Extended Data Fig. 4: PCA of spectral data.
a, Whole spectra-based PCA of all modern (n = 4 biologically independent samples) and fossil (n = 14 biologically independent samples) eggshell and sediment samples (n = 12 independent samples). Sediment samples cluster together (green), and do not overlap the cluster of eggshell samples (grey-to-yellow). Eggshell biomolecules and sediment organics are distinct. Within the eggshell cluster, extant material is separated from fossil material. The proximity of unpigmented, protoporphyrin IX-bearing and biliverdin-rich extant eggshell material emphasizes that the taphonomic signal overprints the pigment signal at the level of a whole spectrum-based PCA. PC1 (73.116%) and PC2 (10.977%) are characterized by high support values and explain most of the variation in the eggshell and sediment sample set. b, PCA based on the pigment fingerprint region (1,500–1,650 cm−1 ± 2 cm−1) of protoporphyrin IX and biliverdin in fossil eggshell material (n = 12 biologically independent samples). The exclusion of fresh and ‘subfossil’ (P. rothschildi and ornithoid ratite) eggshell material and the extraction of the pigment fingerprint region enable a chemo-space separation based on the eggshell pigment signal. Pigmented fossil eggshells form a cluster (yellow) that is separated from the cluster (grey) of unpigmented fossil eggshells (Extended Data Fig. 5). The pigment fingerprint region includes—besides protoporphyrin IX and biliverdin—structurally similar PFPs as well as pigment fossilization products, which account for the distribution of samples within each cluster of fossil eggshells (pigmented and unpigmented). PC1 represents sample variation based on pigment type, concentration and PFP contents, and PC2 separates samples based on the presence or absence of eggshell pigments (Extended Data Fig. 5).
