Phylogeny of early (2020–2022) SARS-CoV-2 sequences plotted by number of nucleotide substitutions from the most recent common ancestor on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right). Tips in the tree and embeddings are colored by their Nextstrain clade assignment. Line segments in each embedding reflect phylogenetic relationships with internal node positions calculated from the mean positions of their immediate descendants in each dimension (see Methods). Line thickness in the embeddings scales by the square root of the number of leaves descending from a given node in the phylogeny. Clade labels in the tree and embeddings highlight larger clades.