds of genes and hundreds of thousands of letters of genetic code from each sample; This is many times higher than previous methods.
A key advantage of the team’s approach is that it makes it possible to sequence a wide range of plant material, old and new, even if the DNA is severely damaged. Vast treasures of dried plant material, comprising approximately 400 million scientific plant specimens in herbarium collections around the world, can now be examined genetically.
“In many ways, this new approach has allowed us to collaborate with botanists of the past using large amounts of data stored in historic herbarium specimens, some dating back to the early 19th century,” Baker said. Senior scientist at Q’s Tree of Life Initiative.
“Our famous ancestors, such as Charles Darwin or Joseph Hooker, could not have foreseen how important these samples would be for genomic research today. Even DNA had not been discovered in their lifetimes. Our work shows how important these incredible botanical museums are for groundbreaking research into life on Earth. Who knows what undiscovered scientific possibilities lie hidden?”
More than 3,400 of the 9,506 species listed come from material obtained from 163 herbaria in 48 countries.
“Collecting herbarium specimens to study plant relationships makes collecting samples from different parts of the world much more possible than having to travel to get fresh material from the field,” said Rabeler, a retired UM research assistant and former collector. Head of the Medical University Herbarium.
For the Tree of Life project, Rabeler helped authenticate the herbarium specimens selected for selection and analyzed the resulting data.
Flowering plants alone account for approximately 90% of all known plant life on land and are found almost everywhere on the planet, from the steamiest tropics to the rocky outcroppings of the Antarctic Peninsula. But our understanding of how these plants came to dominate the scene so soon after their origins has baffled generations of scientists, including Darwin.
Flowering plants appeared 140 million years ago and then rapidly displaced other vascular plants, including their closest living relatives, the gymnosperms (non-flowering plants with bare seeds, such as cycads, conifers, and ginkgos).
Darwin was astonished by the sudden appearance of such diversity in the fossil record. In an 1879 letter to Hooker, his close confidant and director of the Royal Botanical Gardens at Kew, he wrote: “The rapid development of all higher plants in recent geological ages is, so far as we can judge, a terrible mystery.”
Using 200 fossils, the authors scaled trees of life over time to show how flowering plants evolved over geological time. They found that early-blooming plants exploded in diversity, giving rise to more than 80% of the major lineages that exist today shortly after their origin.
However, this trend declined to a more stable rate over the next 100 million years until a further increase in diversification around 40 million years ago, coinciding with the decline in global temperature. These new ideas would fascinate Darwin and will undoubtedly help modern scientists trying to understand how and why species diversify.
Creating such a large-scale tree of life would not have been possible without the collaboration of Kew scientists with many partners around the world. In total, 279 authors representing different nationalities from 138 organizations in 27 countries were included in the study.
“The plant community has a long history of collaborating and coordinating molecular alignment to create a more complete and robust plant tree of life. The effort that led to this paper continues that tradition but expands significantly,” said UM’s Smith.
The flowering plant tree of life has tremendous potential in biodiversity research. Because just as you can predict the properties of an element based on its position in the periodic table, the position of a species in the tree of life allows you to predict its properties. Thus, new data will be invaluable for the development of not only science but also many branches of science.
To make this possible, the tree and all the data supporting it have been made freely available to both the public and the scientific community, including the Kew Tree of Life Explorer. Open access will help scientists make the most of data; for example, by combining data with artificial intelligence to predict which plant species may contain molecules with medicinal potential. Similarly, the tree of life can be used to better understand and predict how pests and diseases will affect plants in the future. Ultimately, the use of these data will depend on the creativity of the scientists who access them, the authors note.
Source: Port Altele
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