  Manuscripts have a complex development process with multiple influencing
factors. Reconstructing this process is difficult without large-scale,
comparable data on different versions of manuscripts. Preprints are
increasingly available and may provide access to the earliest manuscript
versions. Here, we matched 6,024 preprint-publication pairs across multiple
fields and examined changes in their reference lists between the manuscript
versions as one aspect of manuscripts' development. We also qualitatively
analysed the context of references to investigate the potential reasons for
changes. We found that 90 percent of references were unchanged between versions
and 8 percent were newly added. We found that manuscripts in the natural and
medical sciences undergo more extensive reframing of the literature while
changes in engineering mostly focused on methodological details. Our
qualitative analysis suggests that peer review increases the methodological
soundness of scientific claims, improves the communication of findings, and
ensures appropriate credit for previous research.
