FIGURE 2 in Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.

FIGURE 2. Species-coalescence tree of the orchid family inferred from 292 maximum likelihood (ML) gene trees. Pie diagrams at nodes represent quartet support values, with q1 (deep blue portion) representing the proportion of gene tree quartets that support the main (depicted) branch, q2 (blue portion) representing the proportion of quartets supporting the first alternative branch, and q3 (gray portion) representing the proportion of quartets supporting the second alternative branch (an explanation of how the quartet values are computed is available at https://github.com/smira rab/ASTRAL/blob/master/astral-tutorial.md). (Inset): ML tree derived from a supermatrix of 292 low copy nuclear genes. Terminal names with alternative positions to those obtained by the species-tree coalescence analysis are highlighted in bold and red. Adetailed version of the tree is presented in Appendix S4.