Here, from macrophylogeographic mtDNA empirical data, we proposed
a scenario of the evolution and speciation of two important forest
trees, European Black Pine and Scotch Pine, and their multiple
subspecies and varieties. Molecular clock simulations revealed that
INDELs variability in the Pinus mitochondrial genome is
relatively old, i.e., from the Pliocene-Miocene epoch, and related to
historical tectonic continental fluctuations rather than climate change
on a large geographic scale. Special attention is paid to the
relationships between different speciation models and historical
migration patterns and between peripheral and central populations.
Species evolution involves the mixing of different speciation modes
rather than only one of them, and one speciation mode has different
results/effects on different DNA types (e.g., mitochondrial vs.
chloroplast vs. nuclear DNA). The misbalance between different
meta-population census size vs. effective population size
contributions for asymmetric migration pattern is a result of different
genotypes (and sub-phylogenetic lines) responding to selection pressing
and adaptive evolution.