Insects have repeatedly forged symbioses with heritable microbes, gaining novel traits. For the microbe, the transition to symbioses can lead to the degeneration of the symbiont’s genome through transmission bottlenecks, isolation, and the loss of DNA repair enzymes. However, some insect-microbial symbioses have persisted for millions of years, suggesting natural selection slows genetic drift and maintains functional consistency between symbiont populations. By sampling in multiple countries, we examine genomic diversity within a symbiont species, a heritable symbiotic bacterium found only in human head lice. We find that human head louse symbionts contain genetic diversity that appears to have arisen contemporaneously with the appearance of anatomically modern humans within Africa and/or during the colonization of Eurasia by humans. We predict that the observed genetic diversity underlies functional differences in extant symbiont lineages, through the inactivation of genes involved in symbiont membrane construction. Furthermore, we find evidence of additional gene losses prior to the appearance of modern humans, also impacting the symbiont membrane. From this, we conclude that symbiont genome degeneration is proceeding, via gene inactivation and subsequent loss, in human head louse symbionts, while genomic diversity is maintained. Collectively, our results provide a look into the genomic diversity within a single symbiont species and highlight the shared evolutionary history of humans, lice, and bacteria.

中文翻译：

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人头虱内共生细菌的基因组多样性

昆虫反复与可遗传的微生物形成共生关系，获得新的特征。对于微生物来说，向共生体的转变可能会因传播瓶颈、隔离和 DNA 修复酶的丧失而导致共生体基因组的退化。然而，一些昆虫-微生物共生体已经持续了数百万年，这表明自然选择减缓了遗传漂变并保持了共生体种群之间功能的一致性。通过在多个国家采样，我们检查了共生物种内的基因组多样性，共生物种是一种仅在人类头虱中发现的可遗传的共生细菌。我们发现，人类头虱共生体含有遗传多样性，这些遗传多样性似乎与非洲和/或人类殖民欧亚大陆期间解剖学上的现代人类的出现同时出现。我们预测，通过参与共生体膜构建的基因失活，观察到的遗传多样性是现存共生体谱系功能差异的基础。此外，我们发现了在现代人类出现之前额外基因丢失的证据，这也影响了共生体膜。由此，我们得出结论，在人类头虱共生体中，通过基因失活和随后的损失，共生体基因组退化正在发生，而基因组多样性得以维持。总的来说，我们的结果提供了对单个共生物种内基因组多样性的了解，并强调了人类、虱子和细菌的共同进化历史。