Fig. 3

Metagenome-based population genomics [103]. Metagenome-assembled genomes (MAGs), Single Amplified Genomes (SAGs; Fig. 2), or genomes from isolates are generated after sampling or retrieved from collections. In parallel, marine metagenomes (MetaG) are produced from community DNA or retrieved from databases. Subsequently, unassembled metagenomes (reads) are mapped against MAGs, SAGs, or sequenced isolates. After mapping, the abundance and the horizontal and vertical coverages of each MAG, SAG, or isolate are calculated, and Single Nucleotide Variants (SNVs) are called. Based on the SNVs, population-level diversity, and structure (based on the Fst index) can be assessed. The trajectory of the TARA Oceans sampling campaign is shown as an example. See an application of this approach in Fig. 4