Ultrametric spaces are widely used to depict evolutionary times in phylogenetic trees, since they assume that every population/species is located at the tips of divergent branches. The discrete branching of ultrametric trees permits the measurement of distances between pairs of individuals that are proportional to their divergence time. Here we overturn the traditional ultrametric concept of divergent phylogenetic tree and introduce a new type of non-ultrametric diagram to describe gene flows in terms of convergent branches. To provide an operational example, we examine the paleoanthropological issue of Neanderthal genome’s introgression in non-African humans. Neanderthals and ancient humans are not anymore two species that exchange chunks of DNA, rather become a novel cluster that must be considered by itself. Our converging, non-ultrametric phylogenetic trees permit the calibration of molecular clocks with a twofold benefit. When the date of the branching of two population/species from a common ancestor is known, our method allows to calculate the time of subsequent introgressions. On the contrary, when the date of the introgression between two population/species is known, our method allows to detect the time of their previous branching from a common ancestor.