Additional file 1: of Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation

Table S1. List of samples with accession numbers and sequencing properties. Figure S1. Simulation results for CHR2 detection with MELT at varying depth of coverage using dataset specific parameters. Figure S2 Frequency of filters applied by MELT to exclude low-quality CHR2 calls. Figure S3 Phylogenetic trees of baleen whales reconstructed with CHR2 insertions. A) Dollo-Parsimony tree reconstructed in PAUP*. Asteriks indicate 100 % bootstrap support (500 replicates), lower bootstrap support is given as numbers. B) Bayesian inference tree with posterior probability given for nodes. Figure S4 Three alternative relationships in the rorqual radiation and the number of CHR2 insertion that support them. Figure S5 Phylogenetic tree of rorquals with frequency of heterozygous insertions per branch. Figure S6 CHR2 insertion rates per generation. Figure S7 Repeat landscapes of minke whale and bowhead whale based on available assemblies. (PDF 475 kb