水平基因转移下细菌基因组的进化
Evolution of bacterial genomes under horizontal gene transfer
摘要：
今天，利用越来越多的基因组数据，可以解开塑造细菌多样性的进化力量。虽然真核生物的基因组是高度稳定的，但来自同一物种的细胞的细菌基因组在基因内容上差异很大。基因含量的这种巨大变化导致了细菌的分布式基因组及其泛基因组的概念（Tettelin等人，2005; Ehrlich等人，2005年）。我们提出了一个种群遗传模型的基因内容的进化，占几种机制。从环境中的基因摄取是仿照事件的基因增益沿系谱树有关的人口。假基因化可导致基因缺失，并伴有基因丢失。Huson和Steel（2004）使用固定的系统发育树研究了这两种机制。采用由聚结剂给出的随机系谱（Kingman，1982; Hudson，1983），我们研究了Baumdicker等人（2010）已经产生的基因组多样性。在本文中，我们扩展了该模型，以将事件的种间水平基因转移。在这个模型中，我们得到的基因频谱和其他感兴趣的数量的期望。
英文摘要：
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in gene content. This huge variation in gene content led to the concepts of the distributed genome of bacteria and their pangenome (Tettelin et al.,2005; Ehrlich et al.,2005). We present a population genetic model for gene content evolution which accounts for several mechanisms. Gene uptake from the environment is modeled by events of gene gain along the genealogical tree relating the population. Pseudogenization may lead to deletion of genes and is incoporated by gene loss. These two mechanisms were studied by Huson and Steel (2004) using a fixed phylogenetic tree. Taking the random genealogy given by the coalescent (Kingman, 1982; Hudson, 1983), we studied the resulting genomic diversity already in Baumdicker et al. (2010). In the present paper, we extend the model in order to incorporate events of interspecies horizontal gene transfer. Within this model, we derive expectations for the gene frequency spectrum and other quantities of interest.
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