Effect of ghost lineages on observed divergence times in gene trees following or not the species tree topology.

The evolution of genomes (3,000 genes) was simulated on 2 trees, 1 with only extant species (A), the other with all species (B). Mean T1 and T2 were computed for all genes supporting each 1 of the 3 possible topologies (orange, green, and blue trees).The true topology (orange) is the one supported by the trees with the highest mean T1 and T2 when considering only extant species (C), but when considering also extinct lineages (D), the gene trees with the highest T1 and T2 support instead an incorrect topology. One-tailed t test p-values: * 10.5281/zenodo.6901799) and GitHub (https://github.com/theotricou/Ghost_branch_length/tree/main/2_Anopheles/Sup_dataset). (EPS)