Large-scale variation in SNP density within the laboratory axolotl (Ambystoma mexicanum)

To better resolve the distribution and origins of genetic variation with A. mexicanum, we compared DNA sequence data for two laboratory A. mexicanum and one A. tigrinum to identify 710 million high confidence polymorphisms distributed across the 32 Gb genome. While the wild-caught A. tigrinum was generally more polymorphic in a genome-wide sense, several multi-megabase regions were identified from A. mexicanum genomes that were actually more polymorphic than A. tigrinum. Analysis of polymorphism and repeat content reveals that these regions likely originated from the intentional hybridization of A. mexicanum and A. tigrinum that was used to introduce the albino mutation into laboratory stocks.