Fig. 1: Whole-genome sequencing of 11 wild-caught individuals of the bdelloid rotifer A. vaga.

a Microphotograph of an A. vaga individual. Scale bar is approximately 100 μm, based on the characteristic size of A. vaga mastax⁵¹. The photograph was taken for the illustrative purposes. From each of the 11 wild-caught rotifers matching the morphological description of A. vaga, a clonal lineage has been established and sequenced on the Illumina HiSeq to the coverage of ~40–100×. Rotifers were collected in one of the two locations: the Moscow region of Russia or the Kostroma region of Russia, 550 km to NE. All sequenced clonal lineages collected in the same location were started from individuals sampled from separate trees at least 20 m apart. b Tetraploidy in the A. vaga L1 reference genome. The plot shows the mean number of synonymous substitutions between collinear genes per site (Ks) versus the fraction of collinear genes for each syntenic block. Only blocks with 5 or more collinear genes are shown (n = 1769). Blocks with average Ks values <0.4 are in blue; those with average Ks ≥ 0.4 in red (see Supplementary Methods). c Genetic differentiation among the 11 sequenced individuals L1-L11. The first two dimensions from multidimensional scaling (MDS) analysis of pairwise identity-by-state distances are shown. Individuals of the small cluster (L1-L3) and of the large cluster (L4-L11) are shown in blue and green respectively (see Supplementary Methods). Clustering does not reflect geography of sampling: the small cluster is comprised of three individuals (L1-L3) collected in the Moscow region of Russia, while the large cluster contains the rest of individuals collected in the Moscow region (L4, L6-L10), as well as two individuals (L5 and L11) collected in the Kostroma region. See also Supplementary Fig. 8 for a SNP-based neighbor-joining tree of L1-L11.