A new model for ancient DNA decay based on paleogenomic meta-analysis

Abstract

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.

Optimized DNA sampling of ancient bones using Computed Tomography scans

“…For example, cytosine deamination has been frequently used for the validation of ancient DNA data authenticity (Gansauge & Meyer, 2014;Ginolhac et al, 2011;Meyer et al, 2016;Sawyer, Krause, Guschanski, Savolainen, & P€ a€ abo, 2012), which our results show may vary by a factor of up to 1.36 for data sets obtained from different regions of the very same sample. Both cytosine deamination and DNA fragmentation have been used to study the decay kinetics of DNA over time (Allentoft et al, 2012;Kistler et al, 2017). Our results further suggest that sample micropreservation may represent an important factor to be taken into account for empirical investigations of these processes (Allentoft et al, 2012).…”

“…(g) Total DNA yield was not measured for DNA obtained using the conventional sampling method. Note that, for comparisons of conventional sampling, data were also collected from the trabecular region of the same bone, resulting in two comparisons, respectively, with the outermost layer, which are not truly independent (see Table 1) environmental variables (Kistler, Ware, Smith, Collins, & Allaby, 2017) proposed a similar hypothesis. The authors argued that DNA degradation proceeds more by leaching of DNA from bones rather than by fragmentation, but that certain bone structures and environments may be resistant to this bulk diffusion process "closed systems".…”

Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

“…formalin) and those which are much older or 'ancient' (e.g. archaeological samples thousands of years old) are likely to present a different set of complications(Kistler, Ware, Smith, Collins, & Allaby, 2017;McDonough et al, 2018;Zimmermann et al, 2008).…”

Comparison and optimization of genetic tools used for the identification of ancient fish remains recovered from archaeological excavations and museum collections in the Mediterranean region

“…This variation is likely a result of both the age of the specimens and the environmental conditions (temperature, humidity, pH, microorganisms) to which they were exposed since the death of the animal (Sawyer et al, 2012). Several studies have also demonstrated variation in DNA preservation between archaeological sites and environments (Burger, Hummel, Herrmann, & Henke, 1999;Kistler, Ware, Smith, Collins, & Allaby, 2017). The environmental conditions in which fish remains are buried is particularly influential on the extent to which DNA is preserved (Alonso, Häberle, Plogmann, Schibler, & Schlumbaum, 2017;Speller et al, 2012).…”