The scale of population structure in Arabidopsis thaliana.
The scale of population structure in Arabidopsis thaliana.
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DOI：
10.1371/journal.pgen.1000843
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发表时间：
2010-02-12
期刊：
影响因子：
4.5
通讯作者：
Borevitz JO
中科院分区：
文献类型：
--
作者：
Platt A;Horton M;Huang YS;Li Y;Anastasio AE;Mulyati NW;Agren J;Bossdorf O;Byers D;Donohue K;Dunning M;Holub EB;Hudson A;Le Corre V;Loudet O;Roux F;Warthmann N;Weigel D;Rivero L;Scholl R;Nordborg M;Bergelson J;Borevitz JO
生物体的种群结构反映了其进化历史并影响其进化轨迹。它限制了遗传多样性的组合并揭示了过去基因流动的模式。了解它是检测选择下的基因组区域、预测种群扰动的影响或建模基因流的先决条件。本文研究了拟南芥的详细全球种群结构。通过使用从全球各地收集的 5,707 株植物并在 149 个 SNP 上进行基因分型，我们发现虽然拟南芥作为一个物种在 97% 的时间内进行自体受精，但当地群体之间存在相当大的差异。这种水平的异交极大地限制了观察到的杂合性，但足以产生相当大的局部单倍型多样性。我们还发现，在其原生的欧亚大陆范围内，拟南芥在每个地理尺度上都表现出连续的距离隔离，没有与经典种群概念相对应的自然中断。相比之下，在北美洲，拟南芥作为外来物种存在，在大陆范围内几乎没有或没有种群结构，但局部隔离距离延伸数百公里。这表明了一种通过距离进行隔离的发展模式，这种模式可以在生物体填充新的栖息地范围后不久就建立起来。它还对许多标准群体遗传学模型的普遍适用性提出了疑问。任何基于可互换个体的离散集群的模型都不太适合像拟南芥这样的生物体，因为它们在许多尺度上表现出连续的距离隔离。现代群体遗传学领域的大部分内容都是以有机体群体结构及其行为的特定模型为前提的。经典模型通常从达到进化平衡的单个随机交配群体的想法开始。许多模型放宽了其中一些假设，允许诸如选型交配、具有迁移的离散亚群、自体受精和性别比例扭曲等现象。然而，几乎所有模型的核心前提都是这样的概念：存在可交换个体的类别，每个类别代表该类别分布中的相同、独立的样本。对于某些生物体，例如果蝇，这些模型可以很好地描述种群的运作方式。对于其他生物体，例如人类，这些模型可以是合理的近似值，但在组装样本时需要非常小心，并且随着采样变得局部密集，这些模型可能会开始崩溃。对于绝大多数生物体来说，这些模型的适用性从未被研究过。
The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales. Much of the modern field of population genetics is premised on particular models of what an organism's population structure is and how it behaves. The classic models generally start with the idea of a single randomly mating population that has reached an evolutionary equilibrium. Many models relax some of these assumptions, allowing for phenomena such as assortative mating, discrete sub-populations with migration, self-fertilization, and sex-ratio distortion. Virtually all models, however, have as their core premise the notion that there exist classes of exchangeable individuals each of which represents an identical, independent sample from that class' distribution. For certain organisms, such as Drosophila melanogaster, these models do an excellent job of describing how populations work. For other organisms, such as humans, these models can be reasonable approximations but require a great deal of care in assembling samples and can begin to break down as sampling becomes locally dense. For the vast majority of organisms the applicability of these models has never been investigated.
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