Department of Biology, University of North Carolina Greensboro, Greensboro, North Carolina, 321 McIver Street, PO Box 26170, Greensboro, NC, 27402, USA.
Genome Biol. 2022 Nov 10;23(1):239. doi: 10.1186/s13059-022-02809-5.
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.
尽管最初认为细菌是通过克隆进化的，但研究表明大多数细菌会交换 DNA。然而，基因流动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仍然不清楚。
在这里，我们分析了超过 2600 种细菌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，这表明在自然界中纯无性物种是罕见的。我们进一步证明，用于定义细菌物种的95%基因组序列同一性的分类标准不能准确地代表阻止细菌物种之间基因流动的有效障碍。基因流动的中断可以在不同的谱系中以各种序列同一性发生，通常在 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在经验上被判断为定义细菌物种的良好近似值。我们的研究结果支持一种普遍机制，即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是多孔的，因为许多不同的物种保持一定程度的基因流动，类似于有性生物中的基因渗入。
总体而言，细菌的进化和物种形成可能是由类似的力量塑造的，这些力量推动了有性生物的进化。我们的研究结果支持这样一种模式，即基因流动的中断——尽管不一定是物种形成的最初原因——导致了永久性和不可逆转的物种边界的建立。
