Report

Teaser, summary, work performed and final results

Periodic Reporting for period 3 - ComplEvol (Evolutionary origins of complex ecological adaptations)

Teaser

During evolution, organisms adapt to diverse environmental conditions by evolving new morphological and/or biochemical traits, some of which are of impressive complexity. This is for example the case of eyes, wings or complex biochemical pathways, which all involve multiple...

Summary

During evolution, organisms adapt to diverse environmental conditions by evolving new morphological and/or biochemical traits, some of which are of impressive complexity. This is for example the case of eyes, wings or complex biochemical pathways, which all involve multiple components. The evolution of such complex traits has always intrigued evolutionary biologists, including Charles Darwin, and is still only partially understood. How can natural selection on random mutations lead over time to novel complex ecological adaptations that allow organisms to thrive in diverse environments?

This question is addressed in this project by studying a species complex that presents exceptional variation in a key ecological adaptation, namely C4 photosynthesis. This trait results from multiple anatomical and biochemical components that function together to increase plant productivity in warm, high light environments. Capitalizing on a species complex of grasses that includes C4 as well as the ancestral C3 photosynthetic types and multiple intermediate states, the project combines methods from different fields to infer (i) the history of mutations that generated components for C4 photosynthesis during the dispersal into different ecological conditions, (ii) the factors controlling the spread of these mutations among populations, (iii) the effects of these mutations on the properties of the encoded C4 enzymes, (iv) the effects of different anatomical and biochemical C4 components on the performance of the plants (fundamental niche), and (v) the relationships between these components and the distribution of individuals in contrasted environments (realised niche).

The project is subdivided in six parts, which are inter-related and study in parallel the same accessions of the grass Alloteropsis semialata, but using different techniques. Each part addresses a set of subquestions, which will come together to elucidate the microevolutionary processes that lead over time to major ecological innovations.

Work performed

During the first 2.5 years of this project, we have assembled a large collection of Alloteropsis semialata accessions, via repeated field trips, collaborations with colleagues abroad, and using museum collections. These accessions have been genotypes, using genomic scans and transcriptome sequencing, and phenotyped at the biochemistry, anatomy and physiology levels.

Our investigations have already shown that the species includes more variation than previously suspected, with intermediate populations present in parts of Africa in addition to the previously described C3 and C4 groups. A careful investigation of the anatomical and transcriptome variation among populations of Alloteropsis semialata and its congeners showed that the C4 phenotype evolved at least twice independently in the small genus, and one of these origins encompasses two independent realizations of the C4 phenotype from a common ancestor with some C4 components. However, analyses of gene trees also revealed that key genes for the C4 pathway have been introgressed among congeners, effectively disconnecting the species and gene trees.

Within the species Alloteropsis semialata, the different photosynthetic types form distinct genetic groups that exchange genes occasionally. A phylogeographic analysis suggested that C4 genes were acquired independently in geographically isolated populations and were later combined during secondary contacts. Some C4 loci were then rapidly spread to populations with a different genomic background.

Ongoing work is now exploring the phenotyping variation, which will be analysed in a phylogenetic framework provided by our sequencing efforts, to resolve the events that led to the rise and diversification of the C4 photosynthetic apparatus.

Final results

Detailed physiological and biochemical analyses of the first batch of Alloteropsis semialata accessions grown in Sheffield unambiguously demonstrated that some populations from Southern Tanzania are proper C3-C4 intermediates that perform a weak C4 cycle. Therefore, the grass Alloteropsis semialata, besides C4 accessions spread around the world and C3 individuals in Southern Africa, encompasses intermediate phenotypes, which are associated with the Miombo woodlands of the Zambezian region (Lundgren et al. 2016 Plant Cell Environ 39:1874-1885).

Transcriptome and leaf anatomy analyses of members of the Alloteropsis genus revealed that one of the species (A. cimicina) uses different genes/enzymes and parts of the leaf for the C4 pathway, unambiguously demonstrating a distinct C4 origin. The two other species (A. angusta and A. semialata) use the same genes/enzymes and leaf compartments, but selection analyses indicate that they adapted their enzymes for the C4 context independently, which we interpret as independent realizations of the C4 pathway from a common ancestor with some C4 components. This complex history moreover involves movements of C4-adaptive loci across species boundaries, effectively disconnecting the species and gene trees (Dunning et al. 2017, Evolution 71:1541-1555).

We sequenced at low coverage the genomes of 17 accessions of A. semialata and congenerics. The data were used to infer phylogenetic trees based on different parts of the genome, and test for conflicting histories. Our investigations revealed that the different photosynthetic types form distinct genetic groups, but these undergo rare yet recurrent gene flow. We suggest that photosynthetic diversification occurred in isolated populations, but genes were later exchanged when these populations came again into contact, probably during interglacial periods. In particular, laterally-acquired genes that have been incorporated into the C4 machinery of some isolated populations were later passed to other groups via secondary contacts (Olofsson et al. 2016, Mol Ecol 25:6107-6123).

Ongoing investigations are expected to determine how different anatomical and biochemical components contribute to the physiological performance of accessions with contrasted photosynthetic types. In addition, population genomics are currently investigating the selective pressures on different loci, and the processes that allow photosynthetic diversification within a species.