Metabolic fingerprints tell the evolutionary history of plants

A new method for analyzing chemical compositions is tested in Andean plants and shows how they became geographically distributed, leading to an understanding of their evolutionary history.

By Maria Fernanda Ziegler  |  Agência FAPESP – The endemic plants of the genus Espeletia found in the páramo, a moist alpine biome unique to the northern Andes, could be the key to understanding the history of speciation and specie distributions in this region of South America. 

In an article published on August 18 in Scientific Reports, researchers at the University of São Paulo’s Ribeirão Preto School of Pharmaceutical Sciences (FCFRP-USP) in Brazil use metabolic fingerprinting for the first time to explain the evolutionary history and biogeographic characteristics of Espeletia.

The study confirms a longstanding hypothesis about the evolution of this genus, which inhabits the world’s most diverse high-altitude ecosystem. With 72 species currently identified, Espeletia is abundant in the páramo and is considered an outstanding example of adaptive success.

Studies of this kind are usually based on genomics, DNA marker analysis or morphological comparisons. In this case, the researchers used metabolomics, which focuses on the metabolites synthesized by the plants, to map the chemical compositions of each species with a combination of techniques involving plant extracts, geographic data and multivariate statistics.

“Basically, we took the chemical compositions of the species of Espeletia and their metabolome and found a correlation with their geographic origins. Species present in the same locations display similar chemical profiles. The same link had already been found using molecular markers but on a larger geographic scale. This shows that the geography of the Andes not only determined the evolution of this plant group, and possibly of other plant groups in the region but also shaped the chemical compositions of these species,” said Federico Padilla, one of the authors of the article, in an interview with Agência FAPESP.

The study relates to a Thematic Project (“Morphoanatomical, metabolomic and molecular studies as subsidies to the systematic of Asteraceae species and access to their pharmacological potential”) and a regular research grant from FAPESP.

The researchers stress that analogous models to that described in the article can be used to obtain metabolic fingerprints for other plants with the aim of analyzing their biogeographic and evolutionary histories.

“This new model can be used in agriculture, or for medicinal plants, or even by the police, for example, to identify the origin of marijuana consumed in a particular region,” said Professor Fernando Batista da Costa, Padilla’s supervisor and a co-author of the article published in Scientific Reports.

According to the researchers, this approach can be used to study practically all of a plant’s metabolites at the same time. 

“In classical phytochemistry, we studied one plant at a time and usually identified a few chemical substances,” Padilla said. “With the new techniques and equipment, such as the liquid chromatography coupled with mass spectrometry that we used, we can now assemble 100 or more plant extracts, analyze them all at the same time, and obtain a data matrix potentially representing more than 1,000 chemical compounds.”

Mauricio Diazgranados, a biologist at the Royal Botanic Gardens, Kew (United Kingdom), collaborated on the study. “He supplied material collected during a period of more than three years from páramos in Venezuela and Colombia, for a project linked to his PhD research on phylogeny and taxonomy,” Padilla said. “After the samples arrived, we spent three years doing metabolomic analysis and using computational tools.”

Andean barrier

The article confirms a hypothesis on the origin and migration routes of Espeletia along the northern Andes proposed by researchers at the US National Museum of Natural History, part of the Smithsonian Institution, in the 1990s, which was hitherto partially supported by molecular markers.

According to this hypothesis, the original stock of Espeletia diversified when the first population of the genus started expanding in two directions from the western part of the Cordillera de Mérida, the largest massif in Venezuela. One branch moved along the Venezuelan Andes, while the other moved west and southwest along the Colombian Andes and into northern Ecuador. 

“Historically, this kind of analysis has been based on molecular markers. However, genetic analysis is unable to determine specific biogeographic trends with satisfactory precisions in groups that have evolved recently, such as the genus Espeletia, for which it merely identifies two groups, the Venezuelan and Colombian species, ” Padilla said.

The Smithsonian hypothesis was confirmed by an analysis of the secondary metabolites (i.e., the chemical compounds involved in plants’ adaptations to the ecosystem), which pointed to patterns of geographic distributions and chemical diversifications in the Andean páramos.

“Each kind of marker has advantages and disadvantages,” Batista da Costa said. “Unlike animals, plants can’t move in order to adapt to this or that environment. Instead, they produce a vast array of chemical compounds that help them adapt to the place where they grow.”

The rugged topography of the Andes makes the páramo a highly fragmented biome, biologically and geographically comparable to an archipelago in which “islands” of open grassland vegetation are separated by dense forests or deep valleys that prevent plant species from communicating with other páramos.

According to the article, this geographic isolation is a particularly influential factor for species with limited seed dispersal and a lack of long-distance pollinators, as is the case for Espeletia.

“We prove that their isolation favored allopatric speciation, meaning speciation occurring in separate regions because of geographic barriers. Darwin proposed this kind of speciation in his evolutionary theory as a result of his observations in the Galapagos Archipelago. He saw there that different islands had different species and that these species were related to each other,” Batista da Costa said.

The researchers’ analyses of the chemical compositions showed that species of Espeletia in different páramos differ not only genetically and morphologically but also chemically.

“In each páramo, most species accumulate different chemical compounds that may possibly be linked to their adaptation to that particular geographic area,” Padilla said. “We demonstrate, using chemical evidence, that allopatric speciation occurred in these páramos and groups of species, as had been proposed in the 1990s.”

Padilla has begun his PhD research, also on Espeletia, at the University of São Paulo and is currently doing a research internship at the University of Hohenheim in Germany.

“I’m now studying the genetics to find out whether the metabolic differences between the species found in different páramos are due to genetic differences or if there’s simply a difference in the expressions of certain genes. These genes could be silenced or mutated,” he said.

The article “Biogeography shaped the metabolome of the genus Espeletia: a phytochemical perspective on an Andean adaptive radiation” by Guillermo F. Padilla-González, Maurício Diazgranados and Fernando D. da Costa can be read in Scientific Reports at nature.com/articles/s41598-017-09431-7.