Plants that survived dinosaur extinction pulled nitrogen from air

Once a favored food of grazing dinosaurs, an ancient lineage of plants called cycads helped sustain these and other prehistoric animals during the Mesozoic Era, starting 252 million years ago, by being plentiful in the forest understory. Today, just a few species of the palm-like plants survive in tropical and subtropical habitats.

Like their lumbering grazers, most cycads have gone extinct. Their disappearance from their prior habitats began during the late Mesozoic and continued into the early Cenozoic Era, punctuated by the cataclysmic asteroid impact and volcanic activity that mark the K-Pg boundary 66 million years ago. However, unlike the dinosaurs, somehow a few groups of cycads survived to the present.

A new study appearing Nov. 16 in the journal Nature Ecology & Evolution has concluded that the cycad species that survived relied on symbiotic bacteria in their roots, which provide them with nitrogen to grow. Just like modern legumes and other plants that use nitrogen fixation, these cycads trade their sugars with bacteria in their roots in exchange for nitrogen plucked from the atmosphere.

What originally interested lead author Michael Kipp is that the tissues of nitrogen-fixing plants can provide a record of the composition of the atmosphere they grew up in. He combines geochemistry with the fossil record to try to understand the Earth's climate history.

Knowing already that modern cycads are nitrogen-fixers, Kipp began analyzing some very old plant fossils during his Ph.D. work at the University of Washington to see if he could get a different look at ancient atmospheres. Most of the old cycads revealed that they weren't nitrogen-fixers, but these also turned out to be the extinct lineages.

"Instead of being a story about the atmosphere, we realized this was a story about the ecology of these plants that changed through time," said Kipp, who spent nearly a decade on this finding, first at UW and then as a postdoctoral researcher at CalTech.

Kipp is joining the Duke faculty this year as an assistant professor of Earth and Climate Sciences in the Nicholas School of the Environment to continue using the fossil record to understand Earth's climate history so that we can understand its possible future.

Much of what we know about ancient atmospheres comes from chemical studies of ancient sea life and sediments, Kipp said. Applying some of those methods to terrestrial plants is a new wrinkle.

"Going into the project, there were no published nitrogen isotope data from fossilized plant foliage," Kipp said. It took a while for him to fine-tune the method and to secure samples of precious plant fossils that museum curators were reluctant to see vaporized to get the data.

"In the few fossil samples that are of surviving (cycad) lineages, and that are not so old -- 20, 30 million years -- we see the same nitrogen signature as we see today," Kipp said. That means their nitrogen came from symbiotic bacteria. But in the older and extinct cycad fossils, that nitrogen signature was absent.

What is less clear is how nitrogen fixation helped the surviving cycads. It may have helped them weather the dramatic shift in climate or it may have allowed them to compete better with the faster-growing angiosperm plants that flourished after the extinction, "or it could be both."

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How intensive agriculture turned a wild plant into a pervasive weed

New research in Science is showing how the rise of modern agriculture has turned a North American native plant, common waterhemp, into a problematic agricultural weed.

An international team led by researchers at the University of British Columbia (UBC) compared 187 waterhemp samples from modern farms and neighbouring wetlands with more than 100 historical samples dating as far back as 1820 that had been stored in museums across North America. Much like the sequencing of ancient human and neanderthal remains has resolved key mysteries about human history, studying the plant's genetic makeup over the last two centuries allowed the researchers to watch evolution in action across changing environments.

"The genetic variants that help the plant do well in modern agricultural settings have risen to high frequencies remarkably quickly since agricultural intensification in the 1960s," said first author Dr. Julia Kreiner, a postdoctoral researcher in UBC's Department of Botany.

The researchers discovered hundreds of genes across the weed's genome that aid its success on farms, with mutations in genes related to drought tolerance, rapid growth and resistance to herbicides appearing frequently. "The types of changes we're imposing in agricultural environments are so strong that they have consequences in neighbouring habitats that we'd usually think were natural," said Dr. Kreiner.

The findings could inform conservation efforts to preserve natural areas in landscapes dominated by agriculture. Reducing gene flow out of agricultural sites and choosing more isolated natural populations for protection could help limit the evolutionary influence of farms.

Common waterhemp is native to North America and was not always a problematic plant. Yet in recent years, the weed has become nearly impossible to eradicate from farms thanks to genetic adaptations including herbicide resistance.

"While waterhemp typically grows near lakes and streams, the genetic shifts that we're seeing allow the plant to survive on drier land and to grow quickly to outcompete crops," said co-author Dr. Sarah Otto, Killam University Professor at the University of British Columbia. "Waterhemp has basically evolved to become more of a weed given how strongly it's been selected to thrive alongside human agricultural activities."

Notably, five out of seven herbicide-resistant mutations found in current samples were absent from the historical samples. "Modern farms impose a strong filter determining which plant species and mutations can persist through time," said Dr. Kreiner. "Sequencing the plant's genes, herbicides stood out as one of the strongest agricultural filter determining which plants survive and which die."

Waterhemp carrying any of the seven herbicide resistant mutations have produced an average of 1.2 times as many surviving offspring per year since 1960 compared to plants that don't have the mutations.

