Population Genomics of a Cave‐Dwelling Arachnid (Palpigradi, Eukoeneniidae) From the South‐Western Italian Alps

ABSTRACT Palpigradi, an order of miniaturised arachnids, includes over 100 species inhabiting mostly subterranean environments, including caves and deep soil strata. Palpigrades are known to be poor dispersers, making them an ideal model system to study local speciation and to test short‐scale biogeographic patterns. However, genomic data for this group are extremely limited due to their small size, rarity and inaccessibility to their habitats, resulting in reduced detectability. Here we generate the first genomic‐scale data set for palpigrades based on ultraconserved element (UCE) data. Leveraging these data, we examined phylogeographic patterns at a fine geographic scale for two species from caves in NW Italy, while also testing the efficacy of the widely used arachnid UCE probe set for studies at extremely shallow population levels. For these purposes, we analysed a matrix of 808 UCE loci in populations of Eukoenenia bonadonai and E. strinatii (Eukoeneniidae) from five caves located in the south‐western Italian Alps. Our phylogenetic and population genetic analyses using genomic‐scale data demonstrate the existence of strong population genetic structure for both species, supporting the existence of limited gene flow between caves and potential overlooked taxonomic diversity. Despite being designed for an extremely ancient and divergent lineage, the arachnid UCE probe set continues to prove useful at shallow population‐level analyses in yet another arachnid order.