Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis

Abstract

C4 photosynthesis has independently evolved from the ancestral C3 pathway in at least 60 plant lineages, but, as with other complex traits, how it evolved is unclear. Here we show that the polyphyletic appearance of C4 photosynthesis is associated with diverse and flexible evolutionary paths that group into four major trajectories. We conducted a meta-analysis of 18 lineages containing species that use C3, C4, or intermediate C3–C4 forms of photosynthesis to parameterise a 16-dimensional phenotypic landscape. We then developed and experimentally verified a novel Bayesian approach based on a hidden Markov model that predicts how the C4 phenotype evolved. The alternative evolutionary histories underlying the appearance of C4 photosynthesis were determined by ancestral lineage and initial phenotypic alterations unrelated to photosynthesis. We conclude that the order of C4 trait acquisition is flexible and driven by non-photosynthetic drivers. This flexibility will have facilitated the convergent evolution of this complex trait.Plants rely on carbon for their growth and survival: in a process called photosynthesis, they use energy from sunlight to convert carbon dioxide and water into carbohydrates and oxygen gas. The chemical reactions that make up photosynthesis are powered by a chain of enzymes, and plants must ensure that these enzymes—which are in the leaves of the plant—are supplied with enough carbon dioxide and water. Carbon dioxide from the atmosphere enters plants through pores in their leaves, but water must be carried up the plant from the roots.The type of photosynthesis used by about 90% of flowering plant species—including tomatoes and rice—is called C3 photosynthesis. The first step in this process begins with an enzyme called RuBisCO, which reacts with carbon dioxide and a substance called RuBP to form molecules that contain three carbon atoms (hence the name C3 photosynthesis).In a hot climate, however, a plant can lose a lot of water through the pores in its leaves: closing these pores allows the plant to retain water, but this also reduces the supply of carbon dioxide. Under these circumstances this causes problems because RuBisCO uses oxygen to break down RuBP, instead of creating sugars, when carbon dioxide is not readily available. To prevent this process, which wastes a lot of energy and resources, some plants—including maize, sugar cane and many other agricultural staples—have evolved an alternative process called C4 photosynthesis. Although it is more complex than C3 photosynthesis, and required many changes to be made to the structure of leaves, C4 photosynthesis has evolved on more than 60 different occasions.In C4 plants, the mesophyll—the region that is associated with the capture of carbon dioxide by RuBisCO in C3 plants—contains high levels of an alternative enzyme called PEPC that converts carbon dioxide molecules into an acid that contains four carbon atoms. To avoid carbon dioxide being captured by both enzymes, C4 plants evolved to relocate RuBisCO from the mesophyll to a second set of cells in an airtight structure known as the bundle sheath. The four-carbon acids produced by PEPC diffuse to the cells in the bundle sheath, where they are broken down into carbon dioxide molecules, and photosynthesis then proceeds as normal. This process allows photosynthesis to continue when the level of carbon dioxide in the leave is low because the plant has closed its pores to retain water.Since C4 plants grow faster than C3 plants, and also require less water, plant biologists would like to introduce certain C4 traits into C3 crop plants. To help with this process, Williams, Johnston et al. have used computational methods to explore how C4 photosynthesis evolved from ancestral C3 plants. This involved investigating the prevalence of 16 traits that are common to C4 plants in a total of 73 species that undergo C3 or C4 photosynthesis (including 37 species that possess characteristics of both C3 and C4).Williams, Johnston et al. then went on to produce a new mathematical model that represents evolutionary processes as pathways across a multi-dimensional “landscape”. The model shows that traits can be acquired in various orders, and that C4 photosynthesis evolved through a number of independent pathways. Some traits that evolved early in the transitions to C4 photosynthesis influenced how evolution proceeded, providing “foundations” upon which further changes evolved.Interestingly, the structure of the leaf itself appeared to change before any of the photosynthetic enzymes changed. This led Williams, Johnston et al. to conclude that climate change—in particular, the declines in carbon dioxide levels that occurred in prehistoric times—was probably not responsible for the original evolution of C4 photosynthesis. Nevertheless, these results could help with efforts to adapt important C3 crop plants to on-going changes in our climate.