Gene flow and introgression are pervasive forces shaping the evolution of bacterial species.
Gene flow and introgression are pervasive forces shaping the evolution of bacterial species.
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DOI：
10.1186/s13059-022-02809-5
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发表时间：
2022-11-10
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
--
作者：
尽管最初认为是克隆进化，但研究表明，大多数细菌都交换了DNA。然而，目前尚不清楚基因流在多大程度上塑造了细菌基因组的进化，并维持了物种的凝聚力。在这里，我们分析了2600个细菌物种内部和之间的基因流动模式。我们的结果表明，只有不到10%的细菌物种是真正的克隆，这表明纯粹的无性物种在自然界中是罕见的。我们进一步证明，常规用于定义细菌物种的~95%基因组序列同源性的分类标准并不能准确地代表对跨细菌物种的基因流动施加有效障碍的分歧水平。基因流的中断可以发生在不同谱系的不同序列同一性上，通常从90%到98%的基因组同一性。这可能解释了为什么~95%的基因组序列同一性阈值被经验地判断为定义细菌物种的良好近似值。我们的结果支持一种普遍的机制，即启动同源重组所需的相同基因组DNA片段的可用性是细菌中基因流动和物种边界的主要决定因素。我们表明，这些基因流动的障碍仍然存在，因为许多不同的物种保持着一定水平的基因流动，类似于有性生物的渗入。总体而言，细菌进化和物种形成很可能是由推动有性有机体进化的类似力量塑造的。我们的发现支持一个模型，在这个模型中，基因流动的中断--尽管不一定是物种形成的最初原因--会导致永久和不可逆转的物种边界的建立。网上版载有补充材料，可在10.1186/s13059-022-02809-5查阅。
Although originally thought to evolve clonally, studies have revealed that most bacteria exchange DNA. However, it remains unclear to what extent gene flow shapes the evolution of bacterial genomes and maintains the cohesion of species. Here, we analyze the patterns of gene flow within and between >2600 bacterial species. Our results show that fewer than 10% of bacterial species are truly clonal, indicating that purely asexual species are rare in nature. We further demonstrate that the taxonomic criterion of ~95% genome sequence identity routinely used to define bacterial species does not accurately represent a level of divergence that imposes an effective barrier to gene flow across bacterial species. Interruption of gene flow can occur at various sequence identities across lineages, generally from 90 to 98% genome identity. This likely explains why a ~95% genome sequence identity threshold has empirically been judged as a good approximation to define bacterial species. Our results support a universal mechanism where the availability of identical genomic DNA segments required to initiate homologous recombination is the primary determinant of gene flow and species boundaries in bacteria. We show that these barriers of gene flow remain porous since many distinct species maintain some level of gene flow, similar to introgression in sexual organisms. Overall, bacterial evolution and speciation are likely shaped by similar forces driving the evolution of sexual organisms. Our findings support a model where the interruption of gene flow—although not necessarily the initial cause of speciation—leads to the establishment of permanent and irreversible species borders. The online version contains supplementary material available at 10.1186/s13059-022-02809-5.
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