Survival and spread of arctic plants in response to climate change: DNA-based evidence

MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

“…Recent discussions on the challenges of working with sedaDNA have also focused on challenges associated with conventional paleoecological research (Smith et al, 2015;Chen and Ficetola, 2020;Cribdon et al, 2020;Edwards, 2020;Dussex et al, 2021). This has included wider discussions of the issues of understanding the source area and catchment of sedaDNA, the role of taphonomic processes in the formation of the biomolecular archives, and how preservation conditions impact its contribution as a tool for paleoecological reconstruction (Alsos et al, 2018(Alsos et al, , 2020bParducci et al, 2018;Giguet-Covex et al, 2019;Marianne et al, 2020). This in turn has led to improvements in approaches to bioinformatic processing, such as increasing confidence in the phylogenetic assignation of taxa within ancient metagenomic sequences (Smith et al, 2015;Cribdon et al, 2020).…”

“…The number of sedaDNA studies using the shotgun sequencing approach is still limited (Smith et al, 2015;Pedersen et al, 2016;Seersholm et al, 2016;Slon et al, 2017;Ahmed et al, 2018;Parducci et al, 2019;Stahlschmidt et al, 2019;Ardelean et al, 2020;Armbrecht et al, 2020;Gaffney et al, 2020;Schulte et al, 2020;Murchie et al, 2021b;Thomas et al, 2021). The alternative, a targeted amplicon sequencing approach using organism range specific primers [e.g., chloroplast trnL (UAA) gene specific for plants; Taberlet et al, 2007] known as metabarcoding sequencing (Bell et al, 2016;Parducci et al, 2018;Edwards, 2020) has proven far more popular, with not just demonstrative capabilities of high resolution amplification of plant taxa for palaeoenvironmental reconstruction (e.g., Sønstebø et al, 2010;Jørgensen et al, 2012;Parducci et al, 2012Parducci et al, , 2013Parducci et al, , 2015Parducci et al, , 2019Pedersen et al, 2013;Giguet-Covex et al, 2014Epp et al, 2015;Pansu et al, 2015;Alsos et al, 2016Alsos et al, , 2020bSjögren et al, 2017;Clarke et al, 2018;Zale et al, 2018;Crump et al, 2019;Liu et al, 2020;Volstad et al, 2020), but for addressing key barriers in molecular research, such as financial cost (Parducci et al, 2018) and higher computational processing requirements needed for the analysis of metagenomic data...…”

MetaDamage Tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

“…The number of sedaDNA studies using the shotgun sequencing approach is still limited (Smith et al, 2015;Pedersen et al, 2016;Seersholm et al, 2016;Slon et al, 2017;Ahmed et al, 2018;Parducci et al, 2019;Stahlschmidt et al, 2019;Ardelean et al, 2020;Armbrecht et al, 2020;Gaffney et al, 2020;Schulte et al, 2020;Murchie et al, 2021b;Thomas et al, 2021). The alternative, a targeted amplicon sequencing approach using organism range specific primers [e.g., chloroplast trnL (UAA) gene specific for plants; Taberlet et al, 2007] known as metabarcoding sequencing (Bell et al, 2016;Parducci et al, 2018;Edwards, 2020) has proven far more popular, with not just demonstrative capabilities of high resolution amplification of plant taxa for palaeoenvironmental reconstruction (e.g., Sønstebø et al, 2010;Jørgensen et al, 2012;Parducci et al, 2012Parducci et al, , 2013Parducci et al, , 2015Parducci et al, , 2019Pedersen et al, 2013;Giguet-Covex et al, 2014Epp et al, 2015;Pansu et al, 2015;Alsos et al, 2016Alsos et al, , 2020bSjögren et al, 2017;Clarke et al, 2018;Zale et al, 2018;Crump et al, 2019;Liu et al, 2020;Volstad et al, 2020), but for addressing key barriers in molecular research, such as financial cost (Parducci et al, 2018) and higher computational processing requirements needed for the analysis of me...…”