Herbicide resistant mutations were also discovered in natural habitats, albeit at a lower frequency, which raises questions about the costs of these adaptations for plant life in non-agricultural settings. "In the absence of herbicide applications, being resistant can actually be costly to a plant, so the changes happening on the farms are impacting the fitness of the plant in the wild," said Dr. Kreiner.

Agricultural practices have also reshaped where particular genetic variants are found across the landscape. Over the last 60 years, a weedy southwestern variety has made an increasing progression eastward across North America, spreading their genes into local populations as a result of their competitive edge in agricultural contexts.

"These results highlight the enormous potential of studying historical genomes to understand plant adaptation on short timescales," says Dr. Stephen Wright, co-author and Professor in Ecology and Evolutionary Biology at the University of Toronto. "Expanding this research across scales and species will broaden our understanding of how farming and climate change are driving rapid plant evolution."

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Plant study hints evolution may be predictable

Evolution has long been viewed as a rather random process, with the traits of species shaped by chance mutations and environmental events -- and therefore largely unpredictable.

But an international team of scientists led by researchers from Yale University and Columbia University has found that a particular plant lineage independently evolved three similar leaf types over and over again in mountainous regions scattered throughout the neotropics.

The findings provided the first examples in plants of a phenomenon known as "replicated radiation," in which similar forms evolve repeatedly within different regions, suggesting that evolution is not always such a random process but can be predicted.

The study is published July 18 in the journal Nature Ecology & Evolution.

"The findings demonstrate how predictable evolution can actually be, with organismal development and natural selection combining to produce the same forms again and again under certain circumstances," said Yale's Michael Donoghue, Sterling Professor Emeritus of Ecology & Evolutionary Biology and co-corresponding author. "Maybe evolutionary biology can become much more of a predictive science than we ever imagined in the past."

For the study, the research team studied the genetics and morphology of the plant lineage Viburnum, a genus of flowering plants that began to spread south from Mexico into Central and South America some 10 million years ago. Donoghue studied this same plant group for his Ph.D. dissertation at Harvard 40 years ago. At the time, he argued in favor of an alternative theory in which large, hair-covered leaves and small smooth leaves evolved early in the evolution of the group and then both forms migrated separately, being dispersed by birds, through the various mountain ranges.

The new genetic analyses reported in the paper, however, show that the two different leaf types evolved independently, in parallel, in each of a number of mountain regions.

"I came to the wrong conclusion because I lacked the relevant genomic data back in the 1970s," Donoghue said.

The team found that a very similar set of leaf types evolved in nine of 11 regions studied. However, the full array of leaf types may have yet to evolve in places where Viburnum has only more recently migrated. For instance, the mountains of Bolivia lack the large hairy leaf types found in other wetter areas with little sunshine in the cloud forest in Mexico, Central America, and northern South America.

"These plants arrived in Bolivia less than a million years ago, so we predict that the large, hairy leaf form will eventually evolve in Bolivia as well," Donoghue said.

Several examples of replicated radiation have been found in animals, such as Anolis lizards in the Caribbean. In that case, the same set of body forms, or "ectomorphs," evolved independently on several different islands. With a plant example now in hand, evolutionary biologists will try to discover the general circumstances under which solid predictions can be made about evolutionary trajectories.

"This collaborative work, spanning decades, has revealed a wonderful new system to study evolutionary adaptation," said Ericka Edwards, professor of ecology and evolutionary biology at Yale and co-corresponding author of the paper. "Now that we have established the pattern, our next challenges are to better understand the functional significance of these leaf types and the underlying genetic architecture that enables their repeated emergence."

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Dinosaur extinction changed plant evolution

With the extinction of large, non-flying dinosaurs 66 million years ago, large herbivores were missing on Earth for the subsequent 25 million years. Since plants and herbivorous animals influence each other, the question arises whether, and how this very long absence and the later return of the so-called "megaherbivores" affected the evolution of the plant world.

To answer this question, a research team led by iDiv and Leipzig University analysed fossil and living palms today. Genetic analyses enabled the researchers to trace the evolutionary developments of plants during and after the absence of megaherbivores. Thus, they first confirmed the common scientific assumption that many palm species at the time of the dinosaurs bore large fruits and were covered with spines and thorns on their trunks and leaves.

However, the research team found that the "evolutionary speed" with which new palm species with small fruits arose during the megaherbivore gap decreased, whereas the evolutionary speed of those with large fruits remained almost constant. The size of the fruits themselves, however, also increased. So, there were palms with large fruits even after the extinction of the dinosaurs. Apparently, much smaller animals could also eat large fruits and spread the seeds with their excretions. "We were thus able to refute the previous scientific assumption that the presence of large palm fruits depended exclusively on megaherbivores," says the study's first author Dr Renske Onstein from iDiv and Leipzig University. "We therefore assume that the lack of influence of large herbivores led to denser vegetations in which plants with larger seeds and fruits had an evolutionary advantage."

However, the defence traits of the plants; spines and thorns on leaves and stems, showed a different picture: the number of palm species with defence traits decreased during the megaherbivore gap. "Defence traits without predators apparently no longer offered evolutionary advantages," says Onstein, who heads the junior research group Evolution and Adaptation at iDiv. "However, they returned in most palm species when new megaherbivores evolved, in contrast to the changes in fruits, which persisted."

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