I don't see what concerns there could be about the Duke article, it clearly says that they threw out mtDNA use due to the results not being what they expected:
But the current molecular method of using mitochondrial DNA to classify how mammals evolved is so flawed that it might have erroneously linked very different mammals, the scientists said. The mitochondrial DNA method of analyzing mammals has turned on its head the common-sense approach of linking mammals by similar anatomical traits or "morphology," they said.
The above is 'evolutionize' for saying, hey, this test does not agree with our evolutionary assumptions so we must throw it out. The following is an even more blatant example on the same subject:
A quite interesting example of evolution "science" is at Mammalian Genome (PDF file).
First evolutionists tried to use mitochondrial DNA to show the relationships between the monotremes (platypus), the eutherians (kangaroos) and the placentals (all other mammals). The mtDNA did not give them the desired results "The value and accuracy of decades of morphological study have been discounted recently by mytochondrial DNA evidence". So of course the evos could not let that happen, so they had to try again. They then tried DNA hybridization. However, under this method also Darwinian theory was refuted "It is significant that apomorphies of the theran ancestors, such as the braincase, cranial nerve architecture, and reproductive physiology" had to be reclassified as convergences under these two tests. So of course they had to pick another test to get the results they wished - a totally new one called MP6/IG2FR!
The problem in both the Duke test and the one in Mammalian Genome is that the platypus lays eggs, but the kangaroos have live birth, nevertheless the platypus mtDNA was closer to the placentals than the kangaroos which of course destroys tons of evolutionist assumptions. They cannot for one thing continue to say that mtDNA proves their 'tree of life'. But what is worse is the blatant disregard for experiments when they disagree with their assumptions. Experiments are supposed to test theories, not the other way around. However, evolutionists do not test their theories, they test reality and if it does not fit their theory, they ignore it.