Question

How is it possible that phylogenies based on sequences from nuclear genomes and organellar genomes (i.e., chloroplasts and mitochondria) from the same group of species yield phylogenetic trees with different branching orders? the genome of the endosymbiont is more closely related to members of the group in which it originally evolved, while the nuclear genome of the engulfing organism has its own evolutionary trajectory.for organelles like chloroplasts, no mutations can occur or photosynthesis would stop and the organism would die. the nuclear genome can accumulate mutations, so it can continue to evolve.nuclear and organellar genes evolved at different rates, obscuring evolutionary relationships.transfer of genetic material from the genome of the endosymbiont to the host results in two phylogenies, host and endosymbiont. the host genome continues to accumulate mutations, but the endosymbiont genome cannot?

Answer 1

How is it possible that phylogenies based on sequences from nuclear genomes and organellar genomes (i.e., chloroplasts and mitochondria) from the same group of species yield phylogenetic trees with different branching orders? 
Answer : The genome of the endosymbiont is more closely related to members of the group in which it originally evolved, while the nuclear genome of the engulfing organism has its own evolutionary trajectory.