Patterns of gene flow define species of thermophilic Archaea.
Patterns of gene flow define species of thermophilic Archaea.
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DOI：
10.1371/journal.pbio.1001265
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发表时间：
2012-02
期刊：
影响因子：
9.8
通讯作者：
Whitaker RJ
中科院分区：
文献类型：
--
作者：
Cadillo-Quiroz H;Didelot X;Held NL;Herrera A;Darling A;Reno ML;Krause DJ;Whitaker RJ
古生代物种形成的基因组观点表明，共存的微生物物种内的基因流动率高于它们之间的基因流动率。尽管人们越来越多地认识到它们在自然界中的巨大多样性，但细菌和古生物的物种形成机制却知之甚少。在这里，我们使用高通量基因组测序来鉴定嗜热嗜酸古细菌Sulfolobus islandicus中正在进行的物种形成。来自俄罗斯堪察加单一温泉的12个菌株基因组之间的同源基因流动模式表明，内部的基因流动水平高于两个持续共存的群体之间的基因流动，表明这些微生物符合生物物种的概念。此外，两个物种之间的基因流动速度随着时间的推移而下降，这与初始物种形成的方式是一致的。与其他被研究的微生物不同，我们没有观察到遗传分化与沿染色体重组的频率之间的关系，也没有观察到其他会减少谱系之间基因流动的物理机制。每个物种都有自己的遗传岛，编码独特的生理功能和独特的生长表型，这可能表明生态专门化。这些共存群体之间的遗传分化发生在大的基因组“大陆”上，这表明在物种形成过程中基因组分歧的拓扑结构并不统一，并且在强多样化选择下不与单个基因座相关联。这些数据支持一个模型，在该模型中，物种不需要对基因流动设置物理障碍，但通过生态分化来维持。来自生命树细菌和古生物领域的微生物构成了地球上最广泛的生物多样性。然而，微生物对物种形成(生物多样性的产生)的基本进化过程知之甚少。争论的根本问题是，克隆繁殖微生物的个体之间的基因流动是否足够快，以提供共存谱系内部的一致性，并防止共存谱系之间的物种形成。我们使用微生物基因组的完整测序来观察作用中的物种形成。我们专注于从俄罗斯堪察加Mutnovsky火山的地热温泉中收集的名为Sulfolobus islandicus的古生物，它的物理隔离使我们能够准确地将进化过程定位在一个位置。与微生物的理论预测相反，我们提供的证据表明，尽管两个新的谱系发生了重组，但它们正在变得在生态上截然不同，并在进化上独立。我们观察到的差异并不是在整个基因组中均匀发生，因为某些基因组区域比其他区域更容易在物种之间分化。这一发生在单个自然微生物种群内物种形成过程的基因组观点有助于我们理解古生代生物多样性的产生，并进一步加深我们对生命树上物种形成的理解。
A genomic view of speciation in Archaea shows higher rates of gene flow within coexisting microbial species than between them. Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic “continents,” indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation. Microorganisms from the bacterial and archaeal domains of the tree of life comprise the greatest breadth of biodiversity on earth. Yet the essential evolutionary process of speciation (through which biodiversity is generated) is poorly understood in microbes. At issue is the fundamental question of whether gene flow among individuals of clonally reproducing microorganisms is rapid enough to provide coherence within—and prevent speciation between—coexisting lineages. We use complete sequencing of microbial genomes to observe speciation in action. We focus on Archaea called Sulfolobus islandicus gathered from a geothermal hot spring from the Mutnovsky Volcano in Kamchatka, Russia, whose physical isolation allows us to pinpoint evolutionary processes to one location. Contrary to the theoretical predictions for microbes, we provide evidence that two novel lineages are in the process of becoming ecologically distinct and evolutionarily independent despite the fact that they recombine. The divergence we observe is not happening uniformly across the genome because certain genomic regions are more prone to become differentiated between species than others. This genomic view of the process of speciation occurring within a single natural microbial population contributes to our understanding of the generation of biodiversity in Archaea and furthers our understanding of speciation across the tree of life.
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影响因子：
1.5
作者：
Cohan, FM
通讯作者：
Cohan, FM
DOI：
10.1093/bioinformatics/btp347
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Assefa S;Keane TM;Otto TD;Newbold C;Berriman M
通讯作者：
Berriman M
影响因子：
3.3
作者：
Didelot, Xavier;Falush, Daniel
通讯作者：
Falush, Daniel
影响因子：
11
作者：
Doroghazi, James R.;Buckley, Daniel H.
通讯作者：
Buckley, Daniel H.
影响因子：
9.8
作者：
Davison, A;Chiba, S;Clarke, B
通讯作者：
Clarke, B