Figure 2: Manihot genetic diversity.

(a) Midpoint-rooted chloroplast genome phylogeny of sequenced Manihot accessions. Bootstrap values for nodes with support of 500 or more (out of 1,000) shown in red. For groups of accessions with identical nuclear and chloroplast genomes, only one accession is shown. Note that M. pseudoglaziovii and the “wild cassava” W14 group with M. glaziovii, and almost all cultivated cassava in our collection have one of two cpDNA haplotypes. The M. esc. flabellifolia form a sister clade to cassava with much greater apparent haplotype diversity. One outlier cassava, BRA 856 (asterisked), groups among the M. esc. flabellifolia, suggesting possible maternal ancestry/admixing with M. esc. flabellifolia. (b) Principal component analysis based on SNVs revealing distinct clusters of nuclear genome types associated with M. glaziovii (blue), cultivated cassava and some M. esc. flabellifolia (orange), and the remaining M. esc. flabellifolia (gray). The fraction of population variance explained by each principal component is in parentheses. (c) Model-based clustering of nuclear genomes identifies the same groupings as principal component analysis, and identifies some accessions as admixed. Each vertical bar represents the fraction of an individual's genome attributable to one or more hypothetical ancestral populations. Note, for example, that Tree Cassava lies between clusters in b and is identified as admixed in c. Color key as in b. (d–h) Histograms of SNV heterozygosity (gray) and homozygous non-reference SNVs (blue) in 500 kb windows for cultivated cassava accession Albert (d), M. esc. flabellifolia FLA 433-2 (e), M. esc. flabellifolia FLA 444-1 (f), M. glaziovii(R) (g), and the “wild cassava” W14 (h). Note the similarity between M. glaziovii and W14, and between FLA 433-2 and Albert.