Intra-Alpine Islands: Population genomic inference reveals isolation between freshwater spring ecosystems

Headwater stream sections and spring ecosystems have long been considered as highly isolated habitats. This pattern, however, was only weakly supported by data obtained from springs in extreme environments, community composition of geographically widely distributed species, or spring-related species that also appear in other habitats. To assess the applicability of this fundamental hypothesis in crenobiology, we investigated gene flow patterns between populations of Partnunia steinmanni Walter, 1906, a crenobiont Hydrachnidia species, and examined the degree of spring habitat interconnection. We investigated populations in major protected areas across the Alps. From east to west, 12 spring populations located in major protected areas were investigated. Spring P. steinmanni populations were sampled by hand-net. Subsequently, population genomic inferences were assessed by sequencing RADseq libraries of 256 individuals, yielding information about 2'263 variant loci. We assessed gene flow patterns between the populations by investigating admixture, the phylogenetic placement of individuals, and calculated statistical significance of isolation by distance as well as population differentiation based on genetic structure. An overall high degree of genetic differentiation between spring populations was observed. Each spring was shown to manifest its specific genetic setting. Low amounts of gene flow and admixture were present mainly within sampling areas, confirmed by phylogenetic placement. Furthermore, a southwestern genotype extended into eastern populations but was absent in adjacent northern populations. The insularity of headwater areas and freshwater springs can be considered substantial, and we assume Pleistocene intra-alpine isolation in combination with limited dispersal abilities of P. steinmanni as primary drivers for this pattern. Our findings reassure the original hypothesis of spring habitat isolation and highlight the importance of alpine protected areas to conserve springs as substantial sources of biodiversity.