Hop phylogeny pseudo-phylogeny of our full dataset · TENTATIVE

BIONJ backbone of 692 ApeKI-GBS plants (100 bootstraps over 5 Mb blocks) with 61 tips of other assays placed on it (WGS, low-pass WGS, RNA-seq, GRAS-Di, PstI+ApeKI GBS, 13 assembly haplotypes); 753 tips. The root is a midpoint display root, not an inferred root. Placed tips carry placement uncertainty; assay offsets remain (see the report). Zhang 2017 HapMap is not drawn.

Layout Clades max tips Labels Rings: subspecies label assay cohort atlas category bootstrap ≥ % values tips by local affinity Search

Legend

Selected tip

Hover a tip for details; click it to select (and add it to the local-affinity heatmap). Wheel = zoom, drag = pan.

WGS-only trees

Tree Chromosome Window

Local affinity along the genome

For each plant and 25 Mb window, the nearest of five WGS reference groups (mean relative read-allele distance; the plant is left out of its own group). Opacity = margin (2nd − 1st)/1st, full at ≥ 0.3. Grey = no data.

Rows Window