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. 2021 Dec 13;39(1):msab354. doi: 10.1093/molbev/msab354

Fig. 3.

Fig. 3.

Alignments of positively selected sites. Amino acid sequence alignments of positively selected sites in all TLRs (excluding gene-converted regions of the TLR1/2 family). Sequence logo is colored according to the RasMol coloring convention, where amino acids of similar properties are grouped. Amino acids in the alignments are colored according to physicochemical conservation. Pseudogenes were excluded from the analysis, and are indicated by yellow boxes. Gray boxes in alignments indicate missing data. Site position (relative to the Afo coding sequence) is given below the alignment, and is colored according to whether the selected site is proximal to a site of known function (orange: the site is within 5 Å of a site of known function; red: the site has a known function; gray: distance from sites of known function could not be measured). For each site, “other tools” indicates whether a site was also found to be under positive selection by using the alternative methods of MEME and FUBAR, implemented in Datamonkey. Additionally, an indication is given under the alignment (“prior evidence for selection”) as to whether the site has previously been described as being positively selected in birds and/or mammals, or whether the site is a novel selected site in penguins (see supplementary table S2, Supplementary Material online for details). Sequence alignments and images were generated in the msa (v. 1.18.0) package in R (Bodenhofer et al. 2015) which implements the MUSCLE algorithm (Edgar 2004). Abbreviations: Afo, Aptenodytes forsteri (Emperor penguin); Apa, Aptenodytes patagonicus (King penguin); Pad, Pygoscelis adeliae (Adélie penguin); Pan, Pygoscelis antarcticus (Chinstrap penguin); Ppa, Pygoscelis papua (Gentoo penguin); Sma, Spheniscus magellanicus (Magellanic penguin); Shu, Spheniscus humboldti (Humboldt penguin); Sme, Spheniscus mendiculus (Galapagos penguin); Sde, Spheniscus demersus (African penguin); Eno, Eudyptula novaehollandiae (Fairy penguin); Emial, Eudyptula minor albosignata (White-flippered penguin); Emimi, Eudyptula minor minor (Little penguin); Manan, Megadyptes antipodes antipodes (Yellow-eyed penguin); Echch, Eudyptes chrysolophus chrysolophus (Macaroni penguin); Echsh, Eudyptes chrysolophus schlegeli (Royal penguin); Emo, Eudyptes moseleyi (Northern Rockhopper penguin); Efi, Eudyptes filholi (Eastern Rockhopper penguin); Ech, Eudyptes chrysocome (Southern Rockhopper penguin); Esc, Eudyptes sclateri (Erect-crested penguin); Ero, Eudyptes robustus (Snares Crested penguin); Epa Eudyptes pachyrhynchus (Fiordland penguin).