plosone-phylo
pone.0004933.g002.png
Phylogenetic tree using the actual or predicted DNA sequences of spliced interferon lambda genes or pseudogenes in human, mouse, dog and guinea pig.
Human and mouse gene loci are labeled as in Lasfar et. al. [18]. The labels for dog and guinea pig are not intended to be suggestions for permanent names. The “dog1” gene is the single exon gene from dog on chromosome 24, while “dog2” and “dog3” are multi exon genes located near each other on chromosome 1 (see Supplementary Figure S1 for gene sequences). The sequence for the more distant mouse pseudogene, named interferon lambda 4 in Lasfar et. al., was excluded because we were unable to find the locus. The optimal tree is drawn to scale, with bootstrap values shown at branch points and branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree (sum of branch length = 1.0194). All positions containing gaps and missing data were eliminated from the dataset, and the full codons were used. There were a total of 314 nucleotide positions in the final dataset, compared to the longest sequence of 622 nucleotides (the pseudogenes shortened the total number of columns which were available for alignment).
pone.0004933.g002.png
Phylogenetic tree using the actual or predicted DNA sequences of spliced interferon lambda genes or pseudogenes in human, mouse, dog and guinea pig.
Human and mouse gene loci are labeled as in Lasfar et. al. [18]. The labels for dog and guinea pig are not intended to be suggestions for permanent names. The “dog1” gene is the single exon gene from dog on chromosome 24, while “dog2” and “dog3” are multi exon genes located near each other on chromosome 1 (see Supplementary Figure S1 for gene sequences). The sequence for the more distant mouse pseudogene, named interferon lambda 4 in Lasfar et. al., was excluded because we were unable to find the locus. The optimal tree is drawn to scale, with bootstrap values shown at branch points and branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree (sum of branch length = 1.0194). All positions containing gaps and missing data were eliminated from the dataset, and the full codons were used. There were a total of 314 nucleotide positions in the final dataset, compared to the longest sequence of 622 nucleotides (the pseudogenes shortened the total number of columns which were available for alignment).