A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

Abstract

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

Importance of eDNA taphonomy and provenance for robust ecological inference: insights from interfacial geochemistry

“…We recently recovered DNA from sediments dated to 2.4 Ma where the thermal age predicted no DNA survival. 12 Additionally, that study showed that the amount of DNA sediment adsorbs and retains depends on its mineralogic composition. In this communication, the term preservation is considered a function of DNA stabilization offered by the substrate (degree of immobilization and binding capacity) as well as resistance to biological, chemical and thermal degradation of the mineral-bound DNA.…”

“…Different surfaces will interact with DNA in different ways, depending on their composition and surface charge. For example, clay minerals, which adsorb an order of magnitude more DNA compared to other minerals, 12 are composed of layers of silica tetrahedra (T) and layers of magnesium or aluminum octahedra (O) (Fig. 1A)).…”

“…The Kap København formation is a 2.4 Ma marine sandy deposit that contains the oldest DNA recovered to date. 12 The sediment profile can be divided in two depositional environments with similar overall mineral composition but of varying ratios. Excluding the amorphous fraction (both organic and inorganic), the formation contains on average 69 wt% of quartz and 7.3 wt% of clay minerals: the rest of the major minerals are feldspars, pyroxene and amphiboles (Fig.…”

“…Adsorption capacity of major minerals from Kap København formation. 12 The adsorbed DNA is shown as a function of the DNA equilibrium concentration, i.e. the concentration of DNA in solution once the equilibrium was reached.…”

Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer

“…4–7 However, advances made in the field of sedimentary ancient DNA (SedaDNA) underlines that, DNA can be preserved for at least 2 Ma years, and the adsorption of the DNA to mineral surfaces are argued to be key for the preservation. 8 In principle, all sedimentary minerals all hold a potential to adsorb some amount of extracellular DNA. Currently there is about 0.45 Gt of extracellular DNA associated with sediments in the top 10 cm of the ocean floor, and more than 90% of that DNA extracellular.…”