Figure 2.

Simplified phylogenetic tree of the Tlrs from Nototheniidae and other vertebrates. The phylogenetic tree was constructed using the BI method and the full tree is available as Supplementary Figure 3 . Branches corresponding to the six vertebrate TLR superfamilies are identified: S1 indicates the TLR1 superfamily (orange); S3 identifies the TLR3 superfamily (red); S4 identifies the TLR4 superfamily (pink); S5 identifies the TLR5 superfamily; S7 identifies the TLR7 superfamily (blue); and S11 identifies the TLR11 superfamily (green). Some branches of the phylogenetic tree are collapsed to facilitate visualization and three subsections of the same phylogenetic tree are shown: (A) the TLR1 superfamily, (B) the TLR11 and TLR3 superfamilies, and (C) the TLR5, TLR7, and TLR4 superfamilies. The tetrapod branches were also collapsed. The accession numbers of the sequences used to construct the phylogenetic tree are available in Supplementary Table 1 . The teleost tlr2 duplicates were named, tlr2a and tlr2b, and TLR15 was not included in the phylogenetic tree since it was only found in chicken and lizard. The phylogenetic tree was rooted with the Cnidarian Tlr clade (31). The sea lamprey tlrs within the vertebrate TLR1 and TLR7 superfamilies are named Pma_X and Pma_Y, respectively, since their assignment to the Tlr subfamilies was ambiguous. Only the posterior probability values for the main branches are indicated. A phylogenetic tree generated by the ML method is available as Supplementary Figure 2 . Members from Antarctic species are indicated with squares and with a Notothenia cartoon to facilitate identification. The other member of the Perciform order, G. aculeatus, is indicated by a black dot and the Pleuronectiformes is indicated by a black star.