Hybridization of distinct populations or species is an important evolutionary driving force. For invasive species, hybridization can enhance their competitive advantage in the non-native range as a source of adaptive novelty by introgression of selectively favoured alleles. We use single-nucleotide polymorphism arrays (SNP-chips) to assess genetic diversity and population structure in the invasive ctenophore Mnemiopsis leidyi in native habitats along the USA east coast. Hybrids are present at the distribution border of the two lineages. However, our data suggests selection against hybrids in stable habitats, while hybrids are selected for in fluctuating environments. Hybrid populations thriving in extreme and unstable environments of the native range, such as the Chesapeake Bay, could accelerate the invasion success if translocated. For M. leidyi, this is especially relevant as low salinity currently limits its invasion range in western Eurasia. Hybridization status is thus important but currently disregarded to determine high-risk areas for ballast water exchange.

All individuals were genotyped at a total of 96 single nucleotide polymorphisms (SNPs) using a high throughput low-density SNP-chip array developed from whole-genome re-sequencing data (Pujolar et al. 2022). SNP genotyping was performed using Fluidigm 96.96 Dynamic Arrays (Fluidigm Corporation, San Francisco, CA, USA). The Fluidigm system uses nano-fluidic circuitry to allow for the simultaneous genotyping of up to 96 samples with 96 loci (described in Seeb et al. 2009). Genotypes were called and compiled using the Fluidigm SNP Genotyping Analysis software.