Patterns of microbiome variation among infrapopulations of permanent bloodsucking parasites

Abstract

While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved metagenomic and metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.

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

“…Indeed, our phylogenomic trees, between‐individual kinship coefficients, and estimates of among‐infrapopulation F ST 's consistently showed that lice collected from the same Saimaa ringed seal individual are on average genetically more similar than are individuals collected at random from the host population. Notably, the population‐genetic differentiation found across lice collected from different seal individuals is not the only aspect that is affected by the fact that seal lice are distributed into distinct infrapopulations: Using the same specimens that were analysed in this study, Doña et al (2021) found that infrapopulation identity explained a major proportion of the variation in microbiome composition within individual lice.…”