The clouded apollo (Parnassius mnemosyne) has a wide distribution that spans from central Asia to western Europe, but the species shows declining numbers and increasing fragmentation in many countries (Bolotov et al., 2013; Eliasson et al., 2005; Gratton et al., 2008). In Fennoscandia, the clouded apollo can currently be found in Finland, Sweden and Norway, but it has been extinct in Denmark since the early 1960:s (Eliasson et al., 2005). Within Sweden, the distribution range was previously more or less continuous from the far southern region, along the east coast, up to central Sweden (Artdatabanken, 2020, 2021) and it was classified into two different subspecies (P. m. argiope in southernmost Sweden and P. m. romani in the north of the southernmost provinces) based on differences in size and pigmentation (Eliasson et al., 2005; Liljeblad, 2021). Over the last decades, the distribution range has decreased and currently the clouded apollo is limited to three comparatively small and geographically isolated regions; Blekinge, Roslagen and Västernorrland (Fig. 1) (Artdatabanken, 2020, 2021). Besides retreating from large parts of the historical distribution, population sizes have also decreased dramatically - the clouded apollo is currently red-listed (classified as an endangered species) and since 2008 it has been subject to a national action plan initiated by the Swedish Environmental Protection Agency (SEPA, Naturvårdsverket) (Artdatabanken, 2020; Franzén & Imby, 2008). Recurrent efforts to estimate the census sizes within each geographic region have been conducted. In 1994–1995, clouded apollos were observed in 43 different localities within the three distribution areas and the numbers of individuals were estimated to be approximately 1,500 in Roslagen and Västernorrland, respectively, and 150–200 in Blekinge (Artdatabanken, 2021). Since, both the number of inhabited localities within the different geographic areas and the number of individuals has decreased further (Artdatabanken, 2021; Eliasson, 2021; Holst et al., 2021). The current status is that the situation for the species is critical in Blekinge in 2020, for example – while the situation seems to be more stable in Västernorrland (Artdatabanken, 2021; Holst et al., 2021).
The most likely reason for the dramatic decline of the clouded apollo across the distribution range is continuous loss of suitable breeding habitat (Holst et al., 2021). The species prefers sheltered landscapes with a mosaic of moderately grazed pastures or mowed meadows, deciduous forest edges and shrubs and access to larval host plants (Corydalis sp.) and a rich flora of flowering plants for nectar feeding imagines (Franzén & Imby, 2008). As a consequence of the transition from small-scale agricultural practices to centralized land management, such habitats have been lost at a high rate due to locally heavier grazing pressure and overgrowth of small meadows that are no longer used as temporary pastures or for mowing/haymaking (Johansson et al., 2017). Efforts to restore preferred habitats in Roslagen and Blekinge have resulted in temporary breaks in the negative population trends, but it is likely that more regular and large-scale restoration initiatives will be needed to prevent further population fragmentation (Holst et al., 2021) and loss of genetic diversity as a consequence of genetic drift and inbreeding (e.g. Frankham et al., 2012; Sherpa et al., 2021).
Genetic tools to characterize and quantify potential population differentiation and levels of genetic diversity in the clouded apollo have previously been limited to a few microsatellites (Meglecz & Solignac, 1998) and mitochondrial gene sequences (Gratton et al., 2008). Here, we use tissue samples from clouded apollos collected in the three geographically distinct Swedish natural populations and samples from a captive population at Nordens Ark and apply whole genome re-sequencing to generate polymorphism data. The data are used to quantify the levels of intra-population genetic diversity, levels of inter-population genetic differentiation and assess relatedness coefficients to characterize inbreeding in each population. Our results reveal comparatively low genetic diversity in all populations and significant genetic differentiation both between isolated populations and between subpopulations within Roslagen. We also find evidence for postglacial colonization of clouded apollo in Scandinavia from two directions.