Ancient DNA from pollen: a genetic record of population history in Scots pine

Abstract

Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100-year old and 10 000-year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.

Pollen DNA barcoding: current applications and future prospects

“…The study of fossil pollen has various applications in paleoecology, archaeology, as well as anthropology, including the reconstruction of ancient plant communities (Jørgensen et al 2012a;Pedersen et al 2013), the study of population dynamics in single plant species (Parducci et al 2005;Magyari et al 2011), and the investigation of biodiversity with the aim of endemic species conservation (Wilmshurst et al 2014) inter alia. Mathewes (2006) also showed how the study of ancient pollen plays an important role in forensics (see Forensic palynology section, below).…”

Ancient plant DNA in archaeobotany

“…Coniferous pollen from sediment cores was reported to contain DNA (Suyama et al 2003;Parducci et al 2005). Reconstruction of temporal vegetation changes was attempted from faeces (Hofreiter et al 2003) and the potential of genetic analysis of frozen sediments for the reconstruction of past vegetation over thousands of years in correlation to climate changes was demonstrated .…”

Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene–Holocene cave deposit on Kangaroo Island, South Australia

“…Sequences were identified using BLAST (Altschul et al, 1990), and results interpreted with MEGAN (Huson et al, 2007) (Table 2). As with previous sedimentary ancient plant DNA literature using these chloroplast loci (Jorgensen et al, 2011;Parducci et al, 2005), taxonomic resolution is reliant upon comparative database coverage, and within certain families is constrained by the degree of interspecific variation. Nevertheless, the results provide some interesting insights.…”