Figure 4

Diversity of the 185/333 gene elements. Nucleotide diversity scores (black bars) and amino acid diversity scores (gray bars) of individual exon elements are shown. The average element nucleotide diversity is indicated by a dashed black line and average element amino acid diversity is shown as a dashed gray line. The absolute range of diversity scores is 0 (entirely conserved) to 1.609 for nucleotide alignments (based on an even distribution of five states: four nucleotides and a gap) or 3.044 for amino acid alignments (21 possible states) [30]. The highest element diversity score previously observed was from element 11 (0.5381) from a set of cDNAs isolated from bacterially-challenged coelomocytes pooled from five animals [30]. This score was similar to that obtained from a modeled element in which 40% of the positions contained four different states in 20% of the sequences. Elements with a diversity score of 0 were omitted (Ex11, Ex15a, Ex15c, and Ex15f-g of the cDNA-based alignment (A) and Er7, Er10a, Er10c, Er10f-g, Er12 -13, Er18, and Er20 of the repeat-based alignment (B). The number (#), length in nucleotides (L) and nucleotide to amino acid diversity ratio (R) are indicated in the table to the left of the graphs. Ex25 includes both Ex25a and Ex25b. Ex25a includes all sequences from the start of Ex25 up to and including the first stop codon. Ex25b includes only the sequence following the first stop codon to the second stop codon (Additional file 2 and Additional file 3). Element Er27 in the repeat-based alignment (B) is treated similarly.