Leveraging Nanopore Sampling for Identification of Admixture in Wild Mammal Populations

Hey, Alexander

Publication

Leveraging Nanopore Sampling for Identification of Admixture in Wild Mammal Populations

Hey, Alexander

Abstract

Hybrid zones serve as natural laboratories for studying evolutionary processes. Yet the detection and characterization of hybrid zones in nature remains challenging, especially in cases where parental populations or species are not morphologically distinct. Historically, molecular identification of hybrids, from sample collection to genetic diagnosis, has taken months and requires high upfront sequencer costs, complicating global biodiversity research and delaying management action. Here, we test the efficacy of a portable, third-generation sequencing technology for the detection of interspecific gene flow in a woodrat (Neotoma) hybrid zone. We use Nanopore Adaptive Sampling to generate complete mitochondrial genomes and enrich 999 40-kb nuclear targets constructed around exons selected randomly from across the nuclear genome. We consistently found evidence of mito-nuclear discordance and nuclear admixture. Our results document a three-species contact zone between N. floridana, N. micropus, and N. leucodon in southwestern Kansas, and record the first genetic record of N. leucodon in the state. A signal of admixture was also evident when Nanopore reads were treated as low coverage, whole-genome data. We highlight the potential and pitfalls of Nanopore Adaptive Sampling methods, especially in remote or lesser resourced areas. With improvements to adaptive sampling, we see potential for Nanopore sequencing technologies to dynamically adjust field sampling approaches in response to local ancestry patterns.