Highly-resolved strain-level population dynamics of Wolbachia from large-scale metagenomes

Symbiosis studies typically focus on a given bacterial species associated with a specific host organism, yet little is known about how endosymbionts vary within and between hosts. We address this issue in the bacterial enodysmbiont Wolbachia, the common intracellular manipulator of invertebrate biology. While it has been already studied from a macroevolutionary point of view (i.e. phylogeny and comparative genomics), little is known about its diversity and evolution within its different hosts. Here, we compiled 10 Wolbachia strain datasets from a collection of >1,000 Wolbachia genomes sampled from 10 populations of insect and nematode hosts. These large-scale datasets allowed us to explore, at an unprecedented depth, how an intracellular bacterial parasite evolves in different hosts. We first found that Wolbachia recombination is highly heterogenetic among hosts, both in terms of frequency and fragment sizes, and that it is not responsible for incongruences between Wolbachia and host phylogenies. Nucleotide polymorphism patterns indicate that each strain is characterized by distinct demographic histories and has likely undergone distinct selective pressures in different hosts. Overall, our results suggest that the diversity and the evolutionary history of Wolbachia are driven by a combination of horizontal transmission and adaptation to the host.