I think this really depends on the students' interests and the strengths of the individual institution. For instance, here at Pitt we have a greater number in Neuroscience, Bioengineering, and Immunology. But in theory we can do our PhD in any Dept at Pitt or CMU, even non-science ones.
Personally my PhD is in Pathology. Our Dept has the 5th highest NIH funding in the country, but only a handful of MSTP students (and we're a pretty student-friendly dept too!). Go figure
Here at Penn the largest graduting MD/PhD group is from the PhD group called Cell and Molecular Biology (CAMB). I don't know the statistics by group to be able to tell you who ranks second among the groups like Immuno, Neuro, etc...
We have the following PhD Departments represented (sorted by # of students):
Immunology
Neuroscience
Biochemistry
Molecular Biology
Pharmacology
Genetics
Physiology & Biophysics
Microbiology
Anatomy & Cell Biology
Biosciences
Epidemiology
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