The maturing relationship between Quaternary paleoecology and ancient sedimentary DNA

Abstract

In the two decades or so since ancient sedimentary DNA (sedaDNA) took its place as a new Quaternary paleo-proxy, there have been large advances in the scope of its applications and its reliability. The two main approaches, metabarcoding and shotgun sequencing, have contributed exciting insights into areas such as floristic diversity change, plant-herbivore interactions, extinction, conservation baselines and impacts of invasive species. Early doubts as to its potential to contribute novel information have been dispelled; more is now understood about the passage of sedaDNA from the original organism to a component of soil or sediment and about the range of uncertainties that must be addressed in the interpretation of data. With its move into the mainstream, it is now time to develop effective data archives for sedaDNA, refine our understanding of central issues such as taphonomy, and further expand the potential for describing, both qualitatively and quantitatively, the history of past ecosystems.

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

“…By Charline Giguet-Covex 2 , Francesco Gentile Ficetola 14,15 and Pierre Taberlet 6,15 We tested if adding a concentration step to a DNA extraction protocol can improve the performance of extraction of sedaDNA. From the established DNA extraction protocol combining the use of a Phosphate Buffer step with the NucleoSpin Soil kit protocol (Taber-let2012 protocol), successfully used in several studies analyzing lake sedaDNA (e.g., [31,32,51]), we added a step with Amicon ® ultra-15 10k centrifugal filters (Millipore) to concentrate the DNA extract (AmTaberlet2012 protocol).…”

“…A more recent alternative that is now gaining in popularity is to target nucleic acids (DNA) preserved in the sediment archive. The sequencing of targeted genetic regions or the metagenome (all DNA present) extracted from sedimentary DNA can be used to reconstruct changes in biodiversity i.e., distribution of species based on the genetic diversity-over a range of temporal and spatio-ecological scales [13][14][15][16]. Depending on the state of degradation-affected by age, temperature and other environmental variables [17]-sedDNA can be regarded as sedimentary DNA (younger and better preserved) or as sedimentary ancient DNA (sedaDNA; often older, and more poorly preserved).…”

“…In recent years, sedaDNA has shown a great potential for reconstructing past biological assemblages within lakes and their terrestrial catchments (for review see [13][14][15][19][20][21][22]). Following extraction of sedaDNA, several analytical methods have been used (Table S1) including: (i) methods aiming to detect or quantify the occurrence of specific target organisms on the basis of endpoint PCR assays, quantitative real-time qPCR and special applications such as droplet digital ddPCR; (ii) DNA metabarcoding-based methods combining PCR amplification of marker loci (often described as "barcodes") with highthroughput sequencing; (iii) metagenomic approaches based on untargeted shotgun sequencing of the total pool of DNA recovered from the sediment; (iv) hybridization-based target enrichment methods to recover DNA fragments of interest from the sediment metagenome (see Section 3.8).…”

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

“…Ancient metagenomics can be broadly defined as the study of the total genetic content of samples that have degraded over time 3 . Areas of study that fall under ancient metagenomics include studies of host-associated microbial communities (e.g., ancient microbiomes 4 ), genome reconstruction and analysis of specific microbial taxa (e.g., ancient pathogens 5 ), and environmental reconstructions using sedimentary aDNA (sedaDNA)0 6 . Endogenous genetic material obtained from ancient samples has undergone a variety of degradation processes that can cause the original genetic signal to be overwhelmed by modern contamination.…”

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

“…Ancient metagenomics can be broadly defined as the study of the total genetic content of temporally-degraded samples 2 . Areas of study that fall under ancient metagenomics include studies of host-associated microbial communities (e.g., ancient microbiome studies of dental calculus or paleofeces 3 ), genome reconstruction and analysis of specific microbial taxa (e.g., ancient pathogens 4 ), and environmental reconstructions using sedimentary ancient DNA (sedaDNA) 5 . Genetic material obtained from ancient samples has undergone a variety of degradation processes that can cause the original genetic signal to be overwhelmed by modern contamination, requiring large DNA sequencing efforts to detect, quantify, and authenticate the remaining truly aDNA 6,7 .…”