From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo-diversity in sedimentary ancient DNA over the last ~14,500 years

Geobiology. 2018 Nov;16(6):628-639. doi: 10.1111/gbi.12307. Epub 2018 Jul 23.


Most studies that utilize ancient DNA have focused on specific groups of organisms or even single species. Instead, the whole biodiversity of eukaryotes can be described using universal phylogenetic marker genes found within well-preserved sediment cores that cover the post-glacial period. Sedimentary ancient DNA samples from Lake Lielais Svētiņu, eastern Latvia, at a core depth of 1,050 cm in ~150 year intervals were used to determine phylotaxonomy in domain Eukaryota. Phylotaxonomic affiliation of >1,200 eukaryotic phylotypes revealed high richness in all major eukaryotic groups-Alveolata, Stramenopiles, Cercozoa, Chlorophyta, Charophyta, Nucletmycea, and Holozoa. The share of organisms that originate from terrestrial ecosystems was about one third, of which the most abundant molecular operational taxonomic units were Fungi and tracheal/vascular plants, which demonstrates the usefulness of using lake sediments to reconstruct the terrestrial paleoecosystems that surround them. Phylotypes that originate from the lake ecosystem belonged to various planktonic organisms; phyto-, proto,- and macrozooplankton, and vascular aquatic plants. We observed greater richness of several planktonic organisms that can be associated with higher trophic status during the warm climate period between 4,000 and 8,000 years ago and an increase in eukaryotic richness possibly associated with moderate human impact over the last 2,000 years.

Keywords: 18S rRNA gene amplicon sequencing; paleoenvironment; paleome species richness.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA, Ancient / analysis*
  • Geologic Sediments / microbiology*
  • RNA, Ribosomal, 18S / analysis
  • Sequence Analysis, DNA
  • Vertebrates


  • DNA, Ancient
  • RNA, Ribosomal, 18S

Associated data

  • GENBANK/ERS1444172
  • GENBANK/ERS1444423
  • GENBANK/X68484
  • GENBANK/BR000309
  • GENBANK/DQ768723
  • GENBANK/U42447
  • GENBANK/DQ079914
  • GENBANK/HO794266
  • GENBANK/EF526333
  • GENBANK/AF051798