Ancient Plant Genomics in Archaeology, Herbaria, and the Environment

Abstract

The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.

Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA

“…Archaeogenetics is the field in which we analyze DNA material derived from post mortem degraded tissues of living organisms (for example, old bones, sediments, seeds, shells) for the purpose of its genetic characterization. Due to temporal provenance of such samples, archaeogenetics has been an extraordinary tool for studying evolutionary histories of species, mechanisms of evolution in general Kistler, Bieker, et al, 2020;B. Shapiro & Hofreiter, 2014), as well as biological anthropology and archaeology.…”

“…Archaeogenetics is the field in which we analyze DNA material derived from post mortem degraded tissues of living organisms (for example, old bones, sediments, seeds, shells) for the purpose of its genetic characterization. Due to temporal provenance of such samples, archaeogenetics has been an extraordinary tool for studying evolutionary histories of species, mechanisms of evolution in general (Gutaker & Burbano, 2017; Kistler, Bieker, et al., 2020; B. Shapiro & Hofreiter, 2014), as well as biological anthropology and archaeology. The early successes of archaeogenetic studies through molecular cloning (Higuchi, Bowman, Freiberger, Ryder, & Wilson, 1984; S. Pääbo, 1985) were soon overshadowed by a high number of irreproducible PCR‐based results (Svante Pääbo et al., 2004).…”

Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

“…This paves the way for community‐level Angiosperms353 studies. The studies noted above indicate that the potential of Angiosperms353 could be considerable for species‐ and population‐level applications and has potential as a novel tool for DNA barcoding for the molecular identification of modern, historical, ancient, and mixed environmental samples (Kistler et al, 2020; Folk et al, 2021).…”

Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

“…In addition, genome-skimming (Straub et al, 2012) has allowed short-reads to be obtained in a cost-effective way, which is suitable for the relatively small size of organelle genomes. Biodiversity projects have started to regard organelles as "super-barcodes, " since these sequences could still be obtained from degraded museum and herbarium samples (see Kistler et al, 2020). Thus, genome sequencing of plastids in plants and mitochondria in animals has become an essential tool in the study of evolution.…”