New evidence contradicts the rapid spread of invasive genes into a threatened native species

When introduced species hybridize with native relatives, spread of advantageous invasive genes into native populations (introgression) is a conservation concern. Genome-scale SNP (single nucleotide polymorphism) analysis can be a powerful approach to detect hybridization and identify candidate loci experiencing selection in hybrid zones. However, followup studies are critical to verify and interpret potentially impactful patterns of introgression. In an earlier publication we identified three outlier loci (out of 68 unlinked SNPs) where non-native alleles appeared to have introgressed 90 km into the range of a threatened native salamander, while the other 65 markers showed no evidence of spread further than 12 km. This was consistent with strong selection favoring a few invasive traits, but our inferences necessarily depended on limited reference samples of the native species. Here, we further tested our initial interpretation by interrogating the outlier markers in greater detail. First, we isolated DNA from two museum specimens of native salamanders collected several decades before the introduction. Both had the putatively invasive SNPs, indicating that the SNP alleles were present before the introduction and therefore not diagnostic for nonnative ancestry. Second, we developed a novel genealogical analysis of DNA sequences (rather than SNPs) to infer allelic ancestry, since genealogical analysis of haplotypes minimizes the ancestry assignment errors that can occur with SNPs. When applied to the original loci, this analysis confirmed that the genotypes formerly interpreted as ‘superinvasive’ are native variants, and non-native alleles remain limited to areas near the original introduction sites.