Accurate identification of hybrids using genome admixture analysis: implications for genomic surveillance.

, the cotton bollworm moth, is one of the world's most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasive has been reported to hybridize with local populations of . The correct identification of hybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitate pesticide resistance and host plant range via introgression of genes. Here, we present a genome admixture analysis of high quality genome sequences generated from two F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8% and 48.9% for the two F1 hybrids, confirming its accuracy. Genome sequences from five and one that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four genomes generated from a previous study are predicted to possess a proportion of genetic material. Using unsupervised clustering to identify non-hybridized and genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis of hybrids, and suggest measures that will improve such analyses.