ABI 3700 capillary instrument. Sequence trace files were evaluated using the Phred, Phrap and Consed programs, and potential variants were identified by using the PolyPhred program [66],[67]. Single nucleotide polymorphisms (SNPs) were verified by manual evaluation of the individual forward and reverse sequence traces. In addition, all sequence assemblies were manually scanned for insertions, deletions and polymorphic positions undetected by PolyPhred. Tag SNPs were selected using the ldSelect algorithm [68] with an r2 cutoff value of 0.64 on all SNPs with a minor allele frequency >5%.
