Bobay Louis-Marie, Ochman Howard
Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
Genome Biol Evol. 2017 Feb 10;9(3):491-501. doi: 10.1093/gbe/evx026.
Delineation of species is fundamental to organizing and understanding biological diversity. The most widely applied criterion for distinguishing species is the Biological Species Concept (BSC), which defines species as groups of interbreeding individuals that remain reproductively isolated from other such groups. The BSC has broad appeal; however, many organisms, most notably asexual lineages, cannot be classified according to the BSC. Despite their exclusively asexual mode of reproduction, Bacteria and Archaea can transfer and exchange genes though homologous recombination. Here we show that barriers to homologous gene exchange define biological species in prokaryotes with the same efficacy as in sexual eukaryotes. By analyzing the impact of recombination on the polymorphisms in thousands of genome sequences, we find that over half of named bacterial species undergo continuous recombination among sequenced constituents, indicative of true biological species. However, nearly a quarter of named bacterial species show sharp discontinuities and comprise multiple biological species. These interruptions of gene flow are not a simple function of genome identity, indicating that bacterial speciation does not uniformly proceed by the gradual divergence of genome sequences. The same genomic approach based on recombinant polymorphisms retrieves known species boundaries in sexually reproducing eukaryotes. Thus, a single biological species definition based on gene flow, once thought to be limited only to sexually reproducing organisms, is applicable to all cellular lifeforms.
物种的界定是组织和理解生物多样性的基础。区分物种最广泛应用的标准是生物物种概念（BSC），它将物种定义为能够相互交配的个体群体，这些群体与其他此类群体保持生殖隔离。生物物种概念具有广泛的吸引力；然而，许多生物，最显著的是无性谱系，无法根据生物物种概念进行分类。尽管细菌和古菌完全采用无性繁殖方式，但它们可以通过同源重组转移和交换基因。在这里，我们表明，同源基因交换的障碍在原核生物中界定生物物种的效力与在有性真核生物中相同。通过分析重组对数千个基因组序列多态性的影响，我们发现超过一半的已命名细菌物种在测序的组分之间进行持续重组，这表明它们是真正的生物物种。然而，近四分之一的已命名细菌物种表现出明显的间断性，包含多个生物物种。这些基因流动的中断并非基因组同一性的简单函数，这表明细菌物种形成并非通过基因组序列的逐渐分化而统一进行。基于重组多态性的相同基因组方法在有性繁殖的真核生物中检索到了已知的物种界限。因此，一个基于基因流动的单一生物物种定义，曾经被认为仅适用于有性繁殖的生物体，现在适用于所有细胞生命形式。
