An article was published a few days ago (March 21) that is going to cause textbooks to be re-written because of what they found. Thompson and Tucker used transgenic mice to track the developmental process of the middle ear. The mechanism that they found gives a reason why the ear is prone to infection. Two types of tissues are used when developing the middle ear, which are the neural crest and the endoderm. The difference between these two types of tissues is that the endoderm gives rise to the tissue lining that is covered with cilia; whereas, the neural crest gives rise to he tissue lining with absence of the cilia. The purpose of cilia is to remove debris from the ear. Therefore, the tissue that originate from the neural tube are not efficient at removing debris due to the lack of cilia.
The middle ear is a air filled space, something that is unique to mammals. Reptiles and birds do not have this air filled space, probably because they only have one ear bone, while mammals have three. It is suggested that the evolved air filled spaced was needed to proved room for the additional two bones. Thus, the two types of tissue lining in the middle ear might have evolved due to the air filled space. Even though the evolution of these two types of tissues was to make space for the additional two bones needed for hearing in the mammals ear, it allowed the chances of infection to increase. The lining with no cilia cannot efficiently remove debris from the ear, leading it to be more prone to infection. This was discussed in the review as an "evolutionary glitch".
Hannah Thompson and Abigail S. Tucker. Dual Origin of the Epithelium of the Mammalian Middle Ear. Science, 2013; 339 (6126): 1453-1456 DOI: 10.1126/science.1232862