Additional file 1 of Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)

Additional file 1: Fig. S1. Synteny of aligned P. strophiata genome with zebra finch genome and these two genomes showed high collinearity. Fig. S2. Polytomy test for the MP-EST and ASTRAL species trees as the guide trees. Fig. S3. Tree topology weights vary with recombination rate (estimated from PyRho). Fig. S4. Interplay between topology and variation in introgression rate. Fig. S5. Hi-C heatmap reconstructed for Prunella strophiata genome. Table S1. Statistics of the assembly of Prunella strophiata genome. Table S2. Completeness of the genome assembly of Prunella strophiata evaluated by BUSCO. Table S3. Chromosome synteny of aligned Red-breasted accentor genome with zebra finch genome. Table S4. List of the species were used for phylogenetic analyses. Table S5. Resequencing information and genome wide coverage of 36 individuals used in this study. Table S6. Gene concordance factor (gCF) for the nodes (1–7, Fig. 4a-b) that support the species tree (gCF), the two most common alternative topologies (gDF1 and gDF2), and the relative frequency of all other topologies (gDFp)