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.

古基因组学极大地增加了我们对过去进化和生态变化的了解，但仅限于研究以化石形式保存或保存在化石内的物种。在这里，我们展示了霰弹枪宏基因组学的潜力，它揭示了一种没有保存在身体化石记录中的分类群，即藻类Nannochloropsis 的种群基因组信息。我们对可追溯到末次盛冰期的两个湖泊沉积物样本进行了霰弹枪测序，并重建了完整的叶绿体和线粒体基因组，以探索湖内种群基因组变异。这揭示了每个细胞器基因组的两个主要单倍群，它们可以分配给已知的N. limnetica品种，尽管我们使用我们的最小单倍型多样性估计方法表明至少存在三种单倍型。这些方法证明了湖泊沉积古 DNA ( sed aDNA) 在种群基因组分析中的实用性，从而为环境古基因组学打开了大门，这将释放sed aDNA的全部潜力。