Department of Biological Sciences, Dartmouth College, Hanover, NH 03755.
Department of Biological Sciences, Dartmouth College, Hanover, NH 03755;
Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):E5414-E5423. doi: 10.1073/pnas.1619993114. Epub 2017 Jun 19.
Whether prokaryotes (Bacteria and Archaea) are naturally organized into phenotypically and genetically cohesive units comparable to animal or plant species remains contested, frustrating attempts to estimate how many such units there might be, or to identify the ecological roles they play. Analyses of gene sequences in various closely related prokaryotic groups reveal that sequence diversity is typically organized into distinct clusters, and processes such as periodic selection and extensive recombination are understood to be drivers of cluster formation ("speciation"). However, observed patterns are rarely compared with those obtainable with simple null models of diversification under stochastic lineage birth and death and random genetic drift. Via a combination of simulations and analyses of core and phylogenetic marker genes, we show that patterns of diversity for the genera , , and are generally indistinguishable from patterns arising under a null model. We suggest that caution should thus be taken in interpreting observed clustering as a result of selective evolutionary forces. Unknown forces do, however, appear to play a role in , and some individual genes in all groups fail to conform to the null model. Taken together, we recommend the presented birth-death model as a null hypothesis in prokaryotic speciation studies. It is only when the real data are statistically different from the expectations under the null model that some speciation process should be invoked.
原核生物（细菌和古菌）是否自然地组织成表型和遗传上具有凝聚力的单位，类似于动物或植物物种，这仍然存在争议，这使得估计可能存在多少这样的单位，或识别它们所扮演的生态角色变得困难。对各种密切相关的原核群体中的基因序列的分析表明，序列多样性通常组织成不同的聚类，并且周期性选择和广泛重组等过程被理解为聚类形成的驱动因素（“物种形成”）。然而，观察到的模式很少与随机谱系诞生和死亡以及随机遗传漂变下简单的多样化无偏模型所获得的模式进行比较。通过模拟和核心及系统发育标记基因的分析相结合，我们表明，属的多样性模式与无偏模型产生的模式通常无法区分。因此，在将观察到的聚类解释为选择性进化力量的结果时应谨慎。然而，未知的力量似乎确实在发挥作用，并且所有群体中的一些个别基因都不符合无偏模型。总的来说，我们建议将所提出的出生-死亡模型作为原核生物物种形成研究中的一个无偏假设。只有当真实数据在统计上与无偏模型下的预期不同时，才应该调用一些物种形成过程。
