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

Abstract

Abstract:The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to 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 is likely due to a bulk diffusion process, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. Introduction:The genomic era of massively parallel DNA sequencing has driven a revolutionary body of research using ancient DNA-based genomics (1, 2). Paleogenomics has led to the re-writing of recent hominin evolutionary history (3), nuanced understandings of historical human movements and interactions around the globe (4, 5), breakthroughs in Quaternary paleontology (6-8), evolutionary ecology, the biology of extinct species (9), impacts of humans on ancient ecosystems and biodiversity (10), and the evolution and movements of domestic plants and animals (11)(12)(13)(14). The successful probing of ancient epigenomes, microbiomes, and metagenomes further illustrates the flexibility and information value of ancient DNA-based research in the genomic age (15-17). In sum, time-series genomic datasets have proven extremely valuable in diverse research avenues.

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, ; McDonough et al, ; Zimmermann et al, ).…”

Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

“…In Quaternary floras, these affect the transportation, incorporation and preservation of aeDNA in sediments (Birks & Birks, ). For mammal bones, the propensity for tissues and environments to create closed systems appears to be of greater importance than the absolute age of the aeDNA (Kistler, Ware, Smith, Collins, & Allaby, ). To date, there is little knowledge of how taphonomic processes affect the preservation of aeDNA from aquatic habitats, though assemblages derived from aeDNA have been shown to be stable over decadal timescales in lake sediments (Capo, Domaizon, Maier, Debroas, & Bigler, ).…”

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, ). Several studies have also demonstrated variation in DNA preservation between archaeological sites and environments (Burger, Hummel, Herrmann, & Henke, ; Kistler, Ware, Smith, Collins, & Allaby, ). 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, ; Speller et al, ).…”