Data from: Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

Few experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment showed that recombination did not accelerate adaptation, despite increasing genetic variation relative to asexual controls. However, the resolution in that previous work was limited to only a few genetic markers. We sought to clarify and understand these puzzling results by sequencing complete genomes from each population. The effects of recombination were highly variable: one lineage was mostly derived from the donors, while another acquired almost no donor DNA. In most lineages, some regions showed repeated introgression and others almost none. Regions with high introgression tended to be near the donors’ origin of transfer sites. To determine whether introgressed alleles imposed a genetic load, we extended the experiment for 200 generations without recombination and sequenced whole-population samples. Beneficial alleles in the recipient populations were occasionally driven extinct by maladaptive donor-derived alleles. On balance, our analyses indicate that the plasmid-mediated recombination was sufficiently frequent to drive donor alleles to fixation without providing much, if any, selective advantage.鲜有实验研究考察性重组在细菌进化中的作用，涵盖水平基因转移（horizontal gene transfer）对基因组结构的影响。为填补这一研究局限，我们对一项实验的基因组数据展开分析：实验中将大肠杆菌K-12高频重组株（Escherichia coli K-12 Hfr，high frequency recombination）供体周期性引入12个处于进化过程中的大肠杆菌B（E. coli B）种群，使其在1000代的实验周期内反复发生接合生殖。此前针对该实验中进化菌株的分析显示，尽管相较于无性对照种群，重组提升了遗传变异水平，但并未加速适应性进化进程。然而，此前的研究仅依托少量遗传标记开展分析，分辨率存在局限。我们通过对每个种群的完整基因组进行测序，旨在阐明并解析这些令人费解的实验结果。重组的影响呈现高度异质性：一个谱系的遗传物质大多源自供体菌株，而另一谱系则几乎未获取供体DNA。在多数谱系中，部分区域出现了反复的基因渐渗（introgression），其余区域则几乎无此现象。基因渐渗频率较高的区域往往紧邻供体的转移起始位点。为探究渐渗的等位基因是否造成遗传负荷（genetic load），我们将实验在无重组的条件下延续200代，并对全种群样本进行测序。受体种群中的有益等位基因偶尔会被供体来源的适应不良等位基因淘汰。综合而言，我们的分析表明，质粒介导的重组频率足以使供体等位基因在种群中固定，即便未提供可观的选择优势（即使存在选择优势，也微乎其微）。