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EDF 4. PHYLOGENY Phylogenetic tree of pan-vertebrate conserved non-coding elements (pvCNEs), rooted by elephant shark. Alignments were done by MUSCLE, and the maximum-likelihood tree was built by PhyML. Branch length scale shown on bottom. The difference in branch lengths of tetrapods follows the same topology as the protein-coding tree (Fig. 2b).Complete phylogenetic tree from Fig. 2a, with divergence times computed by r8s.Distribution of Ks and Ka on specific subgenomes during the time between L and S speciation, before X. laevis and X. borealis speciation. We find accelerated mutations rates between T2 and T3 in Ks and Ka (p=1.4e-5 (left), 8.6e-3 (right)).Distribution of Ks and Ka on specific subgenomes during the time after laevis and borealis speciation. We do not find significantly accelerated substitution rates. (p= 0.10 (left) and 0.03 (right)).Table showing the number of homeologs and singletons identified as homeologs from the ancient vertebrate duplication (or ohnologs as they are historically called)63. 79.9% of ohnologs retain both copies in X. laevis today, significantly more than the 54.3% of the rest of the genome after excluding ohnologs (χ2 test p-value= 4.44E-69).Table showing the branch lengths of bootstrapped maximum likelihood trees described in Supplemental Note 12.5. The columns refer to the X. tropicalis (XTR), L chromosome of X. laevis (XLA.L), S chromosome of X. laevis (XLA.S), and XLA.L/XLA.S branch lengths respectively. The first row is triplets where all genes show expression, the second row is triplets where L is a thanagene, and the third row is triplets where S is a thanagene. The L branch length is significantly smaller when all genes are expressed, or when S is a thanagene (Wilcoxon p-value=1.7E-216 and 6.4E-212 respectively). The S branch length is smaller when L is a thanagene (p=2.4E-223). The ratio of branch lengths (L/S) is significantly different for either L or S thanagene datasets compared to when all genes are expressed (p=3.55E-214 and 7.48E-220 respectively). The ratio is different between the two thanagene datasets as well (p=1.79E-217).

Image published in: Session AM et al. (2016)

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