Data and scripts from: Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava

The genus Manihot, with around 120 known
species, is native to a wide range of habitats and regions in the
tropical and subtropical Americas. Its high species richness and recent
diversification only ~6Mya have significantly complicated previous
phylogenetic analyses. Several basic elements
of Manihot evolutionary history therefore remain
unresolved. Here, we conduct a comprehensive phylogenomic analysis
of Manihot, focusing on exhaustive sampling of South American
taxa.  We find that two recently described species from northeast
Brazil’s Atlantic forest were the earliest to diverge, strongly suggesting
a South American common ancestor of Manihot. Ancestral state
reconstruction indicates early Manihot diversification
in dry forests, with numerous independent episodes of new habitat
colonization including into savannas and rainforests within South America.
We identify the closest wild relatives to M.
esculenta including the crop cassava, and we quantify extensive
wild introgression into the cassava gene pool from at least five wild
species including M. glaziovii, a species used widely in
breeding programs. Finally, we show that this wild-to-crop introgression
substantially shapes the mutation load in cassava. Our findings provide a
detailed case study for neotropical evolutionary history in a diverse and
widespread group, and a robust phylogenomic framework for
future Manihot and cassava research.