A study of referencing changes in preprint-publication pairs across multiple fields

•Using change in reference list of preprint-publication pairs from multiple fields to investigate manuscript development process.•90% of references were unchanged between versions and 8% were newly added.•Manuscripts in the natural and medical sciences undergo more extensive reframing of the literature.•Changes in engineering mostly focused on methodological details.•Our validation study provides detail on the shortcoming of reference lists in data sources. 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 6024 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% of references were unchanged between versions and 8% 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.