Mink by mink: stitching together signatures of subspecies adaptation through a pangenome of threatened mustelids

Abstract

The American mink (Neogale vison), a semi-aquatic Mustelidae carnivoran with broad ecological range across North America, includes several putative subspecies of conservation concern. To investigate the evolutionary history and adaptive signatures of mink subspecies, chromosome-scale genome assemblies were generated for six individuals representing three southern subspecies: N. vison evergladensis, N. vison vulgivaga, and N. vison lutensis. Genomes were assembled using Illumina short reads, scaffolded with Oxford Nanopore long reads, and aligned to the phased N. vison reference genome. Assemblies ranged from 75.9% to 97.8% completeness, with five meeting thresholds for pangenome construction. A reference-free pangenome revealed an open architecture, highlighting considerable subspecies diversity. Subspecies-specific gene enrichment reflected adaptation: N. vison evergladensis showed enrichment in traits related to reproduction and sensory function; N. vison vulgivaga in cytoskeletal remodeling and oxidative stress; and N. vison lutensis in neuronal development, synaptic plasticity and cellular stress pathways. Assessment of the mitogenomes resolved N. vison lutensis as a distinct lineage, while nuclear data supported broader subspecies divergence but lacked fine scale resolution. N. vison evergladensis showed multiple signatures of small population size, including inbreeding coefficients (FROH) above 0.5, and displayed consistent population decline over time via demographic inference. Our findings support evergladensis as a distinct subspecies, supported by both the mitogenome phylogeny, and significant functional differentiation. As the first pangenome for Mustelidae, this study demonstrates the power of integrating cross-platform sequencing with natural history specimens to improve the resolution on signatures of adaptation and inform conservation policy and management of threatened populations.