Supplementary phylogenetic methods and simulation results for Independent evolution of whale gigantism linked with Plio-Pleistocene ocean dynamics

Phylogenetic Inference Morphological character data for living and fossil mysticetes were sourced from Marx and Fordyce’s comprehensive treatment, with the following edits and additions. All undescribed or unidentified fossil taxa (n=13) were removed, as were the 3 odontocete taxa. We retained the archaeocete Zygorhiza kochii. We also replaced the composite taxon Eubalaena spp. with coded characters for the three extant Eubalaena species. These edits resulted in 3 invariant characters (characters 63 65) that were previously used to resolve odontocete relationships, and which were subsequently deleted from the character matrix. The final morphological matrix contained 76 taxa (13 extant, 63 extinct) coded for 269 characters. We downloaded 11 nuclear loci (AMBN exons 6 and 13, ATP7A, BDNF, CSN2, DMP1, ENAM, PRM1, RAG1, SRY, and TBX4 ) and complete mitochondrial genomes, where available, for all 15 extant mysticete species from Genbank (Table S1). Sequences were aligned using MUSCLE through Geneious v. 8.0 and checked by eye. We extracted only protein coding genes from mitochondrial genomes, ensuring that reading frames were maintained and that overlapping regions were assinged to one gene only. We then used PartitionFinder v 1.1.1 to determine the optimal partitioning scheme for the 11 nuclear loci and 3 mitochondrial partitions, corresponding to 1st through 3rd codon positions, under the Bayesian Information Criterion. We simultaneously inferred phylogeny and branch lengths for living and extinct mysticetes using BEAST 2.2.1, accessed through the CIPRES Science Gateway. Five morphological partitions, each corresponding