Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.
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DOI：
10.1038/ismej.2015.241
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发表时间：
2016-07
期刊：
影响因子：
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通讯作者：
Malmstrom RR
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文献类型：
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作者：
Bendall ML;Stevens SL;Chan LK;Malfatti S;Schwientek P;Tremblay J;Schackwitz W;Martin J;Pati A;Bushnell B;Froula J;Kang D;Tringe SG;Bertilsson S;Moran MA;Shade A;Newton RJ;McMahon KD;Malmstrom RR
多个模型描述了不同微生物系统发育组的形成和进化。这些进化模型对适应性等位基因如何在种群中传播以及遗传多样性如何维持做出了不同的预测。通过竞争进化模型预测的过程，例如，全基因组选择性扫描与基因特异性扫描，可以使用时间序列宏基因组学在自然种群中捕获，如果该方法应用于足够长的时间框架。对这两种过程的直接观察将有助于解决不同微生物群体如何进化的问题。在这里，从一个淡水湖的9年宏基因组研究（2005-2013），我们探讨了单核苷酸多态性（SNP）频率和基因获得和丢失的模式在30个细菌种群的变化。SNP分析揭示了这些群体内的大量遗传异质性，尽管异质性程度在群体之间变化>1000倍。SNP等位基因频率也随着时间的推移在一些人群中发生了显着变化。有趣的是，几乎所有的SNP变体都在几年内从一个绿色硫细菌群体中缓慢清除，而同时多个基因要么被清除，要么从这个群体中丢失。这些模式与正在进行的全基因组选择性扫描一致，这是一个由物种形成的“生态型模型”预测的过程，但以前在自然界中没有观察到。相比之下，其他人群包含大的，无SNP的基因组区域，这些区域似乎在研究之前独立地席卷了人群，而没有清除基因组中其他地方的多样性。全基因组和基因特异性扫描的证据表明，不同的细菌物种形成模型可能适用于共存于同一环境中的不同种群。
Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.