The Plant Press

Ancient hybridization and genome doubling explain the origin of the apple tribe

From Plant Press, Vol. 25, No. 2, April 2022.

In the 1930s, biologists studying chromosomes in the rose family (Rosaceae) noticed that species in the apple tribe (Maleae) had approximately twice as many chromosomes (base chromosome number = 17) as every other species in the rose family (base chromosome number = 7, 8, or 9). Over the ensuing decades, researchers proposed hypotheses of hybridization and/or genome doubling to explain the evolutionary origin of the apple tribe and the unusually high chromosome counts in the apple tribe.

There were two competing hypotheses explaining the evolutionary origin of the apple tribe, but it was difficult to test them rigorously with the data available at the time. For many years, botanists tested these hypotheses using morphological characters, chromosome count data, and more recently, single-locus genetic data. Until a few years ago, researchers did not have access to genome-scale genetic data to test hypotheses of ancient hybridization and/or genome doubling.

An ancient hybridization event gave rise to the apple tribe (Maleae) in the rose family, Rosaceae. Maleae taxa include (from left) sweet crabapple (Malus coronaria), Callery pear (Pyrus calleryana), and Canadian serviceberry (Amelanchier canadensis). (photos by Richie Hodel and Jun Wen)

Smithsonian scientists Richie Hodel, Liz Zimmer, Bin-Bin Liu, and Jun Wen synthesized recently published phylogenomic data from the nuclear and chloroplast genomes of multiple species in the rose family, and applied novel phylogenetic network and multiply-labeled tree analyses to resolve the origin of the apple tribe. They found that an ancient hybridization event occurred between ancestors of the Rosaceae tribes Sorbarieae and Spiraeeae, likely between approximately 65-50 million years ago. Phylogenetic network analyses indicated this hybridization event gave rise to the clade Gillenieae + Maleae. The tribe Gillenieae is a small clade with follicular fruit sister to the larger pome-bearing apple tribe. In contrast to the Maleae, the Gillenieae do not have elevated chromosome counts, indicating that this hybridization event promoted the diversification of the clade Gillenieae + Maleae, but does not explain the high chromosome number in Maleae.

Another key result was that subsequent allopolyploidy (genome doubling involving two distinct species) between ancestors of the apple tribe likely occurred between approximately 50-35 million years ago. Multiply-labeled tree analyses indicated this event probably followed the divergence of the Gillenieae and Maleae lineages. This genome doubling event explains the elevated chromosome numbers observed in the Maleae by researchers over the past century. The research is published in Frontiers in Plant Science (https://doi.org/10.3389/fpls.2021.820997).

Rosaceae tribe, Amygdaleae, which includes (from left) Japanese apricot (Prunus mume) and almond (Prunus dulcis), was once hypothesized to have played a role in a hybridization event leading to the apple tribe, but recent research indicates the participants in the ancient hybridization event were likely ancestors of the tribes Spiraeeae and Sorbarieae. (photos by Richie Hodel and Jun Wen)

Explosive fossil fruit found buried beneath ancient Indian lava flows

From Plant Press, Vol. 25, No. 2, April 2022.

-Adapted from Jerald Pinson (The Florida Museum of Natural History).

Just before the closing scenes of the Cretaceous Period, India was a rogue subcontinent on a collision course with Asia. Before the two landmasses merged, however, India rafted over a “hot spot” within the Earth’s crust, triggering one of the largest volcanic eruptions in Earth’s history, which likely contributed to the extinction of the dinosaurs.

In a recent study published in the International Journal of Plant Sciences (183: 128-138; 2022 https://doi.org/10.1086/717691) scientists excavating the fossilized remains of plant material wedged between layers of volcanic rock describe a new plant species based on the presence of distinctive fruit capsules that likely exploded to disperse their seeds. The fossils may be the oldest fruit discovered to date of the spurge family (Euphorbiaceae), a group of plants with more than 7,000 species, with well-known representatives that include poinsettia, castor oil plant, rubber trees, and crotons.

The fruit of Euphorbiotheca deccanensis is potentially the oldest ever discovered of the spurge family (Euphorbiaceae). Based on the preserved fibers within the fossilized fruit, researchers think it likely exploded to disperse its seeds. (photo by Kristen Grace, Florida Museum of Natural History)

The fossilized fruits were discovered near the village of Mohgaon Kalan in central India, where the remains of the once-widespread volcanic rock lie just beneath the surface in a complex mosaic.

Living in harmony with nature: Winners, losers, and the Convention on Biological Diversity

From Plant Press, Vol. 25, No. 2, April 2022.

By W. John Kress.

A recently published scientific paper documents the imminent decline of thousands of species of plants as a result of the degradation and deterioration of natural environments caused by human greed and recklessness (Plants People Planet; https://doi.org/10.1002/ppp3.10252). As coauthors of that paper, Gary Krupnick and I worked to compile and analyze mountains of data on every species of plant for which we could find information about its current status on the planet.

