Environmental DNA barcoding to track ancient Arctic ecosystem changes

Abstract

Sedimentary ancient DNA can be preserved for several hundred thousand years under optimal depositional conditions, such as permanently very low temperatures. This DNA can be used to infer species’ presence, even in the absence of macrofossils. PCR-based amplification coupled with second-generation sequencing techniques potentially allows multi-taxon studies on species distributions through time, and the analyses of past ecosystem composition. To obtain meaningful information, the genetic data generated must be informative, so as to allow taxonomic identification, and the markers employed must be short to be retrievable from severely degraded DNA. In the BarFrost project (barcoding of permafrost) we design optimal markers to retrieve a maximum of information on former species composition from degraded environmental samples. We apply our markers to ancient permafrost samples collected throughout the Arctic and ranging in age from recent to several hundred thousand years before present. Using newly developed bioinformatic tools we have systematically designed and evaluated a range of new mini-barcodes for different groups found in the arctic (bryophytes, fungi, vertebrates, insects, springtails). These markers have been optimised experimentally and tested on arctic permafrost samples of different ages. We find that the level of detection in ancient permafrost samples varies substantially among organismic groups, but that we are able to gain information for a number of taxa from single small samples. This enables a more detailed view of past ecosystems than previously possible, and allows us to study structure and change of biotic assemblages through time and their response to climatic variation.