Science Advances

Supplementary Materials

This PDF file includes:

  • fig. S1. Possible tree topologies for baleen whales that were evaluated by the AU test.
  • fig. S2. Phylogenetic content of GFs.
  • fig. S3. AU test for increasing GF sizes.
  • fig. S4. MSC-based species trees generated by ASTRAL using 34,192 GFs, with each GF being 20 kbp long.
  • fig. S5. Phylogenetic tree from mitochondrial genomes for baleen whales.
  • fig. S6. A majority-rule consensus tree from 34,192 individual GF ML trees (table S6) calculated with the program CONSENSE of the PHYLIP package.
  • fig. S7. Consensus networks for baleen whales from 34,192 gene trees (10-kbp GF) at different minimum thresholds of gene trees to form an edge.
  • fig. S8. ML estimates of genome-wide heterozygosity estimated with mlRho.
  • fig. S9. Blue whale heterozygosity for different sequencing depth.
  • fig. S10. Demographic histories for each individual whale genome with 100 bootstrap replicates.
  • table S1. Sequencing and mapping statistics.
  • table S2. Occurrences of repetitive elements in the bowhead whale genome.
  • table S3. Number of called substitutions for each whale genome.
  • table S4. Library and sequencing information for the hippopotamus genome assembly.
  • table S5. Summary of repetitive elements in the hippopotamus genome.
  • table S6. A majority-rule consensus analysis of 34,192 individual GF ML trees.
  • table S7. Common names, scientific names, accession numbers, and source database of additional genomes that were included in the divergence time analyses.
  • table S8. Calibration points used for the divergence time tree, node age estimates in million years ago, and references.
  • table S9. Divergence time estimates for Artiodactyla and Cetacea for nodes in the divergence time tree (Fig. 5).

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Other Supplementary Material for this manuscript includes the following:

  • data S1 (Microsoft Excel format). D statistics results.
  • data S2 (Microsoft Excel format). DFOIL results.

Files in this Data Supplement: