Genome variation in three Anthophora bee species reflects divergent demographic histories

Population genomics can reveal trends and drivers of biodiversity loss but it is still unclear how best to use measures of genome variation to understand population vulnerability in insects. Here we study genome variation in three species of Anthophora bees, that show contrasting population trends in northern Europe. Two species, Anthophora plagiata and Anthophora retusa, have experienced declines and recoveries of different magnitudes in the last fifty years whereas a third species, Anthophora quadrimaculata, has relative population stability. We generate highly-contiguous genome assemblies and use them to study genome variation in 136 samples of these species collected throughout Sweden. We find exceedingly low genetic variation in A. plagiata, which has experienced a severe recent bottleneck, but high genetic variation in A. retusa, despite a similar recent population trajectory. Fragmented populations of the threatened species A. plagiata appear isolated from each other, but in A. retusa there is a lack of deep population structure among geographically separated subpopulations. We infer population size in the distant past using MSMC2 and recent past using GONE. These methods are remarkably concordant, and indicate ancient fluctuations in population size dating back to the Pleistocene with moderate expansions in the past century in all three species. These results are comparable to some other studies of endangered insects, which have experienced population declines that predate the modern era. We detect long blocks of identity-by-state in A. plagiata, indicative of severe recent inbreeding. Translocations between isolated populations of this species could have a positive effect on their resilience. Supplementary Material File (taliadoros_anthophora_24apr25.docx) - Download - 245.43 KB Information & Authors Information Version history Peer review timeline Published Molecular Ecology Version of Record12 Dec 2025Published Copyright This work is licensed under a Non Exclusive No Reuse License. Collection

Authors Metrics & Citations Metrics Article Usage 793views 332downloads Citations Download citation Demetris Taliadoros, André Elias Rodrigues Soares, Guilherme Dias, et al. Genome variation in three Anthophora bee species reflects divergent demographic histories. Authorea. 25 April 2025. DOI: https://doi.org/10.22541/au.174560061.17013923/v1 DOI: https://doi.org/10.22541/au.174560061.17013923/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu.