The here provided data and reconstructions did not resolve anything beyond what already the ITS and 5S-IGS data of Forest et al. (2005) showed (see also fig. 1 in Grimm & Renner, 2013 illustrating the not insubstantial information content in the data available back then). The identification of highly-divergent plastid regions may indeed open the door for in-detail intra-generic analyses, but it h...

The idea of ancestral area reconstruction is to reconstruct ancestral areas. For this, each tip taxon has to be coded for its modern area (ideally not more than one, because all AARs tend to end up with ambiguous reconstructions the deeper the node).

You coded each species for the entire area of the genus, in your data mostly represented exclusively by (sometime geographically very restricted,...

Both Forest et al. (2005) and Grimm & Renner (2013) provide dated trees.

PS This paragraph includes a common error: "Our molecular dating analysis supported Betulaceae to be originated at the end of Cretaceous (∼70.49 Mya), which is very close to the above results" – is nonsense. Origin would be the stem age, but your tree lacks the needed stem node (= MRCA Ticodendron and Betulaceae). This is...

It is a poor argument for phylogenomic tree inference, when one has to cite long outdated (pre-2000) phylogenies based on morphology alone or single genes (Pre-2000, molecular phylogenetics were in their infancy, and many trees of that time where quickly refined or rejected).

These graphs are not based on two data partitions, but one (B, only intergenic spacers, ie. noncoding parts) is a subset of the other (complete plastome, A). Wouldn't it have made more sense to compare an amino-acid/codon-based tree vs. one based only on the non-coding regions?

This may have helped regarding "advantages of using chloroplast genome data to illuminate those phylogenies that have...