The effects of sample age and taxonomic origin on the success rate of DNA barcoding when using herbarium material

Abstract

We have produced DNA barcodes for Finnish plant taxa. In this study, we specifically report the barcoding success for herbarium materials varying widely in age, also paying attention on success rate variation and genetic distances among different plant families. Additionally, we investigated whether the level of intraspecific variation differs between native and introduced species. The specimens had been collected between years 1867 and 2013. Among all studied specimens, the average success rates for any barcode (matK or rbcL), rbcL, matK and both barcodes equaled 81, 79, 55 and 53%, respectively, and among species (at least one specimen per species barcoded successfully) 95, 95, 74 and 73%, respectively. We found significant age effects on the barcoding success, the greatest decline being visible in over 100-year-old samples. Plant families showed differences in overall success rates and sample age effects, as well as in intraspecific and interspecific variation levels, while the average level of intraspecific variation appeared similar among native and introduced species. Besides being valuable for the identification of species, DNA barcoding with sufficient sampling is also a tool to investigate specific evolutionary questions, such as biogeographic patterns or the adaptive capacity of invasive and other alien plant species.

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

“…Also for capture probes, the target enrichment efficiency declines with age [53]. This is in contrast to what has been observed for Sanger sequencing [35,54]. Similarly, while we in an earlier Sanger sequencing study observed that specimens collected later in the growing season had poorer success rate (boldsystems.org, project NNOR, n = 1805), time of season caused no problem for genome skimming.…”

A molecular‐based identification resource for the arthropods of Finland

“…Despite initial skepticism from national funding agencies, FinBOL has delivered primary research results of the very type traditionally supported by them. Deliverables to date include insights into the protein structure of the barcode region (Pentinsaari et al, 2016), species interactions (Kaartinen et al, 2010; Mutanen, Ovaskainen, et al, 2020; Nyman et al, 2015; Rytkönen et al, 2019; Vesterinen et al, 2013, 2016), taxonomy (Boonstra et al, 2018; Haarto & Ståhls, 2014; Hausmann et al, 2013; Huemer et al, 2020; Huemer & Mutanen, 2015; Ivanov et al, 2018; Kirichenko et al, 2016; Kozlov et al, 2017; Landry et al, 2013; Landvik et al, 2013; Lee et al, 2020; Liston et al, 2019; Mutanen, Aarvik, Huemer, et al, 2012; Mutanen et al, 2012, 2013, 2015, 2016, 2020; Nieminen et al, 2018; Pentinsaari et al, 2014; Pentinsaari et al, 2014; Pilipenko et al, 2012; Pohjoismäki & Haarto, 2015; Pohjoismäki et al, 2016; Prous et al, 2016, 2020; Pykälä & Myllys, 2016; Salmela et al, 2014; Sihvonen et al, 2020; Ståhls et al, 2015; Tabell et al, 2019; van Nieukerken et al, 2012; Wikström et al, 2020; Wilson et al, 2011), phylogenetics (Heikkilä et al, 2014; Kaila et al, 2020; Karsholt et al, 2013), faunistics (Korpelainen & Pietiläinen, 2017; Paukkunen & Kozlov, 2015), biogeography (Huemer et al, 2014, 2018; Mutanen, Hausmann, et al, 2012; Salmela, 2012), methodology (Kekkonen et al, 2015; Korpelainen & Pietiläinen, 2...…”