![]() In general, both stochastic (e.g., dispersal, or ecological drift) and deterministic (e.g., host immunological regulation, or microbe–microbe interactions) processes operate across multiple spatial scales to shape the composition of animal microbiomes ( Adair and Douglas, 2017 Kohl, 2020). For instance, particular microbiome compositions have been found to drive genomic adaptation ( Rudman et al., 2019) or to confer protection against pathogens ( Velazquez et al., 2019). Patterns of inter- and intraspecific variation in microbiome composition of animals have received much attention because the microbiome may influence many biological processes that have considerable effects on the host ( Clemente et al., 2012 Le Chatelier et al., 2013 Rothschild et al., 2018 Rudman et al., 2019 Velazquez et al., 2019). 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. ![]() Both genome-resolved and read-based 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. 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. 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). 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). 5Natural Resources Institute Finland, Joensuu, Finland.4Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.3Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway.2Departamento de Biología Animal, Universidad de Granada, Granada, Spain.1Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States.Jorge Doña 1,2* Stephany Virrueta Herrera 1 Tommi Nyman 3 Mervi Kunnasranta 4,5 Kevin P.
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