Comparative Genomic Analysis of Co‐Occurring Hybrid Zones of House Mouse Parasites <i>Pneumocystis murina</i> and <i>Syphacia obvelata</i> Using Genome Polarisation

Parasites are expected to hybridise in similar ways to free-living organisms, although this may be modified by their reduced genome architecture. Recombinant strains and taxa of hybrid origin can be studied in nature where hosts come into secondary contact. Here we apply genome-wide analysis to parasites from a contact previously characterised for many individuals using classical markers. The host contact is the European house mouse hybrid zone; the parasites are lung fungus Pneumocystis and gut pinworm Syphacia. The genomic (many loci) and classical (many-individual) results are broadly consistent in scale and centring of transitions across the host hybrid zone. Whole mitogenome comparisons confirm earlier suggestions that parasite divergence is low compared to their hosts, perhaps due to reduced-genome stabilising selection. In the recombining genome, we are able to show blocks of the parasite genome of alternating host origin, including one Pneumocystis strain which appears to be an F3+ cross and one recombinant Syphacia strain found over multiple localities. Functional analyses of introgressing genes show enrichment for genes likely important for parasitic lifestyle. Our work confirms that evolutionary models of hybridisation apply equally to hosts and their parasites.