In bacteria, pan-genomes are the result of an evolutionary “tug of war” between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes. We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high Ne estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport. Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.

中文翻译：

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从濒临灭绝的绿洲中分离出的弧菌科种群基因组学揭示了环境扰动后的局部适应。

在细菌中，泛基因组是选择和水平基因转移 (HGT) 之间进化“拉锯战”的结果。高 HGT 率增加了遗传库和有效种群大小 (Ne)，导致开放的泛基因组。相比之下，选择压力可以通过清除 HGT 和突变引入的变异来导致局部适应，从而导致封闭的泛基因组和克隆谱系。在这项研究中，我们探索了这两种假设，阐明了墨西哥 Cuatro Ciénegas 盆地 (CCB) 濒临灭绝的绿洲发生扰动事件后弧菌科分离株的泛基因组，并在其基因组中寻找适应环境的信号。我们获得了分布在六个谱系中的 42 个弧菌科基因组，其中两个在数据库中没有显示任何密切的参考菌株。其中五个谱系显示出封闭的泛基因组，并且与水或沉积物环境有关；他们的高 Ne 估计表明，这些谱系并非来自最近的起源。在两种环境中都发现了唯一具有开放泛基因组的进化枝，并且由十个低 Ne 基因组形成，表明其起源最近。重组和突变估计量 (r/m) 范围从 0.005 到 2.725，这与海洋弧菌科估计值相似。然而，我们确定了 367 个具有正选择信号的基因家族，其中大部分存在于核心基因组中；表明尽管重组，自然选择将弧菌科 CCB 谱系移动到局部适应，清除基因组并保持封闭的泛基因组模式。此外，我们确定了与非结构化环境相关的 598 个 SNP；与这些 SNP 相关的一些基因与钠转运有关。不同的证据表明，采样的弧菌科是通常生活在饥荒条件下的稀有生物圈的一部分。其中两个谱系是首次报道。CCB 的大多数弧菌科谱系适应其微生境而不是采样环境。这种适应模式与封闭的泛基因组和局部适应的关联是一致的。