  This paper provides insight into the changes manuscripts undergo during peer
review, the potential reasons for these changes, and the differences between
scientific fields. A growing body of literature is assessing the effect of peer
review on manuscripts, however much of this research currently focuses on the
social and medical sciences. We matched more than 6,000 preprint-publication
pairs across multiple fields and quantified the changes in their reference
lists. We also quantified the change in references per full-text section for
565 pairs from PLOS journals. In addition, we conducted manual checks of a
randomly chosen sample of 98 pairs to validate our results, and undertook a
qualitative analysis based on the context of the reference to investigate the
potential reasons for reference changes. We found 10 disciplines, mostly in the
natural sciences with high levels of removed references. Methods sections
undergo the most relative change in the natural sciences, while in the medical
and health sciences, the results and discussion sections underwent the most
changes. Our qualitative analysis identified issues with our results due to
incomplete preprint reference lists. In addition, we deduced 10 themes for
changing references during peer review. This analysis suggested that
manuscripts in the natural and medical sciences undergo more extensive
reframing of the literature used to situate and interpret the results of
studies than the social and agricultural sciences, which are further embedded
in the existing literature through peer review. Peer review in engineering
tends to focus on methodological details. Our results are useful to the body of
literature examining the effectiveness of peer review in fulfilling its
intended purposes.
