High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal

Host-specialist parasites of endangered large vertebrates are in many
cases more endangered than their hosts. In particular, low host population
densities and reduced among-host transmission rates are expected to lead
to inbreeding within parasite infrapopulations living on single host
individuals. Furthermore, spatial population structures of
directly-transmitted parasites should be concordant with those of their
hosts. Using population genomic approaches, we investigated inbreeding and
population structure in a host-specialist seal louse (Echinophthirius
horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis),
which is endemic to Lake Saimaa in Finland and is one of the most
endangered pinnipeds in the world. We conducted genome resequencing of
pairs of lice collected from 18 individual Saimaa ringed seals throughout
the Lake Saimaa complex. Our analyses showed high genetic similarity and
inbreeding between lice inhabiting the same individual seal host,
indicating low among-host transmission rates. Across the lake, genetic
differentiation among individual lice was correlated with their geographic
distance, and assignment analyses revealed a marked break in the genetic
variation of the lice in the middle of the lake, indicating substantial
population structure. These findings indicate that movements of Saimaa
ringed seals across the main breeding areas of the fragmented Lake Saimaa
complex may in fact be more restricted than suggested by previous
population-genetic analyses of the seals themselves.