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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 values^3,4. 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.

SUBMITTER: Kjær KH

PROVIDER: S-EPMC9729109 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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

Kjær Kurt H KH Winther Pedersen Mikkel M De Sanctis Bianca B De Cahsan Binia B Korneliussen Thorfinn S TS Michelsen Christian S CS Sand Karina K KK Jelavić Stanislav S Ruter Anthony H AH Schmidt Astrid M A AMA Kjeldsen Kristian K KK Tesakov Alexey S AS Snowball Ian I Gosse John C JC Alsos Inger G IG Wang Yucheng Y Dockter Christoph C Rasmussen Magnus M Jørgensen Morten E ME Skadhauge Birgitte B Prohaska Ana A Kristensen Jeppe Å JÅ Bjerager Morten M Allentoft Morten E ME Coissac Eric E Rouillard Alexandra A Simakova Alexandra A Fernandez-Guerra Antonio A Bowler Chris C Macias-Fauria Marc M Vinner Lasse L Welch John J JJ Hidy Alan J AJ Sikora Martin M Collins Matthew J MJ Durbin Richard R Larsen Nicolaj K NK Willerslev Eske E

Nature 20221207 7939

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 describin ...[more]

PMID: 36477129

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Project description:Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years. IMPORTANCE The nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor are unknown. Subseafloor populations have ultralow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits. Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting that the genome evolution of these bacteria has been dominated by genetic drift. Thus, reduced recombination, stemming from long-term physical isolation, resulted in small clonal populations of Thalassospira that have accumulated mutations in their genomes over millions of years.

Dataset Information

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

Publications

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

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