Differences between clades and estimated recombination breakpoints. (a) Fixed differences between clades A and B. The region shown is from bp 415 to bp 771, with exons represented as gray bars and introns as horizontal black lines. Vertical dashes represent fixed differences between the A and B clades. Triangles above exon positions 224 and 363 mark the two amino acid substitutions. "+" symbols indicate three polymorphisms that would be fixed differences except for one allele in NCZ26. (b) Recombination breakpoints for sequences NCE19, NYZ25, NYE32. These inferred recombinant alleles share similarity to both clades A and B for different parts of the Δ11 desaturase gene region. Light bars indicate identity to clade A, and dark bars indicate identity to clade B. Recombination breakpoints are estimated from the fixed differences between clades A and B and are displayed as the midpoint between two fixed differences for which the recombinant's haplotype changes from one clade to the other. Most stretches of similarity are supported by multiple fixed differences (compare to (a) to see how many sites (vertical dashes) support that stretch of similarity). Two inferred recombination events are supported by only one nucleotide change and may represent point mutations.