Department of Statistics, Oxford University, Oxford, United Kingdom.
PLoS Genet. 2011 Jul;7(7):e1002191. doi: 10.1371/journal.pgen.1002191. Epub 2011 Jul 28.
Salmonella enterica is a bacterial pathogen that causes enteric fever and gastroenteritis in humans and animals. Although its population structure was long described as clonal, based on high linkage disequilibrium between loci typed by enzyme electrophoresis, recent examination of gene sequences has revealed that recombination plays an important evolutionary role. We sequenced around 10% of the core genome of 114 isolates of enterica using a resequencing microarray. Application of two different analysis methods (Structure and ClonalFrame) to our genomic data allowed us to define five clear lineages within S. enterica subspecies enterica, one of which is five times older than the other four and two thirds of the age of the whole subspecies. We show that some of these lineages display more evidence of recombination than others. We also demonstrate that some level of sexual isolation exists between the lineages, so that recombination has occurred predominantly between members of the same lineage. This pattern of recombination is compatible with expectations from the previously described ecological structuring of the enterica population as well as mechanistic barriers to recombination observed in laboratory experiments. In spite of their relatively low level of genetic differentiation, these lineages might therefore represent incipient species.
肠炎沙门氏菌是一种细菌病原体，可导致人类和动物的肠热病和肠胃炎。尽管其种群结构长期以来被描述为克隆的，基于通过酶电泳分型的位点之间的高度连锁不平衡，但最近对基因序列的检查表明，重组在进化中起着重要作用。我们使用重测序微阵列对 114 株肠炎沙门氏菌的核心基因组进行了约 10%的测序。我们的基因组数据应用两种不同的分析方法（Structure 和 ClonalFrame），可以在肠炎沙门氏亚种内定义五个明确的谱系，其中一个谱系比其他四个谱系早五倍，是整个亚种的三分之二。我们表明，其中一些谱系比其他谱系显示出更多的重组证据。我们还证明，这些谱系之间存在一定程度的性隔离，因此重组主要发生在同一谱系的成员之间。这种重组模式与之前描述的肠炎沙门氏菌种群的生态结构以及实验室实验中观察到的重组机制障碍相一致。尽管这些谱系的遗传分化程度相对较低，但它们可能代表着初生的物种。
