Methodological Changes in the Field of Paleogenetics

Abstract

Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges.

Exploring the complex pre-adaptations of invasive plants to anthropogenic disturbance: a call for integration of archaeobotanical approaches

“…Some types of samples, such as sediment or coprolites, can contain several species' microremains or fragments of macroremains that are too small to be identified and are therefore analyzed through metabarcoding or metagenomics, which can provide an overview of the past community's taxonomic composition (Figure 2B) (Taberlet et al, 2012;Pedersen et al, 2016;Parducci et al, 2017). Excellent reviews have summarized the most recent aDNA analysis techniques, such as Hofreiter et al (2015); Orlando et al (2015), and Danielewski et al (2023). Information on ancient species' evolution can be gathered also from morphometric analyses of archaeobotanical macroremains, which, if applied to charred materials needs careful consideration due to the possible deformations as consequence of the charring process (Charles et al, 2015).…”

Mitochondrial DNA control region typing from highly degraded skeletal remains by single‐multiplex next‐generation sequencing

“…Some authenticity criteria for DNA from ancient and forensic samples were established several years ago [21,22]. However, the ancient DNA community has incorporated bioinformatic tools to authenticate endogenous DNA, mainly based on patterns of DNA damage across genomic sequences generated by NGS [23]. These tools can eliminate PCR duplicates (essentially in PCR based techniques) and can identify the DNA damage markers that are typically observed in ancient samples [11,15,[24][25][26][27][28][29][30].…”