The untapped potential of macrofossils in ancient plant DNA research

Abstract

Summary The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high‐throughput sequencing, and bioinformatics, ancient genome‐scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state‐of‐the‐art, address important challenges, and highlight new research avenues to inspire future research.

A range‐wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence

“…Given our current knowledge of the history of P. cembra , we see various opportunities for further in‐depth research along the time axis. From a historical perspective, palaeo‐genomics using, for example, macro‐remains (Schmid et al, 2017; Schwörer et al, 2022) may enhance our understanding of the spatiotemporal dynamics of migration of specific genetic lineages. For example, lake sediment archives that contain macrofossils (Figure 3b) or currently melting glaciers that occasionally disclose logs and trunks of P. cembra at elevations beyond the current tree line (Nicolussi & Schlüchter, 2012), provide evidence of the species' past presence and, thus, stepping‐stone populations that could be genetically characterised (Danusevicius et al, 2021; Parducci et al, 2012).…”

“…Their large quantities of pollen accumulate in sediments and provide a spatiotemporal record of past species' presences and abundances. Moreover, larger tissue parts (fruits, leaves, wood) can be incorporated into sediments (Schwörer et al, 2022). Such macro‐remains (macrofossils) enable inferring the local presence of a species within a few tens of metres around distributional sites, because they are less widely transported than wind‐borne pollen.…”

Paleogenomics (short review)

“…В целом, флора продемонстрировала устойчивость к изменяющемуся климату, поэтому, если будущее потепление будет ограничено 2 °C, можно ожидать лишь незначительных флористических изменений в этом регионе (хотя летопись голоцена не дает аналогов большему потеплению) (Alson et al 2016). Таким образом, анализ древних геномов макрофоссилий растений может найти применение в реконструкции послеледниковых сдвигов ареалов, отслеживании генетического разнообразия во времени и тестировании адаптивного потенциала растений к изменению климата (Schwörer et al 2022). Древнюю ДНК из отложений можно использовать для характеристики тенденций биоразнообразия, освещения прошлой динамики пищевых сетей, реконструкции долгосрочных экологических изменений в водных экосистемах, а также прослеживания кратко-и долгосрочных трендов антропогенного воздействия (Nguen 2022).…”