On Darwin's birthday, IU study sheds new light on plant evolution

Genetically sequencing 'Darwin's tomatoes' reveals that small changes in genes can create big differences in traits like climate resilience, color

  • Feb. 12, 2016


BLOOMINTON, Ind. -- On Charles Darwin’s 207th birthday, a study from Indiana University is shedding new light on the importance of genetic diversity in plants.

The work, reported today in the journal PLOS Biology, employs genome-wide sequencing to reveal highly specific details about the evolutionary mechanisms that drove genetic divergence in 13 species of wild tomatoes that share a recent common ancestor.

The in-depth genetic analysis was led by Leonie C. Moyle, professor in the IU Bloomington College of Arts and Sciences’ Department of Biology.

"This study reveals new details about the unexpectedly complex genetic mechanisms that drive the diversification of plant species," said Moyle, who conducted the research as the primary investigator on a $1.18 million grant from the National Science Foundation.

The research may also contribute to future efforts to create more resilient crop plants in a time of changing climate by boosting resistance to pests or severe weather using cross-breeding methods rather than genetic engineering.

Tomatoes were the species used in the study because they are an ecologically and reproductively diverse plant group, said Moyle, who was part of a team of researchers on a mission to Ecuador in May 2014 to collect different populations of tomato native to the Andes Mountains, a "hotspot" for biodiversity.

Although most famous for his work on finches, Darwin also hunted on the Galapagos Islands of Ecuador for wild tomatoes, one of the hundreds of plant and animal species collected by the British naturalist during his landmark trip to the archipelago in 1835.

"Nearly 200 years later, these plants are still revealing important new insights into evolution," Moyle said.

By bringing modern technology to bear on these tomatoes, the IU study was able to clarify phylogenetic relationships and assess the "flow" of genes between these wild plant species -- as well as reveal the genetic root of specific environmental adaptations.

The team also found evidence to support three major genetic "strategies" behind the tomato's ability to rapidly adapt to ecological change: the "recruitment" of genes from a common ancestral pool; trading genes between species through "introgression," or natural cross-breeding; and new genes arising from "de novo" evolution.

This latter category was highlight by the surprising number of new mutations in genes found in the tomatoes. Of the four main groups of the wild tomatoes in the study, IU scientists discovered hundreds to thousands of genes with protein-coding changes that were unique to each of these ecologically diverse sub-groups.

All species in the "red-fruited" group -- the closest relatives of the domesticated tomato -- shared changes in 10 enzymes in the specific chemical pathway responsible for making the red pigment in ripe fruits, for example.

Other specific genetic variations resulted in more extreme differences, producing tomato species able to survive "the driest deserts on Earth and the high peaks of the Andes," according to James B. Pease, a postdoctoral researcher at the University of Michigan who was a Ph.D. student at IU at the time of the study.

"Although wild tomato species are very different in many traits from the domesticated tomatoes we eat by the millions, they are surprisingly similar at the genomic level," he said.

Greater knowledge about how such small changes in genetic diversity create big differences in species could eventually lead to the ability to pinpoint specific genes responsible for certain desirable traits -- such as pest resistance or hardiness -- many of which may have been lost due to historical breeding practices.

"There are lots of potentially valuable traits in wild tomatoes," Moyle said. "Our ability to precisely trace genetic histories in these species might help plant breeders identify desirable traits that can be re-introduced from wild species into commercial types using cross-breeding."

Other contributors to the study were Matthew W. Hahn, professor in the IU School of Informatics and Computing and Department of Biology, and David C. Haak of Virginia Tech, who was a postdoctoral researcher at IU at the time of the study.

Currant tomato

The wild currant tomato, a potential source for enhancing natural genetic trait diversity in domesticated tomatoes. | Photo by David Haak

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Leonie Moyle, right, and Natasha Sherman, a former postdoctoral researcher at IU, collect a wild tomato plant for genetic analysis near the city of Cuenca in southern Ecuador.

Leonie Moyle, right, and Natasha Sherman, a former postdoctoral researcher at IU, collect a wild tomato plant for genetic analysis near the city of Cuenca in southern Ecuador. | Photo by Leonie Moyle

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Leonie Moyle

Leonie Moyle | Photo by Indiana University

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Kevin Fryling

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