1Anthropology, McMaster University, 2Archaeology, University of Cambridge, 3Archaeology, University of Bourgogne Franche-Comté, 4Biology, McMaster University, 5Biochemistry, McMaster University, 6Toronto, University Health Network, 7Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 8Earth and Atmospheric Sciences, University of Alberta
April 18, 2020 , Platinum Ballroom
Two major limitations in palaeoenvironmental metagenomics are DNA loss during extraction and the carryover of enzymatic inhibitors. PCR metabarcoding can overcome some degree of inhibition, but this technique can be vulnerable to differential amplification rates and a subsequent bias in taxonomic profiles, especially if there was substantial DNA loss with overly thorough inhibitor removal treatments. Alternatively, sedimentary ancient DNA extracted with techniques designed to maximize ancient DNA recovery are prone to the carryover of enzymatic inhibitors, which can result in failed PCR amplifications or failed adapter ligation during library preparation, impeding shotgun and targeted enrichment strategies.
Here, we report on a new sedimentary ancient DNA extraction protocol paired with targeted enrichment for reconstructing past environments. Our approach averages a 14.6-fold increase in on-target plant and animal DNA compared to a commercial soil extraction kit, and a 22.6-fold increase compared to a PCR metabarcoding approach. To illustrate the effectiveness of our PalaeoChip protocol, we present results of plant and animal presence from permafrost samples and the new potential evidence for the late survival (ca. 9685 BP) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike Region of Yukon, Canada. Our approach translates to a more diverse and sensitive dataset with increased sequencing efficiency of human ecologically informative sedaDNA.