Local population genetic structure of Andrena flavipes (Hymenoptera, Andrenidae), a nest-philopatric communal mining bee, reveals isolation-by-distance and high inbreeding

Wild bee populations are declining globally and understanding how species-intrinsic traits like nest-philopatry shape local population genetic structure is increasingly important for their conservation. However, few studies have explored this at local spatial scales. To fill this gap, we used SNPs in the nuclear vitellogenin (Vg) gene to assess the local population structure and genetic diversity of the philopatric yellow-legged mining bee, Andrena flavipes, in the Netherlands, one of the most fragmented and urbanized countries in Europe. We investigated whether its reported nest-philopatry, combined with a fragmented landscape, would lead to genetic differentiation and isolation-by-distance (IBD) between populations, and low genetic diversity and inbreeding within populations. A total of 144 A. flavipes bees were sequenced for the full-length Vg gene and genotyped for SNPs. Despite high overall genetic variation, we found a heterozygote deficit and positive inbreeding coefficient in most populations, suggesting non-random mating. Low genetic differentiation was detected between populations, with no distinct genetic clusters, but with a pattern of IBD. These results suggest extensive but spatially structured gene flow, consistent with philopatric behaviour, and indicate that increasing isolation between nest-aggregations potentially leads to genetic differentiation over time. Our findings demonstrate that even in a common and widespread species, nest-philopatry and landscape fragmentation can drive inbreeding and spatially structured gene flow at local scales, highlighting the importance of maintaining habitat connectivity and semi-natural elements in agricultural and urbanized landscapes to sustain wild bee populations.