Screening archaeological bone for palaeogenetic and palaeoproteomic studies

Abstract

The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals' size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.

Fig 1. Endogenous DNA-crystallinity relationship.

(a) Correlation of IRSF with endogenous DNA yields. The black line at 3.7 IRSF represents the proposed ‘strict’ threshold, while the red line at 4.2 IRSF represents the ‘moderate’ threshold. The circles represent the petrous bones, and the rhombuses the other skeletal elements. (b) Distribution of samples with well- (> 10%; green/solid diamond), moderately- (1–10%; yellow/large checkerboard), and poorly-preserved (< 1%; red/dotted) endogenous DNA in categories based on crystallinity.

Fig 2. Endogenous DNA-carbonate content relationship.

(a) Correlation of C/P with endogenous DNA yields. Line represents the proposed C/P = 0.13 cut-off point. The circles represent the petrous bones and rhombuses the other skeletal elements. (b) Distribution of samples with well- (>10%; green/solid dimond), moderately- (1–10%; yellow/large checkerboard), and poorly-preserved (< 1%; red/dotted) endogenous DNA in categories based on carbonate content.

Fig 3. Endogenous DNA-collagen content relationship.

(a) Endogenous DNA preservation shows poor correlation with collagen wt. %. Line represents the proposed collagen wt. % = 5 cut-off point. The circles represent the petrous bones, while the rhombuses represent the other skeletal elements. (b) Distribution of samples with well- (> 10%; green/solid diamond), moderately- (1–10%; yellow/large checkerboard), and poorly-preserved (< 1%; red/dotted) endogenous DNA in categories based on collagen yield.

Fig 4. Am/P-collagen content relationship.

(a) Collagen preservation shows strong polynomial (order 2) correlation with Am/P. The red line represents the proposed Am/P = 0.02 cut-off point. The circles represent the petrous bones and rhombuses the other skeletal elements. (b) Distribution of samples with well- (≥ 3%; green/solid diamond), and poorly-preserved (< 3%; red/dotted) collagen in categories based on Am/P.