Fig. 3
Divergence time and gene flow estimated for Juglans regia and J. sigillata with an IMa3 model that included a ghost population (Methods), and a phylogeny of shell-thickness gene sequences. a Each group is represented by a box of a width proportional to its estimated effective population size (ancestral Ne is given for scale). Confidence intervals are indicated as dashed-line boxes aligned with the corresponding population’s box on the left side. Green arrows represent an effective number of migrant gene copies per generation (2Nm) from the source population to the receiving population. Only statistically significant migration rates are shown (*P < 0.05; **P < 0.01; ***P < 0.001). b Maximum likelihood phylogeny obtained from 20 haplotypes of the shell-thickness gene from J. regia and J. sigillata. The blue lines represent 8 haplotypes of J. regia that are shared with J. sigillata. Ultrafast bootstrap (UFBoot) support values ≥ 50 shown at nodes