Here’s a very interesting butterfly paper where they leveraged evolutionary genetic and evo-devo data to look at the history of phenotypes and populations:

Wing patterning gene redefines the mimetic history of Heliconius butterflies

Population phylogeny based on neutral markers is a mess and reflects geography more than history due to episodes of hybridization.  On the other, phylogeny based on the gene responsible for part of the wing color pattern reveals the evolutionary history of that phenotype.  This should be true in a lot of cases – the best way to understand the evolution of phenotypes is to identify the genetic changes responsible for those phenotypes.  Mapping phenotypic characters on trees constructed from random loci will not always give you the true answer.  All the more reason to go after the causative genes!