Continental scale genetic diversity supports geo-clustered ecoregions connectivity

Connectivity is fundamental to ensuring that ecosystems can recover after impact. The genetic information in DNA metabarcoding can provide insight into connectivity at different timescales. We compared structural connectivity, represented by an adjacency matrix of ecoregions, and functional connectivity at different levels of organization, represented by the β-diversity of exact sequence variants and species, between ecoregions, focusing on benthic arthropods. While structural and functional connectivity were correlated, there was a distinct divide between eastern and western ecoregions that approximately aligned with the Rocky Mountains. Within the western ecoregions, species β-diversity was not correlated with ecoregion adjacency and had higher intraspecific genetic differentiation. This implies that gene flow is more restricted in this area. Understanding how gene flow can be limited is important to conservation planning.