Into the Blue: Exploring genetic mechanisms behind the evolution of baleen whales

Table S1. PAML results per species – Results for the branch-site tests for all the 10,159 cetartiodactyla orthologous genes on seventeen species separated per group; genes tested for each group (Mysticeti, Odontoceti and Land) are shown on a different sheet. Columns signify the following: the likelihood ratio test (LRT) used to compare different evolutionary models, specifically, LRT0 compares M2a vs M0, LRT1 compares M2a vs M2a1, and LRT2 compares M2a vs M2a_rel; w0 (ω Zero), representing the ratio of non-synonymous to synonymous substitutions (dN/dS) under the null model where the value for the lineage is constrained to be zero; wF (ω Foreground), indicating the dN/dS ratio for the foreground branch (the lineage of interest) where positive selection is hypothesized and the value can be greater than 1; wB (ω Background), showing the dN/dS ratio for the background branches (all other lineages in the phylogeny) with values ranging between 0 and 1; and Sig (Significance), which indicates whether the test result is statistically significant based on the LRT value and the models being tested, with significance determined by comparing the LRT value to a critical value specific to each model. When the three LRT values are significant then the gene is considered a candidate gene.

Table S2. List of genes where positive selection is estimated to have occurred using the PAML analysis for each species of balaenopterids and eschrichtid. All positive selection events have their corresponding Gene Ontology (GO) and Kegg Orthology (KO) terms retrieved from different sources using the BUSCO2GKO.pm in-house script available at https://github.com/Yuma248/MELFUnction/.

Table S3. PAML results bifurcation of branches in mysticetes – Results for the branch-site tests for the sequences present in the branches of nine species using three models in PAML (M0, M2a and M2a1); candidate genes of each splitting branch within the mysticeti and the outgroup (P. macrocephalus) are shown on a different sheet. Columns signify the following: the likelihood ratio test (LRT) used to compare different evolutionary models, specifically, LRT0 compares M2a vs M0, LRT1 compares M2a vs M2a1, and LRT2 compares M2a vs M2a_rel; w0 (ω Zero), representing the ratio of non-synonymous to synonymous substitutions (dN/dS) under the null model where the value for the lineage is constrained to be zero; wF (ω Foreground), indicating the dN/dS ratio for the foreground branch (the lineage of interest) where positive selection is hypothesized and the value can be greater than 1; wB (ω Background), showing the dN/dS ratio for the background branches (all other lineages in the phylogeny) with values ranging between 0 and 1; and Sig (Significance), which indicates whether the test result is statistically significant based on the LRT value and the models being tested, with significance determined by comparing the LRT value to a critical value specific to each model. When the three LRT values are significant then the gene is considered a candidate gene.

Table S4. List of genes where positive selection is estimated to have occurred using the PAML analysis for each bifurcation of the tree within mysticetes. Sheet1 has a figure with the tree and the corresponding numbers for each bifurcation of the other sheets. All positive selection events have their corresponding Gene Ontology (GO) and Kegg Orthology (KO) terms retrieved from different sources using the BUSCO2GKO.pm in-house script available at https://github.com/Yuma248/MELFUnction/.

Table S5. List of all genes previously reported in the literature taxa within the mysticeti species and ancestral branch of mysticeti (Cao et al., 2021; Ding et al., 2022; Keane et al., 2015; Kishida & Thewissen, 2012; McGowen et al., 2020; Nam et al., 2017; Seim et al., 2014; Sun et al., 2019; Tollis et al., 2019; Tsagkogeorga et al., 2015; Wang et al., 2015; Xu et al., 2012; Yim et al., 2014; Zhou et al., 2018) compared to all the balaenopterids and eschrichtid positive selected unique genes found in the analyses of this paper.

Table S6. List of enrichment analysis mainly focus on Mammalian Phenotype Terms with their corresponding number of genes matched per term and p-values using a Bonferroni correction (p-value<0.05) for each species and each bifurcation shown on different sheets. Highlighted in green are the duplicated terms along the species or bifurcations.