2.5.2 Treemix
Genetic relationships were visualized for the 12 present-day blue whale samples from the NA, three historical samples from the NA and one historical sample from Antarctica using TREEMIX v1.13 setting a NA fin whale as the root. The blue whale samples included here showed low levels of introgression from fin whales. Each individual whale was plotted with a maximum likelihood graph (with option -nos) using genome-wide allele frequencies and a Gaussian distribution to account for genetic drift, allowing for two migration events. Treemix was run independently 10 times to verify that the edges were consistent across runs. Migration edges were fitted iteratively by analyzing the residual plots and confirming gene flow events with D-statistics.