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

Abstract

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 c. 6 million years ago 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 Manihot esculenta, including the crop cassava, and we quantify extensive wild introgression into the cassava gene pool from at least five wild species, including Manihot 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.

Morphometrics and Phylogenomics of Coca (Erythroxylum spp.) Illuminate Its Reticulate Evolution, With Implications for Taxonomy

“… Pironon et al 2024 ). Plant classification at this scale is often non-trivial, since it involves elucidating the plants’ evolutionary trajectories within a wider pool of genetic diversity comprising crop wild relatives, hybrids, and semi-domesticated forms ( Pellicer et al 2018 ; Pérez-Escobar et al 2021 , 2022 ; Simon et al 2022 ). For coca, its naming system has a further layer of relevance, being directly linked to the existence of legal frameworks, which on one side aim to hamper trafficking, but on the other hold the possibility of promoting opportunities for local communities that depend upon coca cultivation for traditional uses.…”

“…ICA in turn considers all gene trees with a decreasing logarithmic weight ( Salichos et al 2014 ). We computed these metrics using a custom script designed to consider well-supported bipartitions on the basis of gene-tree bootstrap values in gene trees with variable support among branches ( Simon et al 2022 ). Finally, using fasta alignments, we also computed site concordance factors ( Minh et al 2020 ), which measure the percentage of decisive sites supporting a branch in the reference tree, using IQ-TREE2 ( Minh et al 2020 ).…”

Morphometrics and phylogenomics of coca (Erythroxylumspp.) illuminate its reticulate evolution, with implications for taxonomy

“…Establishing a robust taxonomic framework is vital for research into plants that are medicinally, nutritionally or culturally valuable to humans. This is because plant classification at this scale involves elucidating the plants’ evolutionary trajectories within a wider pool of genetic diversity comprising crop wild relatives, hybrids and semi- domesticated forms (Pellicer et al, 2018; Pérez-Escobar et al, 2021; Simon et al, 2022). A point in case is coca, a plant so highly prized for its tropane alkaloids that it has become a lynchpin of socioeconomic chaos – the naming system of coca is directly linked to legal ramifications around its cultivation and trafficking.…”

“…ICA in turn considers all gene trees with a decreasing logarithmic weight (Salichos et al, 2014). We computed these metrics using a custom script designed to consider well-supported bipartitions on the basis of gene tree bootstrap values in gene trees with variable support among branches (Simon et al, 2022). Finally, using fasta alignments, we also computed site concordance factors (sCF; Minh et al, 2020), which measure the percentage of decisive sites supporting a branch in the reference tree.…”

Pre-Columbian cultivation of vegetatively propagated and fruit tree tropical crops in the Atacama Desert

“…flabellifolia in the cerrado and the lowland rainforests of the Amazon basin (Allem, 1994(Allem, , 1999Schaal, 1999, 2001). A more recent phylogenomic study of a large assemblage of cassava varieties confirmed its wild ancestry and identified numerous instances of hybridization with other wild Manihot species, but also suggests that because of the vegetatively propagated nature of its dispersion, a spatial structure to its diffusion may be challenging to map out (Simon et al, 2022). The timing of cassava domestication is uncertain, but cultivated varieties might have reached the Andean Pacific Coast and Mesoamerica by the early Middle Holocene (Isendahl, 2011).…”