Abstract
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.
Highlights
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils
While techniques such as DNA metabarcoding allow for the inventorying of groups of organisms[29,30], either deep shotgun sequencing or target enrichment of sedimentary ancient DNA (sedaDNA) is required for palaeogenomic reconstruction, which would allow for robust species-level identification[12,14,24] and the potential exploration of population genomic variation
All of our analyses identified Nannochloropsis as the best represented identifiable eukaryotic taxon in the Last Glacial Maximum (LGM) lake sediments from Andøya, which is consistent with a previous plant DNA metabarcoding study of the same site[41]
Summary
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore withinlake population genomic variation This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. Lake sedaDNA is used to infer the taxonomic composition of past communities[27,28], regardless of whether those taxa preserve in the body fossil record While techniques such as DNA metabarcoding allow for the inventorying of groups of organisms[29,30], either deep shotgun sequencing or target enrichment of sedaDNA is required for palaeogenomic reconstruction, which would allow for robust species-level identification[12,14,24] and the potential exploration of population genomic variation. Nannochloropsis has not been reported from macrofossil and pollen/spore profiles, and may only be identifiable using sedaDNA10,41,50
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