Fig. 7. Phylogenetics of L1-L11 haplotypes hints at hybrid origin of the small cluster.

Midpoint-rooted phylogenetic trees constructed for four segments simultaneously phased in all 11 A. vaga individuals (L1-L11) from both genetic clusters and suggestive of the hybrid origin of the individuals of the small cluster. Haplotypes from the individuals of the small cluster are represented by blue boxes. Overall, in 100 out of 152 tested segments, we detected a well-supported monophyletic group formed by three haplotypes, one haplotype from each of the individuals L1, L2, and L3 (as in a–d). Among those 100 segments, in 36 cases midpoint rooting separated a monophyletic clade comprising three haplotypes of L1, L2, and L3 from the rest of the tree (as in c, d). The displayed phylogenies were constructed for four phased segments located on different contigs in the L1 diploid assembly and spanning 1058 (a), 1452 (b), 1782 (c), and 1824 (d) base pairs. Trees were built using the maximum likelihood method in PhyML⁷⁴ under the GTR + G model with 1000 bootstrap replicates. The bootstrap support values ≥50% are shown next to branches or next to brackets. Bootstrap support values are rounded to the nearest integer. Only those SNPs that satisfied all filtering criteria and were simultaneously phased in L1-L11 were used to reconstruct phylogenies (n = 46, 32, 43, and 30 non-singleton SNPs in a–d, respectively); the remaining sites were treated as monomorphic (see “Methods” section). Indices 1 and 2 designate the two haplotypes of a single individual. Source data are provided as a Source Data file.