Evolution of microbial genomes: Sequence acquisition and loss
Evolution of microbial genomes: Sequence acquisition and loss
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DOI：
10.1093/oxfordjournals.molbev.a004050
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发表时间：
2002-12-01
影响因子：
10.7
通讯作者：
Kurland, CG
中科院分区：
文献类型：
--
作者：
Berg, OG;Kurland, CG
我们提出了描述微生物种群中新序列的获取和删除的模型。我们推断，大多数新的序列是中性的。因此，共享相同环境的生物体之间的序列复制和基因转移很少能产生适应功能。考虑了两类模型：(1)具有恒定大小的均匀种群；(2)通过缓慢迁移将种群细分为相互接触的斑块的岛屿模型。基因频率的分布是在世代重叠的Moran模型中得到的。我们发现，微生物中新颖的、中性或近中性的编码序列不会在全球范围内固定，因为它们为突变提供了很大的靶标大小，而且种群太大。至多，这类基因可能只在一小部分人群中短暂存在。因此，微生物种群预计会有非常大的瞬变中性基因含量的多样性。只有在全局或单个补丁中处于强选择下的序列才有望保持不变。我们认为，在微生物中，基因组大小是通过一种准稳态机制保持的，在这种机制中，有效获取和缺失率的随机波动导致基因组大小因斑块而异。我们将全球种群的基因组身份分配给那些在维持种群基因组一致性的遗传扫描中参与斑块所需的基因。相反，我们强调序列丢失对全球种群中新斑块的分离和分歧(物种形成)的影响。
We present models describing the acquisition and deletion of novel sequences in populations of microorganisms. We infer that most novel sequences are neutral. Thus, sequence duplications and gene transfer between organisms sharing the same environment are rarely expected to generate adaptive functions. Two classes of models are considered: (1) a homogeneous population with constant size, and (2) an island model in which the population is subdivided into patches that are in contact through slow migration. Distributions of gene frequencies are derived in a Moran model with overlapping generations. We find that novel, neutral or near-neutral coding sequences in microorganisms will not be fixed globally because they offer large target sizes for mutations and because the populations are so large. At most, such genes may have a transient presence in only a small fraction of the population. Consequently, a microbial population is expected to have a very large diversity of transient neutral gene content. Only sequences that are under strong selection, globally or in individual patches, can be expected to persist. We suggest that genome size is maintained in microorganisms by a quasi-steady state mechanism in which random fluctuations in the effective acquisition and deletion rates result in genome sizes that vary from patch to patch. We assign the genomic identity of a global population to those genes that are required for the participation of patches in the genetic sweeps that maintain the genomic coherence of the population. In contrast, we stress the influence of sequence loss on the isolation and the divergence (speciation) of novel patches from a global population.