We categorized each species as a “winner” or “loser” according to how it has responded to the “Lords of the Biosphere,” as our own species has been called by Professor John McNeill of Georgetown University. Plants that are useful to people, such as crops and plantation timber trees, or take advantage of environments altered by humans, such as invasive species, stand a good chance of surviving the current perils facing the planet, which include unrelentless habitat destruction, out-of-control climate change, rampant pollution, and escalating diseases. Such species will be the winners that survive the hazards of the Anthropocene to flourish once again in a future, perhaps hundreds or thousands of years from now, when humans will have less impact. Species that are not useful to people and inhabit threatened ecosystems or are exploited for their useful properties, such as wild medicinal plants, will be the losers. These species will succumb to human-dominated habitats, will decline in number, and may eventually go extinct.

Losers that are useful to humans tend to be overexploited wild species that may be medicinal, ornamental or used for timber. One such species is Ceratozamia kuesteriana, is a cycad threatened by habitat loss and over-collecting. Endemic to the Sierra Madre Oriental of Mexico, the one remaining population of this species numbers less than 300 plants. Credit: this image is in the public domain.

Although our conclusions were not what we were hoping for, we were not surprised by the results: among the tens of thousands of plant species we analyzed, the losers by far outnumbered the winners. No, it was not a good outcome. In fact, the result is extremely discouraging, and another indicator that humans, the world’s biodiversity, and the planet are on a dangerous and tragic trajectory if we do not change fast.

It is no coincidence that a week after this publication went to press (although certainly not because of this paper) thousands of international delegates and concerned observers met in Geneva, Switzerland, to prepare for the 15^th meeting of the Conference of the Parties of the United Nations Convention on Biological Diversity (CBD), which will convene in Kunming, China, later this year. The long-anticipated meeting in Geneva, which is really three separate meetings taking place at the same time: SBSTTA-24 (called the Twenty-fourth meeting of the Subsidiary Body on Scientific, Technical and Technological Advice), SBI-03 (Third meeting of the Subsidiary Body on Implementation), and WG2020-03 (Third meeting of the Open-ended Working Group on the Post-2020 Global Biodiversity Framework), took place over a two-week period, from March 14 -29, to facilitate long-term discussions on how to prevent further loss of biodiversity while at the same time making the benefits of Nature available for human well-being. I participated in the Geneva meetings over those 16 long days as a virtual official Observer representing the Earth BioGenome Project.

Smithsonian study finds more ‘losers’ than ‘winners’ among plants in the age of humans

From Plant Press, Vol. 25, No. 2, April 2022.

A new analysis spanning more than 86,000 plant species from John Kress, botany curator emeritus at the Smithsonian’s National Museum of Natural History, and Gary Krupnick, head of the museum’s plant conservation unit, finds that on this human-dominated planet, many more species of plants are poised to “lose” rather than “win.” The study was published in the journal Plants, People, Planet (https://doi.org/10.1002/ppp3.10252).

Losers that are useful to humans tend to be overexploited wild species that may be medicinal, ornamental or used for timber. One such species is Ekman’s magnolia tree (Magnolia ekmanii), a critically endangered tree only found in Haiti that was most likely harvested for its wood to produce charcoal and building materials. Credit: Copyright Martin Reith, some rights reserved (CC BY-NC)

From changing Earth’s climate to destroying, degrading and altering ecosystems on a massive scale, human choices now largely dictate the environmental conditions across much of the globe and, as a result, which species of plants and animals can survive and persist and which will go extinct. Species lucky enough to be directly or indirectly aided by human activities are likely to survive and can be thought of as “winners,” while those that are pushed to ecological irrelevance or extinction by those same activities are the ultimate “losers” in evolutionary terms.

Kress encountered this concept of evolutionary winners and losers in the age of humans (known to some researchers as the Anthropocene), in the writings of John McNeill and wanted to see if it might be possible to tally the plant species that were winning and losing now and in the future.

“I actually started this project from a place of optimism,” Kress said. “I had just planted all these trees around my house in Vermont and thought to myself that maybe there are actually more winners than losers, and we are just focused on everything that’s disappearing.”

In the summer of 2019, Kress brought Krupnick into the fold to help compile and analyze the mountains of data required to put every plant species for which there was enough information into the categories of winners and losers. The researchers split the winners and losers into species that are and are not useful to humans.

In addition to these four categories, Kress and Krupnick created four others: Species that appeared likely to win or lose in the future were deemed tentative winners or potential losers, and species that do not seem to be winning or losing at present were considered currently neutral. A fourth and final category included 571 species that have already gone extinct.

To place plants in these categories, Kress and Krupnick combed through databases that listed endangered plant species, economically important species such as crops, invasive and weedy plants, and endangered plants that are involved in legal and illegal global trade.

In total, the researchers were able to place 86,592 species of vascular plants—a large group of plants that have vascular tissue which transport water, nutrients and other substances—into the eight categories that describe their prospects for survival in the Anthropocene. That may sound like an inconceivably large number of species, but it is actually just under 30% of the nearly 300,000 known species of vascular plants. There simply was not enough data to categorize the remaining 70% of global plant diversity, which reflects how much is left to learn about Earth’s botanical riches, Kress said.

The analysis revealed that losers currently outnumber winners, and that losers are likely to continue to outpace winners in the future if human impact on the planet maintains its current trajectory. Kress and Krupnick categorized 20,293 species of plants as losers, with the vast majority of those losing species being identified as not useful to humans. By contrast, the researchers found just 6,913 species of winners, with all but 164 of those species having some human use.