Endosymbiosis plays an important role in ecology and evolution, but fundamental aspects of the origin of intracellular symbionts remain unclear. The extreme age of many symbiotic relationships, lack of data on free-living ancestors and uniqueness of each event hinder investigations. Here, we describe multiple strains of the bacterium Polynucleobacter that evolved independently and under similar conditions from closely related, free-living ancestors to become obligate endosymbionts of closely related ciliate hosts. As these genomes reduced in parallel from similar starting states, they provide unique glimpses into the mechanisms underlying genome reduction in symbionts. We found that gene loss is contingently lineage-specific, with no evidence for ordered streamlining. However, some genes in otherwise disrupted pathways are retained, possibly reflecting cryptic genetic network complexity. We also measured substitution rates between many endosymbiotic and free-living pairs for hundreds of genes, which showed that genetic drift, and not mutation pressure, is the main non-selective factor driving molecular evolution in endosymbionts.

Department of Biology University of Pisa Pisa 56126 Italy

Department of Botany University of British Columbia Vancouver BC V6T 1Z4 Canada

Department of Chemistry University of Konstanz Konstanz 78464 Germany

Department of Integrative Biology University of Guelph Guelph ON N1G 2W1 Canada

Department of Zoology University of British Columbia Vancouver BC V6T 1Z4 Canada

Institute of Parasitology Biology Centre Czech Academy of Sciences Prague 370 05 Czech Republic

Nat Ecol Evol. 2017 Aug;1(8):1062-1063. doi: 10.1038/s41559-017-0263-y. PubMed

Nat Ecol Evol. 2018 Apr;2(4):750. doi: 10.1038/s41559-018-0484-8. PubMed

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