In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host–microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.

中文翻译：

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系统发育协调：充分利用基因组来了解微生物生态学和进化


近年来，系统发育协调已成为研究微生物生态学和进化的一种有前途的方法。其核心思想是模拟基因树如何沿着物种树进化，并通过基因复制、转移和丢失等进化事件来解释它们之间的差异。在这里，我们描述了系统发育协调如何为研究基因组进化提供一个自然框架，并重点介绍了最近的应用，包括祖先基因内容推断、物种树的生根，以及对代谢进化和它们产生的生态转变的见解。协调分析阐明了从衣原体到阿斯加德古细菌的不同微生物谱系的进化，揭示了生态适应、宿主-微生物相互作用和共生关系。然而，该方法在微生物学领域有很多更广泛应用的机会。不断改进以使协调模型更加现实和可扩展，并整合栖息地、pH、温度和氧气使用等生态元数据，为了解丰富的微生物生命提供了巨大的潜力。