Supplementary code for: Empirical evidence from Last Glacial Maximum eggshells improves predictions of climate-driven range shifts in breeding birds

This repository contains supplementary code accompanying the manuscript: Yeomans, L., Alba, R., Codlin, M.C., Dekker, J., Martínez-Haya, B., Parmaksız, R., Garrard, A., Martin, L., Chamberlain, D., Demarchi, B. *Empirical evidence from Last Glacial Maximum eggshells improves predictions of climate-driven range shifts in breeding birds.* ## Species distribution modelling Author: Riccardo Alba This component contains code for generating Figure 4, Table 1, and Table S5 of the associated manuscript. It models present-day and Last Glacial Maximum (LGM) breeding suitability for Mute Swan (*Cygnus olor*) and Greylag Goose (*Anser anser*), with a focus on Uwaynid 18 in the Azraq Basin, Jordan. It compares a climate-only ensemble (M1) with an ensemble incorporating climate variables and the Topographic Wetness Index (M2). ## Proteomic analysis of archaeological eggshells Author: Maria C. Codlin This component contains code for generating supplementary Figures S3 and S4–S11. ### Figure S3: Injection-blank peptide counts The code extracts identified peptide counts from PEAKS output files for injection blanks and plots the counts in the first, second, and third blanks run after each sample. These plots assess sample carry-over: peptide counts decrease across successive blanks and are absent or very low in the third blank, indicating minimal residual carry-over by that stage. ### Figures S4–S11: Peptide alignments and coverage The code extracts peptide sequences from PEAKS output files for archaeological eggshells and aligns them to reference proteins for *Anser* and *Cygnus*. It then generates CSV matrices recording amino acid identities and peptide coverage at each position relative to the reference sequences for Greylag Goose (*Anser anser*) or Mute Swan (*Cygnus olor*). These matrices are used to generate stacked peptide coverage figures, with individual eggshell samples distinguished by colour and taxonomically informative single amino acid polymorphisms (SAPs) highlighted. ## Using this repositoryAll information required to reproduce figures, tables or run scripts is provided separately for each component as a .md or .rmd file.