Department of Organismic and Evolutionary Biology, Harvard University.
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Mol Biol Evol. 2015 Jun;32(6):1382-95. doi: 10.1093/molbev/msv089. Epub 2015 Apr 10.
Whole-genome duplication, which leads to polyploidy, has been implicated in speciation and biological novelty. In plants, many species exhibit ploidy variation, which is likely representative of an early stage in the evolution of polyploid lineages. To understand the evolution of such multiploidy systems, we must address questions such as whether polyploid lineage(s) had a single or multiple origins, whether admixture occurs between ploidies, and the timescale over which ploidy variation affects the evolution of populations. Here we analyze three genomic data sets using nonparametric and parametric analyses, including coalescent-based methods, to study the evolutionary history of a geographically widespread autotetraploid variant of Arabidopsis arenosa, a new model system for understanding the molecular basis of autopolyploid evolution. Autotetraploid A. arenosa populations are widely distributed across much of Northern and Central Europe, whereas diploids occur in Eastern Europe and along the southern Baltic coast; the two ploidies overlap in the Carpathian Mountains. We find that the widespread autotetraploid populations we sampled likely arose from a single ancestral population approximately 11,000-30,000 generations ago in the Northern Carpathians, where its closest extant diploid relatives are found today. Afterward, the tetraploid population split into at least four major lineages that colonized much of Europe. Reconstructions of population history suggest that substantial interploidy admixture occurred in both directions, but only among geographically proximal populations. We find two cases in which selection likely acted on an introgressed locus, suggesting that persistent interploidy gene flow has a local influence on patterns of genetic variation in A. arenosa.
全基因组复制会导致多倍体的产生，这与物种形成和生物创新有关。在植物中，许多物种表现出倍性变异，这可能代表了多倍体谱系进化的早期阶段。为了了解这种多倍性系统的进化，我们必须解决多倍体谱系是单一起源还是多起源、倍性之间是否存在混合以及倍性变异影响种群进化的时间尺度等问题。在这里，我们使用非参数和参数分析，包括基于合并的方法，分析了三个基因组数据集，以研究广泛分布于欧洲北部和中部的拟南芥 Arenosa 同源四倍体变体的进化历史，这是一个新的模型系统，用于理解同源多倍体进化的分子基础。广泛分布的拟南芥 Arenosa 同源四倍体群体分布在欧洲北部和中部的大部分地区，而二倍体则分布在东欧和波罗的海南部海岸；这两个倍性在喀尔巴阡山脉重叠。我们发现，我们采样的广泛分布的同源四倍体群体可能是由大约 11000-30000 代前在北喀尔巴阡山脉的一个单一祖先群体产生的，其现存的最接近的二倍体亲缘种今天就在那里。之后，四倍体群体分裂成至少四个主要谱系，这些谱系殖民了欧洲的大部分地区。种群历史的重建表明，在两个方向上都发生了大量的倍性混合，但仅限于地理上接近的种群。我们发现了两个选择可能作用于一个渐渗基因座的情况，这表明持续的倍性基因流对拟南芥 Arenosa 中遗传变异模式有局部影响。
