25 26Recent studies in eukaryotes have demonstrated the translation of alternative open 27 reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We 28show that a large number of small proteins could in fact be coded by altORFs. The 29 putative alternative proteins translated from altORFs have orthologs in many species and 30 evolutionary patterns indicate that altORFs are particularly constrained in CDSs that 31 evolve slowly. Thousands of predicted alternative proteins are detected in proteomic 32 datasets by reanalysis using a database containing predicted alternative proteins. Protein 33 domains and co-conservation analyses suggest a potential functional relationship between 34 small and large proteins encoded in the same genes. This is illustrated with specific 35 examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein 36 encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting 37 mitochondrial fission. Our results suggest that many coding genes code for more than one 38 protein that are often functionally related.

In the absence of strong reproductive barriers, genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes, and influence rates of hybridisation. How these dynamics affect the emergence and spread of novel ecological strategies remains only partially understood. We use phylogenomics and population genomics to retrace the origin of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. We report the existence of a previously undescribed ecotype inhabiting miombo woodlands and grasslands. The two ecotypes have divergent nuclear genomes. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can reach the seeds of the other via pollen movements, with strong selection subsequently sorting nuclear alleles by habitat. The contrasting ecotypes of A. angusta can use each other as a gateway to new locations across a large part of Africa. Coupled with newly discovered hybridisation with the sister species A. semialata, our results show that hybridisation can facilitate the geographical dispersal of distinct ecotypes of the same grass species.